Sample records for 35s enhancer sequence


    Lifescience Database Archive (English)

    Full Text Available nhance gene expression; Inverted GAGA; See also S000405, S000427 (GAGA); (TC)4T; CaMV 35S; enhancer; Cauliflower mosaic virus (CaMV) TCTCTCTCT ... ...) found in a 60-nucleotide region (S1) downstream of the transcription start site of the CaMV 35S RNA; Can e

  2. Both the constitutive Cauliflower Mosaic Virus 35S and tissue-specific AGAMOUS enhancers activate transcription autonomously in Arabidopsis thaliana (United States)

    The presence of multiple enhancers and promoters within a single vector often provokes complicated mutual interaction and crosstalk, thereby, altering promoter specificity, which causes serious problems for precisely engineering gene function and agronomic traits in transgenic plants. Enhancer elem...

  3. Enhanced virome sequencing using targeted sequence capture. (United States)

    Wylie, Todd N; Wylie, Kristine M; Herter, Brandi N; Storch, Gregory A


    Metagenomic shotgun sequencing (MSS) is an important tool for characterizing viral populations. It is culture independent, requires no a priori knowledge of the viruses in the sample, and may provide useful genomic information. However, MSS can lack sensitivity and may yield insufficient data for detailed analysis. We have created a targeted sequence capture panel, ViroCap, designed to enrich nucleic acid from DNA and RNA viruses from 34 families that infect vertebrate hosts. A computational approach condensed ∼1 billion bp of viral reference sequence into <200 million bp of unique, representative sequence suitable for targeted sequence capture. We compared the effectiveness of detecting viruses in standard MSS versus MSS following targeted sequence capture. First, we analyzed two sets of samples, one derived from samples submitted to a diagnostic virology laboratory and one derived from samples collected in a study of fever in children. We detected 14 and 18 viruses in the two sets, comprising 19 genera from 10 families, with dramatic enhancement of genome representation following capture enrichment. The median fold-increases in percentage viral reads post-capture were 674 and 296. Median breadth of coverage increased from 2.1% to 83.2% post-capture in the first set and from 2.0% to 75.6% in the second set. Next, we analyzed samples containing a set of diverse anellovirus sequences and demonstrated that ViroCap could be used to detect viral sequences with up to 58% variation from the references used to select capture probes. ViroCap substantially enhances MSS for a comprehensive set of viruses and has utility for research and clinical applications.

  4. Neuropeptides labelled with [sup 35]S

    Energy Technology Data Exchange (ETDEWEB)

    Kaspersen, F.M.; Nispen, J.W. van; Sperling, E.M.G.; Vader, J.F. (Organon Int BV, Oss (Netherlands))


    Methionine and cysteine containing peptides can be labelled with [sup 35]S by coupling of [sup 35]S-cysteine or [sup 35]S-methionine with a large excess of suitability protected peptide precursors. This is illustrated for [pGlu[sup 4], Cyt[sup 6

  5. Complete nucleotide sequences and construction of full-length infectious cDNA clones of cucumber green mottle mosaic virus (CGMMV) in a versatile newly developed binary vector including both 35S and T7 promoters. (United States)

    Park, Chan-Hwan; Ju, Hye-Kyoung; Han, Jae-Yeong; Park, Jong-Seo; Kim, Ik-Hyun; Seo, Eun-Young; Kim, Jung-Kyu; Hammond, John; Lim, Hyoun-Sub


    Seed-transmitted viruses have caused significant damage to watermelon crops in Korea in recent years, with cucumber green mottle mosaic virus (CGMMV) infection widespread as a result of infected seed lots. To determine the likely origin of CGMMV infection, we collected CGMMV isolates from watermelon and melon fields and generated full-length infectious cDNA clones. The full-length cDNAs were cloned into newly constructed binary vector pJY, which includes both the 35S and T7 promoters for versatile usage (agroinfiltration and in vitro RNA transcription) and a modified hepatitis delta virus ribozyme sequence to precisely cleave RNA transcripts at the 3' end of the tobamovirus genome. Three CGMMV isolates (OMpj, Wpj, and Mpj) were separately evaluated for infectivity in Nicotiana benthamiana, demonstrated by either Agroinfiltration or inoculation with in vitro RNA transcripts. CGMMV nucleotide identities to other tobamoviruses were calculated from pairwise alignments using DNAMAN. CGMMV identities were 49.89% to tobacco mosaic virus; 49.85% to pepper mild mottle virus; 50.47% to tomato mosaic virus; 60.9% to zucchini green mottle mosaic virus; and 60.96% to kyuri green mottle mosaic virus, confirming that CGMMV is a distinct species most similar to other cucurbit-infecting tobamoviruses. We further performed phylogenetic analysis to determine relationships of our new Korean CGMMV isolates to previously characterized isolates from Canada, China, India, Israel, Japan, Korea, Russia, Spain, and Taiwan available from NCBI. Analysis of CGMMV amino acid sequences showed three major clades, broadly typified as 'Russian,' 'Israeli,' and 'Asian' groups. All of our new Korean isolates fell within the 'Asian' clade. Neither the 128 nor 186 kDa RdRps of the three new isolates showed any detectable gene silencing suppressor function.

  6. Resolution enhancement of color video sequences. (United States)

    Shah, N R; Zakhor, A


    We propose a new multiframe algorithm to enhance the spatial resolution of frames in video sequences. Our technique specifically accounts for the possibility that motion estimation will be inaccurate and compensates for these inaccuracies. Experiments show that our multiframe enhancement algorithm yields perceptibly sharper enhanced images with significant signal-to-noise ratio (SNR) improvement over bilinear and cubic B-spline interpolation.

  7. Detection of deep stratospheric intrusions by cosmogenic 35S (United States)

    Lin, Mang; Su, Lin; Shaheen, Robina; Fung, Jimmy C. H.; Thiemens, Mark H.


    The extent to which stratospheric intrusions on synoptic scales influence the tropospheric ozone (O3) levels remains poorly understood, because quantitative detection of stratospheric air has been challenging. Cosmogenic 35S mainly produced in the stratosphere has the potential to identify stratospheric air masses at ground level, but this approach has not yet been unambiguously shown. Here, we report unusually high 35S concentrations (7,390 atoms m-3; ˜16 times greater than annual average) in fine sulfate aerosols (aerodynamic diameter less than 0.95 µm) collected at a coastal site in southern California on May 3, 2014, when ground-level O3 mixing ratios at air quality monitoring stations across southern California (43 of 85) exceeded the recently revised US National Ambient Air Quality Standard (daily maximum 8-h average: 70 parts per billion by volume). The stratospheric origin of the significantly enhanced 35S level is supported by in situ measurements of air pollutants and meteorological variables, satellite observations, meteorological analysis, and box model calculations. The deep stratospheric intrusion event was driven by the coupling between midlatitude cyclones and Santa Ana winds, and it was responsible for the regional O3 pollution episode. These results provide direct field-based evidence that 35S is an additional sensitive and unambiguous tracer in detecting stratospheric air in the boundary layer and offer the potential for resolving the stratospheric influences on the tropospheric O3 level.

  8. Enhanced Dynamic Algorithm of Genome Sequence Alignments

    Directory of Open Access Journals (Sweden)

    Arabi E. keshk


    Full Text Available The merging of biology and computer science has created a new field called computational biology that explore the capacities of computers to gain knowledge from biological data, bioinformatics. Computational biology is rooted in life sciences as well as computers, information sciences, and technologies. The main problem in computational biology is sequence alignment that is a way of arranging the sequences of DNA, RNA or protein to identify the region of similarity and relationship between sequences. This paper introduces an enhancement of dynamic algorithm of genome sequence alignment, which called EDAGSA. It is filling the three main diagonals without filling the entire matrix by the unused data. It gets the optimal solution with decreasing the execution time and therefore the performance is increased. To illustrate the effectiveness of optimizing the performance of the proposed algorithm, it is compared with the traditional methods such as Needleman-Wunsch, Smith-Waterman and longest common subsequence algorithms. Also, database is implemented for using the algorithm in multi-sequence alignments for searching the optimal sequence that matches the given sequence.

  9. Soil 35S Transformation and Availability to Plants

    Institute of Scientific and Technical Information of China (English)



    Sulfur transformation in 3 soils maintained in a closed incubation system and its availability to plants were investigated using carrier-free 35S-SO42- and 35S-labeled ryegrass straw.For carrier-free Na235SO4 treatment,78%,70%and 64% of 35S applied were found in Ca(H2PO4)2-extractale S fraction,4%,5% and 7% in slowly soluble inorganic S,11%,15%and 18%in C-O-S,5%,7%,and 6% in C-bonded S,and 5%,7% and 6% in unidentified organic S120 days after incubation in black soil,cinnamon soil and chestnut soil,respectively.Most of 35S uptake by plants came from extractable 35SO42-,and little from C-O-35S and C-bonded 35S,In the treatment with 35S-labeled straw,51%,46%and 36% of 35S incorporated were found in Ca(H2PO4)2-extractable S fraction,7%,6% and 7% in slowly soluble inorganic S,13%,15%and 18% in C-O-S,8%,8%and 6% in C-bonded S,and 18%,25%and 35% in unidentified organic S at the end of incubation in above-mentoned three soils,respectively.Higher availability of C-O-35S,C-bonded 35S and unidentified organic 35S from 35S-labeled straw was observed in 35S-labeled straw treatment compared to carrier-free Na235SO4 treatment.

  10. The effect of ethanol on sup 35 -S-TBPS binding to mouse brain membranes in the presence of chloride

    Energy Technology Data Exchange (ETDEWEB)

    Liljequist, S.; Culp, S.; Tabakoff, B. (Laboratory for Studies of Neuroadaptive Processes, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda (USA))


    The effect of in vitro and in vivo administration of ethanol on the binding of {sup 35}S-t-butyl-bicyclophosphorothionate ({sup 35}S-TBPS) to cortical brain membranes of C57B1 mice was investigated using KCl containing assay media. The in vitro addition of ethanol produced a dose-dependent inhibition of basal {sup 35}S-TBPS binding. In the presence of chloride ions, GABA and pentobarbital had a biphasic action on {sup 35}S-TBPS binding, whereas diazepam only stimulated the binding. Ethanol reduced the stimulatory effects of GABA and pentobarbital in a dose-dependent manner, but had no effect on the enhancement of {sup 35}S-TBPS binding produced by diazepam. {sup 35}S-TBPS binding to cortical brain membranes was inhibited by the putative Cl{sup -} channel blocking agent DIDS. This inhibitory action of DIDS was significantly, and dose-dependently reduced by ethanol. Chronic ethanol ingestion in vivo, which produced tolerance to and physical dependence on ethanol in the animals, did not alter the stimulatory and inhibitory effects of GABA and pentobarbital on {sup 35}S-TBPS binding. The enhancement of {sup 35}S-TBPS binding produced by diazepam was slightly, but significantly, enhanced in brain membranes from animals which had undergone 24 hours of ethanol withdrawal. Chronic ethanol treatment did not change the potency of picrotoxin and of the peripheral BDZ-receptor ligand RO 5-4864 to competitively inhibit {sup 35}S-TBPS binding. Our results suggest that in vitro addition of ethanol alters the activity of the activity of the GABA benzodiazepine (BDZ) receptor complex. Although there was no change in basal {sup 35}S-TBPS binding following chronic in vivo ethanol administration, our curent data suggest that chronic ethanol ingestion may cause specific changes of the GABA BDZ receptor proteins, in this study revealed as an altered modulation of {sup 35}S-TBPS binding by diazepam.

  11. Discriminative prediction of mammalian enhancers from DNA sequence. (United States)

    Lee, Dongwon; Karchin, Rachel; Beer, Michael A


    Accurately predicting regulatory sequences and enhancers in entire genomes is an important but difficult problem, especially in large vertebrate genomes. With the advent of ChIP-seq technology, experimental detection of genome-wide EP300/CREBBP bound regions provides a powerful platform to develop predictive tools for regulatory sequences and to study their sequence properties. Here, we develop a support vector machine (SVM) framework which can accurately identify EP300-bound enhancers using only genomic sequence and an unbiased set of general sequence features. Moreover, we find that the predictive sequence features identified by the SVM classifier reveal biologically relevant sequence elements enriched in the enhancers, but we also identify other features that are significantly depleted in enhancers. The predictive sequence features are evolutionarily conserved and spatially clustered, providing further support of their functional significance. Although our SVM is trained on experimental data, we also predict novel enhancers and show that these putative enhancers are significantly enriched in both ChIP-seq signal and DNase I hypersensitivity signal in the mouse brain and are located near relevant genes. Finally, we present results of comparisons between other EP300/CREBBP data sets using our SVM and uncover sequence elements enriched and/or depleted in the different classes of enhancers. Many of these sequence features play a role in specifying tissue-specific or developmental-stage-specific enhancer activity, but our results indicate that some features operate in a general or tissue-independent manner. In addition to providing a high confidence list of enhancer targets for subsequent experimental investigation, these results contribute to our understanding of the general sequence structure of vertebrate enhancers.

  12. Transformation of Lesquerella Fendleri with the New Binary Vector pGPro4-35S

    Directory of Open Access Journals (Sweden)

    Grace Q. Chen


    Full Text Available Problem statement: Crop genetic engineering requires the use of various promoters to control the expression of introduced transgenes. Some of the binary vectors currently available for promoter characterization in dicotyledonous plants have pitfalls due to their construction, such as containing a selectable marker cassette with enhancer sequences that can potentially interfere with the expression specificity of nearby promoters. Also, many binary vectors are quite large in size and contain few useful restriction sites making their in vitro manipulation technically challenging. Approach: A small (7698 bp and flexible binary vector named pGPro4 was constructed to possess unique features favorable for promoter analysis in dicot plants. A nopaline synthase (nos promoter was used to control the expression of the selectable marker of pGPro4 to prevent the problem of interference with the neighboring promoter-reporter fusion. In pGPro4, the nos promoter and hygromycin phosphotransferase II (hptII sequences are flanked by loxP sites, which allow for Cre recombinase-mediated removal when hygromycin resistance is no longer desired. pGPro4 also contains a bifunctional β-glucuronidase-enhanced Green Fluorescent Protein (gusA-eGFP reporter gene that provides visual detection of reporter gene expression using either fluorescence in live cells or histochemical detection of β-glucuronidase activity. Results and Conclusion: To demonstrate the usefulness of the pGPro4 vector, a CaMV35S promoter was fused to gusA-eGFP and the resulting plasmid, pGPro4-35S, was used to transform Lesquerella fendleri. Primary shoots were generated from explants at an expected frequency of 10-27.5%, indicating that the nos promoter drove sufficient hptII expression to generate hygromycin resistant plants. Six independent transgenic L. fendleri lines were grown to maturity and generated T1 seeds. The bifunctionality of the gusA-eGFP reporter gene was verified by detecting both green

  13. SYNTHESIS OF [35S]-ALBENDAZOLE%35S-丙硫苯咪唑合成工艺路线

    Institute of Scientific and Technical Information of China (English)

    刘永良; 李芬


    @@ 本文描述了广谱驱虫剂35S-两硫苯咪唑的合成方法.它是由元素35S和氰化钾反应生成35S-硫氰化钾开始,经过五步合成完成.总放化收率20%,比放射性7.59mCi/mM,放化纯度94.5%.

  14. Temporal Resolution Enhancement in Compressed Video Sequences

    Directory of Open Access Journals (Sweden)

    Robert L. Stevenson


    Full Text Available Compressed video may possess a number of artifacts, both spatial and temporal. Spatial compression artifacts arise as a result of quantization of the transform-domain coefficients, and are often manifested as blocking and ringing artifacts. Temporal limitations in compressed video occur when the encoder, in an effort to reduce bandwidth, drops frames. Omitting frames decreases the reconstructed frame rate, which can cause motion to appear jerky and uneven. This paper discusses a method to increase the frame rate of video compressed with the DCT by inserting images between received frames of the sequence. The Bayesian formulation of the restoration prevents spatial compression artifacts in the received frames from propagating to the reconstructed frames.

  15. Measuring 35S of Aerosol Sulfate: Techniques and First Results (United States)

    Brothers, L. A.; Dominguez, G.; Bluen, B.; Corbin, A.; Abramian, A.; Thiemens, M. H.


    On a global and regional level, the cycling of sulfur in the environment has consequences for air quality, human health, and may contribute to global climate change. Due to its multiple oxidation states, the sulfur cycle is very complex and poorly understood. Stable isotopes are currently used to understand reaction pathways as well as sources and sinks of sulfurous compounds in the environment. Sulfur also has one short lived (τ1/2 ~87 d) radioactive isotope (35S) which is continuously made in the atmosphere by the cosmic ray spallation of argon, is then quickly oxidized to 35SO2 and enters the atmospheric sulfur cycle. The short-lived radioactive nature of this isotope of sulfur provides us with potentially powerful tracer for understanding the time scales at which sulfur is oxidized, deposited, and transported in the atmosphere and the deposition of atmospheric sulfate into rivers and water catchments. However, despite its potential, the use of 35S as a tracer of aerosol chemistry has not been fully exploited, Here we present details of instrumental set up for measuring 35S in aerosol sulfate and some preliminary results of measurements of 35S abundances in aerosols from Riverside (inland) and La Jolla (coastal) CA and discuss the sensitivity and limitations of the measurements in providing insights into day/night aerosol chemistry (Riverside) as well as the uptake of SO2 pollution in coastal environments by sea-salt aerosols. Also, we present preliminary results from measurement of sulfate in river water in Ecuador before and after precipitation events.

  16. Enhanced sequencing coverage with digital droplet multiple displacement amplification. (United States)

    Sidore, Angus M; Lan, Freeman; Lim, Shaun W; Abate, Adam R


    Sequencing small quantities of DNA is important for applications ranging from the assembly of uncultivable microbial genomes to the identification of cancer-associated mutations. To obtain sufficient quantities of DNA for sequencing, the small amount of starting material must be amplified significantly. However, existing methods often yield errors or non-uniform coverage, reducing sequencing data quality. Here, we describe digital droplet multiple displacement amplification, a method that enables massive amplification of low-input material while maintaining sequence accuracy and uniformity. The low-input material is compartmentalized as single molecules in millions of picoliter droplets. Because the molecules are isolated in compartments, they amplify to saturation without competing for resources; this yields uniform representation of all sequences in the final product and, in turn, enhances the quality of the sequence data. We demonstrate the ability to uniformly amplify the genomes of single Escherichia coli cells, comprising just 4.7 fg of starting DNA, and obtain sequencing coverage distributions that rival that of unamplified material. Digital droplet multiple displacement amplification provides a simple and effective method for amplifying minute amounts of DNA for accurate and uniform sequencing.

  17. In Vivo Enhancer Analysis Chromosome 16 Conserved NoncodingSequences

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Ahituv, Nadav; Moses, Alan M.; Nobrega,Marcelo; Prabhakar, Shyam; Shoukry, Malak; Minovitsky, Simon; Visel,Axel; Dubchak, Inna; Holt, Amy; Lewis, Keith D.; Plajzer-Frick, Ingrid; Akiyama, Jennifer; De Val, Sarah; Afzal, Veena; Black, Brian L.; Couronne, Olivier; Eisen, Michael B.; Rubin, Edward M.


    The identification of enhancers with predicted specificitiesin vertebrate genomes remains a significant challenge that is hampered bya lack of experimentally validated training sets. In this study, weleveraged extreme evolutionary sequence conservation as a filter toidentify putative gene regulatory elements and characterized the in vivoenhancer activity of human-fish conserved and ultraconserved1 noncodingelements on human chromosome 16 as well as such elements from elsewherein the genome. We initially tested 165 of these extremely conservedsequences in a transgenic mouse enhancer assay and observed that 48percent (79/165) functioned reproducibly as tissue-specific enhancers ofgene expression at embryonic day 11.5. While driving expression in abroad range of anatomical structures in the embryo, the majority of the79 enhancers drove expression in various regions of the developingnervous system. Studying a set of DNA elements that specifically droveforebrain expression, we identified DNA signatures specifically enrichedin these elements and used these parameters to rank all ~;3,400human-fugu conserved noncoding elements in the human genome. The testingof the top predictions in transgenic mice resulted in a three-foldenrichment for sequences with forebrain enhancer activity. These datadramatically expand the catalogue of in vivo-characterized human geneenhancers and illustrate the future utility of such training sets for avariety of iological applications including decoding the regulatoryvocabulary of the human genome.

  18. Some dipeptides reverse the inhibitory effect of GABA on /sup 35/S-TBPS binding

    Energy Technology Data Exchange (ETDEWEB)

    Squires, R.F.; Saederup, E.


    All known GABA-A receptor blocker reverse the inhibitory effect of GABA on /sup 35/S-t-butylphosphorothionate (TBPS) binding to rat brain membranes in vitro. This system has already been used to identify several novel GABA antagonists. The authors now report that 12 out of 52 dipeptides tested (all containing L-amino acids), at 1 mM, significantly reverse the inhibitory effect of 1 GABA, which inhibits specific /sup 35/S-TBPS binding about 60%. Most of the active dipeptides contain an aromatic and a basic amino acid. Tryptophan usually conferred greater activity than phe or tyr, while arg usually conferred greater activity than lys or his. Several larger peptides containing the HFRW sequence found in ACTH were also GABA antagonists; ACTH(1-24), ACTH(1-18), ACTH(1-13), ACTH(4-10) and ..gamma..-MSH while ACTH(11-24) was inactive. The excitatory effects of these later peptides may be in part due to blockade of GABA-A receptors.

  19. Possible consequences of the overlap between the CaMV 35S promoter regions in plant transformation vectors used and the viral gene VI in transgenic plants. (United States)

    Podevin, Nancy; du Jardin, Patrick


    Multiple variants of the Cauliflower mosaic virus 35S promoter (P35S) are used to drive the expression of transgenes in genetically modified plants, for both research purposes and commercial applications. The genetic organization of the densely packed genome of this virus results in sequence overlap between P35S and viral gene VI, encoding the multifunctional P6 protein. The present paper investigates whether introduction of P35S variants by genetic transformation is likely to result in the expression of functional domains of the P6 protein and in potential impacts in transgenic plants. A bioinformatic analysis was performed to assess the safety for human and animal health of putative translation products of gene VI overlapping P35S. No relevant similarity was identified between the putative peptides and known allergens and toxins, using different databases. From a literature study it became clear that long variants of the P35S do contain an open reading frame, when expressed, might result in unintended phenotypic changes. A flowchart is proposed to evaluate possible unintended effects in plant transformants, based on the DNA sequence actually introduced and on the plant phenotype, taking into account the known effects of ectopically expressed P6 domains in model plants.

  20. Detection of nonauthorized genetically modified organisms using differential quantitative polymerase chain reaction: application to 35S in maize. (United States)

    Cankar, Katarina; Chauvensy-Ancel, Valérie; Fortabat, Marie-Noelle; Gruden, Kristina; Kobilinsky, André; Zel, Jana; Bertheau, Yves


    Detection of nonauthorized genetically modified organisms (GMOs) has always presented an analytical challenge because the complete sequence data needed to detect them are generally unavailable although sequence similarity to known GMOs can be expected. A new approach, differential quantitative polymerase chain reaction (PCR), for detection of nonauthorized GMOs is presented here. This method is based on the presence of several common elements (e.g., promoter, genes of interest) in different GMOs. A statistical model was developed to study the difference between the number of molecules of such a common sequence and the number of molecules identifying the approved GMO (as determined by border-fragment-based PCR) and the donor organism of the common sequence. When this difference differs statistically from zero, the presence of a nonauthorized GMO can be inferred. The interest and scope of such an approach were tested on a case study of different proportions of genetically modified maize events, with the P35S promoter as the Cauliflower Mosaic Virus common sequence. The presence of a nonauthorized GMO was successfully detected in the mixtures analyzed and in the presence of (donor organism of P35S promoter). This method could be easily transposed to other common GMO sequences and other species and is applicable to other detection areas such as microbiology.

  1. Development and Validation of a P-35S, T-nos, T-35S and P-FMV Tetraplex Real-time PCR Screening Method to Detect Regulatory Genes of Genetically Modified Organisms in Food. (United States)

    Eugster, Albert; Murmann, Petra; Kaenzig, Andre; Breitenmoser, Alda


    In routine analysis screening methods based on real-time PCR (polymerase chain reaction) are most commonly used for the detection of genetically modified (GM) plant material in food and feed. Screening tests are based on sequences frequently used for GM development, allowing the detection of a large number of GMOs (genetically modified organisms). Here, we describe the development and validation of a tetraplex real-time PCR screening assay comprising detection systems for the regulatory genes Cauliflower Mosaic Virus 35S promoter, Agrobacterium tumefaciens nos terminator, Cauliflower Mosaic Virus 35S terminator and Figwort Mosaic Virus 34S promoter. Three of the four primer and probe combinations have already been published elsewhere, whereas primers and probe for the 35S terminator have been developed in-house. Adjustment of primer and probe concentrations revealed a high PCR sensitivity with insignificant physical cross-talk between the four detection channels. The sensitivity of each PCR-system is sufficient to detect a GMO concentration as low as 0.05% of the containing respective element. The specificity of the described tetraplex is high when tested on DNA from GM maize, soy, rapeseed and tomato. We also demonstrate the robustness of the system by inter-laboratory tests. In conclusion, this method provides a sensitive and reliable screening procedure for the detection of the most frequently used regulatory elements present in GM crops either authorised or unauthorised for food.

  2. Saturable binding of /sup 35/S-t-butylbicyclophosphorothionate to the sites linked to the GABA receptor and the interaction with gabaergic agents

    Energy Technology Data Exchange (ETDEWEB)

    Wong, D.T.; Threlkeld, P.G.; Bymaster, F.P.; Squires, R.F.


    /sup 35/-S-t-Butylbicyclophosphorothionate (/sup 35/S-TBPS) binds in a concentration-saturable manner to specific sites on membranes from rat cerebral cortex. Using a filtration assay at 25/sup 0/C, in 250 mM NaCl, specific binding of /sup 35/S-TBPS constitutes about 84 to 94 percent of total binding, depending on radioligand concentrations. /sup 35/S-TBPS binding is optimal in the presence of NaCl or NaBr and substantially less in the presence of NaI or NaF. It is sensitive to the treatment with 0.05 percent Triton X-100 but not to repeated freezing and thawing, procedures which increase /sup 3/H-GABA binding. Pharmacological studies show that /sup 35/S-TBPS binding is strongly inhibited by GABA-A receptor agonists (e.g., GABA and muscimol) and by the noncompetitive antagonist, picrotoxin, but not the competitive antagonist, bicuculline. Compounds which enhance binding of radioactive GABA and benzodiazepines, such as the pyrazolopyridines, cartazolate and trazolate, and a diaryl-triazine, LY81067, are also potent inhibitors of /sup 35/S-TBPS binding, with LY81067 being the most effective. The effects of GABA, picrotoxin

  3. Saturable binding of /sup 35/S-t-butylbicyclophosphorothionate to the sites linked to the GABA receptor and the interaction with gabaergic agents

    Energy Technology Data Exchange (ETDEWEB)

    Wong, D.T.; Threlkeld, P.G.; Bymaster, F.P.; Squires, R.F.


    /sup 35/S-t-Butylbicyclophosphorothionate (/sup 35/S-TBPS) binds in a concentration-saturable manner to specific sites on membranes from rat cerebral cortex. Using a filtration assay at 25/sup 0/C, in 250 mM NaCl, specific binding of /sup 35/S-TBPS constitutes about 84 to 94 percent of total binding, depending on radioligand concentrations. /sup 35/S-TBPS binding is optimal in the presence of NaCl or NaBr and substantially less in the presence of NaI or NaF. It is sensitive to the treatment with 0.05 percent Triton X-100 but not to repeated freezing and thawing, procedures which increase /sup 3/H-GABA binding. Pharmacological studies show that /sup 35/S-TBPS binding is strongly inhibited by GABA-A receptor agonists (e.g., GABA and muscimol) and by the noncompetitive antagonist, picrotoxin, but not the competitive antagonist, bicuculline. Compounds which enhance binding of radioactive GABA and benzodiazepines, such as the pyrazolopyridines, cartazolate and tracazolate, and a diaryltriazine, LY81067, are also potent inhibitors of /sup 35/S-TBPS binding, with LY81067 being the most effective. The effects of GABA, picrotoxin and LY81067 on the saturable binding of /sup 35/S-TBPS in cortical membranes are compared. The present findings are consistent with the interpretation that /sup 35/S-TBPS bind at or near the picrotoxin-sensitive anion recognition sites of the GABA/benzodiazepine/picrotoxin receptor complex.

  4. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)


    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic aci...

  5. Effect of chemical carcinogens and partial hepatectomy on in vivo ( sup 35 S)methionine interaction with rat liver tRNA

    Energy Technology Data Exchange (ETDEWEB)

    Kanduc, D.; Aresta, A.; Rossiello, M.R.; Ranieri, T.; Quagliariello, E. (Universita di Bari (Italy))


    The effect of carcinogens given by a single or multiple injections on the extent of ({sup 35}S)methionine interaction with hepatic tRNA was studied in normal and partially hepatectomized rats. Either partial hepatectomy or administration of ethionine (100 or 330 mg/kg body weight) and dimethylnitrosamine (120 mg/kg body weight) by multiple i.p. injections inhibited the ({sup 35}S)methionine-tRNA interaction, while administration of hepatocarcinogenic chemicals plus PH resulted rather in a stimulation. Methylnitrosourea enhanced the extent of interaction when administered in a single dose (100 mg per kg body weight) 18 h after partial hepatectomy.

  6. Enhancement of the nucleosomal pattern in sequences of lower complexity

    DEFF Research Database (Denmark)

    Bolshoy, Alexander; Shapiro, Kevin; Trifonov, Edward N.;


    in those of higher linguistic complexity. The nucleosome DNA positioning pattern is one of the weakest (highly degenerate) sequence patterns. It has been extracted recently by specially designed multiple alignment procedures. We applied the most sensitive of these procedures to nearly equal subsets...

  7. Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers

    Directory of Open Access Journals (Sweden)

    Kuzin Alexander


    Full Text Available Abstract Background The presence of highly conserved sequences within cis-regulatory regions can serve as a valuable starting point for elucidating the basis of enhancer function. This study focuses on regulation of gene expression during the early events of Drosophila neural development. We describe the use of EvoPrinter and cis-Decoder, a suite of interrelated phylogenetic footprinting and alignment programs, to characterize highly conserved sequences that are shared among co-regulating enhancers. Results Analysis of in vivo characterized enhancers that drive neural precursor gene expression has revealed that they contain clusters of highly conserved sequence blocks (CSBs made up of shorter shared sequence elements which are present in different combinations and orientations within the different co-regulating enhancers; these elements contain either known consensus transcription factor binding sites or consist of novel sequences that have not been functionally characterized. The CSBs of co-regulated enhancers share a large number of sequence elements, suggesting that a diverse repertoire of transcription factors may interact in a highly combinatorial fashion to coordinately regulate gene expression. We have used information gained from our comparative analysis to discover an enhancer that directs expression of the nervy gene in neural precursor cells of the CNS and PNS. Conclusion The combined use EvoPrinter and cis-Decoder has yielded important insights into the combinatorial appearance of fundamental sequence elements required for neural enhancer function. Each of the 30 enhancers examined conformed to a pattern of highly conserved blocks of sequences containing shared constituent elements. These data establish a basis for further analysis and understanding of neural enhancer function.

  8. Protoneus-sequence: extended fluid-attenuated inversion recovery MR imaging without and with contrast enhancement

    Energy Technology Data Exchange (ETDEWEB)

    Nasel, Christian [Division of Neuroradiology, Department of Radiology, Medical University of Vienna, Waehringerguertel 18-20, A-1090 Vienna (Austria)]. E-mail:


    Fluid-attenuated inversion recovery imaging (=flair imaging) is widely used as primary screening sequence in various investigation protocols, due to its high lesion contrast and sensitivity in detection of parenchymatous and leptomeningeal disease. An additional increase of sensitivity for detection of lesions may be achieved by contrast-enhanced flair imaging. Based on flair imaging a dual-echo inversion recovery imaging sequence (=proton echo usage [=protoneus] - sequence) was developed, which could significantly extend the possibilities of conventional flair imaging.

  9. The expression of foreign gene under the control of cauliflower mosaic virus 35s RNA promoter

    Institute of Scientific and Technical Information of China (English)

    WangHao; BaiYongyan


    The promoter region of cauliflower mosaic virus (CaMV) 35s RNA was employed to construct an intermediate expression vector which can be used in Ti plasmid system of Agrobacterium iumefaciens.The original plasmid,which contains a polylinker between CaMV 35s RNA and its 3' termination signal in pUC18 was modified to have another antibiotic resistance marker (kanamycin resistance gene Kmr) to facilitate the selection of recombinant with Ti plasmid.Octopine synthase (ocs) structural gene was inserted into this vector downstream of CaMV 35s RNA promoter.This chimaeric gene was introduced into integrative Ti plasmid vector pGV 3850,and then transformed into Nicotiana tobaccum the chimaeric gene into tobacco cells.In both cases,the expression of ocs gene was demonstrated.The amount of octopine was much more than the nopaline synthesized by nopaline synthase (nos) gene transferred at the same time with Ti plasmid vector.This demonstrated that CaMV 35s RNA promoter is stronger in transcriptional function than the promoter of nos in tobacco cells.

  10. Noribogaine stimulates naloxone-sensitive [35S]GTPgammaS binding. (United States)

    Pablo, J P; Mash, D C


    Noribogaine is formed in vivo by the O-demethylation of the indole alkaloid ibogaine. We report here that noribogaine acts as a full agonist at the mu-opioid receptor. Noribogaine-stimulated guanylyl 5'gamma-[35S]thio]triphosphate ([35S]GTPgammaS) was studied in rat thalamic membranes to measure activation of guanine nucleotide binding proteins (G-proteins) in the presence of excess GDP. Noribogaine caused a 170% increase above basal [35S]GTPgammaS binding at sub-micromolar effective concentrations (EC50) in a naloxone-sensitive manner, confirming that this effect was an opioid receptor-mediated process. The level of intrinsic activity for noribogaine in these assays was comparable to the full agonists DAMGO and morphine. In contrast, ibogaine had no significant effect on [35S]GTPgammaS binding over a similar concentration range. The efficacy of noribogaine as a full mu-opioid agonist may explain ibogaine's ability to block the acute signs of opiate withdrawal and its suppressive effects on morphine self-administration.

  11. PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. (United States)

    Pei, Jimin; Grishin, Nick V


    Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structures in public databases could be used to improve alignment quality. PROMALS3D is a tool for protein MSA construction enhanced with additional evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure databases for input proteins, derives structure-based constraints from alignments of three-dimensional structures, and combines them with sequence-based constraints of profile-profile alignments in a consistency-based framework to construct high-quality multiple sequence alignments. PROMALS3D output is a consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D Web server and package are available at

  12. Peptide Nucleic Acids Having Enhanced Binding Affinity, Sequence Specificity and Solubility

    DEFF Research Database (Denmark)


    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and solubility. The peptide nucleic acids comprise ligands selected from a group consisting of naturally......-occurring nucleobases and non-naturally-occurring nucleobases attached to a polyamide backbone, and contain C1-C8 alkylamine side chains. Methods of enhancing the solubility, binding affinity and sequence specificity of PNAs are provided....

  13. Diagnostic accuracy of unenhanced, contrast-enhanced perfusion and angiographic MRI sequences for pulmonary embolism diagnosis: results of independent sequence readings

    Energy Technology Data Exchange (ETDEWEB)

    Revel, Marie Pierre [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Hotel-Dieu, Service de Radiologie, Paris (France); Sanchez, Olivier; Meyer, Guy [Hopital Europeen Georges Pompidou, APHP, Respiratory and intensive care and, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM Unite 765, Paris (France); Lefort, Catherine; Couchon, Sophie; Hernigou, Anne; Frija, Guy [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Niarra, Ralph [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Chatellier, Gilles [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM CIC-EC E4, Paris (France)


    To independently evaluate unenhanced, contrast-enhanced perfusion and angiographic MR sequences for pulmonary embolism (PE) diagnosis. Prospective investigation, including 274 patients who underwent perfusion, unenhanced 2D steady-state-free-precession (SSFP) and contrast-enhanced 3D angiographic MR sequences on a 1.5-T unit, in addition to CTA (CT angiography). Two independent readers evaluated each sequence independently in random order. Sensitivity, specificity, predictive values and inter-reader agreement were calculated for each sequence, excluding sequences judged inconclusive. Sensitivity was also calculated according to PE location. Contrast-enhanced angiographic sequences showed the highest sensitivity (82.9 and 89.7 %, reader 1 and reader 2, respectively), specificity (98.5 and 100 %) and agreement (kappa value 0.77). Unenhanced angiographic sequences, although less sensitive overall (68.7 and 76.4 %), were sensitive for the detection of proximal PE (92.7 and 100 %) and showed high specificity (96.1 and 99.1 %) and good agreement (kappa value 0.62). Perfusion sequences showed lower sensitivity (75.0 and 79.3 %), specificity (84.8 and 89.7 %) and agreement (kappa value 0.51), and a negative predictive value of 84.8 % at best. Compared with contrast-enhanced angiographic sequences, unenhanced sequences demonstrate lower sensitivity, except for proximal PE, but high specificity and agreement. The negative predictive value of perfusion sequences was insufficient to safely rule out PE. (orig.)

  14. Quantifying groundwater travel time near managed recharge operations using 35S as an intrinsic tracer (United States)

    Urióstegui, Stephanie H.; Bibby, Richard K.; Esser, Bradley K.; Clark, Jordan F.


    Identifying groundwater retention times near managed aquifer recharge (MAR) facilities is a high priority for managing water quality, especially for operations that incorporate recycled wastewater. To protect public health, California guidelines for Groundwater Replenishment Reuse Projects require a minimum 2-6 month subsurface retention time for recycled water depending on the level of disinfection, which highlights the importance of quantifying groundwater travel times on short time scales. This study developed and evaluated a new intrinsic tracer method using the naturally occurring radioisotope sulfur-35 (35S). The 87.5 day half-life of 35S is ideal for investigating groundwater travel times on the managers. Natural concentrations of 35S found in water as dissolved sulfate (35SO4) were measured in source waters and groundwater at the Rio Hondo Spreading Grounds in Los Angeles County, CA, and Orange County Groundwater Recharge Facilities in Orange County, CA. 35SO4 travel times are comparable to travel times determined by well-established deliberate tracer studies. The study also revealed that 35SO4 in MAR source water can vary seasonally and therefore careful characterization of 35SO4 is needed to accurately quantify groundwater travel time. More data is needed to fully assess whether or not this tracer could become a valuable tool for managers.

  15. Alpha beta T-cell development is not affected by inversion of TCR beta gene enhancer sequences: polar enhancement of gene expression regardless of enhancer orientation. (United States)

    Huang, Fang; Cabaud, Olivier; Verthuy, Christophe; Hueber, Anne-Odile; Ferrier, Pierre


    V(D)J recombination and expression of the T-cell receptor beta (TCRbeta) gene are required for the development of the alphabeta T lymphocyte lineage. These processes depend on a transcriptional enhancer (Ebeta) which acts preferentially on adjacent upstream sequences, and has little impact on the 5' distal and 3' proximal regions of the TCRbeta locus. Using knock-in mice, we show that alphabeta T-cell differentiation and TCRbeta gene recombination and expression are not sensitive to the orientation of Ebeta sequences. We discuss the implication of these results regarding the mode of enhancer function at this locus during T lymphocyte development.

  16. Ex vivo binding of t-( sup 35 S) butylbicyclophosphorothionate: A biochemical tool to study the pharmacology of ethanol at the gamma-aminobutyric acid-coupled chloride channel

    Energy Technology Data Exchange (ETDEWEB)

    Sanna, E.; Concas, A.; Serra, M.; Santoro, G.; Biggio, G. (Univ. of Cagliari (Italy))


    The effects of acute administration of ethanol on t-(35S)Butylbiclophosphorothionate (35S-TBPS) binding measured ex vivo in unwashed membrane preparations of rat cerebral cortex were investigated. Ethanol, given i.g., decreased in a dose-related (0.5-4 g/kg) and time-dependent manner the binding of 35S-TBPS. This effect was similar to that induced by the administration of diazepam (0.5-4 mg/kg i.p.). Scatchard plot analysis of this radioligand binding revealed that ethanol, differently from diazepam, decreased the apparent affinity of 35S-TBPS recognition sites whereas it failed to change the density of these binding sites. The effect of ethanol on 35S-TBPS binding could not be reversed by the previous administration to rats of the benzodiazepine receptor antagonist, Ro 15-1788 (ethyl-8-fluoro-5,6-dihydro-5-methyl-6-oxo-4H- imidazo (1,5a) (1,4) benzodiazepine-3-carboxylate). Vice versa, the benzodiazepine receptor partial inverse agonist, Ro 15-4513 (ethyl-8-azido-5,6-dihydro-5-methyl-6-oxo-4H- imidazo (1,5a) (4,4) benzodiazepine-3-carboxylate) (8 mg/kg i.p.), prevented completely ethanol-induced decrease of 35S-TBPS binding. The ability of Ro 15-4513 to prevent the action of ethanol was shared by the anxiogenic and proconvulsant beta-carboline derivatives, FG 7142 (N-methyl-beta-carboline-3-carboxamide) (12.5 mg/kg i.p.) and ethyl-beta-carboline-3-carboxylate (0.6 mg/kg i.v.), which, per se, enhanced this parameter. Moreover, ethanol (0.5-4 g/kg) was able to reverse the increase of 35S-TBPS binding elicited by the s.c. injection of isoniazid (350 mg/kg) and to clearly attenuate the severity of tonic-clonic seizures produced by this inhibitor of the GABAergic transmission.

  17. Sequence comparison for non-enhanced MRA of the lower extremity arteries at 7 Tesla.

    Directory of Open Access Journals (Sweden)

    Sören Johst

    Full Text Available In this study three sequences for non-contrast-enhanced MRA of the lower extremity arteries at 7T were compared. Cardiac triggering was used with the aim to reduce signal variations in the arteries. Two fast single-shot 2D sequences, a modified Ultrafast Spoiled Gradient Echo (UGRE sequence and a variant of the Quiescent-Interval Single-Shot (QISS sequence were triggered via phonocardiogram and compared in volunteer examinations to a non-triggered 2D gradient echo (GRE sequence. For image acquisition, a 16-channel transmit/receive coil and a manually positionable AngioSURF table were used. To tackle B1 inhomogeneities at 7T, Time-Interleaved Acquisition of Modes (TIAMO was integrated in GRE and UGRE. To compare the three sequences quantitatively, a vessel-to-background ratio (VBR was measured in all volunteers and stations. In conclusion, cardiac triggering was able to suppress flow artifacts satisfactorily. The modified UGRE showed only moderate image artifacts. Averaged over all volunteers and stations, GRE reached a VBR of 4.18±0.05, UGRE 5.20±0.06, and QISS 2.72±0.03. Using cardiac triggering and TIAMO imaging technique was essential to perform non-enhanced MRA of the lower extremities vessels at 7T. The modified UGRE performed best, as observed artifacts were only moderate and the highest average VBR was reached.

  18. Feasibility of Single Molecule DNA Sequencing using Surface-Enhanced Raman Scattering

    Energy Technology Data Exchange (ETDEWEB)

    Talley, C E; Reboredo, F; Chan, J; Lane, S M


    We have used a combined theoretical and experimental approach in order to assess the feasibility of using surface-enhanced Raman scattering (SERS) for DNA sequencing at the single molecule level. We have developed a numerical tool capable of calculating the E-field and resulting SERS enhancement factors for metallic structures of arbitrary size and shape. Measurements of the additional SERS enhancement by combining SERS with coherent antistokes Raman scattering (CARS) show that only modest increases in the signal are achievable due to thermal damage at higher laser powers. Finally, measurements of the SERS enhancement from nanoparticles coated with an insulating layer show that the SERS enhancement is decreased by as much as two orders of magnitude when the molecule is not in contact with the metal surface.

  19. New metabolic labelling medium for Trichomonas vaginalis and Tritrichomonas foetus using 35S methionine

    Energy Technology Data Exchange (ETDEWEB)

    Torian, B.E.; Kenny, G.E.


    A metabolic labelling medium was devised for Trichomonas vaginalis and Tritrichomonas foetus utilizing 35S methionine. T. vaginalis cultured for 24h in the medium took up approximately 27% of the available label and increased greater than two fold in number. Counts per microgram of protein were 32,555 +/- 10% between different strains or identical strains in different labelling runs. T. foetus took up approximately 5% of the available label and increased greater than two fold in 24h. This resulted in specific labelling of 12,704 cpm/ug protein +/- 10% between different runs with the same strain.

  20. Molecular Identification of Transgenic Tomato in Iran by P35S PromoterBased PCR

    Directory of Open Access Journals (Sweden)

    Parastoo Khanmohammad


    Full Text Available Background: With the increasing population of the world, we should face food shortages in the near future. In this regard, agriculture of transgenic crops becomes very important. However, ensuring of GM products labeling is of great importance. Tomato is one of the most important food crops and for this reason it has undergone many genetic changes. This study aims to introduce a rapid, sensitive, and accurate method to identify non-labeled transgenic tomatoes in Iran market. Results: In this study, after optimization of PCR test based on P35S promoter, the amplicon was cloned in the plasmid PTZ57R in Escherichia coli JM107 to confirm and make positive control. After optimized PCR test of 50 tomatoes it was found that 4% of the Iranian markets’ tomatoes contain P35S promoter and are probably transgenic while none of the samples have been labeled in this regard. Conclusion: PCR technique is a suitable, available, fast and accurate method for screening transgenic products such as tomatoes.

  1. Method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation in conjunction with mass spectrometric analysis (United States)

    Laskin, Julia [Richland, WA; Futrell, Jean H [Richland, WA


    The invention relates to a method and apparatus for enhanced sequencing of complex molecules using surface-induced dissociation (SID) in conjunction with mass spectrometric analysis. Results demonstrate formation of a wide distribution of structure-specific fragments having wide sequence coverage useful for sequencing and identifying the complex molecules.

  2. Development of an intra-molecularly shuffled efficient chimeric plant promoter from plant infecting Mirabilis mosaic virus promoter sequence. (United States)

    Acharya, Sefali; Sengupta, Soumika; Patro, Sunita; Purohit, Sukumar; Samal, Sabindra K; Maiti, Indu B; Dey, Nrisingha


    We developed an efficient chimeric promoter, MUASMSCP, with enhanced activity and salicylic acid (SA)/abscisic acid (ABA) inducibility, incorporating the upstream activation sequence (UAS) of Mirabilis mosaic virus full-length transcript (MUAS, -297 to -38) to the 5' end of Mirabilis mosaic virus sub-genomic transcript (MSCP, -306 to -125) promoter-fragment containing the TATA element. We compared the transient activity of the MUASMSCP promoter in tobacco/Arabidopsis protoplasts and in whole plant (Petunia hybrida) with the same that obtained from CaMV35S and MUAS35SCP promoters individually. The MUASMSCP promoter showed 1.1 and 1.5 times stronger GUS-activities over that obtained from MUAS35SCP and CaMV35S promoters respectively, in tobacco (Xanthi Brad) protoplasts. In transgenic tobacco (Nicotiana tabacum, var. Samsun NN), the MUASMSCP promoter showed 1.1 and 2.2 times stronger activities than MUAS35SCP and CaMV35S(2) promoters respectively. We observed a fair correlation between MUASMSCP-, MUAS35SCP- and CaMV35S(2)-driven GUS activities with the corresponding uidA-mRNA level in transgenic plants. X-gluc staining of transgenic germinating seed-sections and whole seedlings also support above findings. Protein-extracts made from tobacco protoplasts expressing GFP and human-IL-24 genes driven individually by the MUASMSCP promoter showed enhanced expression of the reporters compared to that obtained from the CaMV35S promoter. Furthermore, MUASMSCP-driven protoplast-derived human IL-24 showed enhanced cell inhibitory activity in DU-145 prostate cancer cells compared to that obtained from the CaMV35S promoter. We propose chimeric MUASMSCP promoter developed in the study could be useful for strong constitutive expression of transgenes in both plant/animal cells and it may become an efficient substitute for CaMV35S/CaMV35S(2) promoter.

  3. Thick-target external-bremsstrahlung spectra of 147Pm and 35S β rays (United States)

    Dhaliwal, A. S.; Powar, M. S.; Singh, M.


    External-bremsstrahlung spectra excited by soft β particles of 147Pm (Emaxβ=225 keV) and 35S (Emaxβ=167 keV) in targets of Al, Cu, Sn, and Pb have been studied. The experimental and theoretical results are compared in terms of the number of photons of energy k per m0c2 per unit photon yield to exclude the uncertainty in the source strength measurement and overcome the inherent inadequacy of the normalization procedure used by earlier workers. The results of present measurements for medium- and high-Z elements show better agreement with the theory of Tseng and Pratt [Phys. Rev. A 3, 1714 (1976)] than with Elwert's corrections [Ann. Phys. (N.Y.) 34, 78 (1939)] to the Bethe-Heitler theory [Proc. R. Soc. London Ser. A 14, 83 (1934)], particularly at the higher-energy ends. However, for low-Z elements, both theories are found to be adequate.

  4. Use of natural 35S to trace sulphate cycling in small lakes, Flattops Wilderness Area, Colorado, U.S.A. (United States)

    Michel, Robert L.; Turk, John T.; Campbell, Donald H.; Mast, M. Alisa


    Measurements of the cosmogenically-produced 35S, a radioisotope of sulphur (t1/2 = 87 days), are reported for the Ned Wilson Lake watershed in Colorado. The watershed contains two small lakes and a flowing spring presumed to be representative of local ground water. The watershed is located in the Flattops Wilderness Area and the waters in the system have low alkalinity, making them sensitive to increases in acid and sulphate deposition. Time series of 35S measurements were made during the summers of 1995 and 1996 (July–September) at all three sites. The system is dominated by melting snow and an initial concentration of 16–20 mBq L-1was estimated for snowmelt based on a series of snow samples collected in the Rocky Mountains. The two lakes had large initial 35S concentrations in July, indicating that a large fraction of the lake water and sulphate was introduced by meltwater from that year's snowpack. In 1995 and 1996, 35S concentrations decreased more rapidly than could be accounted for by decay, indicating that other processes were affecting 35S concentrations. The most likely explanation is that exchange with sediments or the biota was removing 35S from the lake and replacing it with older sulphate devoid of 35S. In September of 1995 and 1996, 35S concentrations increased, suggesting that atmospheric deposition is important in the sulphate flux of these lakes in late summer. Sulphur-35 concentrations in the spring water were highly variable but never higher than 3.6 mBq L-1 and averaged 2 mBq L-1. Using a simple mixing model, it was estimated that 75% of the spring water was derived from precipitation of previous years.

  5. Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences.

    Directory of Open Access Journals (Sweden)

    Mohammed Bakkali

    Full Text Available Among the many bacteria naturally competent for transformation by DNA uptake-a phenomenon with significant clinical and financial implications- Pasteurellaceae and Neisseriaceae species preferentially take up DNA containing specific short sequences. The genomic overrepresentation of these DNA uptake enhancing sequences (DUES causes preferential uptake of conspecific DNA, but the function(s behind this overrepresentation and its evolution are still a matter for discovery. Here I analyze DUES genome dynamics and evolution and test the validity of the results to other selectively constrained oligonucleotides. I use statistical methods and computer simulations to examine DUESs accumulation in Haemophilus influenzae and Neisseria gonorrhoeae genomes. I analyze DUESs sequence and nucleotide frequencies, as well as those of all their mismatched forms, and prove the dependence of DUESs genomic overrepresentation on their preferential uptake by quantifying and correlating both characteristics. I then argue that mutation, uptake bias, and weak selection against DUESs in less constrained parts of the genome combined are sufficient enough to cause DUESs accumulation in susceptible parts of the genome with no need for other DUES function. The distribution of overrepresentation values across sequences with different mismatch loads compared to the DUES suggests a gradual yet not linear molecular drive of DNA sequences depending on their similarity to the DUES. Other genomically overrepresented sequences, both pro- and eukaryotic, show similar distribution of frequencies suggesting that the molecular drive reported above applies to other frequent oligonucleotides. Rare oligonucleotides, however, seem to be gradually drawn to genomic underrepresentation, thus, suggesting a molecular drag. To my knowledge this work provides the first clear evidence of the gradual evolution of selectively constrained oligonucleotides, including repeated, palindromic and protein

  6. Sequence-selective DNA recognition and enhanced cellular up-take by peptide-steroid conjugates. (United States)

    Ruiz García, Yara; Iyer, Abhishek; Van Lysebetten, Dorien; Pabon, Y Vladimir; Louage, Benoit; Honcharenko, Malgorzata; De Geest, Bruno G; Smith, C I Edvard; Strömberg, Roger; Madder, Annemieke


    Several GCN4 bZIP TF models have previously been designed and synthesized. However, the synthetic routes towards these constructs are typically tedious and difficult. We here describe the substitution of the Leucine zipper domain of the protein by a deoxycholic acid derivative appending the two GCN4 binding region peptides through an optimized double azide-alkyne cycloaddition click reaction. In addition to achieving sequence specific dsDNA binding, we have investigated the potential of these compounds to enter cells. Confocal microscopy and flow cytometry show the beneficial influence of the steroid on cell uptake. This unique synthetic model of the bZIP TF thus combines sequence specific dsDNA binding properties with enhanced cell-uptake. Given the unique properties of deoxycholic acid and the convergent nature of the synthesis, we believe this work represents a key achievement in the field of TF mimicry.

  7. Nucleotide sequence and infectious cDNA clone of the L1 isolate of Pea seed-borne mosaic potyvirus. (United States)

    Olsen, B S; Johansen, I E


    The complete nucleotide sequence of Pea seed-borne mosaic potyvirus isolate L1 has been determined from cloned virus cDNA. The PSbMV L1 genome is 9895 nucleotides in length excluding the poly(A) tail. Computer analysis of the sequence revealed a single long open reading frame (ORF) of 9594 nucleotides. The ORF potentially encodes a polyprotein of 3198 amino acids with a deduced Mr of 363537. Nine putative proteolytic cleavage sites were identified by analogy to consensus sequences and genome arrangement in other potyviruses. Two full-length cDNA clones, p35S-L1-4 and p35S-L1-5, were assembled under control of an enhanced 35S promoter and nopaline synthase terminator. Clone p35S-L1-4 was constructed with four introns and p35S-L1-5 with five introns inserted in the cDNA. Clone p35S-L1-4 was unstable in Escherichia coli often resulting in amplification of plasmids with deletions. Clone p35S-L1-5 was stable and apparently less toxic to Escherichia coli resulting in larger bacterial colonies and higher plasmid yield. Both clones were infectious upon mechanical inoculation of plasmid DNA on susceptible pea cultivars Fjord, Scout, and Brutus. Eight pea genotypes resistant to L1 virus were also resistant to the cDNA derived L1 virus. Both native PSbMV L1 and the cDNA derived virus infected Chenopodium quinoa systemically giving rise to characteristic necrotic lesions on uninoculated leaves.

  8. Enhancing distributive mixing of immiscible polyethylene/thermoplastic starch blend through zeolite ZSM-5 compounding sequence. (United States)

    Thipmanee, Ranumas; Lukubira, Sam; Ogale, Amod A; Sane, Amporn


    The aim of this work was to explore the effect of zeolite ZSM-5 (ZSM5) incorporation sequence on the phase morphology, microstructure, and performance of polyethylene/thermoplastic starch (PE/TPS) films. Two processing sequences were used for preparing PE/TPS/ZSM5 composites at a weight ratio of PE to TPS of 70:30 and ZSM5 concentrations of 1-5 wt%: (i) melt compounding of PE with ZSM5 prior to melt blending with TPS (SI); and (ii) TPS was compounded with ZSM5 prior to blending with PE (SII). Distributive mixing and mechanical properties of PE/TPS blend were greatly enhanced when ZSM5 was incorporated via SII. These were caused by both the higher affinity between PE and ZSM5, compared to that of TPS and ZSM5, and the reduction of TPS viscosity after compounding with ZSM5, leading to migration of ZSM5 from TPS dispersed phase toward PE matrix and increase in breakup of TPS droplets during SII sequence.

  9. Investigating atmospheric transport processes using cosmogenic 35S and oxygen isotopic anomaly (Δ17O) in sulfate (United States)

    Hill-Falkenthal, J. C.; Pandey, A.; Coupal, E.; Kim, S. D.; Dominguez, G.; Thiemens, M. H.


    Sulfate aerosols have been recognized to possess hazardous impact on both climate and human health. Improved understanding of the SO2 residence time and sulfate aerosol transport is needed for assessing its influences on climate. Cosmogenically produced 35S (half-life~87 days)1 measurements have been used to understand the atmospheric transport process, boundary layer dynamics and its effect on the tropospheric SO2 oxidation rate constant. Our method involves determining 35S in gaseous SO2 and aerosol sulfate samples collected twice a week at Scripps Institute of Oceanography Pier (La Jolla, CA) for a year along with the determination of oxygen isotopes in both coarse and fine particle samples. The oxygen isotopes measurement in sulfate and 35S measurements were done by isotope ratio mass spectrometry and low-noise liquid scintillation spectroscopy2, respectively. The data show that 35S activity is significantly different for coarse and fine particles, with the latter possessing higher activity as it is mainly produced from the gas phase oxidation of SO2 at higher altitude. The fluctuation in 35S activity in fine particles indicates mixing of air masses from higher altitude. The coarse particles show nearly constant 35S activity which is either due to the constant uptake rate of SO2 by sea salt aerosol or the coagulation of fine particles together. The normalized activity 35S/S is about 5 times higher in both coarse and fine particles during Santa Ana wind event. Santa Ana wind is characterized by low humidity (<20%) and relatively high temperature and may have an impact on SO2 oxidation. We are investigating the sulfate oxygen isotope signature and the correlation between oxygen anomaly and 35S activity in sulfate. 1. Lal D., P. K. Malhotra, and B. Peters, On the production of radioisotopes in the atmosphere by cosmic radiation and their application in meteorology, J. Atmos. AndTerrest. Phys. 12, 306, 1958 2. Brother, L.A., G. Dominguez, A. Abramian, A. Corbin

  10. Recombinase polymerase amplification (RPA) of CaMV-35S promoter and nos terminator for rapid detection of genetically modified crops. (United States)

    Xu, Chao; Li, Liang; Jin, Wujun; Wan, Yusong


    Recombinase polymerase amplification (RPA) is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37-42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S) promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos) terminator, which are widely incorporated in genetically modified (GM) crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15-25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean). With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops.

  11. Recombinase Polymerase Amplification (RPA of CaMV-35S Promoter and nos Terminator for Rapid Detection of Genetically Modified Crops

    Directory of Open Access Journals (Sweden)

    Chao Xu


    Full Text Available Recombinase polymerase amplification (RPA is a novel isothermal DNA amplification and detection technology that enables the amplification of DNA within 30 min at a constant temperature of 37–42 °C by simulating in vivo DNA recombination. In this study, based on the regulatory sequence of the cauliflower mosaic virus 35S (CaMV-35S promoter and the Agrobacterium tumefaciens nopaline synthase gene (nos terminator, which are widely incorporated in genetically modified (GM crops, we designed two sets of RPA primers and established a real-time RPA detection method for GM crop screening and detection. This method could reliably detect as few as 100 copies of the target molecule in a sample within 15–25 min. Furthermore, the real-time RPA detection method was successfully used to amplify and detect DNA from samples of four major GM crops (maize, rice, cotton, and soybean. With this novel amplification method, the test time was significantly shortened and the reaction process was simplified; thus, this method represents an effective approach to the rapid detection of GM crops.

  12. Metabolism of 35S- and 14C-labeled 1-methyl-2-mercaptoimidazole in vitro and in vivo. (United States)

    Taurog, A; Dorris, M L; Guziec, F S


    We previously described an in vitro incubation system for studying the mechanism of inhibition of thyroid peroxidase (TPO)-catalyzed iodination by the antithyroid drug 1-methyl-2-mercaptoimidazole (MMI). Inhibition of iodination in this system may be reversible or irreversible, depending on the relative concentrations of iodide and MMI and on the TPO concentration. Metabolism of the drug occurs under both conditions, and in the present investigation we used 35S- and 14C-labeled MMI together with reverse phase HPLC to examine the metabolic products associated with reversible and irreversible inhibition of iodination by MMI. Under conditions of reversible inhibition, MMI was rapidly metabolized and disappeared completely from the incubation mixture. With [35S]MMI, the earliest detectable 35S-labeled product was MMI disulfide, which reached a peak after a few minutes and then declined to undetectable levels. Coincident with the decrease in disulfide was the appearance of two 35S peaks, the major one corresponding to sulfate/sulfite, and the other to a component eluting at 7.5 min. Similar results were obtained for the disulfide and for the 7.5 min metabolite with [14C]MMI. The major 14C-labeled metabolite containing no S appeared to be 1-methylimidazole. Under conditions of irreversible inhibition, MMI disulfide was also the earliest detectable 35S-labeled metabolite. However, MMI decreased more slowly, and after reaching a nadir at about 6 min returned gradually to a level about halfway between the initial and the minimum value. The reformation of MMI appeared to involve the nonenzymatic disproportionation of MMI disulfide. Formation of the 7.5 min peak was also observed, but there was no formation of sulfate/sulfite. The difference in metabolic pattern between the reversible and irreversible conditions is primarily related to the rapid inactivation of TPO that occurs under irreversible conditions. The metabolism of [35S]MMI in thyroids of rats injected with the

  13. Video Enhancement and Dynamic Range Control of HDR Sequences for Automotive Applications

    Directory of Open Access Journals (Sweden)

    Giovanni Ramponi


    Full Text Available CMOS video cameras with high dynamic range (HDR output are particularly suitable for driving assistance applications, where lighting conditions can strongly vary, going from direct sunlight to dark areas in tunnels. However, common visualization devices can only handle a low dynamic range, and thus a dynamic range reduction is needed. Many algorithms have been proposed in the literature to reduce the dynamic range of still pictures. Anyway, extending the available methods to video is not straightforward, due to the peculiar nature of video data. We propose an algorithm for both reducing the dynamic range of video sequences and enhancing its appearance, thus improving visual quality and reducing temporal artifacts. We also provide an optimized version of our algorithm for a viable hardware implementation on an FPGA. The feasibility of this implementation is demonstrated by means of a case study.

  14. Exploration of the Brn4-regulated genes enhancing adult hippocampal neurogenesis by RNA sequencing. (United States)

    Guo, Jingjing; Cheng, Xiang; Zhang, Lei; Wang, Linmei; Mao, Yongxin; Tian, Guixiang; Xu, Wenhao; Wu, Yuhao; Ma, Zhi; Qin, Jianbing; Tian, Meiling; Jin, Guohua; Shi, Wei; Zhang, Xinhua


    Adult hippocampal neurogenesis is essential for learning and memory, and its dysfunction is involved in neurodegenerative diseases. However, the molecular mechanisms underlying adult hippocampal neurogenesis are still largely unknown. Our previous studies indicated that the transcription factor Brn4 was upregulated and promoted neuronal differentiation of neural stem cells (NSCs) in the surgically denervated hippocampus in rats. In this study, we use high-throughput RNA sequencing to explore the molecular mechanisms underlying the enhancement of adult hippocampal neurogenesis induced by lentivirus-mediated Brn4 overexpression in vivo. After 10 days of the lentivirus injection, we found that the expression levels of genes related to neuronal development and maturation were significantly increased and the expression levels of genes related to NSC maintenance were significantly decreased, indicating enhanced neurogenesis in the hippocampus after Brn4 overexpression. Through RNA sequencing, we found that 658 genes were differentially expressed in the Brn4-overexpressed hippocampi compared with GFP-overexpressed controls. Many of these differentially expressed genes are involved in NSC division and differentiation. By using quantitative real-time PCR, we validated the expression changes of three genes, including Ctbp2, Notch2, and Gli1, all of which are reported to play key roles in neuronal differentiation of NSCs. Importantly, the expression levels of Ctbp2 and Notch2 were also significantly changed in the hippocampus of Brn4 KO mice, which indicates that the expression levels of Ctbp2 and Notch2 may be directly regulated by Brn4. Our current study provides a solid foundation for further investigation and identifies Ctbp2 and Notch2 as possible downstream targets of Brn4. © 2017 Wiley Periodicals, Inc.

  15. Online feedback enhances early consolidation of motor sequence learning and reverses recall deficit from transcranial stimulation of motor cortex. (United States)

    Wilkinson, Leonora; Steel, Adam; Mooshagian, Eric; Zimmermann, Trelawny; Keisler, Aysha; Lewis, Jeffrey D; Wassermann, Eric M


    Feedback and monetary reward can enhance motor skill learning, suggesting reward system involvement. Continuous theta burst (cTBS) transcranial magnetic stimulation (TMS) of the primary motor area (M1) disrupts processing, reduces excitability and impairs motor learning. To see whether feedback and reward can overcome the learning impairment associated with M1 cTBS, we delivered real or sham stimulation to two groups of participants before they performed a motor sequence learning task with and without feedback. Participants were trained on two intermixed sequences, one occurring 85% of the time (the "probable" sequence) and the other 15% of the time (the "improbable" sequence). We measured sequence learning as the difference in reaction time (RT) and error rate between probable and improbable trials (RT and error difference scores). Participants were also tested for sequence recall with the same indices of learning 60 min after cTBS. Real stimulation impaired initial sequence learning and sequence knowledge recall as measured by error difference scores and impaired sequence knowledge recall as measured by RT difference score. Relative to non-feedback learning, the introduction of feedback during sequence learning improved subsequent sequence knowledge recall indexed by RT difference score, in both real and sham stimulation groups and feedback reversed the RT difference score based sequence knowledge recall impairment from real cTBS that we observed in the non-feedback learning condition. Only the real cTBS group in the non-feedback condition showed no evidence of explicit sequence knowledge when tested at the end of the study. Feedback improves recall of implicit and explicit motor sequence knowledge and can protect sequence knowledge against the effect of M1 inhibition. Adding feedback and monetary reward/punishment to motor skill learning may help overcome retention impairments or accelerate training in clinical and other settings.

  16. Expression of a chemically synthesized gene for human epidermal growth factor under the control of cauliflower mosaic virus 35S promoter in transgenic tobacco. (United States)

    Higo, K; Saito, Y; Higo, H


    Nicotiana tabacum was transformed with a chemically synthesized gene encoding the human epidermal growth factor (hEGF) under control of the CaMV-35S promoter. The hEGF gene sequence was present at one to several copies in the primary transformant plants (R0), and a transcript with the expected length was produced. Slot blot analysis of total RNAs of the progeny (R1) seedlings, originating from self-pollination of the R0 plants, showed that the level of mRNA expression was generally, but not always, heritable. The highest hEGF peptide content per unit of total soluble protein in young (upper) R1 leaves so far examined by an immunological method was about 0.001%. These results suggest that either the hEGF peptide was less stable than the average leaf protein, or the hEGF mRNAs were not efficiently translated.

  17. Bioaggregate of photo-fermentative bacteria for enhancing continuous hydrogen production in a sequencing batch photobioreactor. (United States)

    Xie, Guo-Jun; Liu, Bing-Feng; Wang, Rui-Qing; Ding, Jie; Ren, Hong-Yu; Zhou, Xu; Ren, Nan-Qi


    Hydrogen recovery through solar-driven biomass conversion by photo-fermentative bacteria (PFB) has been regarded as a promising way for sustainable energy production. However, a considerable fraction of organic substrate was consumed for the growth of PFB as biocatalysts, furthermore, these PFB were continuously washed out from the photobioreactor in continuous operation because of their poor flocculation. In this work, PFB bioaggregate induced by L-cysteine was applied in a sequencing batch photobioreactor to enhance continuous hydrogen production and reduce biomass washout. The effects of the hydraulic retention time (HRT), influent concentration and light intensity on hydrogen production of the photobioreactor were investigated. The maximum hydrogen yield (3.35 mol H2/mol acetate) and production rate (1044 ml/l/d) were obtained at the HRT of 96 h, influent concentration of 3.84 g COD/l, and light intensity of 200 W/m(2). With excellent settling ability, biomass accumulated in the photobioreactor and reached 2.15 g/l under the optimum conditions. Structural analysis of bioaggregate showed that bacterial cells were covered and tightly linked together by extracellular polymeric substances, and formed a stable structure. Therefore, PFB bioaggregate induced by L-cysteine is an efficient strategy to improve biomass retention capacity of the photobioreactor and enhance hydrogen recovery efficiency from organic wastes.

  18. Comparison of four enhancement strategies for aerobic granulation in sequencing batch reactors. (United States)

    Gao, Dawen; Liu, Lin; Liang, Hong; Wu, Wei-Min


    Aerobic granules were developed in four identical sequencing batch reactors (SBRs) with synthetic wastewater to compare different strategies for the enhancement of granulation. The SBRs were operated by (a) increasing organic loading rate in R1; (b) reducing settling time in R2; (c) extending starvation period in R3; and (d) increasing shear force in R4. The results showed that four operational strategies were able to enhance aerobic granulation successfully in SBR, but that also showed different effect on the granulation process and characteristics of mature aerobic granules. The rapidest granulation was observed by using short settling time (R2) and the granules had higher extracellular polymeric substance (EPS) than other reactors. Extended starvation period (R3) and high shear force (R4) resulted in longer granulation period and the granules with higher integrity and smaller size. Higher organic loading rate (R1) resulted in the granules with larger size and higher K value. The maximum specific COD removal rates (q(max)) of the granules in all SBRs were at a similar level (0.13-0.16 g COD/h-g VSS) but the granules in R1 and R2 had higher apparent half rate constant (K) of 18 and 16 mg/L, than those in R3 and R4 (2.8 and 3.3 mg/L).

  19. Comparison of four enhancement strategies for aerobic granulation in sequencing batch reactors

    Energy Technology Data Exchange (ETDEWEB)

    Gao Dawen, E-mail: [School of Forestry, Northeast Forestry University, Harbin 150040 (China); State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin 150090 (China); Liu Lin; Liang Hong [School of Forestry, Northeast Forestry University, Harbin 150040 (China); Wu Weimin [Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305-4020 (United States)


    Aerobic granules were developed in four identical sequencing batch reactors (SBRs) with synthetic wastewater to compare different strategies for the enhancement of granulation. The SBRs were operated by (a) increasing organic loading rate in R1; (b) reducing settling time in R2; (c) extending starvation period in R3; and (d) increasing shear force in R4. The results showed that four operational strategies were able to enhance aerobic granulation successfully in SBR, but that also showed different effect on the granulation process and characteristics of mature aerobic granules. The rapidest granulation was observed by using short settling time (R2) and the granules had higher extracellular polymeric substance (EPS) than other reactors. Extended starvation period (R3) and high shear force (R4) resulted in longer granulation period and the granules with higher integrity and smaller size. Higher organic loading rate (R1) resulted in the granules with larger size and higher K value. The maximum specific COD removal rates (q{sub max}) of the granules in all SBRs were at a similar level (0.13-0.16 g COD/h-g VSS) but the granules in R1 and R2 had higher apparent half rate constant (K) of 18 and 16 mg/L, than those in R3 and R4 (2.8 and 3.3 mg/L).

  20. Delay enhancement patterns in apical hypertrophic cardiomyopathy by phase-sensitive inversion recovery sequence

    Institute of Scientific and Technical Information of China (English)

    Zi-Yi Guo; Jing Chen; Qi-Zhou Liang; Hai-Yan Liao; Shui-Xi Fu; Qian-Yu Tang; Cai-Xiang Chen; Xiang-Jun Han; Feng Gao


    Objective:Late gadolinium enhancement (LGE) patterns of cardiovascular magnetic resonance (CMR) relying on PSIR (phase-sensitive inversion recovery sequence) techniques had been used to determine the characteristics of LGE in apical hypertrophic cardiomyopathy (ApHCM). Methods:Forty patients pure ApHCM [age, (60.2±10.4) years, 31 men] were enrolled. LGE images were acquired using PSIR, and analyzed using a 17-segment model. Summing the LGE areas in all short axis slices yielded the total volume of late enhancement, which was subsequently presented as a proportion of total LV myocardium (%LGE). Results:Mean maximal apical wall thickness was (17.9±2.3) mm, and mean left ventricular (LV) ejection fraction was (67.7±8.0)%. LGE was detected in 130 segments of 30 patients (75.0%), occupying (4.9±5.5)%of LV myocardium. LGE was mainly detected at the junction between left and right ventricles in 12 (30%) and at the apex in 28 (70%), although LGE-positive areas were widely distributed, and not limited to the apex. Focal LGE at the non-hypertrophic LV segments was found in some ApHCM patients, even without LGE of hypertrophied apical segments. Conclusions: LGE was frequently observed not only in the thickened apex of the heart but also in other LV segments, irrespective of the presence or absence of hypertrophy. The simple presence of LGE on CMR was not representative of adverse prognosis in this population.

  1. An Enhanced Partial Transmit Sequence Segmentation Schemes to Reduce the PAPR in OFDM Systems

    Directory of Open Access Journals (Sweden)

    Yasir Amer Al-Jawhar


    Full Text Available Although the orthogonal frequency division multiplexing system (OFDM is widely used in high-speed data rate wire and wireless environment, the peak-to- average-power-ratio (PAPR is one of its major obstacles for the real applications. The high PAPR value leads some devices of the OFDM system such as power amplifiers and analog to digital converters to work out of band of these devices. Thus the system efficiency is degraded. Many techniques have been proposed to overcome the high PAPR in OFDM systems such as partial transmit sequences (PTS, selected mapping and interleaving technique. PTS is considered as one of the effective PAPR reduction methods; this scheme depends on segmentation of the input data into several subblocks and then combined again. The three well-known segmentation schemes are pseudo-random, adjacent and interleaving; each scheme has PAPR reduction performance, and computational complexity differs from one to another. In this paper, five types of segmentation schemes are proposed to improve the PAPR reduction execution including sine and cosine shape as well as hybrid interleaving and adjacent schemes in new approaches. From the simulation results, the proposed methods can achieve PAPR reduction performance greater than that of the adjacent and interleaving partition schemes, without increasing the computational complexity of the system. Moreover, the enhanced schemes can realize better PAPR performance with any number of subcarriers.

  2. Effect of BRCA2 sequence variants predicted to disrupt exonic splice enhancers on BRCA2 transcripts

    Directory of Open Access Journals (Sweden)

    Brewster Brooke L


    Full Text Available Abstract Background Genetic screening of breast cancer patients and their families have identified a number of variants of unknown clinical significance in the breast cancer susceptibility genes, BRCA1 and BRCA2. Evaluation of such unclassified variants may be assisted by web-based bioinformatic prediction tools, although accurate prediction of aberrant splicing by unclassified variants affecting exonic splice enhancers (ESEs remains a challenge. Methods This study used a combination of RT-PCR analysis and splicing reporter minigene assays to assess five unclassified variants in the BRCA2 gene that we had previously predicted to disrupt an ESE using bioinformatic approaches. Results Analysis of BRCA2 c.8308 G > A (p.Ala2770Thr by mRNA analysis, and BRCA2 c.8962A > G (p.Ser2988Gly, BRCA2 c.8972G > A (p.Arg2991His, BRCA2 c.9172A > G (p.Ser3058Gly, and BRCA2 c.9213G > T (p.Glu3071Asp by a minigene assay, revealed no evidence for aberrant splicing. Conclusions These results illustrate the need for improved methods for predicting functional ESEs and the potential consequences of sequence variants contained therein.

  3. Method for the typing of Clostridium difficile based on polyacrylamide gel electrophoresis of (/sup 35/S)methionine-labeled proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tabaqchali, S.; O' Farrell, S.; Holland, D.; Silman, R.


    A typing method for Clostridium difficile based on the incorporation of (/sup 35/S)methionine into cellular proteins, their separation by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and their visualization by autoradiography is described. On analysis of the radiolabeled-protein profiles, nine distinct groups were observed (A to E and W to Z). The method, which is simple, reproducible, and readily expandable, has been applied in epidemiological studies to demonstrate cross-infection and hospital acquisition of C. difficile.

  4. Acceptance-Enhanced Behavior Therapy (AEBT) for Trichotillomania and Chronic Skin Picking: Exploring the Effects of Component Sequencing (United States)

    Flessner, Christopher A.; Busch, Andrew M.; Heideman, Paul W.; Woods, Douglas W.


    This pilot study examined the utility of acceptance-enhanced behavior therapy (AEBT) for trichotillomania (TTM) and chronic skin picking (CSP) and the impact of altering treatment sequence on overall treatment efficacy. Participants referred to a TTM and CSP specialty clinic were assessed by an independent evaluator within separate, nonconcurrent,…

  5. Chunk concatenation evolves with practice and sleep-related enhancement consolidation in a complex arm movement sequence

    Directory of Open Access Journals (Sweden)

    Blischke Klaus


    Full Text Available This paper addresses the notion of chunk concatenation being associated with sleep-related enhancement consolidation of motor sequence memory, thereby essentially contributing to improvements in sequence execution speed. To this end, element movement times of a multi-joint arm movement sequence incorporated in a recent study by Malangré et al. (2014 were reanalyzed. As sequence elements differed with respect to movement distance, element movement times had to be purged from differences solely due to varying trajectory lengths. This was done by dividing each element movement time per subject and trial block by the respective “reference movement time” collected from subjects who had extensively practiced each sequence element in isolation. Any differences in these “relative element movement times” were supposed to reflect element-specific “production costs” imposed solely by the sequence context. Across all subjects non-idiosyncratic, lasting sequence segmentation was shown, and four possible concatenation points (i.e. transition points between successive chunks within the original arm movement sequence were identified. Based on theoretical suppositions derived from previous work with the discrete sequence production task and the dual processor model (Abrahamse et al., 2013, significantly larger improvements in transition speed occurring at these four concatenation points as compared to the five fastest transition positions within the sequence (associated with mere element execution were assumed to indicate increased chunk concatenation. As a result, chunk concatenation was shown to proceed during acquisition with physical practice, and, most importantly, to significantly progress some more during retention following a night of sleep, but not during a waking interval.

  6. V(D)J recombination frequency is affected by the sequence interposed between a pair of recombination signals: sequence comparison reveals a putative recombinational enhancer element. (United States)

    Roch, F A; Hobi, R; Berchtold, M W; Kuenzle, C C


    The immunoglobulin heavy chain intron enhancer (Emu) not only stimulates transcription but also V(D)J recombination of chromosomally integrated recombination substrates. We aimed at reproducing this effect in recombination competent cells by transient transfection of extrachromosomal substrates. These we prepared by interposing between the recombination signal sequences (RSS) of the plasmid pBlueRec various fragments, including Emu, possibly affecting V(D)J recombination. Our work shows that sequences inserted between RSS 23 and RSS 12, with distances from their proximal ends of 26 and 284 bp respectively, can markedly affect the frequency of V(D)J recombination. We report that the entire Emu, the Emu core as well as its flanking 5' and 3' matrix associated regions (5' and 3' MARs) upregulate V(D)J recombination while the downstream section of the 3' MAR of Emu does not. Also, prokaryotic sequences markedly suppress V(D)J recombination. This confirms previous results obtained with chromosomally integrated substrates, except for the finding that the full length 3' MAR of Emu stimulates V(D)J recombination in an episomal but not in a chromosomal context. The fact that other MARs do not share this activity suggests that the effect is no mediated through attachment of the recombination substrate to a nuclear matrix-associated recombination complex but through cis-activation. The presence of a 26 bp A-T-rich sequence motif in the 5' and 3' MARs of Emu and in all of the other upregulating fragments investigated, leads us to propose that the motif represents a novel recombinational enhancer element distinct from those constituting the Emu core.

  7. Enhanced adherence of methicillin-resistant Staphylococcus pseudintermedius sequence type 71 to canine and human corneocytes. (United States)

    Latronico, Francesca; Moodley, Arshnee; Nielsen, Søren Saxmose; Guardabassi, Luca


    The recent worldwide spread of methicillin-resistant Staphylococcus pseudintermedius (MRSP) in dogs is a reason for concern due to the typical multidrug resistance patterns displayed by some MRSP lineages such as sequence type (ST) 71. The objective of this study was to compare the in vitro adherence properties between MRSP and methicillin-susceptible (MSSP) strains. Four MRSP, including a human and a canine strain belonging to ST71 and two canine non-ST71 strains, and three genetically unrelated MSSP were tested on corneocytes collected from five dogs and six humans. All strains were fully characterized with respect to genetic background and cell wall-anchored protein (CWAP) gene content. Seventy-seven strain-corneocyte combinations were tested using both exponential- and stationary-phase cultures. Negative binomial regression analysis of counts of bacterial cells adhering to corneocytes revealed that adherence was significantly influenced by host and strain genotype regardless of bacterial growth phase. The two MRSP ST71 strains showed greater adherence than MRSP non-ST71 (p pseudintermedius adherence to canine corneocytes was significantly higher compared to human corneocytes (p < 0.0001), but the MRSP ST71 strain of human origin adhered equally well to canine and human corneocytes, suggesting that MRSP ST71 may be able to adapt to human skin. The genetic basis of the enhanced in vitro adherence of ST71 needs to be elucidated as this phenotypic trait may be associated to the epidemiological success and zoonotic potential of this epidemic MRSP clone.

  8. Peptide consensus sequence determination for the enhancement of the antimicrobial activity and selectivity of antimicrobial peptides (United States)

    Almaaytah, Ammar; Ajingi, Ya’u; Abualhaijaa, Ahmad; Tarazi, Shadi; Alshar’i, Nizar; Al-Balas, Qosay


    The rise of multidrug-resistant bacteria is causing a serious threat to the world’s human population. Recent reports have identified bacterial strains displaying pan drug resistance against antibiotics and generating fears among medical health specialists that humanity is on the dawn of entering a post-antibiotics era. Global research is currently focused on expanding the lifetime of current antibiotics and the development of new antimicrobial agents to tackle the problem of antimicrobial resistance. In the present study, we designed a novel consensus peptide named “Pepcon” through peptide consensus sequence determination among members of a highly homologous group of scorpion antimicrobial peptides. Members of this group were found to possess moderate antimicrobial activity with significant toxicity against mammalian cells. The aim of our design method was to generate a novel peptide with an enhanced antimicrobial potency and selectivity against microbial rather than mammalian cells. The results of our study revealed that the consensus peptide displayed potent antibacterial activities against a broad range of Gram-positive and Gram-negative bacteria. Our membrane permeation studies displayed that the peptide efficiently induced membrane damage and consequently led to cell death through the process of cell lysis. The microbial DNA binding assay of the peptide was found to be very weak suggesting that the peptide is not targeting the microbial DNA. Pepcon induced minimal cytotoxicity at the antimicrobial concentrations as the hemolytic activity was found to be zero at the minimal inhibitory concentrations (MICs). The results of our study demonstrate that the consensus peptide design strategy is efficient in generating peptides. PMID:28096686

  9. An enhanced method for sequence walking and paralog mining: TOPO® Vector-Ligation PCR

    Directory of Open Access Journals (Sweden)

    Davis Thomas M


    Full Text Available Abstract Background Although technological advances allow for the economical acquisition of whole genome sequences, many organisms' genomes remain unsequenced, and fully sequenced genomes may contain gaps. Researchers reliant upon partial genomic or heterologous sequence information require methods for obtaining unknown sequences from loci of interest. Various PCR based techniques are available for sequence walking - i.e., the acquisition of unknown DNA sequence adjacent to known sequence. Many such methods require rigid, elaborate protocols and/or impose narrowly confined options in the choice of restriction enzymes for necessary genomic digests. We describe a new method, TOPO® Vector-Ligation PCR (or TVL-PCR that innovatively integrates available tools and familiar concepts to offer advantages as a means of both targeted sequence walking and paralog mining. Findings TVL-PCR exploits the ligation efficiency of the pCR®4-TOPO® (Invitrogen, Carlsbad, California vector system to capture fragments of unknown sequence by creating chimeric molecules containing defined priming sites at both ends. Initially, restriction enzyme-digested genomic DNA is end-repaired to create 3' adenosine overhangs and is then ligated to pCR4-TOPO vectors. The ligation product pool is used directly as a template for nested PCR, using specific primers to target orthologous sequences, or degenerate primers to enable capture of paralogous gene family members. We demonstrated the efficacy of this method by capturing entire coding and partial promoter sequences of several strawberry Superman-like genes. Conclusions TVL-PCR is a convenient and efficient method for DNA sequence walking and paralog mining that is applicable to any organism for which relevant DNA sequence is available as a basis for primer design.

  10. SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues.

    Directory of Open Access Journals (Sweden)

    Xiaoxia Yang

    Full Text Available Protein-nucleic acid interactions are central to various fundamental biological processes. Automated methods capable of reliably identifying DNA- and RNA-binding residues in protein sequence are assuming ever-increasing importance. The majority of current algorithms rely on feature-based prediction, but their accuracy remains to be further improved. Here we propose a sequence-based hybrid algorithm SNBRFinder (Sequence-based Nucleic acid-Binding Residue Finder by merging a feature predictor SNBRFinderF and a template predictor SNBRFinderT. SNBRFinderF was established using the support vector machine whose inputs include sequence profile and other complementary sequence descriptors, while SNBRFinderT was implemented with the sequence alignment algorithm based on profile hidden Markov models to capture the weakly homologous template of query sequence. Experimental results show that SNBRFinderF was clearly superior to the commonly used sequence profile-based predictor and SNBRFinderT can achieve comparable performance to the structure-based template methods. Leveraging the complementary relationship between these two predictors, SNBRFinder reasonably improved the performance of both DNA- and RNA-binding residue predictions. More importantly, the sequence-based hybrid prediction reached competitive performance relative to our previous structure-based counterpart. Our extensive and stringent comparisons show that SNBRFinder has obvious advantages over the existing sequence-based prediction algorithms. The value of our algorithm is highlighted by establishing an easy-to-use web server that is freely accessible at

  11. SPIO-enhanced MR imaging for HCC detection in cirrhotic patient : comparison of various techniques for optimal sequence selection

    Energy Technology Data Exchange (ETDEWEB)

    Kim, In Hwan; Lee, Jeong Min; Kwak, Hyo Sung; Kim, Chong Soo; Yu, Hee Chul [Chonbuk National University Hospital, Chonju (Korea, Republic of); Kim, Tae Kon; Lee Soo Tiek [Medical School, Chonbuk National University, Chonju (Korea, Republic of)


    To compare the efficacy of breathhold and non-breathhold sequences in the detection of hepatocellular carcinoma (HCC) in cirrhotic patients using superparamagnetic iron oxide (SPIO)-enhanced MR imaging, and to determine the optimal sequence combination. By means of unenhanced and iron-oxide-enhanced MRI, 29 patients with 49 nodular HCCs were evaluated for the presence of HCC nodules. Twenty-one were male and eight were female, and their ages ranged from 38 to 71 (mean, 56) years. Eight different MR sequences were used, including four non-breath-hold sequences and four breath-hold, and images were obtained before and after the administration of SPIO particles. Non-breath-hold sequences included T2-, proton density-weighted SE, and TSE imaging, while breath-hold sequences comprised T1-weighted fast low-angle shot (T1w FLASH), half-Fourier acquisition single shot turbo spine echo (HASTE), T2-weighted fast imaging with steady-state free precession (T2{sup *}wFISP) and T2-weighted breath-hold TSE (T2wBHTSE). Image analysis involved both quantitative and qualitative analysis. The quantitative parameters calculated were signal-to noise (S/N) ratios for livers and tumors, contrast to noise (C/N) ratios for tumors seen on precontrast and postcontrast images, and percentage of signal intensity loss (PSIL) after SPIO injection. Images were analysed qualitatively in terms of image artifacts and lesion conspicuity, and prior to calculating sensitivity, the number of lesions detected using various pulse sequences were counted. SPIO had a marked effect on liver S/N ratio but a minimal effect on tumor S/N ratio. PSIL was best in T2{sup *}wFISP images, while T2wSE images showed the second-best results (p less than 0.05). Tumor-to-liver C/N values were also highest with T2{sup *}wFISP, while T2wTSE and HASTE images were next. Qualitative study showed that non-breath hold images and FISP were better than breath hold images in terms of lesion conspicuity. The latter, however, were

  12. Source of error in the chromatographic study of /sup 35/S-sulfate labeled mucous glycoproteins secreted by the gill epithelium of Mytilus edulis

    Energy Technology Data Exchange (ETDEWEB)

    Sabouni, A.H.; Ma, J.K.; Malanga, C.J.


    HPLC combined with (/sup 35/S)-sulfate/(/sup 3/H)-glucosamine radiolabeling were employed to study the synthesis and secretion of mucous glycoproteins. The secreted radiolabeled glycoproteins were separated from the medium by precipitation with a mixture of trichloroacetic-phosphotungstic acids (TCA/PTA). The redissolved glycoproteins were chromatographed on an anion exchange protein column at varying pH of the mobile phase and fractions were collected for liquid scintillation counting. Varying the pH of the mobile phase from pH 3 to 7 resulted in a decrease of glycoprotein bound (/sup 35/S) from 69.5 to 0.5% of the total recovered (/sup 35/S)-sulfate with the remainder recovered as free (/sup 35/S)-sulfate. The (/sup 3/H)-labeled glycoprotein recovered under the uV peaks at this pH range was 99.5%. When high performance size exclusion chromatography was performed the change in mobile phase pH did not affect the 100% recovery of either (/sup 35/S)-or (/sup 3/H)-labels under the uV peaks. No free (/sup 35/S)-sulfate was obtained when (/sup 35/S)-labeled glycoproteins were separated from the medium using dialysis. These data suggest that the standard method of TCA/PTA precipitation of (/sup 35/S)-labeled glycoproteins may cleave the (/sup 35/S)-sulfate ester linkages to the oligosaccharide chains. The (/sup 35/S)-sulfate may then rebind to the macromolecule by a relatively strong noncovalent bond. This may prove critical in anion exchange protein HPLC studies.

  13. High performance liquid chromatography (HPLC) study of (/sup 35/S)- and (/sup 3/H)-labeled mucus glycoproteins secreted by the isolated mucociliated gill epithelium of Mytilus edulis

    Energy Technology Data Exchange (ETDEWEB)

    Sabouni, A.; Ma, J.K.; Malanga, C.J.


    HPLC combined with (/sup 35/S)-sulfate/(/sup 3/H)-glucosamine radiolabeling were employed to study the synthesis and secretion of mucous glycoproteins. The radiolabeled secreted glycoproteins were separated from the medium by precipitation with a mixture of trichloroacetic-phosphotungstic acids (TCA/PTA). The redissolved glycoproteins were chromatographed on an anion exchange protein column at varying pH of the mobile phase and fractions were collected for liquid scintillation counting. Varying the pH of the mobile phase from pH 3 to 7 resulted in a decrease of glycoprotein bound (/sup 35/S) from 69.5 to 0.5% of the total recovered (/sup 35/S)-sulfate with the remainder recovered as free (/sup 35/S)-sulfate. The (/sup 3/H)-labeled glycoprotein recovered under the uV peaks at this pH range was 99.5%. When high performance size exclusion chromatography was performed the change in mobile phase pH did not affect the 100% recovery of either (/sup 35/S)- or (/sup 3/H)-labels under the uV peaks. No free (/sup 35/S)-sulfate was obtained when (/sup 35/S)-labeled glycoproteins were separated form the medium using dialysis. These data suggest that the standard method of TCA/PTA precipitation of (/sup 35/S)-labeled glycoproteins may cleave the (/sup 35/S)-sulfate ester linkages to the oligosaccharide chains. The (/sup 35/S)-sulfate may then rebind to the macromolecule by a relatively strong noncovalent bond. This may prove critical in anion exchange protein HPLC studies.

  14. Daytime sleep enhances consolidation of the spatial but not motoric representation of motor sequence memory.

    Directory of Open Access Journals (Sweden)

    Geneviève Albouy

    Full Text Available Motor sequence learning is known to rely on more than a single process. As the skill develops with practice, two different representations of the sequence are formed: a goal representation built under spatial allocentric coordinates and a movement representation mediated through egocentric motor coordinates. This study aimed to explore the influence of daytime sleep (nap on consolidation of these two representations. Through the manipulation of an explicit finger sequence learning task and a transfer protocol, we show that both allocentric (spatial and egocentric (motor representations of the sequence can be isolated after initial training. Our results also demonstrate that nap favors the emergence of offline gains in performance for the allocentric, but not the egocentric representation, even after accounting for fatigue effects. Furthermore, sleep-dependent gains in performance observed for the allocentric representation are correlated with spindle density during non-rapid eye movement (NREM sleep of the post-training nap. In contrast, performance on the egocentric representation is only maintained, but not improved, regardless of the sleep/wake condition. These results suggest that motor sequence memory acquisition and consolidation involve distinct mechanisms that rely on sleep (and specifically, spindle or simple passage of time, depending respectively on whether the sequence is performed under allocentric or egocentric coordinates.

  15. BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. (United States)

    Bahr, A; Thompson, J D; Thierry, J C; Poch, O


    BAliBASE is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The database contains high quality, manually constructed multiple sequence alignments together with detailed annotations. The alignments are all based on three-dimensional structural superpositions, with the exception of the transmembrane sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Here we describe version 2.0 of the database, which incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. BAliBASE can be viewed at the web site http://www-igbmc.u-strasbg. fr/BioInfo/BAliBASE2/index.html or can be downloaded from /.

  16. A sequence upstream of canonical PDZ-binding motif within CFTR COOH-terminus enhances NHERF1 interaction. (United States)

    Sharma, Neeraj; LaRusch, Jessica; Sosnay, Patrick R; Gottschalk, Laura B; Lopez, Andrea P; Pellicore, Matthew J; Evans, Taylor; Davis, Emily; Atalar, Melis; Na, Chan-Hyun; Rosson, Gedge D; Belchis, Deborah; Milewski, Michal; Pandey, Akhilesh; Cutting, Garry R


    The development of cystic fibrosis transmembrane conductance regulator (CFTR) targeted therapy for cystic fibrosis has generated interest in maximizing membrane residence of mutant forms of CFTR by manipulating interactions with scaffold proteins, such as sodium/hydrogen exchange regulatory factor-1 (NHERF1). In this study, we explored whether COOH-terminal sequences in CFTR beyond the PDZ-binding motif influence its interaction with NHERF1. NHERF1 displayed minimal self-association in blot overlays (NHERF1, Kd = 1,382 ± 61.1 nM) at concentrations well above physiological levels, estimated at 240 nM from RNA-sequencing and 260 nM by liquid chromatography tandem mass spectrometry in sweat gland, a key site of CFTR function in vivo. However, NHERF1 oligomerized at considerably lower concentrations (10 nM) in the presence of the last 111 amino acids of CFTR (20 nM) in blot overlays and cross-linking assays and in coimmunoprecipitations using differently tagged versions of NHERF1. Deletion and alanine mutagenesis revealed that a six-amino acid sequence (1417)EENKVR(1422) and the terminal (1478)TRL(1480) (PDZ-binding motif) in the COOH-terminus were essential for the enhanced oligomerization of NHERF1. Full-length CFTR stably expressed in Madin-Darby canine kidney epithelial cells fostered NHERF1 oligomerization that was substantially reduced (∼5-fold) on alanine substitution of EEN, KVR, or EENKVR residues or deletion of the TRL motif. Confocal fluorescent microscopy revealed that the EENKVR and TRL sequences contribute to preferential localization of CFTR to the apical membrane. Together, these results indicate that COOH-terminal sequences mediate enhanced NHERF1 interaction and facilitate the localization of CFTR, a property that could be manipulated to stabilize mutant forms of CFTR at the apical surface to maximize the effect of CFTR-targeted therapeutics.

  17. Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation. (United States)

    Garcia, S; Kovařík, A


    In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA locus encoding 18S-5.8S-26S genes (L-type arrangement). Here we used Southern blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the 35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo (∼30% of the species analysed), while the remaining exhibit separate organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short tandems embedded in the 26S-18S rDNA intergenic spacer (IGS). The 5S transcript may be encoded by the same (Ginkgo, Ephedra) or opposite (Podocarpus) DNA strand as the 18S-5.8S-26S genes. In addition, pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have been largely homogenised across the genomes. Phylogenetic relationships based on the comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at least three times in the course of gymnosperm evolution. Frequent transpositions and rearrangements of basic units indicate relatively relaxed selection pressures imposed on genomic organisation of 5S genes in plants.

  18. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

    NARCIS (Netherlands)

    Wiedenheft, Blake; van Duijn, Esther; Bultema, Jelle; Waghmare, Sakharam; Zhou, Kaihong; Barendregt, Arjan; Westphal, Wiebke; Heck, Albert; Boekema, Egbert; Dickman, Mark; Doudna, Jennifer A.


    Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids. In each case, transcripts derived from clustered regularly interspaced short palindromic repeats (CRISPRs) are thought to selectively target invading phage and plasmids in a sequenc

  19. Reverse Engineering of Vaccine Antigens Using High Throughput Sequencing-enhanced mRNA Display

    Directory of Open Access Journals (Sweden)

    Nini Guo


    Research in Context: We used a large number of randomly produced small proteins (“peptides” to identify peptides containing specific protein sequences that bind efficiently to an antibody that can prevent hepatitis C virus infection in cell culture. After the identified peptides were injected into mice, the mice produced their own antibodies with characteristics similar to the original antibody. This approach can provide previously unavailable information about antibody binding and could also be useful in developing new vaccines.

  20. A noncontrast-enhanced pulse sequence optimized to visualize human peripheral vessels

    Energy Technology Data Exchange (ETDEWEB)

    Gjesdal, Kjell-Inge [Sunnmoere MR-Klinikk, Aalesund (Norway); Storaas, Tryggve [Ullevaal University Hospital, Section for Diagnostic Physics, Department of Radiology, Oslo (Norway); Geitung, Jonn-Terje [Haraldsplass University Hospital, Department of Radiology, Bergen (Norway)


    The purpose of this paper is to present a pulse sequence optimized to visualize human peripheral vessels. The optimized MR technique is a 3D multi-shot balanced non-SSFP gradient echo pulse sequence with fat suppression. Several imaging parameters were adjusted to find the best compromise between the contrast of vascular structures and muscle, fat, and bone. Most of the optimization was performed in the knee and calf regions using multi-channel SENSE coils. To verify potential clinical use, images of both healthy volunteers and volunteers with varicose veins were produced. The balanced non-SSFP sequence can produce high-spatial-resolution images of the human peripheral vessels without the need for an intravenous contrast agent. Both arteries and veins are displayed along with other body fluids. Due to the high spatial resolution of the axial plane source or reconstructed images, the need for procedures to separate arteries from veins is limited. We demonstrate that high signals from synovial joint fluid and cystic structures can be suppressed by applying an inversion prepulse but at the expense of reduced image signal-to-noise and overall image quality. (orig.)

  1. Enhanced formation of aerobic granular sludge with yellow earth as nucleating agent in a sequencing batch reactor (United States)

    He, Q. L.; Zhang, S. L.; Zou, Z. C.; Wang, H. Y.


    Enhanced formation of aerobic granulation was investigated by adding yellow earth as a nucleating agent in a sequencing batch reactor with a constant setting time of 10 min. As a result, granules with an average diameter over 1 mm were obtained on the 4th day. The mature granules behaved better than the seed sludge in the water content, specific gravity, sludge volume index, settling velocity, and specific oxygen uptake rate. The yellow earth stimulated the secretion of extracellular polymeric substances, especially proteins. Both chemical oxygen demand and ammonia nitrogen had a removal rate over 90%, and more than 80% of the total inorganic nitrogen was removed even under aeration conditions due to simultaneous denitrification. The enhancement effects of the yellow earth might be based on the unique physicochemical characteristics and short settling time. A settling time of 10 min or more turned out not to be a prerequisite for a rapid granulation process.

  2. Enhanced adherence of methicillin-resistant Staphylococcus pseudintermedius sequence type 71 to canine and human corneocytes

    DEFF Research Database (Denmark)

    Latronico, Francesca; Moodley, Arshnee; Nielsen, Søren Saxmose;


    The recent worldwide spread of methicillin-resistant Staphylococcus pseudintermedius (MRSP) in dogs is a reason for concern due to the typical multidrug resistance patterns displayed by some MRSP lineages such as sequence type (ST) 71. The objective of this study was to compare the in vitro...... characterized with respect to genetic background and cell wall-anchored protein (CWAP) gene content. Seventy-seven strain-corneocyte combinations were tested using both exponential- and stationary-phase cultures. Negative binomial regression analysis of counts of bacterial cells adhering to corneocytes revealed...

  3. Instability strips of main sequence B stars: a parametric study of iron enhancement

    CERN Document Server

    Miglio, A; Montalban, J; Dupret, M A


    The discovery of beta Cephei stars in low metallicity environments, as well as the difficulty to theoretically explain the excitation of the pulsation modes observed in some beta Cephei and SPB stars, suggest that the iron opacity ``bump'' provided by standard models could be underestimated. We investigate, by means of a parametric study, the effect of a local iron enhancement on the location of the beta Cephei and SPB instability strips.

  4. Spatially Enhanced Differential RNA Methylation Analysis from Affinity-Based Sequencing Data with Hidden Markov Model. (United States)

    Zhang, Yu-Chen; Zhang, Shao-Wu; Liu, Lian; Liu, Hui; Zhang, Lin; Cui, Xiaodong; Huang, Yufei; Meng, Jia


    With the development of new sequencing technology, the entire N6-methyl-adenosine (m(6)A) RNA methylome can now be unbiased profiled with methylated RNA immune-precipitation sequencing technique (MeRIP-Seq), making it possible to detect differential methylation states of RNA between two conditions, for example, between normal and cancerous tissue. However, as an affinity-based method, MeRIP-Seq has yet provided base-pair resolution; that is, a single methylation site determined from MeRIP-Seq data can in practice contain multiple RNA methylation residuals, some of which can be regulated by different enzymes and thus differentially methylated between two conditions. Since existing peak-based methods could not effectively differentiate multiple methylation residuals located within a single methylation site, we propose a hidden Markov model (HMM) based approach to address this issue. Specifically, the detected RNA methylation site is further divided into multiple adjacent small bins and then scanned with higher resolution using a hidden Markov model to model the dependency between spatially adjacent bins for improved accuracy. We tested the proposed algorithm on both simulated data and real data. Result suggests that the proposed algorithm clearly outperforms existing peak-based approach on simulated systems and detects differential methylation regions with higher statistical significance on real dataset.

  5. Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery.

    Directory of Open Access Journals (Sweden)

    Dineika Chandrananda

    Full Text Available Pregnant women carry a mixture of cell-free DNA fragments from self and fetus (non-self in their circulation. In recent years multiple independent studies have demonstrated the ability to detect fetal trisomies such as trisomy 21, the cause of Down syndrome, by Next-Generation Sequencing of maternal plasma. The current clinical tests based on this approach show very high sensitivity and specificity, although as yet they have not become the standard diagnostic test. Here we describe improvements to the analysis of the sequencing data by reducing GC bias and better handling of the genomic repeats. We show substantial improvements in the sensitivity of the standard trisomy 21 statistical tests, which we measure by artificially reducing read coverage. We also explore the bias stemming from the natural cleavage of plasma DNA by examining DNA motifs and position specific base distributions. We propose a model to correct this fragmentation bias and observe that incorporating this bias does not lead to any further improvements in the detection of fetal trisomy. The improved bias corrections that we demonstrate in this work can be readily adopted into existing fetal trisomy detection protocols and should also lead to improvements in sub-chromosomal copy number variation detection.

  6. Engineering Proteins with Enhanced Mechanical Stability by Force Specific Sequence Motifs (United States)

    Lu, Wenzhe; Negi, Surendra; Oberhauser, Andres F.; Braun, Werner


    Use of atomic force microscopy (AFM) has recently led to a better understanding of the molecular mechanisms of the unfolding process by mechanical forces; however, the rational design of novel proteins with specific mechanical strength remains challenging. We have approached this problem from a new perspective that generates linear physical-chemical properties (PCP) motifs from a limited AFM data set. Guided by our linear sequence analysis we designed and analyzed four new mutants of the titin I1 domain with the goal of increasing the domain's mechanical strength. All four mutants could be cloned and expressed as soluble proteins. AFM data indicate that at least two of the mutants have increased molecular mechanical strength. This observation suggests that the PCP method is useful to graft sequences specific for high mechanical stability to weak proteins to increase their mechanical stability, and represents an additional tool in the design of novel proteins besides steered molecular dynamics calculations, coarse grained simulations and phi-value analysis of the transition state. PMID:22274941

  7. Investigating and correcting plasma DNA sequencing coverage bias to enhance aneuploidy discovery. (United States)

    Chandrananda, Dineika; Thorne, Natalie P; Ganesamoorthy, Devika; Bruno, Damien L; Benjamini, Yuval; Speed, Terence P; Slater, Howard R; Bahlo, Melanie


    Pregnant women carry a mixture of cell-free DNA fragments from self and fetus (non-self) in their circulation. In recent years multiple independent studies have demonstrated the ability to detect fetal trisomies such as trisomy 21, the cause of Down syndrome, by Next-Generation Sequencing of maternal plasma. The current clinical tests based on this approach show very high sensitivity and specificity, although as yet they have not become the standard diagnostic test. Here we describe improvements to the analysis of the sequencing data by reducing GC bias and better handling of the genomic repeats. We show substantial improvements in the sensitivity of the standard trisomy 21 statistical tests, which we measure by artificially reducing read coverage. We also explore the bias stemming from the natural cleavage of plasma DNA by examining DNA motifs and position specific base distributions. We propose a model to correct this fragmentation bias and observe that incorporating this bias does not lead to any further improvements in the detection of fetal trisomy. The improved bias corrections that we demonstrate in this work can be readily adopted into existing fetal trisomy detection protocols and should also lead to improvements in sub-chromosomal copy number variation detection.

  8. In vitro screening of psychoactive drugs by [(35)S]GTPgammaS binding in rat brain membranes. (United States)

    Nonaka, Ryouichi; Nagai, Fumiko; Ogata, Akio; Satoh, Kanako


    We constructed a reproducible, simple, and small-scale determination method of the psychoactive drugs that acted directly on the monoamine receptor by measuring the activation of [(35)S]guanosine-5'-O-(3-thio)-triphosphate binding to guanine nucleotide-binding proteins (G proteins). This method can simultaneously measure the effects of three monoamines, namely dopamine (DA), serotonin (5-HT), and norepinephrine (NE), in rat brain membranes using a 96-well microplate. Activation of D(1) and D(2) receptors in striatal membranes by DA as well as 5-HT and NEalpha(2) receptors in cortical membranes could be measured. Of 12 tested phenethylamines, 2,5-dimethoxy-4-chlorophenethylamine (2C-C), 2,5-dimethoxy-4-ethylphenethylamine (2C-E), and 2,5-dimethoxy-4-iodophenethylamine (2C-I) stimulated G protein binding. The other phenethylamines did not affect G protein binding. All 7 tryptamines tested stimulated G protein binding with the following rank order of potency; 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT)>5-methoxy-N,N-diallyltryptamine (5-MeO-DALT)>5-methoxy-alpha-methyltryptamine (5-MeO-AMT)>or=5-methoxy-N,N-methylisopropyltryptamine (5-MeO-MIPT)>5-methoxy-N,N-diisopropyltryptamine (5-MeO-DIPT)>N,N-dipropyltryptamine (DPT)>or=alpha-methyltryptamine (AMT). This assay system was able to designate psychoactive drugs as prohibited substances in accordance with criteria set forth by the Tokyo Metropolitan government.

  9. Enhanced DNA sequencing performance through edge-hydrogenation of graphene electrodes

    CERN Document Server

    He, Yuhui; Grigoriev, Anton; Ahuja, Rajeev; Long, Shibing; Huo, ZongLiang; Liu, Ming


    We propose using graphene electrodes with hydrogenated edges for solid-state nanopore-based DNA sequencing, and perform molecular dynamics simulations in conjunction with electronic transport calculations to explore the potential merits of this idea. The results of our investigation show that, compared to the unhydrogenated system, edge-hydrogenated graphene electrodes facilitate the temporary formation of H-bonds with suitable atomic sites in the translocating DNA molecule. As a consequence, the average conductivity is drastically raised by about 3 orders of magnitude while exhibiting significantly reduced statistical variance. We have furthermore investigated how these results are affected when the distance between opposing electrodes is varied and have identified two regimes: for narrow electrode separation, the mere hindrance due to the presence of protruding hydrogen atoms in the nanopore is deemed more important, while for wider electrode separation, the formation of H-bonds becomes the dominant effect....

  10. Analysis of Dengue Virus Enhancing Epitopes Using Peptide Antigens Derived from the Envelope Glycoprotein Gene Sequence (United States)


    WE. 1990. Development of dengue and Japanese encephalitis Vaccines . J Infect Dis 162:577-83. 2. Brandt WE, McCown JM, Gentry MK, and Russell PK. i982...7. 19. Roehrig JT, Johnson AJ, Hunt AR, Bolin RA, •d Chu MC. 1990. Antibodies to dengue 2 Jamaica E-glycopr tein synthetic peptides identify antigenic...AD________ AD-A230 976 ARMY PROJECT NO: 89PP9961 TITLE: ANALYSIS OF DENGUE VIRUS ENHANCING EPITOPES USING PEPTIDE ANTIGENS DERIVED FROM THE ENVELOPE

  11. Technical innovation in dynamic contrast-enhanced magnetic resonance imaging of musculoskeletal tumors: an MR angiographic sequence using a sparse k-space sampling strategy

    Energy Technology Data Exchange (ETDEWEB)

    Fayad, Laura M.; Mugera, Charles; Grande, Filippo del [Johns Hopkins Medical Institutions, Russell H. Morgan Department of Radiology and Radiological Sciences, Baltimore, MD (United States); Soldatos, Theodoros [Johns Hopkins Medical Institutions, Musculoskeletal Imaging Section, Baltimore, MD (United States); University of Athens, Research Unit of Radiology and Medical Imaging, Evgenidion Hospital, Athens (Greece); Flammang, Aaron [Siemens Corporate Research, Center for Applied Medical Imaging, Baltimore, MD (United States)


    We demonstrate the clinical use of an MR angiography sequence performed with sparse k-space sampling (MRA), as a method for dynamic contrast-enhanced (DCE)-MRI, and apply it to the assessment of sarcomas for treatment response. Three subjects with sarcomas (2 with osteosarcoma, 1 with high-grade soft tissue sarcomas) underwent MRI after neoadjuvant therapy/prior to surgery, with conventional MRI (T1-weighted, fluid-sensitive, static post-contrast T1-weighted sequences) and DCE-MRI (MRA, time resolution = 7-10 s, TR/TE 2.4/0.9 ms, FOV 40 cm{sup 2}). Images were reviewed by two observers in consensus who recorded image quality (1 = diagnostic, no significant artifacts, 2 = diagnostic, <25 % artifacts, 3 = nondiagnostic) and contrast enhancement characteristics by static MRI (presence/absence of contrast enhancement, percentage of enhancement) and DCE-MRI (presence/absence of arterial enhancement with time-intensity curves). Results were compared with histological response (defined as <5 % viable tumor [soft tissue sarcoma] or <10 % [bone sarcoma] following resection). Diagnostic quality for all conventional and DCE-MRI sequences was rated as 1. In 2 of the 3 sarcomas, there was good histological response ({<=}5 % viable tumor); in 1 there was poor response (50 % viable tumor). By static post-contrast T1-weighted sequences, there was enhancement in all sarcomas, regardless of response (up to >75 % with good response, >75 % with poor response). DCE-MRI findings were concordant with histological response (arterial enhancement with poor response, no arterial enhancement with good response). Unlike conventional DCE-MRI sequences, an MRA sequence with sparse k-space sampling is easily integrated into a routine musculoskeletal tumor MRI protocol, with high diagnostic quality. In this preliminary work, tumor enhancement characteristics by DCE-MRI were used to assess treatment response. (orig.)

  12. Exploration of the arrest peptide sequence space reveals arrest-enhanced variants. (United States)

    Cymer, Florian; Hedman, Rickard; Ismail, Nurzian; von Heijne, Gunnar


    Translational arrest peptides (APs) are short stretches of polypeptides that induce translational stalling when synthesized on a ribosome. Mechanical pulling forces acting on the nascent chain can weaken or even abolish stalling. APs can therefore be used as in vivo force sensors, making it possible to measure the forces that act on a nascent chain during translation with single-residue resolution. It is also possible to score the relative strengths of APs by subjecting them to a given pulling force and ranking them according to stalling efficiency. Using the latter approach, we now report an extensive mutagenesis scan of a strong mutant variant of the Mannheimia succiniciproducens SecM AP and identify mutations that further increase the stalling efficiency. Combining three such mutations, we designed an AP that withstands the strongest pulling force we are able to generate at present. We further show that diproline stretches in a nascent protein act as very strong APs when translation is carried out in the absence of elongation factor P. Our findings highlight critical residues in APs, show that certain amino acid sequences induce very strong translational arrest and provide a toolbox of APs of varying strengths that can be used for in vivo force measurements.

  13. Embedding constructed wetland in sequencing batch reactor for enhancing nutrients removal: A comparative evaluation. (United States)

    Liu, Ranbin; Zhao, Yaqian; Zhao, Jinhui; Xu, Lei; Sibille, Caroline


    In the present study, a novel green bio-sorption reactor (GBR) was firstly proposed and preliminarily investigated by embedding constructed wetland (CW) into the aeration tank of the conventional activated sludge (CAS). This integrated novel system owns the striking features of adding carriers of wetland substrate (i.e. the dewatered alum sludge in this case) in CAS for robust phosphorus adsorption and enriching the biomass. Meanwhile, the "green" feature of this GBR imparted aesthetic value of CW to the CAS system. The preliminary 3-month trial of GBR based on a sequencing batch reactor (GB-SBR) with diluted piggery wastewater demonstrated an average removal of 96%, 99% and 90% for BOD, TP and TN, respectively. The comparison with moving bed biofilm reactor (MBBR) and integrated fixed-film activated sludge (IFAS) reflected the advantages of GBR over purification performance, aesthetic value and potential carbon sink. Moreover, the carriers used in the GBR are dewatered alum sludge which is in line with the policy of "recycle, reuse and reduce". Overall, this GBR undoubtedly offered a more sustainable and economical solution for retrofitting the aging CAS.

  14. Enhanced intercarrier interference mitigation based on encoded bit-sequence distribution inside optical superchannels (United States)

    Torres, Jhon James Granada; Soto, Ana María Cárdenas; González, Neil Guerrero


    In the context of gridless optical multicarrier systems, we propose a method for intercarrier interference (ICI) mitigation which allows bit error correction in scenarios of nonspectral flatness between the subcarriers composing the multicarrier system and sub-Nyquist carrier spacing. We propose a hybrid ICI mitigation technique which exploits the advantages of signal equalization at both levels: the physical level for any digital and analog pulse shaping, and the bit-data level and its ability to incorporate advanced correcting codes. The concatenation of these two complementary techniques consists of a nondata-aided equalizer applied to each optical subcarrier, and a hard-decision forward error correction applied to the sequence of bits distributed along the optical subcarriers regardless of prior subchannel quality assessment as performed in orthogonal frequency-division multiplexing modulations for the implementation of the bit-loading technique. The impact of the ICI is systematically evaluated in terms of bit-error-rate as a function of the carrier frequency spacing and the roll-off factor of the digital pulse-shaping filter for a simulated 3×32-Gbaud single-polarization quadrature phase shift keying Nyquist-wavelength division multiplexing system. After the ICI mitigation, a back-to-back error-free decoding was obtained for sub-Nyquist carrier spacings of 28.5 and 30 GHz and roll-off values of 0.1 and 0.4, respectively.

  15. Complete genome sequence of virulence-enhancing Siphophage VHS1 from Vibrio harveyi. (United States)

    Khemayan, Krit; Prachumwat, Anuphap; Sonthayanon, Burachai; Intaraprasong, Aungkul; Sriurairatana, Siriporn; Flegel, Timothy W


    Vibrio harveyi siphophage 1 (VHS1) is a tailed phage with an icosahedral head of approximately 66 nm in diameter and an unornamented, flexible tail of approximately 153 nm in length. When Vibrio harveyi 1114GL is lysogenized with VHS1, its virulence for the black tiger shrimp (Penaeus monodon) increases by more than 100 times, and this coincides with production of a toxin(s) associated with shrimp hemocyte agglutination. Curiously, the lysogen does not show increased virulence for the whiteleg shrimp (Penaeus [Litopenaeus] vannamei). Here we present and annotate the complete, circular genome of VHS1 (81,509 kbp; GenBank accession number JF713456). By software analysis, the genome contains 125 putative open reading frames (ORFs), all of which appear to be located on the same DNA strand, similar to the case for many other bacteriophages. Most of the putative ORFs show no significant homology to known sequences in GenBank. Notable exceptions are ORFs for a putative DNA polymerase and putative phage structural proteins, including a portal protein, a phage tail tape measure protein, and a phage head protein. The last protein was identified as a component of the species-specific toxin mixture described above as being associated with agglutination of hemocytes from P. monodon.

  16. RNase MRP is required for entry of 35S precursor rRNA into the canonical processing pathway. (United States)

    Lindahl, Lasse; Bommankanti, Ananth; Li, Xing; Hayden, Lauren; Jones, Adrienne; Khan, Miriam; Oni, Tolulope; Zengel, Janice M


    RNase MRP is a nucleolar RNA-protein enzyme that participates in the processing of rRNA during ribosome biogenesis. Previous experiments suggested that RNase MRP makes a nonessential cleavage in the first internal transcribed spacer. Here we report experiments with new temperature-sensitive RNase MRP mutants in Saccharomyces cerevisiae that show that the abundance of all early intermediates in the processing pathway is severely reduced upon inactivation of RNase MRP. Transcription of rRNA continues unabated as determined by RNA polymerase run-on transcription, but the precursor rRNA transcript does not accumulate, and appears to be unstable. Taken together, these observations suggest that inactivation of RNase MRP blocks cleavage at sites A0, A1, A2, and A3, which in turn, prevents precursor rRNA from entering the canonical processing pathway (35S > 20S + 27S > 18S + 25S + 5.8S rRNA). Nevertheless, at least some cleavage at the processing site in the second internal transcribed spacer takes place to form an unusual 24S intermediate, suggesting that cleavage at C2 is not blocked. Furthermore, the long form of 5.8S rRNA is made in the absence of RNase MRP activity, but only in the presence of Xrn1p (exonuclease 1), an enzyme not required for the canonical pathway. We conclude that RNase MRP is a key enzyme for initiating the canonical processing of precursor rRNA transcripts, but alternative pathway(s) might provide a backup for production of small amounts of rRNA.

  17. CRISPR/Cas9 system as an innovative genetic engineering tool: Enhancements in sequence specificity and delivery methods. (United States)

    Jo, Young-Il; Suresh, Bharathi; Kim, Hyongbum; Ramakrishna, Suresh


    While human gene therapy has gained significant attention for its therapeutic promise, CRISPR/Cas9 technology has made a breakthrough as an efficient genome editing tool by emulating prokaryotic immune defense mechanisms. Although many studies have found that CRISPR/Cas9 technology is more efficient, specific and manipulable than previous generations of gene editing tools, it can be further improved by elevating its overall efficiency in a higher frequency of genome modifications and reducing its off-target effects. Here, we review the development of CRISPR/Cas9 technology, focusing on enhancement of its sequence specificity, reduction of off-target effects and delivery systems. Moreover, we describe recent successful applications of CRISPR/Cas9 technology in laboratory and clinical studies.

  18. Fluorescent in situ hybridization of the ribosomal RNA genes (5S and 35S in the genus Lolium: Lolium canariense, the missing link with Festuca?

    Directory of Open Access Journals (Sweden)

    Inda, Luis A.


    Full Text Available Two groups of taxa can be distinguished within the genus Lolium L. based on the pollination system, chromosome size, chromosomal location of nrDNA (5S and 35S (18S-5.8S-26S] and nrDNA phylogeny. The first group includes self-pollinated taxa (L. temulentum, L. persicum and L. remotum, whereas the second group comprises cross-pollinated species (L. perenne, L. multiflorum and L. rigidum. Here we describe that the autogamous species have two 5S sites and four 35S sites in their genome. Two of the 35S sites are present in the chromosomes containing the 5S regions. The allogamous taxa possess two 5S rDNA sites and 6-10 35S sites per genome, depending on the species. Two of these regions (35S may also be present in the chromosomes bearing 5S sites. Our study also demonstrates that Lolium canariense shows a distinctive pattern. It has two 5S and four 35S sites. In this case, the 35S loci are located in different chromosomes than the 5S. This cytogenetic pattern is consistent with that of Festuca pratensis. Thus, despite being allogamous, Lolium canariense does not entirely fit in either of the groups defined for the genus Lolium. The physical mapping of the nrDNA regions in L. canariense is different, and resembles that of F. pratensis, suggesting that this Macaronesian Lolium could be intermediate between Festuca and Lolium.En trabajos previos se ha descrito que el género Lolium L. está formado por dos grupos de taxones basados en el tipo de polinización, tamaño de los cromosomas, localización cromosómica de los loci del ADN ribosómico [5S y 35S (18S-5.8S-26S] y filogenia molecular basada en secuencias de ADN ribosómico. Los dos grupos son: especies autógamas (L. temulentum, L. persicum y L. remotum y especies alógamas (L. perenne, L. multiflorum y L. rigidum. Aquí describimos que según la localización cromosómica de los loci ribosómicos, las especies autógamas tienen dos sitios 5S y cuatro sitios 35S; dos de las cuales coinciden en

  19. Enhanced pulmonary absorption of a macromolecule through coupling to a sequence-specific phage display-derived peptide. (United States)

    Morris, Christopher J; Smith, Mathew W; Griffiths, Peter C; McKeown, Neil B; Gumbleton, Mark


    With the aim of identifying a peptide sequence that promotes pulmonary epithelial transport of macromolecule cargo we used a stringent peptide-phage display library screening protocol against rat lung alveolar epithelial primary cell cultures. We identified a peptide-phage clone (LTP-1) displaying the disulphide-constrained 7-mer peptide sequence, C-TSGTHPR-C, that showed significant pulmonary epithelial translocation across highly restrictive polarised cell monolayers. Cell biological data supported a differential alveolar epithelial cell interaction of the LTP-1 peptide-phage clone and the corresponding free synthetic LTP-1 peptide. Delivering select phage-clones to the intact pulmonary barrier of an isolated perfused rat lung (IPRL) resulted in 8.7% of lung deposited LTP-1 peptide-phage clone transported from the IPRL airways to the vasculature compared (pprobes. This study shows proof-of principle that array technologies can be effectively exploited to identify peptides mediating enhanced transmucosal delivery of macromolecule therapeutics across an intact organ.


    Directory of Open Access Journals (Sweden)

    Ananya Basu


    Full Text Available In post genomic era with the advent of new technologies a huge amount of complex molecular data are generated with high throughput. The management of this biological data is definitely a challenging task due to complexity and heterogeneity of data for discovering new knowledge. Issues like managing noisy and incomplete data are needed to be dealt with. Use of data mining in biological domain has made its inventory success. Discovering new knowledge from the biological data is a major challenge in data mining technique. The novelty of the proposed model is its combined use of intelligent techniques to classify the protein sequence faster and efficiently. Use of FFT, fuzzy classifier, String weighted algorithm, gram encoding method, neural network model and rough set classifier in a single model and in an appropriate place can enhance the quality of the classification system .Thus the primary challenge is to identify and classify the large protein sequences in a very fast and easy but intellectual way to decrease the time complexity and space complexity

  1. Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein. (United States)

    Burrows, Patricia C; Schumacher, Jörg; Amartey, Samuel; Ghosh, Tamaswati; Burgis, Timothy A; Zhang, Xiaodong; Nixon, B Tracy; Buck, Martin


    Molecular machines belonging to the AAA+ superfamily of ATPases use NTP hydrolysis to remodel their versatile substrates. The presence of an insertion sequence defines the major phylogenetic pre-sensor I insertion (pre-SIi) AAA+ superclade. In the bacterial sigma(54)-dependent enhancer binding protein phage shock protein F (PspF) the pre-SIi loop adopts different conformations depending on the nucleotide-bound state. Single amino acid substitutions within the dynamic pre-SIi loop of PspF drastically change the ATP hydrolysis parameters, indicating a structural link to the distant hydrolysis site. We used a site-specific protein-DNA proximity assay to measure the contribution of the pre-SIi loop in sigma(54)-dependent transcription and demonstrate that the pre-SIi loop is a major structural feature mediating nucleotide state-dependent differential engagement with Esigma(54). We suggest that much, if not all, of the action of the pre-SIi loop is mediated through the L1 loop and relies on a conserved molecular switch, identified in a crystal structure of one pre-SIi variant and in accordance with the high covariance between some pre-SIi residues and distinct residues outside the pre-SIi sequence.

  2. Translational Enhancer of Tobacco mosaic virus Enhancing Expression of Hepatitis B Surface Antigen in Transgenic Panax ginseng C. A. Meyer Callus

    Institute of Scientific and Technical Information of China (English)


    The 5'-nontranslated leader(omega sequence) of Tobacco mosaic virus(TMV) was used as a translational enhancer sequence in the expression of the hepatitis B surface antigen(HBsAg) gene in transgenic ginseng callus cultures.The adr subtype HBsAg gene was placed under the control of the Cauliflower mosaic virus(CaMV) 35S promoter linking to the TMV leader sequence. The antisense omega sequence was used in a control construct. The resulting constructs cloned in the binary vector pBI121 were used to transform the ginseng callus tissue via the Agrobacterium-mediated procedure. The integration and expression of the HBsAg gene were evaluated by PCR and western blot, respectively. Enzyme-linked immunoassays(ELISA) using a monoclonal antibody directed against human serum-derived HBsAg revealed a three to four-fold enhanced expression of HBsAg in ginseng cells conferred by the TMV omega element.

  3. Centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo sequence: improvement of the image quality of oxygen-enhanced MRI

    Energy Technology Data Exchange (ETDEWEB)

    Ohno, Yoshiharu E-mail:; Hatabu, Hiroto; Higashino, Takanori; Kawamitsu, Hideaki; Watanabe, Hirokazu; Takenaka, Daisuke; Cauteren, Marc van; Sugimura, Kazuro


    Purpose: The purpose of the study presented here was to determine the improvement in image quality of oxygen-enhanced magnetic resonance (MR) subtraction imaging obtained with a centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo (c-IR-HASTE) sequence compared with that obtained with a conventional sequentially reordered inversion recovery single-shot HASTE (s-IR-HASTE) sequence for pulmonary imaging. Materials and methods: Oxygen-enhanced MR imaging using a 1.5 T whole body scanner was performed on 12 healthy, non-smoking volunteers. Oxygen-enhanced MR images were obtained with the coronal two-dimensional (2D) c-IR-HASTE sequence and 2D s-IR-HASTE sequence combined with respiratory triggering. For a 256x256 matrix, 132 phase-encoding steps were acquired including four steps for phase correction. Inter-echo spacing for each sequence was 4.0 ms. The effective echo time (TE) for c-IR-HASTE was 4.0 ms, and 16 ms for s-IR-HASTE. The inversion time (TI) was 900 ms. To determine the improvement in oxygen-enhanced MR subtraction imaging by c-IR-HASTE, CNRs of subtraction image, overall image quality, and image degradation of the c-IR-HASTE and s-IR-HASTE techniques were statistically compared. Results: CNR, overall image quality, and image degradation of c-IR-HASTE images showed significant improvement compared to those s-IR-HASTE images (P<0.05). Conclusion: Centrically reordered inversion recovery half-Fourier single-shot turbo spin-echo (c-IR-HASTE) sequence enhanced the signal from the lung and improved the image quality of oxygen-enhanced MR subtraction imaging.

  4. Effects of cysteamine administration on the in vivo incorporation of (/sup 35/S)cysteine into somatostatin-14, somatostatin-28, arginine vasopressin, and oxytocin in rat hypothalamus

    Energy Technology Data Exchange (ETDEWEB)

    Cameron, J.L.; Fernstrom, J.D.


    The effect of cysteamine injection on the in vivo incorporation of (/sup 35/S)cysteine into somatostatin-14 (SRIF-14), SRIF-28, arginine vasopressin (AVP), and oxytocin (OXT) in rat hypothalamus was studied. (/sup 35/S)Cysteine was injected into the third ventricle 1 h, 4 h, or 1 week after cysteamine (300 mg/kg, sc) injection; animals were killed 4 h later. The drug was found to substantially reduce immunoreactive SRIF levels, but not OXT or AVP, 4 h after its injection. Cysteamine also caused large reductions in label incorporation into SRIF-14, SRIF-28, and OXT 1 and 4 h after drug injection. However, (/sup 35/S)cysteine incorporation into AVP was increased substantially at these time points, while that into acid-precipitable protein was normal. One week after cysteamine injection, label incorporation into all hypothalamic peptides was normal. Cysteine specific activity was also measured after (/sup 35/S)cysteine injection and was found to be similar in treatment and control groups. The results suggest that cysteamine inhibits the syntheses of SRIF-14, SRIF-28, and OXT and stimulates that of AVP.

  5. Neutron-activated determination of chlorine, using the /sup 35/Cl(n,p)/sup 35/S reaction as the basis, in thin coatings of silicon dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Perezhogin, G.A.


    The neutron-activation determination of chlorine in thin coatings of silicon dioxide on silicon has been shown to be possible through the use of the /sup 55/Cl(n, P)/sup 35/S reaction. The detection limit of chlorine is 3 x 10/sup -9/ g (5 x 10/sup 13/ atoms).

  6. Contrast enhancement of intracranial lesions at 1.5 T: comparison among 2D spin echo, black-blood (BB) Cube, and BB Cube-FLAIR sequences

    Energy Technology Data Exchange (ETDEWEB)

    Im, SungWoon; Ashikaga, Ryuichiro; Yagyu, Yukinobu; Hyodo, Tomoko; Imaoka, Izumi; Kumano, Seishi; Ishii, Kazunari; Murakami, Takamichi [Kinki University Faculty of Medicine, Department of Radiology, Osaka-Sayama, Osaka (Japan); Wakayama, Tetsuya; Miyoshi, Mitsuharu [GE Healthcare Japan, MR Applications and Workflow, Asia Pacific, Hino, Tokyo (Japan)


    The purpose of this study was to investigate the usefulness of T1W black-blood Cube (BB Cube) and T1W BB Cube fluid-attenuated inversion recovery (BB Cube-FLAIR) sequences for contrast-enhanced brain imaging, by evaluating flow-related artefacts, detectability, and contrast ratio (CR) of intracranial lesions among these sequences and T1W-SE. Phantom studies were performed to determine the optimal parameters of BB Cube and BB Cube-FLAIR. A clinical study in 23 patients with intracranial lesions was performed to evaluate the usefulness of these two sequences for the diagnosis of intracranial lesions compared with the conventional 2D T1W-SE sequence. The phantom study revealed that the optimal parameters for contrast-enhanced T1W imaging were TR/TE = 500 ms/minimum in BB Cube and TR/TE/TI = 600 ms/minimum/300 ms in BB Cube-FLAIR imaging. In the clinical study, the degree of flow-related artefacts was significantly lower in BB Cube and BB Cube-FLAIR than in T1W-SE. Regarding tumour detection, BB Cube showed the best detectability; however, there were no significant differences in CR among the sequences. At 1.5 T, contrast-enhanced BB Cube was a better imaging sequence for detecting brain lesions than T1W-SE or BB Cube-FLAIR. (orig.)

  7. Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector-Coding Sequence Junction

    DEFF Research Database (Denmark)

    Mirzadeh, Kiavash; Martinez, Virginia; Toddo, Stephen;


    are poorly expressed even when they are codon-optimized and expressed from vectors with powerful genetic elements. In this study, we show that poor expression can be caused by certain nucleotide sequences (e.g., cloning scars) at the junction between the vector and the coding sequence. Since these sequences...... lie between the Shine-Dalgarno sequence and the start codon, they are an integral part of the translation initiation region. To identify the most optimal sequences, we devised a simple and inexpensive PCR-based step that generates sequence variants at the vector-coding sequence junction...

  8. Sequencing the hypervariable regions of human mitochondrial DNA using massively parallel sequencing: Enhanced data acquisition for DNA samples encountered in forensic testing. (United States)

    Davis, Carey; Peters, Dixie; Warshauer, David; King, Jonathan; Budowle, Bruce


    Mitochondrial DNA testing is a useful tool in the analysis of forensic biological evidence. In cases where nuclear DNA is damaged or limited in quantity, the higher copy number of mitochondrial genomes available in a sample can provide information about the source of a sample. Currently, Sanger-type sequencing (STS) is the primary method to develop mitochondrial DNA profiles. This method is laborious and time consuming. Massively parallel sequencing (MPS) can increase the amount of information obtained from mitochondrial DNA samples while improving turnaround time by decreasing the numbers of manipulations and more so by exploiting high throughput analyses to obtain interpretable results. In this study 18 buccal swabs, three different tissue samples from five individuals, and four bones samples from casework were sequenced at hypervariable regions I and II using STS and MPS. Sample enrichment for STS and MPS was PCR-based. Library preparation for MPS was performed using Nextera® XT DNA Sample Preparation Kit and sequencing was performed on the MiSeq™ (Illumina, Inc.). MPS yielded full concordance of base calls with STS results, and the newer methodology was able to resolve length heteroplasmy in homopolymeric regions. This study demonstrates short amplicon MPS of mitochondrial DNA is feasible, can provide information not possible with STS, and lays the groundwork for development of a whole genome sequencing strategy for degraded samples.

  9. Automatic classification of lung tumour heterogeneity according to a visual-based score system in dynamic contrast enhanced CT sequences (United States)

    Bevilacqua, Alessandro; Baiocco, Serena


    Computed tomography (CT) technologies have been considered for a long time as one of the most effective medical imaging tools for morphological analysis of body parts. Contrast Enhanced CT (CE-CT) also allows emphasising details of tissue structures whose heterogeneity, inspected through visual analysis, conveys crucial information regarding diagnosis and prognosis in several clinical pathologies. Recently, Dynamic CE-CT (DCE-CT) has emerged as a promising technique to perform also functional hemodynamic studies, with wide applications in the oncologic field. DCE-CT is based on repeated scans over time performed after intravenous administration of contrast agent, in order to study the temporal evolution of the tracer in 3D tumour tissue. DCE-CT pushes towards an intensive use of computers to provide automatically quantitative information to be used directly in clinical practice. This requires that visual analysis, representing the gold-standard for CT image interpretation, gains objectivity. This work presents the first automatic approach to quantify and classify the lung tumour heterogeneities based on DCE-CT image sequences, so as it is performed through visual analysis by experts. The approach developed relies on the spatio-temporal indices we devised, which also allow exploiting temporal data that enrich the knowledge of the tissue heterogeneity by providing information regarding the lesion status.

  10. Enhancing nitrogen removal from low carbon to nitrogen ratio wastewater by using a novel sequencing batch biofilm reactor. (United States)

    Zou, Jinte; Li, Jun; Ni, Yongjiong; Wei, Su


    Removing nitrogen from wastewater with low chemical oxygen demand/total nitrogen (COD/TN) ratio is a difficult task due to the insufficient carbon source available for denitrification. Therefore, in the present work, a novel sequencing batch biofilm reactor (NSBBR) was developed to enhance the nitrogen removal from wastewater with low COD/TN ratio. The NSBBR was divided into two units separated by a vertical clapboard. Alternate feeding and aeration was performed in the two units, which created an anoxic unit with rich substrate content and an aeration unit deficient in substrate simultaneously. Therefore, the utilization of the influent carbon source for denitrification was increased, leading to higher TN removal compared to conventional SBBR (CSBBR) operation. The results show that the CSBBR removed up to 76.8%, 44.5% and 10.4% of TN, respectively, at three tested COD/TN ratios (9.0, 4.8 and 2.5). In contrast, the TN removal of the NSBBR could reach 81.9%, 60.5% and 26.6%, respectively, at the corresponding COD/TN ratios. Therefore, better TN removal performance could be achieved in the NSBBR, especially at low COD/TN ratios (4.8 and 2.5). Furthermore, it is easy to upgrade a CSBBR into an NSBBR in practice.

  11. Optimization of operation conditions for preventing sludge bulking and enhancing the stability of aerobic granular sludge in sequencing batch reactors. (United States)

    Zhou, Jun; Wang, Hongyu; Yang, Kai; Ma, Fang; Lv, Bin


    Sludge bulking caused by loss of stability is a major problem in aerobic granular sludge systems. This study investigated the feasibility of preventing sludge bulking and enhancing the stability of aerobic granular sludge in a sequencing batch reactor by optimizing operation conditions. Five operation parameters have been studied with the aim to understand their impact on sludge bulking. Increasing dissolved oxygen (DO) by raising aeration rates contributed to granule stability due to the competition advantage of non-filamentous bacteria and permeation of oxygen at high DO concentration. The ratio of polysaccharides to proteins was observed to increase as the hydraulic shear force increased. When provided with high/low organic loading rate (OLR) alternately, large and fluffy granules disintegrated, while denser round-shape granules formed. An increase of biomass concentration followed a decrease at the beginning, and stability of granules was improved. This indicated that aerobic granular sludge had the resistance of OLR. Synthetic wastewater combined highly and slowly biodegradable substrates, creating a high gradient, which inhibited the growth of filamentous bacteria and prevented granular sludge bulking. A lower chemical oxygen demand/N favored the hydrophobicity of granular sludge, which promoted with granule stability because of the lower diffusion rate of ammonia. The influence of temperature indicated a relatively low temperature was more suitable.

  12. Proteome scale census of major facilitator superfamily transporters in Trichoderma reesei using protein sequence and structure based classification enhanced ranking. (United States)

    Chaudhary, Nitika; Kumari, Indu; Sandhu, Padmani; Ahmed, Mushtaq; Akhter, Yusuf


    Trichoderma spp. have been acknowledged as potent bio-control agents against microbial pathogens and also as plant growth promoters. Various secondary metabolites are attributed for these beneficial activities. Major facilitator superfamily (MFS) includes the large proportion of efflux-pumps which are linked with membrane transport of these secondary metabolites. We have carried out a proteome-wide identification of MFS transporters using protein sequence and structure based hierarchical method in Trichoderma reesei. 448 proteins out of 9115 were detected to carry transmembrane helices. MFS specific intragenic gene duplication and its context with transport function have been presented. Finally, using homology based techniques, domains and motifs of MFS families have been identified and utilized to classify them. From query dataset of 448 transmembrane proteins, 148 proteins are identified as potential MFS transporters. Sugar porter, drug: H(+) antiporter-1, monocarboxylate porter and anion: cation symporter emerged as major MFS families with 51, 35, 17 and 11 members respectively. Representative protein tertiary structures of these families are homology modeled for structure-function analysis. This study may help to understand the molecular basis of secretion and transport of agriculturally valuable secondary metabolites produced by these bio-control fungal agents which may be exploited in future for enhancing its biotechnological applications in eco-friendly sustainable development.

  13. Two estrogen response element sequences near the PCNA gene are not responsible for its estrogen-enhanced expression in MCF7 cells.

    Directory of Open Access Journals (Sweden)

    Cheng Wang

    Full Text Available BACKGROUND: The proliferating cell nuclear antigen (PCNA is an essential component of DNA replication, cell cycle regulation, and epigenetic inheritance. High expression of PCNA is associated with poor prognosis in patients with breast cancer. The 5'-region of the PCNA gene contains two computationally-detected estrogen response element (ERE sequences, one of which is evolutionarily conserved. Both of these sequences are of undocumented cis-regulatory function. We recently demonstrated that estradiol (E2 enhances PCNA mRNA expression in MCF7 breast cancer cells. MCF7 cells proliferate in response to E2. METHODOLOGY/PRINCIPAL FINDINGS: Here, we demonstrate that E2 rapidly enhanced PCNA mRNA and protein expression in a process that requires ERalpha as well as de novo protein synthesis. One of the two upstream ERE sequences was specifically bound by ERalpha-containing protein complexes, in vitro, in gel shift analysis. Yet, each ERE sequence, when cloned as a single copy, or when engineered as two tandem copies of the ERE-containing sequence, was not capable of activating a luciferase reporter construct in response to E2. In MCF7 cells, neither ERE-containing genomic region demonstrated E2-dependent recruitment of ERalpha by sensitive ChIP-PCR assays. CONCLUSION/SIGNIFICANCE: We conclude that E2 enhances PCNA gene expression by an indirect process and that computational detection of EREs, even when evolutionarily conserved and when near E2-responsive genes, requires biochemical validation.

  14. V(D)J recombination frequency is affected by the sequence interposed between a pair of recombination signals: sequence comparison reveals a putative recombinational enhancer element

    DEFF Research Database (Denmark)

    Roch, F A; Hobi, R; Berchtold, M W;


    The immunoglobulin heavy chain intron enhancer (Emu) not only stimulates transcription but also V(D)J recombination of chromosomally integrated recombination substrates. We aimed at reproducing this effect in recombination competent cells by transient transfection of extrachromosomal substrates. ...

  15. Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens. (United States)

    Shokralla, Shadi; Gibson, Joel F; Nikbakht, Hamid; Janzen, Daniel H; Hallwachs, Winnie; Hajibabaei, Mehrdad


    DNA barcoding is an efficient method to identify specimens and to detect undescribed/cryptic species. Sanger sequencing of individual specimens is the standard approach in generating large-scale DNA barcode libraries and identifying unknowns. However, the Sanger sequencing technology is, in some respects, inferior to next-generation sequencers, which are capable of producing millions of sequence reads simultaneously. Additionally, direct Sanger sequencing of DNA barcode amplicons, as practiced in most DNA barcoding procedures, is hampered by the need for relatively high-target amplicon yield, coamplification of nuclear mitochondrial pseudogenes, confusion with sequences from intracellular endosymbiotic bacteria (e.g. Wolbachia) and instances of intraindividual variability (i.e. heteroplasmy). Any of these situations can lead to failed Sanger sequencing attempts or ambiguity of the generated DNA barcodes. Here, we demonstrate the potential application of next-generation sequencing platforms for parallel acquisition of DNA barcode sequences from hundreds of specimens simultaneously. To facilitate retrieval of sequences obtained from individual specimens, we tag individual specimens during PCR amplification using unique 10-mer oligonucleotides attached to DNA barcoding PCR primers. We employ 454 pyrosequencing to recover full-length DNA barcodes of 190 specimens using 12.5% capacity of a 454 sequencing run (i.e. two lanes of a 16 lane run). We obtained an average of 143 sequence reads for each individual specimen. The sequences produced are full-length DNA barcodes for all but one of the included specimens. In a subset of samples, we also detected Wolbachia, nontarget species, and heteroplasmic sequences. Next-generation sequencing is of great value because of its protocol simplicity, greatly reduced cost per barcode read, faster throughout and added information content.

  16. Synthesis of organic substances labelled with {sup 14}C and {sup 35}S; Syntheses de molecules organiques marquees par le carbone-14 et le soufre-35

    Energy Technology Data Exchange (ETDEWEB)

    Pichat, L. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires


    After a brief history of the development of the Section des Molecules marquees of the Frenchmic Energy Commission, the author gives an outline of the synthesis of the following labelled compounds: benzene {sup 14}C-6; phenyl-p-fluorophenyl, thienyl-2 {beta} alanines {beta} {sup 14}C; noradrenaline {beta} {sup 14}C (arterenol {beta} {sup 14}C), dotriacontane {sup 14}C-16-17, aminoethane sulfinic acid (hypotaurine {sup 35}S). (author)Fren. [French] Apres un bref historique du developpement de la Section des Molecules marquees du Commissariat a l'Energie Atomique fran is, l'auteur donne un resume des syntheses des composes marques suivants: benzene {sup 14}C-6; phenyl-p-fluorophenyl, thienyl-2 {beta} alamines {beta} {sup 14}C; noradrenaline {beta} {sup 14}C (arterenol {beta} {sup 14}C), dotriacontane {sup 14}C-16-17, acide aminoethane sulfinique (hypotaurine {sup 35}S). (auteur)

  17. In vivo biosynthesis of L-(/sup 35/S)Cys-arginine vasopressin, -oxytocin, and -somatostatin: rapid estimation using reversed phase high pressure liquid chromatography. [Rats

    Energy Technology Data Exchange (ETDEWEB)

    Franco-Bourland, R.E.; Fernstrom, J.D.


    L(/sup 35/S)Cys-arginine vasopressin, -oxytocin, and -somatostatin were purified from hypothalami and neurohypophyses 4 h after rats received L(/sup 35/S)Cys via the third ventricle. After acetic acid extraction, Sephadex G-25 filtration, and chemoadsorption to C18-silica (Sep-Pak cartridges), the labeled peptides were rapidly separated by gradient elution, reversed phase, high pressure liquid chromatography (HPLC). The identity and isotopic purity of the labeled peptides were determined by several reversed phase HPLC procedures in conjunction with chemical modification. The labeled peptide fractions were at least 50% radiochemically pure. Using this HPLC isolation procedure, incorporation of L-(/sup 35/S)Cys into each peptide was determined in hydrated and dehydrated rats. Label incorporation into arginine vasopressin and oxytocin in the hypothalamus and the neurohypophysis of dehydrated rats was 2-3 times greater than that in hydrated rats. Incorporation of label into hypothalamic and neurohypophyseal somatostatin was unaffected by the hydration state of the animal. This procedure thus provides a very rapid, but sensitive, set of techniques for studying the control of small peptide biosynthesis in the brain.

  18. Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples. (United States)

    Matranga, Christian B; Andersen, Kristian G; Winnicki, Sarah; Busby, Michele; Gladden, Adrianne D; Tewhey, Ryan; Stremlau, Matthew; Berlin, Aaron; Gire, Stephen K; England, Eleina; Moses, Lina M; Mikkelsen, Tarjei S; Odia, Ikponmwonsa; Ehiane, Philomena E; Folarin, Onikepe; Goba, Augustine; Kahn, S Humarr; Grant, Donald S; Honko, Anna; Hensley, Lisa; Happi, Christian; Garry, Robert F; Malboeuf, Christine M; Birren, Bruce W; Gnirke, Andreas; Levin, Joshua Z; Sabeti, Pardis C


    We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targeted RNase H-based digestion to remove contaminating poly(rA) carrier and ribosomal RNA. This depletion step improves both the quality of data and quantity of informative reads in unbiased total RNA sequencing libraries. We have also developed a hybrid-selection protocol to further enrich the viral content of sequencing libraries. These protocols have enabled rapid deep sequencing of both Lassa and Ebola virus and are broadly applicable to other viral genomics studies.

  19. Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate

    NARCIS (Netherlands)

    Buschmann, Tilo; Zhang, Rong; Brash, Douglas E.; Bystrykh, Leonid V.


    Background: DNA barcodes are short unique sequences used to label DNA or RNA-derived samples in multiplexed deep sequencing experiments. During the demultiplexing step, barcodes must be detected and their position identified. In some cases (e. g., with PacBio SMRT), the position of the barcode and D

  20. Quantitative assessment of hepatic function: modified look-locker inversion recovery (MOLLI) sequence for T1 mapping on Gd-EOB-DTPA-enhanced liver MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jeong Hee [Seoul National University Hospital, Department of Radiology, Seoul (Korea, Republic of); Lee, Jeong Min; Han, Joon Koo; Choi, Byung Ihn [Seoul National University Hospital, Department of Radiology, Seoul (Korea, Republic of); Seoul National University College of Medicine, Institute of Radiation Medicine, Jongno-gu, Seoul (Korea, Republic of); Paek, Munyoung [Siemens Healthcare, Seoul (Korea, Republic of)


    To determine whether multislice T1 mapping of the liver using a modified look-locker inversion recovery (MOLLI) sequence on gadoxetic acid-enhanced magnetic resonance imaging (MRI) can be used as a quantitative tool to estimate liver function and predict the presence of oesophageal or gastric varices. Phantoms filled with gadoxetic acid were scanned three times using MOLLI sequence to test repeatability. Patients with chronic liver disease or liver cirrhosis who underwent gadoxetic acid-enhanced liver MRI including MOLLI sequence at 3 T were included (n = 343). Pre- and postcontrast T1 relaxation times of the liver (T1liver), changes between pre- and postcontrast T1liver (ΔT1liver), and adjusted postcontrast T1liver (postcontrast T1liver-T1spleen/T1spleen) were compared among Child-Pugh classes. In 62 patients who underwent endoscopy, all T1 parameters and spleen sizes were correlated with varices. Phantom study showed excellent repeatability of MOLLI sequence. As Child-Pugh scores increased, pre- and postcontrast T1liver were significantly prolonged (P < 0.001), and ΔT1liver and adjusted postcontrast T1liver decreased (P< 0.001). Adjusted postcontrast T1liver and spleen size were independently associated with varices (R{sup 2} = 0.29, P < 0.001). T1 mapping of the liver using MOLLI sequence on gadoxetic acid-enhanced MRI demonstrated potential in quantitatively estimating liver function, and adjusted postcontrast T1liver was significantly associated with varices. (orig.)

  1. Over-Expression of the Pikh Gene with a CaMV 35S Promoter Leads to Improved Blast Disease (Magnaporthe oryzae) Tolerance in Rice



    Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is ...

  2. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains

    Directory of Open Access Journals (Sweden)

    Bharti Arvind K


    Full Text Available Abstract Background Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR and methylation spanning linker libraries (MSLL. These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to "epigenetic boundaries" where methylation begins or ends. Results A large-scale study in maize generated 40,299 HMPR sequences and 80,723 MSLL sequences, including MSLL clones exceeding 100 kb. The paired end reads of MSLL and HMPR clones were shown to be effective in linking existing gene-rich sequences into scaffolds. In addition, it was shown that the MSLL clones can be used for anchoring these scaffolds to a BAC-based physical map. The MSLL end reads effectively identified epigenetic boundaries, as indicated by their preferential alignment to regions upstream and downstream from annotated genes. The ability to precisely map long stretches of fully methylated DNA sequence is a unique outcome of MSLL analysis, and was also shown to provide evidence for errors in gene identification. MSLL clones were observed to be significantly more repeat-rich in their interiors than in their end reads, confirming the correlation between methylation and retroelement content. Both MSLL and HMPR reads were found to be substantially gene-enriched, with the SalI MSLL libraries being the most highly enriched (31% align to an EST contig, while the HMPR clones exhibited exceptional depletion of repetitive DNA (to ~11%. These two techniques were compared with other gene-enrichment methods, and shown to be complementary. Conclusion MSLL technology provides an unparalleled approach for mapping the epigenetic status of repetitive blocks and for identifying sequences mis-identified as genes. Although the types and natures of

  3. A tandem sequence motif acts as a distance-dependent enhancer in a set of genes involved in translation by binding the proteins NonO and SFPQ

    Directory of Open Access Journals (Sweden)

    Roepcke Stefan


    Full Text Available Abstract Background Bioinformatic analyses of expression control sequences in promoters of co-expressed or functionally related genes enable the discovery of common regulatory sequence motifs that might be involved in co-ordinated gene expression. By studying promoter sequences of the human ribosomal protein genes we recently identified a novel highly specific Localized Tandem Sequence Motif (LTSM. In this work we sought to identify additional genes and LTSM-binding proteins to elucidate potential regulatory mechanisms. Results Genome-wide analyses allowed finding a considerable number of additional LTSM-positive genes, the products of which are involved in translation, among them, translation initiation and elongation factors, and 5S rRNA. Electromobility shift assays then showed specific signals demonstrating the binding of protein complexes to LTSM in ribosomal protein gene promoters. Pull-down assays with LTSM-containing oligonucleotides and subsequent mass spectrometric analysis identified the related multifunctional nucleotide binding proteins NonO and SFPQ in the binding complex. Functional characterization then revealed that LTSM enhances the transcriptional activity of the promoters in dependency of the distance from the transcription start site. Conclusions Our data demonstrate the power of bioinformatic analyses for the identification of biologically relevant sequence motifs. LTSM and the here found LTSM-binding proteins NonO and SFPQ were discovered through a synergistic combination of bioinformatic and biochemical methods and are regulators of the expression of a set of genes of the translational apparatus in a distance-dependent manner.

  4. Evaluation of Dixon Sequence on Hybrid PET/MR Compared with Contrast-Enhanced PET/CT for PET-Positive Lesions

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Ju Hye; Cho, Ihn Ho; Kong, Eun Jung; Chun, Kyung Ah [Yeungnam Univ. Hospital, Daegu (Korea, Republic of)


    Hybrid positron emission tomography and magnetic resonance (PET/MR) imaging performs a two-point Dixon MR sequence for attenuation correction. However, MR data in hybrid PET/MR should provide anatomic and morphologic information as well as an attenuation map. We evaluated the Dixon sequence of hybrid PET/MR for anatomic correlation of PET-positive lesions compared with contrast-enhanced PET/computed tomography (CT) in patients with oncologic diseases. Twelve patients underwent a single injection, dual imaging protocol. PET/CT was performed with an intravenous contrast agent (85±13 min after {sup 18}F-FDG injection of 403± 45 MBq) and then (125±19 min after injection) PET/MR was performed. Attenuation correction and anatomic allocation of PET were performed using contrast-enhanced CT for PET/CT and Dixon MR sequence for hybrid PET/MR. The Dixon MR sequence and contrast-enhanced CT were compared for anatomic correlation of PET-positive lesions (scoring scale ranging from 0 to 3 for visual ratings). Additionally, standardized uptake values (SUVs) for the detected lesions were assessed for quantitative comparison. Both hybrid PET/MR and contrast-enhanced PET/CT identified 55 lesions with increased FDG uptake in ten patients. In total, 28 lymph nodes, 11 bone lesions, 3 dermal nodules, 3 pleural thickening lesions, 2 thyroid nodules, 1 pancreas, 1 liver, 1 ovary, 1 uterus, 1 breast, 1 soft tissue and 2 lung lesions were present. The best performance was observed for anatomic correlation of PET findings by the contrast-enhanced CT scans (contrast-enhanced CT, 2.64± 0.70; in-phase, 1.29±1.01; opposed-phase, 1.29±1.15; water-weighted, 1.71±1.07; fat weighted, 0.56±1.03). A significant difference was observed between the scores obtained from the contrast-enhanced CT and all four coregistered Dixon MR images. Quantitative evaluation revealed a high correlation between the SUVs measured with hybrid PET/MR (SUVmean, 2.63±1.62; SUVmax, 4.30±2.88) and contrast-enhanced

  5. Handling Permutation in Sequence Comparison: Genome-Wide Enhancer Prediction in Vertebrates by a Novel Non-Linear Alignment Scoring Principle.

    Directory of Open Access Journals (Sweden)

    Dirk Dolle

    Full Text Available Enhancers have been described to evolve by permutation without changing function. This has posed the problem of how to predict enhancer elements that are hidden from alignment-based approaches due to the loss of co-linearity. Alignment-free algorithms have been proposed as one possible solution. However, this approach is hampered by several problems inherent to its underlying working principle. Here we present a new approach, which combines the power of alignment and alignment-free techniques into one algorithm. It allows the prediction of enhancers based on the query and target sequence only, no matter whether the regulatory logic is co-linear or reshuffled. To test our novel approach, we employ it for the prediction of enhancers across the evolutionary distance of ~450Myr between human and medaka. We demonstrate its efficacy by subsequent in vivo validation resulting in 82% (9/11 of the predicted medaka regions showing reporter activity. These include five candidates with partially co-linear and four with reshuffled motif patterns. Orthology in flanking genes and conservation of the detected co-linear motifs indicates that those candidates are likely functionally equivalent enhancers. In sum, our results demonstrate that the proposed principle successfully predicts mutated as well as permuted enhancer regions at an encouragingly high rate.

  6. Comparison of different magnetic resonance cholangiography techniques in living liver donors including Gd-EOB-DTPA enhanced T1-weighted sequences.

    Directory of Open Access Journals (Sweden)

    Sonja Kinner

    Full Text Available Preoperative evaluation of potential living liver donors (PLLDs includes the assessment of the biliary anatomy to avoid postoperative complications. Aim of this study was to compare T2-weighted (T2w and Gd-EOB-DTPA enhanced T1-weighted (T1w magnetic resonance cholangiography (MRC techniques in the evaluation of PLLDs.30 PLLDs underwent MRC on a 1.5 T Magnetom Avanto (Siemens, Erlangen, Germany using (A 2D T2w HASTE (Half Fourier Acquisition Single Shot Turbo Spin Echo fat saturated (fs in axial plane, (B 2D T2w HASTE fs thick slices in coronal plane, (C free breathing 3D T2w TSE (turbo spin echo RESTORE (high-resolution navigator corrected plus (D maximum intensity projections (MIPs, (E T2w SPACE (sampling perfection with application optimized contrasts using different flip angle evolutions plus (F MIPs and (G T2w TSE BLADE as well as Gd-EOB-DTPA T1w images without (G and with (H inversion recovery. Contrast enhanced CT cholangiography served as reference imaging modality. Two independent reviewers evaluated the biliary tract anatomy on a 5-point scale subjectively and objectively. Data sets were compared using a Mann-Whitney-U-test. Kappa values were also calculated.Source images and maximum intensity projections of 3D T2w TSE sequences (RESTORE and SPACE proved to be best for subjective and objective evaluation directly followed by 2D HASTE sequences. Interobserver variabilities were good to excellent (k = 0.622-0.804.3D T2w sequences are essential for preoperative biliary tract evaluation in potential living liver donors. Furthermore, our results underline the value of different MRCP sequence types for the evaluation of the biliary anatomy in PLLDs including Gd-EOB-DTPA enhanced T1w MRC.

  7. Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta

    KAUST Repository

    Lafi, Feras Fawzi


    Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated from roots of Cyperus conglomeratus collected at the Red Sea coast in Thuwal, Saudi Arabia. Here, we present a draft genome sequence of this strain, highlighting a number of pathways involved in plant growth promotion under salt stress.

  8. Draft Genome Sequence of Halomonas elongata Strain K4, an Endophytic Growth-Promoting Bacterium Enhancing Salinity Tolerance In Planta (United States)

    Lafi, Feras F.; Ramirez-Prado, Juan S.; Alam, Intikhab; Bajic, Vladimir B.


    Halomonas elongata strain K4 is an endophytic bacterial strain that was isolated from roots of Cyperus conglomeratus collected at the Red Sea coast in Thuwal, Saudi Arabia. Here, we present a draft genome sequence of this strain, highlighting a number of pathways involved in plant growth promotion under salt stress. PMID:27811099

  9. Sequences enhancing cassava mosaic disease symptoms occur in the cassava genome and are associated with South African cassava mosaic virus infection. (United States)

    Maredza, A T; Allie, F; Plata, G; Rey, M E C


    Cassava is an important food security crop in Sub-Saharan Africa. Two episomal begomovirus-associated sequences, named Sequences Enhancing Geminivirus Symptoms (SEGS1 and SEGS2), were identified in field cassava affected by the devastating cassava mosaic disease (CMD). The sequences reportedly exacerbated CMD symptoms in the tolerant cassava landrace TME3, and the model plants Arabidopsis thaliana and Nicotiana benthamiana, when biolistically co-inoculated with African cassava mosaic virus-Cameroon (ACMV-CM) or East African cassava mosaic virus-UG2 (EACMV-UG2). Following the identification of small SEGS fragments in the cassava EST database, the intention of this study was to confirm their presence in the genome, and investigate a possible role for these sequences in CMD. We report that multiple copies of varying lengths of both SEGS1 and SEGS2 are widely distributed in the sequenced cassava genome and are present in several other cassava accessions screened by PCR. The endogenous SEGS1 and SEGS2 are in close proximity or overlapping with cassava genes, suggesting a possible role in regulation of specific biological processes. We confirm the expression of SEGS in planta using EST data and RT-PCR. The sequence features of endogenous SEGS (iSEGS) are unique but resemble non-autonomous transposable elements (TEs) such as MITEs and helitrons. Furthermore, many SEGS-associated genes, some involved in virus-host interactions, are differentially expressed in susceptible (T200) and tolerant TME3) cassava landraces infected by South African cassava mosaic virus (SACMV) of susceptible (T200) and tolerant (TME3) cassava landraces. Abundant SEGS-derived small RNAs were also present in mock-inoculated and SACMV-infected T200 and TME3 leaves. Given the known role of TEs and associated genes in gene regulation and plant immune responses, our observations are consistent with a role of these DNA elements in the host's regulatory response to geminiviruses.

  10. Global analysis of physical and functional RNA targets of hnRNP L reveals distinct sequence and epigenetic features of repressed and enhanced exons. (United States)

    Cole, Brian S; Tapescu, Iulia; Allon, Samuel J; Mallory, Michael J; Qiu, Jinsong; Lake, Robert J; Fan, Hua-Ying; Fu, Xiang-Dong; Lynch, Kristen W


    HnRNP L is a ubiquitous splicing-regulatory protein that is critical for the development and function of mammalian T cells. Previous work has identified a few targets of hnRNP L-dependent alternative splicing in T cells and has described transcriptome-wide association of hnRNP L with RNA. However, a comprehensive analysis of the impact of hnRNP L on mRNA expression remains lacking. Here we use next-generation sequencing to identify transcriptome changes upon depletion of hnRNP L in a model T-cell line. We demonstrate that hnRNP L primarily regulates cassette-type alternative splicing, with minimal impact of hnRNP L depletion on transcript abundance, intron retention, or other modes of alternative splicing. Strikingly, we find that binding of hnRNP L within or flanking an exon largely correlates with exon repression by hnRNP L. In contrast, exons that are enhanced by hnRNP L generally lack proximal hnRNP L binding. Notably, these hnRNP L-enhanced exons share sequence and context features that correlate with poor nucleosome positioning, suggesting that hnRNP may enhance inclusion of a subset of exons via a cotranscriptional or epigenetic mechanism. Our data demonstrate that hnRNP L controls inclusion of a broad spectrum of alternative cassette exons in T cells and suggest both direct RNA regulation as well as indirect mechanisms sensitive to the epigenetic landscape.

  11. Secure Digital Cashless Transactions with Sequence Diagrams and Spatial Circuits to Enhance the Information Assurance and Security Education

    Directory of Open Access Journals (Sweden)

    Dr. Ajantha Herath


    Full Text Available Often students have difficulties mastering cryptographic algorithms. For some time we have been developing with methods for introducing important security concepts for both undergraduate and graduate students in Information Systems, Computer Science and Engineering students. To achieve this goal, Sequence diagrams and spatial circuit derivation from equations are introduced to students. Sequence diagrams represent progression of events with time. They learn system security concepts more effectively if they know how to transform equations and high level programming language constructs into spatial circuits or special purpose hardware. This paper describes an active learning module developed to help students understand secure protocols, algorithms and modeling web applications to prevent attacks and both software and hardware implementations related to encryption. These course materials can also be used in computer organization and architecture classes to help students understand and develop special purpose circuitry for cryptographic algorithms.

  12. Demonstration of the therapeutic effect of /sup 35/S labelled L-cystine in articular and intervertebral cartilage as well as in skeletal musculature

    Energy Technology Data Exchange (ETDEWEB)

    Schmiegelow, P.; Puschmann, M.; Giese, U.


    Clinical experience has obviously shown a positive effect of application of sulfated amino acids on degenerative cartilage diseases. L-Cystin, presumed to be of therapeutic effect, was autoradiographically localized in articular, columnar and intervertebral cartilage as well as in skeletal musculature. In 10 days old NMRI-mice, we had shown a dose-dependent incorporation of the radioactively labelled /sup 35/S-Cystin in hair follicle. These statistically significant differences had been measured by quantitative autoradiographical microscope photometry. The sulfated amino acids are also proven in nail matrix, nail hyponychium as well as in cartilage and skeletal musculature. Besides a localization of radioactively labelled L-Cystin in tissues, presumed as target organs of a therapeutic effect, there is still lacking an experimental proof of efficacy on cell proliferation and functional metabolism e.g. in arthrosis by suitable animal models.

  13. Genome Sequence and Transcriptome Analyses of Chrysochromulina tobin: Metabolic Tools for Enhanced Algal Fitness in the Prominent Order Prymnesiales (Haptophyceae.

    Directory of Open Access Journals (Sweden)

    Blake T Hovde

    Full Text Available Haptophytes are recognized as seminal players in aquatic ecosystem function. These algae are important in global carbon sequestration, form destructive harmful blooms, and given their rich fatty acid content, serve as a highly nutritive food source to a broad range of eco-cohorts. Haptophyte dominance in both fresh and marine waters is supported by the mixotrophic nature of many taxa. Despite their importance the nuclear genome sequence of only one haptophyte, Emiliania huxleyi (Isochrysidales, is available. Here we report the draft genome sequence of Chrysochromulina tobin (Prymnesiales, and transcriptome data collected at seven time points over a 24-hour light/dark cycle. The nuclear genome of C. tobin is small (59 Mb, compact (∼ 40% of the genome is protein coding and encodes approximately 16,777 genes. Genes important to fatty acid synthesis, modification, and catabolism show distinct patterns of expression when monitored over the circadian photoperiod. The C. tobin genome harbors the first hybrid polyketide synthase/non-ribosomal peptide synthase gene complex reported for an algal species, and encodes potential anti-microbial peptides and proteins involved in multidrug and toxic compound extrusion. A new haptophyte xanthorhodopsin was also identified, together with two "red" RuBisCO activases that are shared across many algal lineages. The Chrysochromulina tobin genome sequence provides new information on the evolutionary history, ecology and economic importance of haptophytes.

  14. Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5

    Energy Technology Data Exchange (ETDEWEB)

    Mefford, Megan E., E-mail: [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA (United States); Kunstman, Kevin, E-mail: [Northwestern University Medical School, Chicago, IL (United States); Wolinsky, Steven M., E-mail: [Northwestern University Medical School, Chicago, IL (United States); Gabuzda, Dana, E-mail: [Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA (United States); Department of Neurology (Microbiology and Immunobiology), Harvard Medical School, Boston, MA (United States)


    Macrophages express low levels of the CD4 receptor compared to T-cells. Macrophage-tropic HIV strains replicating in brain of untreated patients with HIV-associated dementia (HAD) express Envs that are adapted to overcome this restriction through mechanisms that are poorly understood. Here, bioinformatic analysis of env sequence datasets together with functional studies identified polymorphisms in the β3 strand of the HIV gp120 bridging sheet that increase M-tropism. D197, which results in loss of an N-glycan located near the HIV Env trimer apex, was detected in brain in some HAD patients, while position 200 was estimated to be under positive selection. D197 and T/V200 increased fusion and infection of cells expressing low CD4 by enhancing gp120 binding to CCR5. These results identify polymorphisms in the HIV gp120 bridging sheet that overcome the restriction to macrophage infection imposed by low CD4 through enhanced gp120–CCR5 interactions, thereby promoting infection of brain and other macrophage-rich tissues. - Highlights: • We analyze HIV Env sequences and identify amino acids in beta 3 of the gp120 bridging sheet that enhance macrophage tropism. • These amino acids at positions 197 and 200 are present in brain of some patients with HIV-associated dementia. • D197 results in loss of a glycan near the HIV Env trimer apex, which may increase exposure of V3. • These variants may promote infection of macrophages in the brain by enhancing gp120–CCR5 interactions.

  15. 环介导等温扩增技术检测含有CaMV35S的转基因玉米%Loop-mediated Isothermal Amplification for the Detection of CaMV35S Promoter in Genetically Modified Maize

    Institute of Scientific and Technical Information of China (English)

    陈金松; 黄丛林; 张秀海; 吴忠义


    The objective is to develop a loop-mediated isothermal amplification method for detection of CaMV-35S promoter in Genetically Modified maize. Loop-mediated isothermal amplification (LAMP) , a novel nucleic acid amplification method, was developed for the rapid detection of Genetically Modified maize. Cauliflower mosaic virus 35S (CaMV35S) promoter gene was amplified by a set of four primers that recognize six distinct sequences of the target. The optimized conditions for LAMP were studied using different Mg2+ , dNTPs, Betaine and primers concentrations. Furthermore, the sensitivity of LAMP was tested comparing with PCR. The LAMP method can detect CaMV35S promoter from genetically modified maize and their test results were consistent with the results of conventional PCR method. LAMP assay results were found to be more sensitive than the conventional PCR. The LAMP assay is an extremely rapid, highly sensitive, specific method, and will be an effective tool for rapid detection of Genetically Modified maize.%DNA环介导等温扩增技术是一种特异、灵敏、快速的新型基因检测技术.针对玉米表达载体的花椰菜花叶病毒35 S启动子(CaMV35S)的6个区域设计4种特异引物,对LAMP反应的MgSO4、dNTPs、Betaine、内引物、外引物各个成分进行了优化,此外还对LAMP和PCR两种不同方法的特异性进行了比较.建立转基因玉米花椰菜花叶病毒35 S启动子环介导等温扩增技术检测方法,LAMP与PCR相比具有更高的灵敏度.环介导等温扩增技术检测方法具有时间少,成本低,特异性高,检测方法多样等优势,为检测转基因玉米花椰菜花叶病毒35 S启动子提供了一种更加简便快速的方法.

  16. Quantum dot-enhanced detection of dual short RNA sequences via one-step template-dependent surface hybridization

    Energy Technology Data Exchange (ETDEWEB)

    Song Wenqing; Qiu Xue; Lau Choiwan [School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education and PLA, Fudan University, 826 Zhangheng Road, Shanghai 201203 (China); Lu Jianzhong, E-mail: [School of Pharmacy, Key Laboratory of Smart Drug Delivery, Ministry of Education and PLA, Fudan University, 826 Zhangheng Road, Shanghai 201203 (China)


    Graphical abstract: A novel multiplexed method for short RNA detection is reported that employed a design strategy in which quantum dots functionalized reporter DNA were used to capture a short single-stranded RNA sequence from a target solution and then to specifically adsorb onto a common capture probe-modified 96-well plate via a one-step template-dependent, surface hybridization for simultaneous fluorescence detection. Highlights: Black-Right-Pointing-Pointer A ligase-free sensor was demonstrated for the specific detection of dual short RNA. Black-Right-Pointing-Pointer The method was sensitive and simultaneous. Black-Right-Pointing-Pointer Quantum dots-modified reporter probes could increase the melting temperature. Black-Right-Pointing-Pointer Quantum dots functionalized reporter DNA hybridized with capture DNA and target RNA. Black-Right-Pointing-Pointer Target RNA was captured via a one-step template-dependent hybridization. - Abstract: A novel multiplexed method for short RNA detection is reported that employs a design strategy in which capture and reporter probes anneal to each other in the presence of a short RNA target via the formation of a stable three-component complex. Quantum dots (QDs) functionalized with reporter DNA are thus specifically bound onto a capture probe-modified 96-well plate by one-step hybridization for simple RNA detection. In comparison with conventional organic dye-modified reporter probes, the use of reporter DNA-modified QD conjugates increase the melting temperature and lead to the detection of short RNA without the need for a ligation reaction. Moreover, QD properties allow multiple short RNA sequences to be simultaneously determined via rapid and simple one-step hybridization, as exemplified herein. The present results clearly demonstrate that this new strategy can be used to detect dual-short RNA sequence at concentrations of 10 pM in 100 {mu}L.

  17. Enhancement of heterologous gene expression in Flammulina velutipes using polycistronic vectors containing a viral 2A cleavage sequence.

    Directory of Open Access Journals (Sweden)

    Yu-Ju Lin

    Full Text Available Agrobacterium tumefaciens-mediated transformation for edible mushrooms has been previously established. However, the enhancement of heterologous protein production and the expression of multi-target genes remains a challenge. In this study, heterologous protein expression in the enoki mushroom Flammulina velutipes was notably enhanced using 2A peptide-mediated cleavage to co-express multiple copies of single gene. The polycistronic expression vectors were constructed by connecting multi copies of the enhanced green fluorescent protein (egfp gene using 2A peptides derived from porcine teschovirus-1. The P2A peptides properly self-cleaved as shown by the formation of the transformants with antibiotic resistant capacity and exciting green fluorescence levels after introducing the vectors into F. velutipes mycelia. The results of western blot analysis, epifluorescent microscopy and EGFP production showed that heterologous protein expression in F. velutipes using the polycistronic strategy increased proportionally as the gene copy number increased from one to three copies. In contrast, much lower EGFP levels were detected in the F. velutipes transformants harboring four copies of the egfp gene due to mRNA instability. The polycistronic strategy using 2A peptide-mediated cleavage developed in this study can not only be used to express single gene in multiple copies, but also to express multiple genes in a single reading frame. It is a promising strategy for the application of mushroom molecular pharming.

  18. Enhancement of heterologous gene expression in Flammulina velutipes using polycistronic vectors containing a viral 2A cleavage sequence. (United States)

    Lin, Yu-Ju; Huang, Li-Hsin; Huang, Ching-Tsan


    Agrobacterium tumefaciens-mediated transformation for edible mushrooms has been previously established. However, the enhancement of heterologous protein production and the expression of multi-target genes remains a challenge. In this study, heterologous protein expression in the enoki mushroom Flammulina velutipes was notably enhanced using 2A peptide-mediated cleavage to co-express multiple copies of single gene. The polycistronic expression vectors were constructed by connecting multi copies of the enhanced green fluorescent protein (egfp) gene using 2A peptides derived from porcine teschovirus-1. The P2A peptides properly self-cleaved as shown by the formation of the transformants with antibiotic resistant capacity and exciting green fluorescence levels after introducing the vectors into F. velutipes mycelia. The results of western blot analysis, epifluorescent microscopy and EGFP production showed that heterologous protein expression in F. velutipes using the polycistronic strategy increased proportionally as the gene copy number increased from one to three copies. In contrast, much lower EGFP levels were detected in the F. velutipes transformants harboring four copies of the egfp gene due to mRNA instability. The polycistronic strategy using 2A peptide-mediated cleavage developed in this study can not only be used to express single gene in multiple copies, but also to express multiple genes in a single reading frame. It is a promising strategy for the application of mushroom molecular pharming.

  19. The upstream regulatory sequence of the light harvesting complex Lhcf2 gene of the marine diatom Phaeodactylum tricornutum enhances transcription in an orientation- and distance-independent fashion. (United States)

    Russo, Monia Teresa; Annunziata, Rossella; Sanges, Remo; Ferrante, Maria Immacolata; Falciatore, Angela


    Diatoms are a key phytoplankton group in the contemporary ocean, showing extraordinary adaptation capacities to rapidly changing environments. The recent availability of whole genome sequences from representative species has revealed distinct features in their genomes, like novel combinations of genes encoding distinct metabolisms and a significant number of diatom-specific genes. However, the regulatory mechanisms driving diatom gene expression are still largely uncharacterized. Considering the wide variety of fields of study orbiting diatoms, ranging from ecology, evolutionary biology to biotechnology, it is thus essential to increase our understanding of fundamental gene regulatory processes such as transcriptional regulation. To this aim, we explored the functional properties of the 5'-flanking region of the Phaeodatylum tricornutum Lhcf2 gene, encoding a member of the Light Harvesting Complex superfamily and we showed that this region enhances transcription of a GUS reporter gene in an orientation- and distance-independent fashion. This represents the first example of a cis-regulatory sequence with enhancer-like features discovered in diatoms and it is instrumental for the generation of novel genetic tools and diatom exploitation in different areas of study.

  20. Enhancing learning through optimal sequencing of web-based and manikin simulators to teach shock physiology in the medical curriculum. (United States)

    Cendan, Juan C; Johnson, Teresa R


    The Association of American Medical Colleges has encouraged educators to investigate proper linkage of simulation experiences with medical curricula. The authors aimed to determine if student knowledge and satisfaction differ between participation in web-based and manikin simulations for learning shock physiology and treatment and to determine if a specific training sequencing had a differential effect on learning. All 40 second-year medical students participated in a randomized, counterbalanced study with two interventions: group 1 (n = 20) participated in a web-based simulation followed by a manikin simulation and group 2 (n = 20) participated in reverse order. Knowledge and attitudes were documented. Mixed-model ANOVA indicated a significant main effect of time (F(1,38) = 18.6, P learning when web-based simulation precedes manikin use. This finding warrants further study.

  1. Sequence-selective recognition of double-stranded RNA and enhanced cellular uptake of cationic nucleobase and backbone-modified peptide nucleic acids. (United States)

    Hnedzko, Dziyana; McGee, Dennis W; Karamitas, Yannis A; Rozners, Eriks


    Sequence-selective recognition of complex RNAs in live cells could find broad applications in biology, biomedical research, and biotechnology. However, specific recognition of structured RNA is challenging, and generally applicable and effective methods are lacking. Recently, we found that peptide nucleic acids (PNAs) were unusually well-suited ligands for recognition of double-stranded RNAs. Herein, we report that 2-aminopyridine (M) modified PNAs and their conjugates with lysine and arginine tripeptides form strong (Ka = 9.4 to 17 × 10(7) M(-1)) and sequence-selective triple helices with RNA hairpins at physiological pH and salt concentration. The affinity of PNA-peptide conjugates for the matched RNA hairpins was unusually high compared to the much lower affinity for DNA hairpins of the same sequence (Ka = 0.05 to 1.1 × 10(7) M(-1)). The binding of double-stranded RNA by M-modified PNA-peptide conjugates was a relatively fast process (kon = 2.9 × 10(4) M(-1) sec(-1)) compared to the notoriously slow triple helix formation by oligodeoxynucleotides (kon ∼ 10(3) M(-1) sec(-1)). M-modified PNA-peptide conjugates were not cytotoxic and were efficiently delivered in the cytosol of HEK293 cells at 10 µM. Surprisingly, M-modified PNAs without peptide conjugation were also taken up by HEK293 cells, which, to the best of our knowledge, is the first example of heterocyclic base modification that enhances the cellular uptake of PNA. Our results suggest that M-modified PNA-peptide conjugates are promising probes for sequence-selective recognition of double-stranded RNA in live cells and other biological systems.

  2. Quantitation of 35S promoter in maize DNA extracts from genetically modified organisms using real-time polymerase chain reaction, part 2: interlaboratory study. (United States)

    Feinberg, Max; Fernandez, Sophie; Cassard, Sylvanie; Bertheau, Yves


    The European Committee for Standardization (CEN) and the European Network of GMO Working Laboratories have proposed development of a modular strategy for stepwise validation of complex analytical techniques. When applied to the quantitation of genetically modified organisms (GMOs) in food products, the instrumental quantitation step of the technique is separately validated from the DNA extraction step to better control the sources of uncertainty and facilitate the validation of GMO-specific polymerase chain reaction (PCR) tests. This paper presents the results of an interlaboratory study on the quantitation step of the method standardized by CEN for the detection of a regulatory element commonly inserted in GMO maize-based foods. This is focused on the quantitation of P35S promoter through using the quantitative real-time PCR (QRT-PCR). Fifteen French laboratories participated in the interlaboratory study of the P35S quantitation operating procedure on DNA extract samples using either the thermal cycler ABI Prism 7700 (Applied Biosystems, Foster City, CA) or Light Cycler (Roche Diagnostics, Indianapolis, IN). Attention was focused on DNA extract samples used to calibrate the method and unknown extract samples. Data were processed according to the recommendations of ISO 5725 standard. Performance criteria, obtained using the robust algorithm, were compared to the classic data processing after rejection of outliers by the Cochran and Grubbs tests. Two laboratories were detected as outliers by the Grubbs test. The robust precision criteria gave values between the classical values estimated before and after rejection of the outliers. Using the robust method, the relative expanded uncertainty by the quantitation method is about 20% for a 1% Bt176 content, whereas it can reach 40% for a 0.1% Bt176. The performances of the quantitation assay are relevant to the application of the European regulation, which has an accepted tolerance interval of about +/-50%. These data

  3. MRI增强序列对胆管细胞癌的诊断价值%Contrast-enhanced MRI sequence in the diagnosis of cholangiocarcinoma

    Institute of Scientific and Technical Information of China (English)

    裴新龙; 苏静; 刘剑羽


    Objective To evaluate contrast-enhanced MRI sequence for diagnosing cholangiocarcinoma.Methods Cholangiocarcinoma was confirmed by surgery and pathology in 17 cases,all underwent preoperative CT and MRI T1-VIBE scan with contrast-enhancement sequence.We retrospectively analyzed imaging signs in two scan methods,including lesion position,number,size,enhancement degree,expansion degree of bile duct,invasion of adjacent artery and portal vein,and portal vein tumor thrombosis.The differences on detecting lesions between two methods were compared.Results The contrast to noise ratio (CNR) between tumor and liver tissue in MRI T1-VIBE images was obviously superior to that in CT images.Peripheral lesion boundary in T1-VIBE enhanced images was clearer than CT.One hemorrhage lesion was shown in T1-VIBE images,and tumor thrombosis was visible in the left branch of portal vein in 1 case.Bile duct wall lesions in T1-VIBE enhanced images was more evident than CT in hilar cholangiocarcinoma and extrahepatic cholangiocarcinoma.The VIBE enhanced images find more lesions in 9 out of 11 multiple focus cases,compared with CT images.Conclusions Contrast-enhanced MRI T1-VIBE sequence can give more comprehensive and clear evaluation on cholangiocarcinoma,and has important clinical diagnostic values.%目的 评估分析MRI增强序列对胆管细胞癌的诊断价值.方法 回顾性分析17例经病理证实的胆管细胞癌患者,均经CT增强检查和MRI T1-VIBE增强序列扫描,分析2种检查方法中的各种影像学征象,分别记录病变的位置、数目、大小、强化程度、胆管扩张程度,观察邻近动脉、门静脉受侵、门静脉内瘤栓情况,重点观察两种不同的检查方法对于病变的显示效果. 结果 MRI TlVIBE图像的肿瘤与无肿瘤肝脏组织的对比明显优于CT图像.肝内病变边界T1-VIBE增强序列更加清晰,1例病灶内可见出血,1例可见门脉左支内瘤栓;肝门部病变和肝外胆管病变VIBE增

  4. The diagnostic efficacy of quantitative liver MR imaging with diffusion-weighted, SWI, and hepato-specific contrast-enhanced sequences in staging liver fibrosis - a multiparametric approach

    Energy Technology Data Exchange (ETDEWEB)

    Feier, Diana [Medical University of Vienna, General Hospital of Vienna (AKH), Department of Biomedical Imaging and Image-guided Therapy, Vienna (Austria); Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Emergency County Hospital, Department of Radiology, Cluj-Napoca (Romania); Balassy, Csilla; Bastati, Nina; Fragner, Romana; Ba-Ssalamah, Ahmed [Medical University of Vienna, General Hospital of Vienna (AKH), Department of Biomedical Imaging and Image-guided Therapy, Vienna (Austria); Wrba, Friedrich [Medical University of Vienna, General Hospital of Vienna (AKH), Department of Pathology, Vienna (Austria)


    To assess the diagnostic efficacy of multiparametric MRI using quantitative measurements of the apparent diffusion coefficient (ADC) of the liver parenchyma on diffusion-weighted imaging (DWI), signal intensity (SI) on susceptibility-weighted imaging (SWI), and gadoxetic acid-enhanced T1-weighted imaging during the hepatobiliary phase for the staging of liver fibrosis. Seventy-seven patients underwent a 3T MRI examination, including DWI/SWI sequences and gadoxetic acid-enhanced T1-weighted MRI. Liver fibrosis according to liver biopsy was staged using the Metavir fibrosis score: F0 (n = 21, 27.3 %); F1 (n = 7, 9.1 %); F2 (n = 8, 10.4 %); F3 (n = 12, 15.6 %); and F4 (n = 29, 37.7 %). SI of the liver was defined using region-of-interest measurements to calculate the ADC values, the relative enhancement (RE) in the hepatobiliary phase, and the liver-to-muscle ratio (LMR) measurements for SWI. The values of RE, LMR, and ADC measurements were statistically significantly different among the five fibrosis stages (p < 0.004). Combining the three parameters in a multiparametric approach, the AUC for detecting F1 stage or greater (≥ F1) was 94 %, for F2 or greater (≥F2) was 95 %, for F3 or greater (≥F3) was 90 %, and for stage F4 was 93 %. Multiparametric MRI is an efficient non-invasive diagnostic tool for the staging of liver fibrosis. (orig.)

  5. Enhanced Biological Phosphorus Removal in Anaerobic/Aerobic Sequencing Batch Reactor Supplied with Glucose as Carbon Source

    Institute of Scientific and Technical Information of China (English)

    LIU Yanan; YU Shui-li; JING Guo-lin; ZHAO Bing-jie; GUO Si-yuan


    Phosphorus removal performance in an aerobic/aerobic sequencing batch reactor (SBR) supplied with glucose as carbon source was investigated. It was found that there was no phosphate release concomitant with the storing of poly-β-hydroxyalkanoate (PHA) during the anaerobic phase. Whereas, glycogen was soon built up followed by rapid consumption, at the same time, glucose was depleted rapidly. Based on the analysis of different fractions of phosphorus in activated sludge, the relative ratio of organically bound phosphorus in sludge changed at the end of anaerobic and aerobic phases. The ratios were 45.3% and51.8% respectively. This showed that the polyphosphate broke down during the anaerobic phase to supply part of energy for PHA synthesis. The reason why there was no phosphate release might be the biosorption effect of extracellular exopolymers (EPS). It was also proved by the analysis of EPS with scanning electron microscopy (SEM)combined with energy dispersive spectrometry (EDS). The phosphorus weight percentage of EPS at the end of anaerobic phase was 9.22%.

  6. Three Medicago MtFUL genes have distinct and overlapping expression patterns during vegetative and reproductive development and 35S:MtFULb accelerates flowering and causes a terminal flower phenotype in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Mauren eJaudal


    Full Text Available The timing of the transition to flowering is carefully controlled by plants in order to optimise sexual reproduction and the ensuing production of seeds, grains and fruits. The genetic networks that regulate floral induction are best characterised in the temperate eudicot Arabidopsis in which the florigen gene FT plays a major role in promoting the transition to flowering. Legumes are an important plant group, but less is known about the regulation of their flowering time. In the model legume Medicago truncatula (Medicago, a temperate annual plant like Arabidopsis, flowering is induced by prolonged cold (vernalisation followed by long day lengths (LD. Recent molecular-genetic experiments have revealed that a FT-like gene, MtFTa1, is a central regulator of flowering time in Medicago. Here, we characterize the three Medicago FRUITFULL (FUL MADS transcription factors, MtFULa, MtFULb and MtFULc using phylogenetic analyses, gene expression profiling through developmental time courses, and functional analyses in transgenic plants. MtFULa and MtFULb have similarity in sequence and expression profiles under inductive environmental conditions during both vegetative and reproductive development while MtFULc is only up regulated in the apex after flowering in LD conditions. Sustained up regulation of MtFULs requires functional MtFTa1 but their transcript levels are not affected during cold treatment. Overexpression of MtFULa and MtFULb promotes flowering in transgenic Arabidopsis plants with an additional terminal flower phenotype on some 35S:MtFULb plants. An increase in transcript levels of the MtFULs was also observed in Medicago plants overexpressing MtFTa1. Our results suggest that the MtFULs are targets of MtFTa1. Overall, this work highlights the conserved functions of FUL-like genes in promoting flowering and other roles in plant development and thus contributes to our understanding of the genetic control of the flowering process in Medicago.

  7. Neuropeptide Y-stimulated [(35) S]GTPγs functional binding is reduced in the hippocampus after kainate-induced seizures in mice

    DEFF Research Database (Denmark)

    Elbrønd-Bek, Heidi; Olling, Janne Damm; Gøtzsche, Casper René;


    Kainate-induced seizures constitute a model of temporal lobe epilepsy where prominent changes are observed in the hippocampal neuropeptide Y (NPY) system. However, little is known about the functional state and signal transduction of the NPY receptor population resulting from kainate exposure. Thus......, in this study, we explored functional NPY receptor activity in the mouse hippocampus and neocortex after kainate-induced seizures using NPY-stimulated [(35) S]GTPγS binding. Moreover, we also studied levels of [(125) I]-peptide YY (PYY) binding and NPY, Y1, Y2, and Y5 receptor mRNA in these kainate-treated mice....... Functional NPY binding was unchanged up to 12 h post-kainate, but decreased significantly in all hippocampal regions after 24 h and 1 week. Similarly, a decrease in [(125) I]-PYY binding was found in the dentate gyrus (DG) 1 week post-kainate. However, at 2 h, 6 h, and 12 h, [(125) I]-PYY binding...

  8. Identification of adenovirus type 12 candidate transformation proteins by radioimmunoprecipitation with antisera to EcoRI-C-fragment. [/sup 35/S tracer technique, rats

    Energy Technology Data Exchange (ETDEWEB)

    Wold, W.S.M. (St. Louis Univ. School of Medicine, MO); Chinnadurai, G.; Green, M.; Mak, S.


    Experiments were performed to identify polypeptides coded by early gene block 1 (which includes the transforming region) of human adenoviruses in group A (Ad12, 18, 31). Two lines, C-1 and C-2, of rat cells transformed by transfection with Ad12 EcoRI-C fragment (left 16% of genome) were inoculated into syngeneic rats to produce tumors (F. Graham and S. Mak, unpublished data). The tumor sera were used to immunoprecipitate (/sup 35/S)methionine-labeled polypeptides from Ad12-early-infected human cells. The polypeptides were resolved by electrophoresis in sodium dodecyl sulfate-polyacrylamide gels, and visualized by fluorography. Two additional sera were also used, from hamsters bearing tumors induced by inoculation with Ad12 or Ad18 virions. The immunoprecipitation results suggest (but do not prove) that early gene block 1 of group A Ads may code a family of related polypeptides with apparent molecular weights ranging from 4OK to 46K or 4OK to 65K, as well as polypeptides of 16.5 K and 10.5K. One or more of these polypeptides may play a role in the initiation and/or maintenance of cell transformation.

  9. Differential regulation of serotonin-1A receptor-stimulated [35S]GTP gamma S binding in the dorsal raphe nucleus by citalopram and escitalopram. (United States)

    Rossi, Dania V; Burke, Teresa F; Hensler, Julie G


    The effect of chronic citalopram or escitalopram administration on 5-HT1A receptor function in the dorsal raphe nucleus was determined by measuring [35S]GTP gamma S binding stimulated by the 5-HT1A receptor agonist (R)-(+)-8-OH-DPAT (1nM-10 microM). Although chronic administration of citalopram or escitalopram has been shown to desensitize somatodendritic 5-HT1A autoreceptors, we found that escitalopram treatment decreased the efficacy of 5-HT1A receptors to activate G proteins, whereas citalopram treatment did not. The binding of [3H]8-OH-DPAT to the coupled, high affinity agonist state of the receptor was not altered by either treatment. Interestingly, escitalopram administration resulted in greater occupancy of serotonin transporter sites as measured by the inhibition of [3H]cyanoimipramine binding. As the binding and action of escitalopram is limited by the inactive enantiomer R-citalopram present in racemic citalopram, we propose that the regulation of 5-HT1A receptor function in the dorsal raphe nucleus at the level of receptor-G protein interaction may be a result of greater inhibition of the serotonin transporter by escitalopram.

  10. Sequencing batch reactor enhances bacterial hydrolysis of starch promoting continuous bio-hydrogen production from starch feedstock

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Shing-Der [Energy and Environment Research Laboratories, Industrial Technology Research Institute, Hsinchu (China); Lo, Yung-Chung; Huang, Tian-I. [Department of Chemical Engineering, National Cheng Kung University, Tainan 701 (China); Lee, Kuo-Shing [Department of Safety Health and Environmental Engineering, Central Taiwan University of Science and Technology, Taichung (China); Chang, Jo-Shu [Department of Chemical Engineering, National Cheng Kung University, Tainan 701 (China); Sustainable Environment Research Center, National Cheng Kung University, Tainan (China)


    Bio-hydrogen production from starch was carried out using a two-stage process combining thermophillic starch hydrolysis and dark H{sub 2} fermentation. In the first stage, starch was hydrolyzed by Caldimonas taiwanensis On1 using sequencing batch reactor (SBR). In the second stage, Clostridium butyricum CGS2 was used to produce H{sub 2} from hydrolyzed starch via continuous dark hydrogen fermentation. Starch hydrolysis with C. taiwanensis On1 was operated in SBR under pH 7.0 and 55 C. With a 90% discharge volume, the reducing sugar (RS) production from SBR reactor reached 13.94 g RS/L, while the reducing sugar production rate and starch hydrolysis rate was 0.92 g RS/h/L and 1.86 g starch/h/L, respectively, which are higher than using other discharge volumes. For continuous H{sub 2} production with the starch hydrolysate, the highest H{sub 2} production rate and yield was 0.52 L/h/L and 13.2 mmol H{sub 2}/g total sugar, respectively, under a hydraulic retention time (HRT) of 12 h. The best feeding nitrogen source (NH{sub 4}HCO{sub 3}) concentration was 2.62 g/L, attaining a good H{sub 2} production efficiency along with a low residual ammonia concentration (0.14 g/L), which would be favorable to follow-up photo H{sub 2} fermentation while using dark fermentation effluents as the substrate. (author)

  11. Integrated processing of contrast pulse sequencing ultrasound imaging for enhanced active contrast of hollow gas filled silica nanoshells and microshells. (United States)

    Ta, Casey N; Liberman, Alexander; Paul Martinez, H; Barback, Christopher V; Mattrey, Robert F; Blair, Sarah L; Trogler, William C; Kummel, Andrew C; Wu, Zhe


    In recent years, there have been increasing developments in the field of contrast-enhanced ultrasound both in the creation of new contrast agents and in imaging modalities. These contrast agents have been employed to study tumor vasculature in order to improve cancer detection and diagnosis. An in vivo study is presented of ultrasound imaging of gas filled hollow silica microshells and nanoshells which have been delivered intraperitoneally to an IGROV-1 tumor bearing mouse. In contrast to microbubbles, this formulation of microshells provided strong ultrasound imaging signals by shell disruption and release of gas. Imaging of the microshells in an animal model was facilitated by novel image processing. Although the particle signal could be identified by eye under live imaging, high background obfuscated the particle signal in still images and near the borders of the tumor with live images. Image processing techniques were developed that employed the transient nature of the particle signal to selectively filter out the background signal. By applying image registration, high-pass, median, threshold, and motion filtering, a short video clip of the particle signal was compressed into a single image, thereby resolving the silica shells within the tumor. © 2012 American Vacuum Society.

  12. Brain histamine depletion enhances the behavioural sequences complexity of mice tested in the open-field: Partial reversal effect of the dopamine D2/D3 antagonist sulpiride. (United States)

    Santangelo, Andrea; Provensi, Gustavo; Costa, Alessia; Blandina, Patrizio; Ricca, Valdo; Crescimanno, Giuseppe; Casarrubea, Maurizio; Passani, M Beatrice


    Markers of histaminergic dysregulation were found in several neuropsychiatric disorders characterized by repetitive behaviours, thoughts and stereotypies. We analysed the effect of acute histamine depletion by means of i. c.v. injections of alpha-fluoromethylhistidine, a blocker of histidine decarboxylase, on the temporal organization of motor sequences of CD1 mice behaviour in the open-field test. An ethogram encompassing 9 behavioural components was employed. Durations and frequencies were only slightly affected by treatments. However, as revealed by multivariate t-pattern analysis, histamine depletion was associated with a striking increase in the number of behavioural patterns. We found 42 patterns of different composition occurring, on average, 520.90 ± 50.23 times per mouse in the histamine depleted (HD) group, whereas controls showed 12 different patterns occurring on average 223.30 ± 20.64 times. Exploratory and grooming behaviours clustered separately, and the increased pattern complexity involved exclusively exploratory patterns. To test the hypothesis of a histamine-dopamine interplay on behavioural pattern phenotype, non-sedative doses of the D2/D3 antagonist sulpiride (12.5-25-50 mg/kg) were additionally administered to different groups of HD mice. Sulpiride counterbalanced the enhancement of exploratory patterns of different composition, but it did not affect the mean number of patterns at none of the doses used. Our results provide new insights on the role of histamine on repetitive behavioural sequences of freely moving mice. Histamine deficiency is correlated with a general enhancement of pattern complexity. This study supports a putative involvement of histamine in the pathophysiology of tics and related disorders.

  13. Assessment of myocardial infarction in mice by Late Gadolinium Enhancement MR imaging using an inversion recovery pulse sequence at 9.4T

    Directory of Open Access Journals (Sweden)

    Herlihy Amy H


    Full Text Available Abstract Purpose To demonstrate the feasibility of using an inversion recovery pulse sequence and to define the optimal inversion time (TI to assess myocardial infarction in mice by late gadolinium enhancement (LGE MRI at 9.4T, and to obtain the maximal contrast between the infarcted and the viable myocardium. Methods MRI was performed at 9.4T in mice, two days after induction of myocardial infarction (n = 4. For cardiovascular MR imaging, a segmented magnetization-prepared fast low angle shot (MP-FLASH sequence was used with varied TIs ranging from 40 to 420 ms following administration of gadolinium-DTPA at 0.6 mmol/kg. Contrast-to-noise (CNR and signal-to-noise ratio (SNR were measured and compared for each myocardial region of interest (ROI. Results The optimal TI, which corresponded to a minimum SNR in the normal myocardium, was 268 ms ± 27.3. The SNR in the viable myocardium was significantly different from that found in the infarcted myocardium (17.2 ± 2.4 vs 82.1 ± 10.8; p = 0.006 leading to a maximal relative SI (Signal Intensity between those two areas (344.9 ± 60.4. Conclusion Despite the rapid heart rate in mice, our study demonstrates that LGE MRI can be performed at 9.4T using a protocol similar to the one used for clinical MR diagnosis of myocardial infarction.

  14. Fusion of a Short HA2-Derived Peptide Sequence to Cell-Penetrating Peptides Improves Cytosolic Uptake, but Enhances Cytotoxic Activity

    Directory of Open Access Journals (Sweden)

    Igor Kitanovic


    Full Text Available Cell-penetrating peptides (CPP have become a widely used tool for efficient cargo delivery into cells. However, one limiting fact is their uptake by endocytosis causing the enclosure of the CPP-cargo construct within endosomes. One often used method to enhance the outflow into the cytosol is the fusion of endosome-disruptive peptide or protein sequences to CPP. But, until now, no studies exist investigating the effects of the fusion peptide to the cellular distribution, structural arrangements and cytotoxic behaviour of the CPP. In this study, we attached a short modified sequence of hemagglutinin subunit HA2 to different CPP and analysed the biologic activity of the new designed peptides. Interestingly, we observed an increased cytosolic distribution but also highly toxic activities in the micromolar range against several cell lines. Structural analysis revealed that attachment of the fusion peptide had profound implications on the whole conformation of the peptide, which might be responsible for membrane interaction and endosome disruption.

  15. Enhancement of the performance of an anaerobic sequencing batch reactor treating low-strength wastewater through implementation of a variable stirring rate program

    Energy Technology Data Exchange (ETDEWEB)

    Rodrigues, J.A.D.; Pinto, A.G.; Ratusznei, S.M.; Gedraite, R. [Instituto Maua de Tecnologia (IMT), Sao Caetano do Sul, SP (Brazil). Escola de Engenharia. Dept. de Engenharia Quimica e de Alimentos]. E-mail:; Zaiat, M. [Sao Paulo Univ., Sao Carlos, SP (Brazil). Escola de Engenharia. Dept. de Hidraulica e Saneamento


    This work focuses on enhancement of the performance of an anaerobic sequencing batch reactor with a six-vertical-blade-disk-turbine impeller, containing granulated biomass treating low-strength synthetic wastewater, through a study of the feasibility of implementing a variable stirring rate program. The reactor was operated at 30 deg C and a six-hour cycle was used to treat approximately 2.0 L of the synthetic substrate with a chemical oxygen demand (COD) of nearly 500 mg/L. Two different stirring rate program were implemented: a constant rate of 50 rpm and a variable rate consisting of 75 rpm for one hour, 50 rpm for four hours and 25 rpm for 0.5 hour. The last 0.5 hour of the cycle was used for the settling step. In both cases, a very short start-up period and unfiltered and filtered substrate removal efficiencies of 81% and 88%, respectively, were attained. However, use of the variable stirring rate enhanced efficiency of the reactor dynamics without impairing biomass morphology, thus resulting in a reduction in the total cycle time and a possible decrease in energy consumption. Additionally, a simplified model of the anaerobic metabolic activity, using apparent kinetic parameters, was proposed as a consecutive first-order kinetic model with substrate and total volatile acid residual concentrations in order to analyze how the variable stirring rate affects reactor performance. (author)

  16. Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5. (United States)

    Mefford, Megan E; Kunstman, Kevin; Wolinsky, Steven M; Gabuzda, Dana


    Macrophages express low levels of the CD4 receptor compared to T-cells. Macrophage-tropic HIV strains replicating in brain of untreated patients with HIV-associated dementia (HAD) express Envs that are adapted to overcome this restriction through mechanisms that are poorly understood. Here, bioinformatic analysis of env sequence datasets together with functional studies identified polymorphisms in the β3 strand of the HIV gp120 bridging sheet that increase M-tropism. D197, which results in loss of an N-glycan located near the HIV Env trimer apex, was detected in brain in some HAD patients, while position 200 was estimated to be under positive selection. D197 and T/V200 increased fusion and infection of cells expressing low CD4 by enhancing gp120 binding to CCR5. These results identify polymorphisms in the HIV gp120 bridging sheet that overcome the restriction to macrophage infection imposed by low CD4 through enhanced gp120-CCR5 interactions, thereby promoting infection of brain and other macrophage-rich tissues.

  17. Evaluation of small ({<=}2 cm) dysplastic nodules and well-differentiated hepatocellular carcinomas with ferucarbotran-enhanced MRI in a 1.0-T MRI unit: Utility of T2*-weighted gradient echo sequences with an intermediate-echo time

    Energy Technology Data Exchange (ETDEWEB)

    Tonan, Tatsuyuki [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan); Fujimoto, Kiminori [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan)], E-mail:; Azuma, Sanae [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan); Ono, Noriyuki [Department of Internal Medicine, Chikugo City Hospital, Chikugo (Japan); Matsushita, Sunao [Department of Radiology, Chikugo City Hospital, 917-1 Izumi, Chikugo 833-0041 (Japan); Kojiro, Masamichi [Department of Pathology, Kurume University School of Medicine, Kurume (Japan); Hayabuchi, Naofumi [Department of Radiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume 830-0011 (Japan)


    Purpose: To evaluate the detectability and signal intensities of small ({<=}2 cm) dysplastic nodules (DNs) and well-differentiated hepatocellular carcinomas (w-HCCs) by T2*-weighted gradient echo (GRE) sequences using an intermediate echo-time (TE) with ferucarbotran in a 1.0-T magnetic resonance imaging (MRI) unit. Materials and methods: Pathologically confirmed DNs (n = 13) and w-HCCs (n = 31) with a median largest dimension of 1.1 cm were scanned using ferucarbotran-enhanced MRI. Conventional T2*-weighted GRE sequences (conventional-T2*-GRE: repetition time, 280 ms; echo time, 14 ms; flip angle, 60 deg.) and specific T2*-weighted GRE sequences using an intermediate-TE (specific-T2*-GRE: repetition time, 140 ms; echo time, 8 ms; flip angle, 30 deg.) were obtained before and after ferucarbotran administration. Two independent observers scored all nodules for visibility and assigned confidence level scores to their observations. To assess the effect of ferucarbotran, the tumor-liver signal contrast-to-noise ratio (tumor-liver-CNR) was also calculated for detected nodules by the same two observers with consensus. Results: There was good interobserver agreement regarding the presence of nodules for both sequence types. Qualitative and quantitative analyses indicated that specific-T2*GRE sequences were superior to conventional-T2*-GRE sequences for detecting DNs and w-HCCs with hypointense signals. The tumor-liver-CNR of DNs was significantly different between specific-T2*-GRE sequences and conventional-T2*-GRE sequences (Mann-Whitney test, P < 0.001). Both qualitative and quantitative analyses indicated that conventional-T2*-GRE sequences were superior to specific-T2*-GRE sequences for detecting w-HCCs with heterogeneous and hyperintense signals. Conclusion: Specific-T2*-GRE sequences with ferucarbotran are useful for detecting DNs and w-HCCs that produce hypointense signals on a 1.0-T MRI unit.

  18. Preparation of {sup 35}SO{sub 4}H{sub 2} and of some other {sup 35}S labeled mineral compounds; Preparation de {sup 35}SO{sub 4}H{sub 2} et de quelques autres composes mineraux simples marques a {sup 35}S

    Energy Technology Data Exchange (ETDEWEB)

    De la Gueronniere, E.; Henry, R. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires


    Methods of preparation, from pile irradiated KCI, of the following labeled molecules are described: - carrier free H{sub 2}SO{sub 4} - SCd (100 m curies/milli mole) - solution of SNa{sub 2} (100 m curies/milli mole) - solution of SK{sub 2} (100 m curies/milli mole) - S metalloid (100 m curies/milli mole) - SO{sub 3}Na{sub 2} (90 m curies/milli mole) - S{sub 2}C{sub 3}Na{sub 2} (50 m curies/mammalia). (author) [French] On decrit les methodes de preparation, a partir de KCl irradie dans les piles, des molecules suivantes marquees au {sup 35}S: - SO{sub 4}H{sub 2} (sans entraineur) - SCd (100 mcuries/millimole) - solution de SNa{sub 2} (100 mcuries/millimole) - solution de SK{sub 2} (100 mcuries/millimole) - S metalloide (100 mcuries/millimole) - Na{sub 2}SO{sub 3} (90 mcuries/millimole) - Na{sub 2}S{sub 2}C{sub 3} (50 mcuries/milIimole). (auteur)

  19. 通过重叠PCR构建2个增强型植物花特异双向启动子%Construction of two enhanced plant flower-specific bidirectional promoters through overlap extension PCR

    Institute of Scientific and Technical Information of China (English)

    张雄飞; 刘雅莉; 娄倩; 祁银燕; 杜灵娟


    Promoter is a key element on gene expression regulation,and it is an emphasis of plant transgenic research.Now,detailed analysis about flower-specific promoters such as chalcone synthase gene promoter from petunia and lily has been made.Enhancer is another kind of regulatory element usually placed at upstream of promoter sequence.In order to precisely regulate gene expression in plant genetic engineering,scientists put forward a method of designing artificial promoter to avoid homology-dependent gene silencing caused by repeatedly using a same promoter sequence.In addition,in order to decrease the size of foreign gene and conform to the trend of multiple genes transformation,the method of using bidirectional promoter was proposed by scientists.According to the previous studies,the present study use core sequence of petunia flower-specific promoter pPCHS and lily flower-specific promoter pLCHS,CaMV 35S enhance sequence,OCS enhance sequence to design and construct two enhanced plant flower-specific bidirectional promoters.We wish to provide some promoters with practical value when we try to use multiple genes transformation method to precisely regulate ornamental traits of some important flower species such as petunia and lily. In this research,according to the procedure of overlap extension PCR method and sequences of petunia flower-specific promoter pPCHS,lily flower-specific promoter pLCHS,CaMV 35S enhancer,OCS enhancer,10 primers were designed and synthesized firstly.In the first round of PCR process,plasmids which contain above-mentioned four sequences were templates; six fragments with overlapping areas were amplified using overlapping primers.These six fragments were named as pPCHS-1-2,pPCHS-1-3,35S-4-5,OCS 6 7,pLCHS-8 10,pLCHS-9-10.Moreover,Prime StarTM HS DNA Polymerase was used in this PCR process and these six products were all blunt-ended.In the second round of PCR process,the mixture of products pPCHS-1-2,35S-4-5,pLCHS-8-10 was a group of template

  20. Enhanced protective efficacy against tuberculosis provided by a recombinant urease deficient BCG expressing heat shock protein 70-major membrane protein-II having PEST sequence. (United States)

    Tsukamoto, Yumiko; Maeda, Yumi; Tamura, Toshiki; Mukai, Tetsu; Mitarai, Satoshi; Yamamoto, Saburo; Makino, Masahiko


    Enhancement of the T cell-stimulating ability of Mycobacterium bovis BCG (BCG) is necessary to develop an effective tuberculosis vaccine. For this purpose, we introduced the PEST-HSP70-major membrane protein-II (MMPII)-PEST fusion gene into ureC-gene depleted recombinant (r) BCG to produce BCG-PEST. The PEST sequence is involved in the proteasomal processing of antigens. BCG-PEST secreted the PEST-HSP70-MMPII-PEST fusion protein and more efficiently activated human monocyte-derived dendritic cells (DCs) in terms of phenotypic changes and cytokine productions than an empty-vector-introduced BCG or HSP70-MMPII gene-introduced ureC gene-depleted BCG (BCG-DHTM). Autologous human naïve CD8(+) T cells and naïve CD4(+) T cells were effectively activated by BCG-PEST and produced IFN-γ in an antigen-specific manner through DCs. These T cell activations were closely associated with phagosomal maturation and intraproteasomal protein degradation in antigen-presenting cells. Furthermore, BCG-PEST produced long-lasting memory-type T cells in C57BL/6 mice more efficiently than control rBCGs. Moreover, a single subcutaneous injection of BCG-PEST more effectively reduced the multiplication of subsequent aerosol-challenged Mycobacterium tuberculosis of the standard H37Rv strain and clinically isolated Beijing strain in the lungs than control rBCGs. The vaccination effect of BCG-PEST lasted for at least 6months. These results indicate that BCG-PEST may be able to efficiently control the spread of tuberculosis in human.

  1. Expression of 5 S rRNA genes linked to 35 S rDNA in plants, their epigenetic modification and regulatory element divergence

    Directory of Open Access Journals (Sweden)

    Garcia Sònia


    Full Text Available Abstract Background In plants, the 5 S rRNA genes usually occur as separate tandems (S-type arrangement or, less commonly, linked to 35 S rDNA units (L-type. The activity of linked genes remains unknown so far. We studied the homogeneity and expression of 5 S genes in several species from family Asteraceae known to contain linked 35 S-5 S units. Additionally, their methylation status was determined using bisulfite sequencing. Fluorescence in situ hybridization was applied to reveal the sub-nuclear positions of rDNA arrays. Results We found that homogenization of L-type units went to completion in most (4/6 but not all species. Two species contained major L-type and minor S-type units (termed Ls-type. The linked genes dominate 5 S rDNA expression while the separate tandems do not seem to be expressed. Members of tribe Anthemideae evolved functional variants of the polymerase III promoter in which a residing C-box element differs from the canonical angiosperm motif by as much as 30%. On this basis, a more relaxed consensus sequence of a plant C-box: (5’-RGSWTGGGTG-3’ is proposed. The 5 S paralogs display heavy DNA methylation similarly as to their unlinked counterparts. FISH revealed the close association of 35 S-5 S arrays with nucleolar periphery indicating that transcription of 5 S genes may occur in this territory. Conclusions We show that the unusual linked arrangement of 5 S genes, occurring in several plant species, is fully compatible with their expression and functionality. This extraordinary 5 S gene dynamics is manifested at different levels, such as variation in intrachromosomal positions, unit structure, epigenetic modification and considerable divergence of regulatory motifs.

  2. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich


    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  3. Overexpression of a novel Arabidopsis gene related to putative zinc-transporter genes from animals can lead to enhanced zinc resistance and accumulation. (United States)

    van der Zaal, B J; Neuteboom, L W; Pinas, J E; Chardonnens, A N; Schat, H; Verkleij, J A; Hooykaas, P J


    We describe the isolation of an Arabidopsis gene that is closely related to the animal ZnT genes (Zn transporter). The protein encoded by the ZAT (Zn transporter of Arabidopsis thaliana) gene has 398 amino acid residues and is predicted to have six membrane-spanning domains. To obtain evidence for the postulated function of the Arabidopsis gene, transgenic plants with the ZAT coding sequence under control of the cauliflower mosaic virus 35S promoter were analyzed. Plants obtained with ZAT in the sense orientation exhibited enhanced Zn resistance and strongly increased Zn content in the roots under high Zn exposure. Antisense mRNA-producing plants were viable, with a wild-type level of Zn resistance and content, like plants expressing a truncated coding sequence lacking the C-terminal cytoplasmic domain of the protein. The availability of ZAT can lead to a better understanding of the mechanism of Zn homeostasis and resistance in plants.

  4. Nano Au/TiO2 hollow microsphere membranes for the improved sensitivity of detecting specific DNA sequences related to transgenes in transgenic plants

    Institute of Scientific and Technical Information of China (English)


    Gold nanoparticles (nano Au)/titanium dioxide (TiO2) hollow microsphere membranes were prepared on the carbon paste electrode (CPE) for enhancing the sensitivity of DNA hybridization detection. The immobilization of nano Au and TiO2 microsphere was investigated with cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The hybridization events were monitored with EIS us-ing [Fe(CN)6]3-/4- as indicator. The sequence-specific DNA of the 35S promoter from cauliflower mosaic virus (CaMV35S) gene was detected with this DNA electrochemical sensor. The dynamic detection range was from 1.0×10-12 to 1.0×10-8 mol/L DNA and a detection limit of 2.3×10-13 mol/L could be ob-tained. The polymerase chain reaction (PCR) amplification of the terminator of nopaline synthase (NOS) gene from the real sample of a kind of transgenic soybean was also satisfactorily detected.

  5. Nicotiana small RNA sequences support a host genome origin of cucumber mosaic virus satellite RNA.

    Directory of Open Access Journals (Sweden)

    Kiran Zahid


    Full Text Available Satellite RNAs (satRNAs are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread. Despite many decades of research, the origin of satRNAs remains unknown. In this study we show that a β-glucuronidase (GUS transgene fused with a Cucumber mosaic virus (CMV Y satellite RNA (Y-Sat sequence (35S-GUS:Sat was transcriptionally repressed in N. tabacum in comparison to a 35S-GUS transgene that did not contain the Y-Sat sequence. This repression was not due to DNA methylation at the 35S promoter, but was associated with specific DNA methylation at the Y-Sat sequence. Both northern blot hybridization and small RNA deep sequencing detected 24-nt siRNAs in wild-type Nicotiana plants with sequence homology to Y-Sat, suggesting that the N. tabacum genome contains Y-Sat-like sequences that give rise to 24-nt sRNAs capable of guiding RNA-directed DNA methylation (RdDM to the Y-Sat sequence in the 35S-GUS:Sat transgene. Consistent with this, Southern blot hybridization detected multiple DNA bands in Nicotiana plants that had sequence homology to Y-Sat, suggesting that Y-Sat-like sequences exist in the Nicotiana genome as repetitive DNA, a DNA feature associated with 24-nt sRNAs. Our results point to a host genome origin for CMV satRNAs, and suggest novel approach of using small RNA sequences for finding the origin of other satRNAs.

  6. Nicotiana small RNA sequences support a host genome origin of cucumber mosaic virus satellite RNA. (United States)

    Zahid, Kiran; Zhao, Jian-Hua; Smith, Neil A; Schumann, Ulrike; Fang, Yuan-Yuan; Dennis, Elizabeth S; Zhang, Ren; Guo, Hui-Shan; Wang, Ming-Bo


    Satellite RNAs (satRNAs) are small noncoding subviral RNA pathogens in plants that depend on helper viruses for replication and spread. Despite many decades of research, the origin of satRNAs remains unknown. In this study we show that a β-glucuronidase (GUS) transgene fused with a Cucumber mosaic virus (CMV) Y satellite RNA (Y-Sat) sequence (35S-GUS:Sat) was transcriptionally repressed in N. tabacum in comparison to a 35S-GUS transgene that did not contain the Y-Sat sequence. This repression was not due to DNA methylation at the 35S promoter, but was associated with specific DNA methylation at the Y-Sat sequence. Both northern blot hybridization and small RNA deep sequencing detected 24-nt siRNAs in wild-type Nicotiana plants with sequence homology to Y-Sat, suggesting that the N. tabacum genome contains Y-Sat-like sequences that give rise to 24-nt sRNAs capable of guiding RNA-directed DNA methylation (RdDM) to the Y-Sat sequence in the 35S-GUS:Sat transgene. Consistent with this, Southern blot hybridization detected multiple DNA bands in Nicotiana plants that had sequence homology to Y-Sat, suggesting that Y-Sat-like sequences exist in the Nicotiana genome as repetitive DNA, a DNA feature associated with 24-nt sRNAs. Our results point to a host genome origin for CMV satRNAs, and suggest novel approach of using small RNA sequences for finding the origin of other satRNAs.

  7. A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data

    NARCIS (Netherlands)

    Y.J. Kim (Young Jin); J. Lee (Juyoung); B.-J. Kim (Bong-Jo); T. Park (Taesung); G.R. Abecasis (Gonçalo); M. Almeida (Marcio); D. Altshuler (David); J.L. Asimit (Jennifer L.); G. Atzmon (Gil); M. Barber (Mathew); A. Barzilai (Ari); N.L. Beer (Nicola L.); G.I. Bell (Graeme I.); J. Below (Jennifer); T. Blackwell (Tom); J. Blangero (John); M. Boehnke (Michael); D.W. Bowden (Donald W.); N.P. Burtt (Noël); J.C. Chambers (John); H. Chen (Han); P. Chen (Ping); P.S. Chines (Peter); S. Choi (Sungkyoung); C. Churchhouse (Claire); P. Cingolani (Pablo); B.K. Cornes (Belinda); N.J. Cox (Nancy); A.G. Day-Williams (Aaron); A. Duggirala (Aparna); J. Dupuis (Josée); T. Dyer (Thomas); S. Feng (Shuang); J. Fernandez-Tajes (Juan); T. Ferreira (Teresa); T.E. Fingerlin (Tasha E.); J. Flannick (Jason); J.C. Florez (Jose); P. Fontanillas (Pierre); T.M. Frayling (Timothy); C. Fuchsberger (Christian); E. Gamazon (Eric); K. Gaulton (Kyle); S. Ghosh (Saurabh); B. Glaser (Benjamin); A.L. Gloyn (Anna); R.L. Grossman (Robert L.); J. Grundstad (Jason); C. Hanis (Craig); A. Heath (Allison); H. Highland (Heather); M. Horikoshi (Momoko); I.-S. Huh (Ik-Soo); J.R. Huyghe (Jeroen R.); M.K. Ikram (Kamran); K.A. Jablonski (Kathleen); Y. Jun (Yang); N. Kato (Norihiro); J. Kim (Jayoun); Y.J. Kim (Young Jin); B.-J. Kim (Bong-Jo); J. Lee (Juyoung); C.R. King (C. Ryan); J.S. Kooner (Jaspal S.); M.-S. Kwon (Min-Seok); H.K. Im (Hae Kyung); M. Laakso (Markku); K.K.-Y. Lam (Kevin Koi-Yau); J. Lee (Jaehoon); S. Lee (Selyeong); S. Lee (Sungyoung); D.M. Lehman (Donna M.); H. Li (Heng); C.M. Lindgren (Cecilia); X. Liu (Xuanyao); O.E. Livne (Oren E.); A.E. Locke (Adam E.); A. Mahajan (Anubha); J.B. Maller (Julian B.); A.K. Manning (Alisa K.); T.J. Maxwell (Taylor J.); A. Mazoure (Alexander); M.I. McCarthy (Mark); J.B. Meigs (James B.); B. Min (Byungju); K.L. Mohlke (Karen); A.P. Morris (Andrew); S. Musani (Solomon); Y. Nagai (Yoshihiko); M.C.Y. Ng (Maggie C.Y.); D. Nicolae (Dan); S. Oh (Sohee); N.D. Palmer (Nicholette); T. Park (Taesung); T.I. Pollin (Toni I.); I. Prokopenko (Inga); D. Reich (David); M.A. Rivas (Manuel); L.J. Scott (Laura); M. Seielstad (Mark); Y.S. Cho (Yoon Shin); X. Sim (Xueling); R. Sladek (Rob); P. Smith (Philip); I. Tachmazidou (Ioanna); E.S. Tai (Shyong); Y.Y. Teo (Yik Ying); T.M. Teslovich (Tanya M.); J. Torres (Jason); V. Trubetskoy (Vasily); S.M. Willems (Sara); A.L. Williams (Amy L.); J.G. Wilson (James); S. Wiltshire (Steven); S. Won (Sungho); A.R. Wood (Andrew); W. Xu (Wang); J. Yoon (Joon); M. Zawistowski (Matthew); E. Zeggini (Eleftheria); W. Zhang (Weihua); S. Zöllner (Sebastian)


    textabstractBackground: Rare variants have gathered increasing attention as a possible alternative source of missing heritability. Since next generation sequencing technology is not yet cost-effective for large-scale genomic studies, a widely used alternative approach is imputation. However, the imp

  8. The VviMYB80 Gene is Abnormally Expressed in Vitis vinifera L. cv. 'Zhong Shan Hong' and its Expression in Tobacco Driven by the 35S Promoter Causes Male Sterility. (United States)

    Zheng, Huan; Yu, Xiaojuan; Yuan, Yue; Zhang, Yaguang; Zhang, Zhen; Zhang, Jiyu; Zhang, Meng; Ji, Chenfei; Liu, Qian; Tao, Jianmin


    Anther development is a very precise and complicated process. In Arabidopsis, the AtMYB80 transcription factor regulates genes involved in pollen development and controls the timing of tapetal programmed cell death (PCD). In this study, we isolated and characterized cDNA for VviMYB80 expressed in flower buds of male-sterile Vitis vinifera L. cv. 'Zhong Shan Hong', a late-maturing cultivar derived from self-progeny of cv. 'Wink'. VviMYB80 belongs to the MYB80 subfamily and clusters with AtMYB35/TDF1 in a distinct clade. We found that in flower buds, expression of the VviMYB80 gene in cv. 'Zhong Shan Hong' sharply increased at the tetrad stage, resulting in a higher and earlier transcript level than that found in cv. 'Wink'. Expression of the VviMYB80 gene, driven by the 35S promoter, caused pleiotropic effects on the stamens, including smaller and shriveled anthers, delayed dehiscence, fewer seeds, shorter anther filaments, distorted pollen shape and a lack of cytoplasm, with the tapetum exhibiting hypertrophy in transformed tobacco. These results suggest that VviMYB80 may play an important role in stamen development and that expression of VviMYB80 driven by the 35S promoter in tobacco induces male sterility.

  9. An Enhanced Method for the Identification of Leishmania spp. using Real-Time PCR and Sequence Analysis of the 7SL RNA Gene Region (United States)

    Stevenson, Lindsay G.; Fedorko, Daniel P.; Zelazny, Adrian M.


    The accurate identification of Leishmania species is important for the treatment of infected patients. Molecular methods offer an alternative to time consuming traditional laboratory techniques for species determination. We redesigned a 7SL rRNA gene based PCR and sequence assay for increased species identification. DNA extracted from 17 reference strains and 10 cultured clinical isolates was examined. Sequence comparison was used successfully to identify organisms to the complex level with intercomplex similarity ranging from 77.5% to 98.4%. Many species within each complex were discriminated accurately by this method including: L. major, L. tropica, L. aethiopica, L. guyanensis, and the previously indistinguishable L. brasiliensis and L. panamensis. The L. donovani complex members remain indistinguishable by this method, as are the representatives of L. amazonensis/L. garnhami and L. mexicana/L. pifanoi. PMID:20226334

  10. MRI of testicular disease. A comparison between Gd-DTPA enhanced scans and unenhanced T[sub 2]-weighted sequences. MR-Tomographie bei Hodenprozessen. Bedeutung Gd-DTPA-verstaerkter Sequenzen im Vergleich mit nativen T[sub 2]-gewichteten Sequenzen

    Energy Technology Data Exchange (ETDEWEB)

    Just, M.; Grebe, P.; Kreitner, K.F.; Thelen, M. (Klinikum der Johannes-Gutenberg-Universitaet Mainz, Radiologische Klinik mit Poliklinik (Germany)); Melchior, S.; Buerger, R.A.; Hohenfellner, R. (Klinikum der Johannes-Gutenberg-Universitaet Mainz, Urologische Klinik und Poliklinik (Germany))


    The value of T[sub 1]-weighted sequences after intravenous administration of Gd-DTPA and of T[sub 2]-weighted sequences was compared in 43 patients suspected of having scrotal abnormalities. T[sub 2]-weighted sequences gave better demonstration of the tunica albuginea and better contrast between tumor and parenchyma. The two techniques were equally sensitive for demonstrating testicular tumors but orchitis was better demonstrated on the contrast enhanced sequences. Motion artifacts were less marked in the T[sub 1]-weighted sequences with contrast enhancement. In selected cases, contrast enhancement may be a valuable addition to native protocols. Our experience has indicated that MRI provides specific findings in cases of orchitis which are clinically atypical; this facilitates the decision to conservative treatment and prevents unnecessary exploration of the testes. (orig.).

  11. Unique C2V3 sequence in HIV-1 envelope obtained from broadly neutralizing plasma of a slow progressing patient conferred enhanced virus neutralization.

    Directory of Open Access Journals (Sweden)

    Rajesh Ringe

    Full Text Available Broadly neutralizing antibodies to HIV-1 usually develops in chronic infections. Here, we examined the basis of enhanced sensitivity of an env clone amplified from cross neutralizing plasma of an antiretroviral naïve chronically infected Indian patient (ID50 >600-fold higher compared to other autologous env clones. The enhanced autologous neutralization of pseudotyped viruses expressing the sensitive envelope (Env was associated with increased sensitivity to reagents and monoclonal antibodies targeting distinct sites in Env. Chimeric viruses constructed by swapping fragments of sensitive Env into resistant Env backbone revealed that the presence of unique residues within C2V3 region of gp120 governed increased neutralization. The enhanced virus neutralization was also associated with low CD4 dependence as well as increased binding of Env trimers to IgG1b12 and CD4-IgG2 and was independent of gp120 shedding. Our data highlighted vulnerabilities in the Env obtained from cross neutralizing plasma associated with the exposure of discontinuous neutralizing epitopes and enhanced autologous neutralization. Such information may aid in Env-based vaccine immunogen design.

  12. Efficient gusA Transient Expression in Porphyra yezoensis Protoplasts Mediated by Endogenous Beta-tubulin Flanking Sequences

    Institute of Scientific and Technical Information of China (English)

    GONG Qianhong; YU Wengong; DAI Jixun; LIU Hongquan; XU Rifu; GUAN Huashi; PAN Kehou


    Endogenous tubulin promoter has been widely used for expressing foreign genes in green algae, but the efficiency and feasibility of endogenous tubulin promoter in the economically important Porphyra yezoensis (Rhodophyta) are tmknown. In this study, the flanking sequences of beta-tubulin gene from P. yezoensis were amplified and two transient expression vectors were constructed to determine their transcription promoting feasibility for foreign gene gusA. The testing vector pATubGUS was constructed by inserting 5'- and 3'-flanking regions (Tub5'and Tub3') up- and down-stream of β-glucuronidase (GUS) gene (gusA), respectively,into pA, a derivative of pCAT(R)3-enhancer vector. The control construct, pAGUSTub3, contains only gusA and Tub3 '. These constructs were electroporated into P. yezoensis protoplasts and the GUS activities were quantitatively analyzed by spectrometry. The results demonstrated that gusA gene was efficiently expressed in P. yezoensis protoplasts under the regulation of 5'-flanking sequence of the beta-tubulin gene. More interestingly, the pATubGUS produced stronger GUS activity in P. yezoensis protoplasts when compared to the result from pBI221, in which the gusA gene was directed by a constitutive CaMV 35 S promoter. The data suggest that the integration of P. yezoensis protoplast and its endogenous beta-tubulin flanking sequences is a potential novel system for foreign gene expression.

  13. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria


    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at:

  14. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj


    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  15. Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Venditti, Vincenzo; Fawzi, Nicolas L.; Clore, G. Marius, E-mail: [National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Laboratory of Chemical Physics (United States)


    Methyl-transverse relaxation optimized spectroscopy is rapidly becoming the preferred NMR technique for probing structure and dynamics of very large proteins up to {approx}1 MDa in molecular size. Data interpretation, however, necessitates assignment of methyl groups which still presents a very challenging and time-consuming process. Here we demonstrate that, in combination with a known 3D structure, paramagnetic relaxation enhancement (PRE), induced by nitroxide spin-labels incorporated at only a few surface-exposed engineered cysteines, provides fast, straightforward and robust access to methyl group resonance assignments, including stereoassignments for the methyl groups of leucine and valine. Neither prior assignments, including backbone assignments, for the protein, nor experiments that transfer magnetization between methyl groups and the protein backbone, are required. PRE-derived assignments are refined by 4D methyl-methyl nuclear Overhauser enhancement data, eliminating ambiguities and errors that may arise due to the high sensitivity of PREs to the potential presence of sparsely-populated transient states.

  16. The value of true-FISP sequence added to conventional gadolinium-enhanced MRA of abdominal aorta and its major branches

    Energy Technology Data Exchange (ETDEWEB)

    Iozzelli, Andrea [University of Milan School of Medicine, Department of Medical and Surgical Sciences, Radiology Unit, IRCCS Policlinico San Donato, via Morandi 30, 20097 San Donato Milanese, Milan (Italy)], E-mail:; D' Orta, Giovanni [University of Milan School of Medicine, Department of Medical and Surgical Sciences, Radiology Unit, IRCCS Policlinico San Donato, via Morandi 30, 20097 San Donato Milanese, Milan (Italy)], E-mail:; Aliprandi, Alberto [University of Milan School of Medicine, Department of Medical and Surgical Sciences, Radiology Unit, IRCCS Policlinico San Donato, via Morandi 30, 20097 San Donato Milanese, Milan (Italy)], E-mail:; Secchi, Francesco [University of Milan School of Medicine, Department of Medical and Surgical Sciences, Radiology Unit, IRCCS Policlinico San Donato, via Morandi 30, 20097 San Donato Milanese, Milan (Italy)], E-mail:; Di Leo, Giovanni [University of Milan School of Medicine, Department of Medical and Surgical Sciences, Radiology Unit, IRCCS Policlinico San Donato, via Morandi 30, 20097 San Donato Milanese, Milan (Italy)], E-mail:; Sardanelli, Francesco [University of Milan School of Medicine, Department of Medical and Surgical Sciences, Radiology Unit, IRCCS Policlinico San Donato, via Morandi 30, 20097 San Donato Milanese, Milan (Italy)], E-mail:


    To test true-fast imaging with steady-state precession (true-FISP) added to gadolinium-based MR angiography (Gd-MRA) for imaging abdominal aorta and major abdominal vessels, 35 consecutive patients (age 67 {+-} 11 years) with known or suspected abdominal and/or peripheral vascular disease were studied with sagittal and axial 2D true-FISP during free breathing and coronal 3D fast low-angle shot (FLASH) Gd-MRA (breath-holding, 0.2 mmol/kg of Gd-DOTA at 2 ml/s). We evaluated: suprarenal aorta, celiac trunk, superior mesenteric artery, right renal artery, left renal artery, infrarenal aorta, inferior mesenteric artery, aortic bifurcation/common iliac arteries, lumbar arteries and aortic atheromasia. The possible presence of accessory renal arteries, collateral vasculature and vascular prosthesis/stent was evaluated. A quality four-point score was assigned to each item on both sequences, from 0 (not visible) to 3 (good-to-excellent image quality) and Wilcoxon test was used. Main diagnoses resulted: normal or atheromasic aorta (n = 25); aortic aneurysm (n = 2); patent aorto-iliac surgical prosthesis (n = 2); patent vascular iliac stent (n = 2); aneurysm of iliac artery (n = 1); patent aortic endovascular prosthesis (n = 1); patent aorto-femural bypass (n = 1) and aorto-iliac surgical prosthesis endoleak (n = 1). We also found three patients with accessory renal arteries, two with collateral circulation, and three with surgical aorto-iliac prosthesis. The score of true-FISP (25.9 {+-} 4.1, median 27) was significantly higher (p = 0.003) than that of Gd-MRA (23.9 {+-} 3.6, median 24). True-FISP was superior for visualizing inferior mesenteric artery (score 2.5 {+-} 1.1 vs. 1.0 {+-} 1.4; p < 0.001) and atheromasic plaques (2.5 {+-} 1.1 vs. 1.2 {+-} 1.1; p < 0.001). One collateral vasculature was demonstrated only with Gd-MRA. Summarizing, true-FISP is a power and fast non-breath-hold sequence to be added to Gd-MRA, obtaining an information increase.

  17. Magnetic resonance imaging of pelvic entheses - a systematic comparison between short tau inversion recovery (STIR) and T1-weighted, contrast-enhanced, fat-saturated sequences

    Energy Technology Data Exchange (ETDEWEB)

    Klang, Eyal; Aharoni, Dvora; Rimon, Uri; Eshed, Iris [Tel Aviv University, Department of Diagnostic Imaging, Sheba Medical Center, Tel Aviv (Israel); Hermann, Kay-Geert [Department of Radiology, Charite University Hospital, Berlin (Germany); Herman, Amir [Sheba Medical Center, Department of Orthopedic Surgery, Tel-Hashomer (Israel); Tel Aviv University, The Sackler School of Medicine, Tel Aviv (Israel); Shazar, Nachshon [Sheba Medical Center, Department of Orthopedic Surgery, Tel-Hashomer (Israel)


    To assess the contribution of contrast material in detecting and evaluating enthesitis of pelvic entheses by MRI. Sixty-seven hip or pelvic 1.5-T MRIs (30:37 male:female, mean age: 53 years) were retrospectively evaluated for the presence of hamstring and gluteus medius (GM) enthesitis by two readers (a resident and an experienced radiologist). Short tau inversion recovery (STIR) and T1-weighted pre- and post-contrast (T1+Gd) images were evaluated by each reader at two sessions. A consensus reading of two senior radiologists was regarded as the gold standard. Clinical data was retrieved from patients' referral form and medical files. Cohen's kappa was used for intra- and inter-observer agreement calculation. Diagnostic properties were calculated against the gold standard reading. A total of 228 entheses were evaluated. Gold standard analysis diagnosed 83 (36 %) enthesitis lesions. Intra-reader reliability for the experienced reader was significantly (p = 0.0001) higher in the T1+Gd images compared to the STIR images (hamstring: k = 0.84/0.45, GM: k = 0.84/0.47). Sensitivity and specificity increased from 0.74/0.8 to 0.87/0.9 in the STIR images and T1+Gd sequences. Intra-reader reliability for the inexperienced reader was lower (p > 0.05). Evidence showing that contrast material improves the reliability, sensitivity, and specificity of detecting enthesitis supports its use in this setting. (orig.)

  18. Comparison of three combined sequencing batch reactor followed by enhanced Fenton process for an azo dye degradation: Bio-decolorization kinetics study. (United States)

    Azizi, A; Alavi Moghaddam, M R; Maknoon, R; Kowsari, E


    The purpose of this research was to compare three combined sequencing batch reactor (SBR) - Fenton processes as post-treatment for the treatment of azo dye Acid Red 18 (AR18). Three combined treatment systems (CTS1, CTS2 and CTS3) were operated to investigate the biomass concentration, COD removal, AR18 dye decolorization and kinetics study. The MLSS concentration of CTS2 reached 7200 mg/L due to the use of external feeding in the SBR reactor of CTS2. The COD concentration remained 273 mg/L and 95 mg/L (initial COD=3270 mg/L) at the end of alternating anaerobic-aerobic SBR with external feeding (An-A MSBR) and CTS2, respectively, resulting in almost 65% of Fenton process efficiency. The dye concentration of 500 mg/L was finally reduced to less than 10mg/L in all systems indicating almost complete AR18 decolorization, which was also confirmed by UV-vis analysis. The dye was removed following two successive parts as parts 1 and 2 with pseudo zero-order and pseudo first-order kinetics, respectively, in all CTSs. Higher intermediate metabolites degradation was obtained using HPLC analysis in CTS2. Accordingly, a combined treatment system can be proposed as an appropriate and environmentally-friendly system for the treatment of the azo dye AR18 in wastewater.


    Directory of Open Access Journals (Sweden)

    Tb. Haeru Rahayu


    Full Text Available The use of local probiotics in the culture of aquatic organisms is increasing with the demand for more environmental-friendly aquaculture practices. The local bacterium isolate considered as a probiotic was added into the water of whiteleg shrimp (Litopenaeus vannamei culture in a field trial. Four rectangular plastic ponds (ca. 20 m x 30 m per pond were used for 100 days experimentation for six consecutive crops in two years experiment. Survival, harvest size, feed conversion ratio (FCR and Vibrio bacterial count was compared with those of shrimp receiving and none of local isolate. Identification based on 16S rRNA gene sequence shown those isolate was Bacillus pumilus strain DURCK14 with 99% homology. Water shrimp pond added a local isolate had significantly higher survival at about 10.0% to 11.7% than shrimp without added the isolate (p<0.05, and better FCR, but no significant different in shrimp harvest size. Vibrio bacterial was undetected by total plate count. Moreover, it shown better projected yields on an annual basis (three crops per year.

  20. Dna Sequencing (United States)

    Tabor, Stanley; Richardson, Charles C.


    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  1. Comparison of contrast-enhanced modified T1-weighted 3D TSE black-blood and 3D MP-RAGE sequences for the detection of cerebral metastases and brain tumours

    Energy Technology Data Exchange (ETDEWEB)

    Kammer, N.N.; Coppenrath, E.; Treitl, K.M.; Saam, T. [Ludwig-Maximilians-University Hospital Munich, Institute for Clinical Radiology, Munich (Germany); Kooijman, H. [Philips Healthcare, Hamburg (Germany); Dietrich, O. [Ludwig-Maximilians-University Hospital Munich, Josef Lissner Laboratory for Biomedical Imaging, Institute for Clinical Radiology, Munich (Germany)


    To compare a modified T1-weighted 3D TSE black-blood sequence with sub-millimetre resolution (T1-mVISTA) with a magnetization-prepared rapid gradient echo (MP-RAGE) sequence for the diagnosis of cerebral malignomas. Forty-six patients with known or suspected intracranial tumours and 15 control patients were included in this retrospective study. All patients underwent T1-mVISTA (0.75-mm isotropic resolution, 4:43 min) and MP-RAGE (0.8-mm isotropic resolution, 4:46 minutes) at 3-Tesla in random order after application of contrast agent. Two experienced radiologists determined the number of lesions. Maximum diameter, diagnostic confidence (DC), visual assessment of contrast enhancement (VCE) and CNR{sub lesion/parenchyma} were assessed for each lesion. Significantly more lesions were detected with T1-mVISTA compared to the MP-RAGE (61 vs. 36; p < 0.05). Further, DC and VCE was rated significantly higher in the T1-mVISTA (p < 0.05 and p < 0.001). Mean CNR{sub lesion/parenchyma} was twofold higher for T1-mVISTA (24.2 ± 17.5 vs. 12.7 ± 11.5, p < 0.001). The 25 lesions detected only in T1-mVISTA were significantly smaller than those detected in both sequences (4.3 ± 3.7 mm vs. 11.3 ± 10.7 mm; p < 0.01). T1-mVISTA increases the contrast of lesions significantly compared to MP-RAGE and might therefore improve detection rates of small lesions in early stages of disease. (orig.)

  2. Elevated O₃ enhances the attraction of whitefly-infested tomato plants to Encarsia formosa. (United States)

    Cui, Hongying; Su, Jianwei; Wei, Jianing; Hu, Yongjian; Ge, Feng


    We experimentally examined the effects of elevated O₃ and whitefly herbivory on tomato volatiles, feeding and oviposition preferences of whiteflies and behavioural responses of Encarsia formosa to these emissions on two tomato genotypes, a wild-type (Wt) and a jasmonic acid (JA) defence-enhanced genotype (JA-OE, 35S). The O₃ level and whitefly herbivory significantly increased the total amount of volatile organic compounds (VOCs), monoterpenes, green leaf volatiles (GLVs), and aldehyde volatiles produced by tomato plants. The 35S plants released higher amount of total VOCs and monoterpene volatiles than Wt plants under O₃+herbivory treatments. The feeding and oviposition bioassays showed that control plants were preferred by adult whiteflies whereas the 35S plants were not preferred by whiteflies. In the Y-tube tests, O₃+herbivory treatment genotypes were preferred by adult E. Formosa. The 35S plants were preferred by adult E. formosa under O₃, herbivory and O₃+herbivory treatments. Our results demonstrated that elevated O₃ and whitefly herbivory significantly increased tomato volatiles, which attracted E. formosa and reduced whitefly feeding. The 35S plants had a higher resistance to B. tabaci than Wt plant. Such changes suggest that the direct and indirect defences of resistant genotypes, such as 35S, could strengthen as the atmospheric O₃ concentration increases.

  3. ABS: Sequence alignment by scanning

    KAUST Repository

    Bonny, Mohamed Talal


    Sequence alignment is an essential tool in almost any computational biology research. It processes large database sequences and considered to be high consumers of computation time. Heuristic algorithms are used to get approximate but fast results. We introduce fast alignment algorithm, called Alignment By Scanning (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the well-known alignment algorithms, the FASTA (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 76% enhancement in alignment score when it is compared with the FASTA Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  4. Fast global sequence alignment technique

    KAUST Repository

    Bonny, Mohamed Talal


    Bioinformatics database is growing exponentially in size. Processing these large amount of data may take hours of time even if super computers are used. One of the most important processing tool in Bioinformatics is sequence alignment. We introduce fast alignment algorithm, called \\'Alignment By Scanning\\' (ABS), to provide an approximate alignment of two DNA sequences. We compare our algorithm with the wellknown sequence alignment algorithms, the \\'GAP\\' (which is heuristic) and the \\'Needleman-Wunsch\\' (which is optimal). The proposed algorithm achieves up to 51% enhancement in alignment score when it is compared with the GAP Algorithm. The evaluations are conducted using different lengths of DNA sequences. © 2011 IEEE.

  5. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Nucleotide Sequence Nucleotide sequence of full length cDNA (trimmed sequence) kome_ine_full_sequence_db ...

  6. Sequences upstream of the homologous cis-elements of the Adh adult enhancer of Drosophila are required for maximal levels of Adh gene transcription in adults of Scaptodrosophila lebanonensis. (United States)

    Papaceit, Montserrat; Orengo, Dorcas; Juan, Elvira


    The evolution of cis-regulatory elements is of particular interest for our understanding of the evolution of gene regulation. The Adh gene of Drosophilidae shows interspecific differences in tissue-specific expression and transcript levels during development. In Scaptodrosophila lebanonensis adults, the level of distal transcripts is maximal between the fourth and eighth day after eclosion and is around five times higher than that in D. melanogaster Adh(S). To examine whether these quantitative differences are regulated by sequences lying upstream of the distal promoter, we performed in vitro deletion mutagenesis of the Adh gene of S. lebanonensis, followed by P-element-mediated germ-line transformation. All constructs included, as a cotransgene, a modified Adh gene of D. melanogaster (dAdh) in a fixed position and orientation that acted as a chromosomal position control. Using this approach, we have identified a fragment of 1.5 kb in the 5' region, 830 bp upstream of the distal start site, which is required to achieve maximal levels of distal transcript in S. lebanonensis. The presence of this fragment produces a 3.5-fold higher level of distal mRNA (as determined by real time quantitative PCR) compared with the D. melanogaster dAdh cotransgene. This region contains the degenerated end of a minisatellite sequence expanding farther upstream and does not correspond to the Adh adult enhancer (AAE) of D. melanogaster. Indeed, the cis-regulatory elements of the AAE have been identified by phylogenetic footprinting within the region 830 bp upstream of the distal start site of S. lebanonensis. Furthermore, the deletions Delta-830 and Delta-2358 yield the same pattern of tissue-specific expression, indicating that all tissue-specific elements are contained within the region 830 bp upstream of the distal start site. PMID:15166155

  7. Cloning of an Erwinia herbicola gene necessary for gluconic acid production and enhanced mineral phosphate solubilization in Escherichia coli HB101: nucleotide sequence and probable involvement in biosynthesis of the coenzyme pyrroloquinoline quinone. (United States)

    Liu, S T; Lee, L Y; Tai, C Y; Hung, C H; Chang, Y S; Wolfram, J H; Rogers, R; Goldstein, A H


    Escherichia coli is capable of synthesizing the apo-glucose dehydrogenase enzyme (GDH) but not the cofactor pyrroloquinoline quinone (PQQ), which is essential for formation of the holoenzyme. Therefore, in the absence of exogenous PQQ, E. coli does not produce gluconic acid. Evidence is presented to show that the expression of an Erwinia herbicola gene in E. coli HB101(pMCG898) resulted in the production of gluconic acid, which, in turn, implied PQQ biosynthesis. Transposon mutagenesis showed that the essential gene or locus was within a 1.8-kb region of a 4.5-kb insert of the plasmid pMCG898. This 1.8-kb region contained only one apparent open reading frame. In this paper, we present the nucleotide sequence of this open reading frame, a 1,134-bp DNA fragment coding for a protein with an M(r) of 42,160. The deduced sequence of this protein had a high degree of homology with that of gene III (M(r), 43,600) of a PQQ synthase gene complex from Acinetobacter calcoaceticus previously identified by Goosen et al. (J. Bacteriol. 171:447-455, 1989). In minicell analysis, pMCG898 encoded a protein with an M(r) of 41,000. These data indicate that E. coli HB101(pMCG898) produced the GDH-PQQ holoenzyme, which, in turn, catalyzed the oxidation of glucose to gluconic acid in the periplasmic space. As a result of the gluconic acid production, E. coli HB101(pMCG898) showed an enhanced mineral phosphate-solubilizing phenotype due to acid dissolution of the hydroxyapatite substrate.

  8. MYB and bHLH transcription factor transgenes increase anthocyanin pigmentation in petunia and lisianthus plants, and the petunia phenotypes are strongly enhanced under field conditions

    Directory of Open Access Journals (Sweden)

    Kathy E Schwinn


    Full Text Available Petunia line Mitchell [MP, Petunia axillaris × (P. axillaris × P. hybrida] and Eustoma grandiflorum (lisianthus plants were produced containing a transgene for over-expression of the R2R3-MYB transcription factor (ROSEA1 that up-regulates flavonoid biosynthesis in Antirrhinum majus. The petunia lines were also crossed with previously produced MP lines containing a Zea mays flavonoid-related bHLH transcription factor transgene (LEAF COLOR, LC, which induces strong vegetative pigmentation when these 35S:LC plants are exposed to high light levels. 35S:ROS1 lisianthus transgenics had limited changes in anthocyanin pigmentation, specifically, precocious pigmentation of flower petals and increased pigmentation of sepals. RNA transcript levels for two anthocyanin biosynthetic genes, chalcone synthase and anthocyanidin synthase, were increased in the 35S:ROS1 lisianthus petals compared to those of control lines. With MP, the 35S:ROS1 calli showed novel red pigmentation in culture, but this was generally not seen in tissue culture plantlets regenerated from the calli or young plants transferred to soil in the greenhouse. Anthocyanin pigmentation was enhanced in the stems of mature 35S:ROS1 MP plants, but the MP white-flower phenotype was not complemented. Progeny from a 35S:ROS1×35S:LC cross had novel pigmentation phenotypes that were not present in either parental line or MP. In particular, there was increased pigment accumulation in the petal throat region, and the anthers changed from yellow to purple colour. An outdoor field trial was conducted with the 35S:ROS1, 35S:LC, 35S:ROS1×35S:LC and control MP lines. Field conditions rapidly induced intense foliage pigmentation in 35S:LC plants, a phenotype not observed in control MP or equivalent 35S:LC plants maintained in a greenhouse. No difference in plant stature, seed germination, or plant survival was observed between transgenic and control plants.

  9. Spatiotemporal correlations of aftershock sequences

    CERN Document Server

    Peixoto, Tiago P; Davidsen, Jörn


    Aftershock sequences are of particular interest in seismic research since they may condition seismic activity in a given region over long time spans. While they are typically identified with periods of enhanced seismic activity after a large earthquake as characterized by the Omori law, our knowledge of the spatiotemporal correlations between events in an aftershock sequence is limited. Here, we study the spatiotemporal correlations of two aftershock sequences form California (Parkfield and Hector Mine) using the recently introduced concept of "recurrent" events. We find that both sequences have very similar properties and that most of them are captured by the space-time epidemic-type aftershock sequence (ETAS) model if one takes into account catalog incompleteness. However, the stochastic model does not capture the spatiotemporal correlations leading to the observed structure of seismicity on small spatial scales.

  10. A 28 nt long synthetic 5′UTR (synJ as an enhancer of transgene expression in dicotyledonous plants

    Directory of Open Access Journals (Sweden)

    Kanoria Shaveta


    Full Text Available Abstract Background A high level of transgene expression is required, in several applications of transgenic technology. While use of strong promoters has been the main focus in such instances, 5′UTRs have also been shown to enhance transgene expression. Here, we present a 28 nt long synthetic 5′UTR (synJ, which enhances gene expression in tobacco and cotton. Results The influence of synJ on transgene expression was studied in callus cultures of cotton and different tissues of transgenic tobacco plants. The study was based on comparing the expression of reporter gene gus and gfp, with and without synJ as its 5′UTR. Mutations in synJ were also analyzed to identify the region important for enhancement. synJ, enhances gene expression by 10 to 50 fold in tobacco and cotton depending upon the tissue studied. This finding is based on the experiments comparing the expression of gus gene, encoding the synJ as 5′UTR under the control of 35S promoter with expression cassettes based on vectors like pBI121 or pRT100. Further, the enhancement was in most cases equivalent to that observed with the viral leader sequences known to enhance translation like Ω and AMV. In case of transformed cotton callus as well as in the roots of tobacco transgenic plants, the up-regulation mediated by synJ was much higher than that observed in the presence of both Ω as well as AMV. The enhancement mediated by synJ was found to be at the post-transcriptional level. The study also demonstrates the importance of a 5′UTR in realizing the full potential of the promoter strength. synJ has been utilized to design four cloning vectors: pGEN01, pBGEN02, pBGEN02-hpt and pBGEN02-ALSdm each of which can be used for cloning the desired transgene and achieving high level of expression in the resulting transgenic plants. Conclusions synJ, a synthetic 5′UTR, can enhance transgene expression under a strong promoter like 35S as well as under a weak promoter like nos in

  11. 35S::GmPM30在拟南芥的根系生长中表现为对ABA的敏感性降低(英文)

    Institute of Scientific and Technical Information of China (English)



    LEA protein,late-embryogenesis-abundant protein,is importantin response to thesalt and drought stresses in plants.Here,weidentified a cDNA full length of LEA from soybean and found that LEA enhance the ability of anti-salinity in transgenic Arabidopsis thaliana.The expression of GmPM30 increases highly under salinity,cold or ABA treatment,and enhances by certain degree under drought stress.The germination rates,primary root lengths and survival rate of GmPM30 over-expression lines are obviously higher than that of the wild-type after suffering the salinity stress.Our studies displays that GmPM30-ox apparently enhances the tolerance to salinity in Arabidopsis thaliana.

  12. Analysis of genetically modified organisms by pyrosequencing on a portable photodiode-based bioluminescence sequencer. (United States)

    Song, Qinxin; Wei, Guijiang; Zhou, Guohua


    A portable bioluminescence analyser for detecting the DNA sequence of genetically modified organisms (GMOs) was developed by using a photodiode (PD) array. Pyrosequencing on eight genes (zSSIIb, Bt11 and Bt176 gene of genetically modified maize; Lectin, 35S-CTP4, CP4EPSPS, CaMV35S promoter and NOS terminator of the genetically modified Roundup ready soya) was successfully detected with this instrument. The corresponding limit of detection (LOD) was 0.01% with 35 PCR cycles. The maize and soya available from three different provenances in China were detected. The results indicate that pyrosequencing using the small size of the detector is a simple, inexpensive, and reliable way in a farm/field test of GMO analysis.

  13. T1 WI BLADE Dark Fluid 序列在头颅增强扫描中的应用价值%The value of contrast-enhanced T1 WI BLADE Dark Fluid sequence in the brain MR imaging

    Institute of Scientific and Technical Information of China (English)

    张海平; 敖国昆; 李利佳; 刘杰爱; 石清磊; 李帅


    (SNRwm )were measured and calculated by the same two radi-ologists.The mean values of the quantitative parameters were compared using the Paired t-test.Results The grading values were 21,9,0 and 0 case in 0,Ⅰ,Ⅱ and Ⅲ grades scanned by T1 WI BLADE Dark Fluid and 8,1 1,6 and 5 cases in group scanned by T1 WI Dark Fluid and the difference between them was significant statistical difference(Z =-5.130,P =0.000);The CNRgw (30.37 ±10.96 )and CNRle (87.36±45.32)of T1 WI BLADE Dark Fluid were superior to the CNRgw (24.48±10.55)and CNRle (60.46 ±25.22)of T1 WI Dark Fluid,with significant statistical difference (P=0.000,P=0.009).The mean values of SNRwm of the two sequences were 84.12±20.08, 79.71±25.37,with no significant statistical difference (P =0.1 69).Conclusion Contrast-enhanced T1 WI BLADE Dark Fluid can significantly weaken the motion artifacts.It has great value in contrast-enhanced T1 WI head MR examination.

  14. Rapid Diagnostics of Onboard Sequences (United States)

    Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.


    Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command

  15. TM6, a novel nuclear matrix attachment region, enhances its flanking gene expression through influencing their chromatin structure. (United States)

    Ji, Lusha; Xu, Rui; Lu, Longtao; Zhang, Jiedao; Yang, Guodong; Huang, Jinguang; Wu, Changai; Zheng, Chengchao


    Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.

  16. Classifying Genomic Sequences by Sequence Feature Analysis

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Liu; Dian Jiao; Xiao Sun


    Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream,exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.

  17. A Novel Thylakoid Ascorbate Peroxidase from Jatrophacurcas Enhances Salt Tolerance in Transgenic Tobacco

    Directory of Open Access Journals (Sweden)

    Zhibin Liu


    Full Text Available Ascorbate peroxidase (APX plays an important role in the metabolism of hydrogen peroxide in higher plants. In the present study, a novel APX gene (JctAPX was cloned from Jatropha curcas L. The deduced amino acid sequence was similar to that of APX of some other plant species. JctAPX has a chloroplast transit peptide and was localized to the chloroplasts by analysis with a JctAPX-green fluorescent protein (GFP fusion protein. Quantitative polymerase chain reaction (qPCR analysis showed that JctAPX was constitutively expressed in different tissues from J. curcas and was upregulated by NaCl stress. To characterize its function in salt tolerance, the construct p35S: JctAPX was created and successfully introduced into tobacco by Agrobacterium-mediated transformation. Compared with wild type (WT, the transgenic plants exhibited no morphological abnormalities in the no-stress condition. However, under 200 mM NaCl treatment, JctAPX over-expressing plants showed increased tolerance to salt during seedling establishment and growth. In addition, the transgenic lines showed higher chlorophyll content and APX activity, which resulted in lower H2O2 content than WT when subjected to 400 mM NaCl stress. These results suggest that the increased APX activity in the chloroplasts from transformed plants increased salt tolerance by enhancing reactive oxygen species (ROS-scavenging capacity under short-term NaCl stress conditions.

  18. Ascorbate peroxidase from Jatropha curcas enhances salt tolerance in transgenic Arabidopsis. (United States)

    Chen, Y; Cai, J; Yang, F X; Zhou, B; Zhou, L R


    Ascorbate peroxidase (APX) plays a central role in the ascorbate-glutathione cycle and is a key enzyme in cellular H2O2 me-tabolism. It includes a family of isoenzymes with different character-istics, which are identified in many higher plants. In the present study, we isolated the APX gene from Jatropha curcas L, which is similar with other previously characterized APXs as revealed by alignment and phylogenetic analysis of its deduced amino acid sequence. Real-time qPCR analysis showed that the expression level of JcAPX transcript significantly increased under NaCl stress. Subsequently, to elucidate the contribution of JcAPX to the protection against salt-induced oxi-dative stress, the expression construct p35S: JcAPX was created and transformed into Arabidopsis and transcribed. Under 150-mM NaCl stress, compared with wild type (WT), the overexpression of JcAPX in Arabidopsis increased the germination rate, the number of leaves, and the rosette area. In addition, the transgenic plants had longer roots, higher total chlorophyll content, higher total APX activity, and lower H2O2 content than the WT under NaCl stress conditions. These results suggested that higher APX activity in transgenic lines increases the salt tolerance by enhancing scavenging capacity for reactive oxygen spe-cies under NaCl stress conditions.

  19. Main: Sequences [KOME

    Lifescience Database Archive (English)

    Full Text Available Sequences Amino Acid Sequence Amino Acid sequence of full length cDNA (Longest ORF) kome_ine_full_sequence_amino_db ...

  20. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.


    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  1. Sequence Read Archive (SRA) (United States)

    U.S. Department of Health & Human Services — The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome...

  2. Multimodal sequence learning. (United States)

    Kemény, Ferenc; Meier, Beat


    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  3. Coordinate cytokine regulatory sequences (United States)

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.


    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  4. The use of a viral 2A sequence for the simultaneous over-expression of both the vgf gene and enhanced green fluorescent protein (eGFP) in vitro and in vivo (United States)

    Lewis, Jo E.; Brameld, John M.; Hill, Phil; Barrett, Perry; Ebling, Francis J.P.; Jethwa, Preeti H.


    Introduction The viral 2A sequence has become an attractive alternative to the traditional internal ribosomal entry site (IRES) for simultaneous over-expression of two genes and in combination with recombinant adeno-associated viruses (rAAV) has been used to manipulate gene expression in vitro. New method To develop a rAAV construct in combination with the viral 2A sequence to allow long-term over-expression of the vgf gene and fluorescent marker gene for tracking of the transfected neurones in vivo. Results Transient transfection of the AAV plasmid containing the vgf gene, viral 2A sequence and eGFP into SH-SY5Y cells resulted in eGFP fluorescence comparable to a commercially available reporter construct. This increase in fluorescent cells was accompanied by an increase in VGF mRNA expression. Infusion of the rAAV vector containing the vgf gene, viral 2A sequence and eGFP resulted in eGFP fluorescence in the hypothalamus of both mice and Siberian hamsters, 32 weeks post infusion. In situ hybridisation confirmed that the location of VGF mRNA expression in the hypothalamus corresponded to the eGFP pattern of fluorescence. Comparison with old method The viral 2A sequence is much smaller than the traditional IRES and therefore allowed over-expression of the vgf gene with fluorescent tracking without compromising viral capacity. Conclusion The use of the viral 2A sequence in the AAV plasmid allowed the simultaneous expression of both genes in vitro. When used in combination with rAAV it resulted in long-term over-expression of both genes at equivalent locations in the hypothalamus of both Siberian hamsters and mice, without any adverse effects. PMID:26300182

  5. Induction and maintenance of DNA methylation in plant promoter sequences by apple latent spherical virus-induced transcriptional gene silencing

    Directory of Open Access Journals (Sweden)

    Tatsuya eKon


    Full Text Available Apple latent spherical virus (ALSV is an efficient virus-induced gene silencing vector in functional genomics analyses of a broad range of plant species. Here, an Agrobacterium-mediated inoculation (agroinoculation system was developed for the ALSV vector, and virus-induced transcriptional gene silencing (VITGS is described in plants infected with the ALSV vector. The cDNAs of ALSV RNA1 and RNA2 were inserted between the CaMV 35S promoter and the NOS-T sequences in a binary vector pCAMBIA1300 to produce pCALSR1 and pCALSR2-XSB or pCALSR2-XSB/MN. When these vector constructs were agroinoculated into Nicotiana benthamiana plants with a construct expressing a viral silencing suppressor, the infection efficiency of the vectors was 100%. A recombinant ALSV vector carrying part of the 35S promoter sequence induced transcriptional gene silencing of the green fluorescent protein gene in a line of N. benthamiana plants, resulting in the disappearance of green fluorescence of infected plants. Bisulfite sequencing showed that cytosine residues at CG and CHG sites of the 35S promoter sequence were highly methylated in the silenced generation 0 plants infected with the ALSV carrying the promoter sequence as well as in progeny. The ALSV-mediated VITGS state was inherited by progeny for multiple generations. In addition, induction of VITGS of an endogenous gene (chalcone synthase-A was demonstrated in petunia plants infected with an ALSV vector carrying the native promoter sequence. These results suggest that ALSV-based vectors can be applied to study DNA methylation in plant genomes, and provide a useful tool for plant breeding via epigenetic modification.

  6. Genomic Signal Enhancement by Clustering

    Institute of Scientific and Technical Information of China (English)

    ZHENG Wei-Mou


    Weight matrix models for signal sequence motif are simple. A main limitation of the models is the assumption of independence between positions. Signal enhancement is achieved by taking the total likelihood as the objective function for maximization to cluster sequences into groups with different patterns. As an example, the initial and terminal signals for translation in rice genome are examined.

  7. Constitutive over-expression of rice chymotrypsin protease inhibitor gene OCPI2 results in enhanced growth, salinity and osmotic stress tolerance of the transgenic Arabidopsis plants. (United States)

    Tiwari, Lalit Dev; Mittal, Dheeraj; Chandra Mishra, Ratnesh; Grover, Anil


    Protease inhibitors are involved primarily in defense against pathogens. In recent years, these proteins have also been widely implicated in response of plants to diverse abiotic stresses. Rice chymotrypsin protease inhibitor gene OCPI2 is highly induced under salt and osmotic stresses. The construct containing the complete coding sequence of OCPI2 cloned downstream to CaMV35S promoter was transformed in Arabidopsis and single copy, homozygous transgenic lines were produced. The transgenic plants exhibited significantly enhanced tolerance to NaCl, PEG and mannitol stress as compared to wild type plants. Importantly, the vegetative and reproductive growth of transgenic plants under unstressed, control conditions was also enhanced: transgenic plants were more vigorous than wild type, resulting into higher yield in terms of silique number. The RWC values and membrane stability index of transgenic in comparison to wild type plants was higher. Higher proline content was observed in the AtOCPI2 lines, which was associated with higher transcript expression of pyrroline-5-carboxylate synthase and lowered levels of proline dehydrogenase genes. The chymotrypsin protease activities were lower in the transgenic as against wild type plants, under both unstressed, control as well as stressed conditions. It thus appears that rice chymotrypsin protease inhibitor gene OCPI2 is a useful candidate gene for genetic improvement of plants against salt and osmotic stress.

  8. Reading biological processes from nucleotide sequences (United States)

    Murugan, Anand

    Cellular processes have traditionally been investigated by techniques of imaging and biochemical analysis of the molecules involved. The recent rapid progress in our ability to manipulate and read nucleic acid sequences gives us direct access to the genetic information that directs and constrains biological processes. While sequence data is being used widely to investigate genotype-phenotype relationships and population structure, here we use sequencing to understand biophysical mechanisms. We present work on two different systems. First, in chapter 2, we characterize the stochastic genetic editing mechanism that produces diverse T-cell receptors in the human immune system. We do this by inferring statistical distributions of the underlying biochemical events that generate T-cell receptor coding sequences from the statistics of the observed sequences. This inferred model quantitatively describes the potential repertoire of T-cell receptors that can be produced by an individual, providing insight into its potential diversity and the probability of generation of any specific T-cell receptor. Then in chapter 3, we present work on understanding the functioning of regulatory DNA sequences in both prokaryotes and eukaryotes. Here we use experiments that measure the transcriptional activity of large libraries of mutagenized promoters and enhancers and infer models of the sequence-function relationship from this data. For the bacterial promoter, we infer a physically motivated 'thermodynamic' model of the interaction of DNA-binding proteins and RNA polymerase determining the transcription rate of the downstream gene. For the eukaryotic enhancers, we infer heuristic models of the sequence-function relationship and use these models to find synthetic enhancer sequences that optimize inducibility of expression. Both projects demonstrate the utility of sequence information in conjunction with sophisticated statistical inference techniques for dissecting underlying biophysical

  9. Combination of low and high resolution T{sub 1}-weighted sequences for improved evaluation of morphologic criteria in dynamic contrast enhanced MRI of the breast; Eine Kombination niedrig und hochaufloesender dynamischer T{sub 1}-gewichteter Sequenzen zur besseren Beurteilung der Morphologie Kontrastmittel aufnehmender Laesionen in der MRT der weiblichen Brust

    Energy Technology Data Exchange (ETDEWEB)

    Vomweg, T.W.; Teifke, A.; Schreiber, W.G.; Thelen, M. [Klinik und Poliklinik fuer Radiologie, Klinikum der Universitaet Mainz (Germany); Schmidt, M. [Klinik und Poliklinik fuer Geburtshilfe und Frauenkrankheiten, Klinikum der Universitaet Mainz (Germany)


    Purpose: Presentation of a new protocol for simultaneous acquisition of both low and high resolution T{sub 1}-weighted images of breast lesions for dynamic contrast-enhanced MR mammography. Demonstration of possible diagnostic improvement with representative measurements in patients with suspected breast cancer by adding morphologic parameters from high resolution sequences to the analysis of the signal-time curve. Materials and Methods: Dynamic MR imaging was performed with a 1.5 T system (Magnetom SONATA, Siemens Medical Systems, Germany) and the manufacturer's double-breast coil. Coronal T{sub 1}-weighted 3D FLASH sequences (spatial resolution 1.25 x 1.25mm{sup 2}; slice thickness 1.7 mm) were acquired once before and five times after administration of contrast medium (Gd-DTPA, 0.15 mmol/kg) injection. In addition, a high resolution T{sub 1}-weighted 3D-FLASH sequence (spatial resolution, 0.63 x 0.63 mm{sup 2}) was obtained before administration of contrast medium and after the third post-contrast low-resolution sequence. Except for the acquisition matrix, all imaging parameters were identical for both 3D pulse sequences. To assure comparison of the measured signal intensities for both T{sub 1}-weighted sequences, calibrating phantom measurements were performed using a dilution series of Gd-DTPA. Results: Phantom measurements demonstrated similar signal intensities and enhancement pattern for both sequences. A combined protocol consisting of both pulse sequences can be employed and does not interfere with the signal-time curve analysis. By measuring one high resolution sequence 3:18 minutes after administration of contrast medium, morphologic features can be evaluated without interference from barely enhancing surrounding tissue. The overall study time is not increased. The improved spatial resolution slightly increases the severity of motion artifacts. (orig.) [German] Ziel: Vorstellung eines neuen Protokolls zur gleichzeitigen Messung von niedrig und

  10. 磁共振T2WI压脂及T1WI压脂增强序列在肛痈及肛漏诊断中的价值%The Value of Mri T2WI Pressure Grease and Fat Enhanced T1WI Pressure Sequence in Diagnosis of Anus Carbuncle and Anal Leakage

    Institute of Scientific and Technical Information of China (English)



    目的:分析磁共振T2WI压脂及T1WI压脂增强序列在肛痈及肛漏诊断中的价值。方法:41例肛痈及肛漏患者均行常规及Gd-DTPA增强磁共振检查,经手术证实,对以上各磁共振扫描序列组合对各种类型肛痈、肛漏及其内口的检出率进行统计分析。结果:肛痈32个,肛漏26个。对于肛痈、肛漏检出率,矢状位平扫及增强T1Wl压脂序列与手术结果比较差异均有统计学意义(P0.05)。结论:轴位联合冠状位T2WI压脂序列及T1WI压脂增强扫描序列可明显提高肛痈、肛漏临床诊断正确率,为手术方式的最佳选择提供科学信息。%Objective:To analyze the value of mri T2WI pressure grease and fat enhanced T1WI pressure sequence in diagnosis of anus carbuncle and anal leakage.Method:41 patients with anal carbuncle and anal leakage both conventional and Gd-DTPA enhanced magnetic resonance examination,confirmed by surgery,the combination of all mri scanning sequences of various types of anal abscess in mouth,anus leakage and its detection rate were analyzed. Result:Anal carbuncle was 32,anal leakage was 26.For abscess,anal leakage inspection rate,sagittal scan and enhanced T1Wl pressure grease series all had significant difference compared with surgical results(P0.05).Conclusion:Shaft joint coronary bits fat T2WI pressure fat sequence and T1WI enhancement scan sequence can obviously improve the anus carbuncle,anal leakage clinical diagnostic accuracy, provide scientific information for the best choice of the surgical procedure.

  11. Analysis of the spacing between the two palindromes of activation sequence-1 with respect to binding to different TGA factors and transcriptional activation potential.


    Krawczyk, Stefanie; Thurow, Corinna; Niggeweg, Ricarda; Gatz, Christiane


    In higher plants, activation sequence-1 (as-1) of the cauliflower mosaic virus 35S promoter mediates both salicylic acid- and auxin-inducible transcriptional activation. Originally found in viral and T-DNA promoters, as-1-like elements are also functional elements of plant promoters activated in the course of a defence response upon pathogen attack. as-1-like elements are characterised by two imperfect palindromes with the palindromic centres being spaced by 12 bp. They are recognised by plan...

  12. DNA damage and photosynthesis in Antarctic and Arctic Sanionia uncinata (Hedw.) Loeske under ambient and enhanced levels of UV-B radiation

    NARCIS (Netherlands)

    Lud, D; Moerdijk, T.C W; van de Poll, W.H.; Buma, A.G.J.; Huiskes, A.H L


    The response of the bipolar moss Sanionia uncinata (Hedw.) Loeske to ambient and enhanced UV-B radiation was investigated at an Antarctic (Leonie Island, 67degrees35' S, 68degrees20' W) and an Arctic (Ny-Alesund, 78degrees55' N, 11degrees56' E) site, which differed in ambient UV-B radiation (UV-BR:

  13. Cadmium resistance in transgenic tobacco plants enhanced by expressing bean heavy metal-responsive gene PvSR2

    Institute of Scientific and Technical Information of China (English)

    CHAI; Tuanyao; (柴团耀); CHEN; Qiong; (陈琼); ZHANG; Yuxiu; (张玉秀); DONG; Juan; (董娟); AN; Chengcai; (安成才)


    PvSR2 (Phaseolus vulgaris stress-related gene) has been cloned from French bean and shown to be expressed specifically upon heavy metal treatment. In order to investigate the role of PvSR2 in plant, PvSR2 gene under the control of cauliflower mosaic virus 35S promoter was introduced into tobacco mediated with Agrobacterium tumefaciens LBA4404. The regenerated plantlets were selected on medium with 100 mg/L kanamycin. PCR and Southern blot analysis showed PvSR2 gene was integrated in tobacco genome. Gus and Northern blot analysis indicated PvSR2 gene was expressed in transgenic seedling. The heavy metal resistance assay showed that the transgenic tobacco seedlings with the PvSR2 coding sequence exhibited higher tolerance to Cd compared with wild-type (WT) under Cd exposure. The Cd content accumulated in root between transgenic and WT seedlings had no obvious difference at lower Cd external concentration (0.05-0.075 mmol/L CdCl2), whereas transgenic plant showed a lower root Cd content than the control at higher external Cd concentration (0.1 mmol/L CdCl2). These results suggested that the expression of PvSR2 can enhance the Cd tolerance, and PvSR2 may be involved in Cd transportation and accumulation at the test concentration of 0.1 mmol/L Cd.

  14. Genome Sequence Databases (Overview): Sequencing and Assembly

    Energy Technology Data Exchange (ETDEWEB)

    Lapidus, Alla L.


    From the date its role in heredity was discovered, DNA has been generating interest among scientists from different fields of knowledge: physicists have studied the three dimensional structure of the DNA molecule, biologists tried to decode the secrets of life hidden within these long molecules, and technologists invent and improve methods of DNA analysis. The analysis of the nucleotide sequence of DNA occupies a special place among the methods developed. Thanks to the variety of sequencing technologies available, the process of decoding the sequence of genomic DNA (or whole genome sequencing) has become robust and inexpensive. Meanwhile the assembly of whole genome sequences remains a challenging task. In addition to the need to assemble millions of DNA fragments of different length (from 35 bp (Solexa) to 800 bp (Sanger)), great interest in analysis of microbial communities (metagenomes) of different complexities raises new problems and pushes some new requirements for sequence assembly tools to the forefront. The genome assembly process can be divided into two steps: draft assembly and assembly improvement (finishing). Despite the fact that automatically performed assembly (or draft assembly) is capable of covering up to 98% of the genome, in most cases, it still contains incorrectly assembled reads. The error rate of the consensus sequence produced at this stage is about 1/2000 bp. A finished genome represents the genome assembly of much higher accuracy (with no gaps or incorrectly assembled areas) and quality ({approx}1 error/10,000 bp), validated through a number of computer and laboratory experiments.

  15. Contamination of sequence databases with adaptor sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yoshikawa, Takeo; Sanders, A.R.; Detera-Wadleigh, S.D. [National Institute of Mental Health, Bethesda, MD (United States)


    Because of the exponential increase in the amount of DNA sequences being added to the public databases on a daily basis, it has become imperative to identify sources of contamination rapidly. Previously, contaminations of sequence databases have been reported to alert the scientific community to the problem. These contaminations can be divided into two categories. The first category comprises host sequences that have been difficult for submitters to manage or control. Examples include anomalous sequences derived from Escherichia coli, which are inserted into the chromosomes (and plasmids) of the bacterial hosts. Insertion sequences are highly mobile and are capable of transposing themselves into plasmids during cloning manipulation. Another example of the first category is the infection with yeast genomic DNA or with bacterial DNA of some commercially available cDNA libraries from Clontech. The second category of database contamination is due to the inadvertent inclusion of nonhost sequences. This category includes incorporation of cloning-vector sequences and multicloning sites in the database submission. M13-derived artifacts have been common, since M13-based vectors have been widely used for subcloning DNA fragments. Recognizing this problem, the National Center for Biotechnology Information (NCBI) started to screen, in April 1994, all sequences directly submitted to GenBank, against a set of vector data retrieved from GenBank by use of key-word searches, such as {open_quotes}vector.{close_quotes} In this report, we present evidence for another sequence artifact that is widespread but that, to our knowledge, has not yet been reported. 11 refs., 1 tab.

  16. Automated DNA Sequencing System

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.; Ekkebus, C.P.; Hauser, L.J.; Kress, R.L.; Mural, R.J.


    Oak Ridge National Laboratory (ORNL) is developing a core DNA sequencing facility to support biological research endeavors at ORNL and to conduct basic sequencing automation research. This facility is novel because its development is based on existing standard biology laboratory equipment; thus, the development process is of interest to the many small laboratories trying to use automation to control costs and increase throughput. Before automation, biology Laboratory personnel purified DNA, completed cycle sequencing, and prepared 96-well sample plates with commercially available hardware designed specifically for each step in the process. Following purification and thermal cycling, an automated sequencing machine was used for the sequencing. A technician handled all movement of the 96-well sample plates between machines. To automate the process, ORNL is adding a CRS Robotics A- 465 arm, ABI 377 sequencing machine, automated centrifuge, automated refrigerator, and possibly an automated SpeedVac. The entire system will be integrated with one central controller that will direct each machine and the robot. The goal of this system is to completely automate the sequencing procedure from bacterial cell samples through ready-to-be-sequenced DNA and ultimately to completed sequence. The system will be flexible and will accommodate different chemistries than existing automated sequencing lines. The system will be expanded in the future to include colony picking and/or actual sequencing. This discrete event, DNA sequencing system will demonstrate that smaller sequencing labs can achieve cost-effective the laboratory grow.

  17. Genetic modification of the soybean to enhance the β-carotene content through seed-specific expression.

    Directory of Open Access Journals (Sweden)

    Mi-Jin Kim

    Full Text Available The carotenoid biosynthetic pathway was genetically manipulated using the recombinant PAC (Phytoene synthase-2A-Carotene desaturase gene in Korean soybean (Glycine max L. cv. Kwangan. The PAC gene was linked to either the β-conglycinin (β or CaMV-35S (35S promoter to generate β-PAC and 35S-PAC constructs, respectively. A total of 37 transgenic lines (19 for β-PAC and 18 for 35S-PAC were obtained through Agrobacterium-mediated transformation using the modified half-seed method. The multi-copy insertion of the transgene was determined by genomic Southern blot analysis. Four lines for β-PAC were selected by visual inspection to confirm an orange endosperm, which was not found in the seeds of the 35S-PAC lines. The strong expression of PAC gene was detected in the seeds of the β-PAC lines and in the leaves of the 35S-PAC lines by RT-PCR and qRT-PCR analyses, suggesting that these two different promoters function distinctively. HPLC analysis of the seeds and leaves of the T(2 generation plants revealed that the best line among the β-PAC transgenic seeds accumulated 146 µg/g of total carotenoids (approximately 62-fold higher than non-transgenic seeds, of which 112 µg/g (77% was β-carotene. In contrast, the level and composition of the leaf carotenoids showed little difference between transgenic and non-transgenic soybean plants. We have therefore demonstrated the production of a high β-carotene soybean through the seed-specific overexpression of two carotenoid biosynthetic genes, Capsicum phytoene synthase and Pantoea carotene desaturase. This nutritional enhancement of soybean seeds through the elevation of the provitamin A content to produce biofortified food may have practical health benefits in the future in both humans and livestock.

  18. sequenceMiner algorithm (United States)

    National Aeronautics and Space Administration — Detecting and describing anomalies in large repositories of discrete symbol sequences. sequenceMiner has been open-sourced! Download the file below to try it out....

  19. DNA sequencing conference, 2

    Energy Technology Data Exchange (ETDEWEB)

    Cook-Deegan, R.M. [Georgetown Univ., Kennedy Inst. of Ethics, Washington, DC (United States); Venter, J.C. [National Inst. of Neurological Disorders and Strokes, Bethesda, MD (United States); Gilbert, W. [Harvard Univ., Cambridge, MA (United States); Mulligan, J. [Stanford Univ., CA (United States); Mansfield, B.K. [Oak Ridge National Lab., TN (United States)


    This conference focused on DNA sequencing, genetic linkage mapping, physical mapping, informatics and bioethics. Several were used to study this sequencing and mapping. This article also discusses computer hardware and software aiding in the mapping of genes.

  20. Anomaly Detection in Sequences (United States)

    National Aeronautics and Space Administration — We present a set of novel algorithms which we call sequenceMiner, that detect and characterize anomalies in large sets of high-dimensional symbol sequences that...

  1. Roles of repetitive sequences

    Energy Technology Data Exchange (ETDEWEB)

    Bell, G.I.


    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  2. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.


    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.

  3. Production of 35S for a Liquid Semiconductor Betavoltaic

    Energy Technology Data Exchange (ETDEWEB)

    Meier, David E.; Garnov, A. Y.; Robertson, J. D.; Kwon, J. W.; Wacharasindhu, T.


    The specific energy density from radioactive decay is five to six orders of magnitude greater than the specific energy density in conventional chemical battery and fuel cell technologies. We are currently investigating the use of liquid semiconductor based betavoltaics as a way to directly convert the energy of radioactive decay into electrical power and potentially avoid the radiation damage that occurs in solid state semiconductor devices due to non-ionizing energy loss. Sulfur-35 was selected as the isotope for the liquid semiconductor demonstrations because it can be produced in high specific activity and it is chemically compatible with known liquid semiconductor media.

  4. Integration of retinal image sequences (United States)

    Ballerini, Lucia


    In this paper a method for noise reduction in ocular fundus image sequences is described. The eye is the only part of the human body where the capillary network can be observed along with the arterial and venous circulation using a non invasive technique. The study of the retinal vessels is very important both for the study of the local pathology (retinal disease) and for the large amount of information it offers on systematic haemodynamics, such as hypertension, arteriosclerosis, and diabetes. In this paper a method for image integration of ocular fundus image sequences is described. The procedure can be divided in two step: registration and fusion. First we describe an automatic alignment algorithm for registration of ocular fundus images. In order to enhance vessel structures, we used a spatially oriented bank of filters designed to match the properties of the objects of interest. To evaluate interframe misalignment we adopted a fast cross-correlation algorithm. The performances of the alignment method have been estimated by simulating shifts between image pairs and by using a cross-validation approach. Then we propose a temporal integration technique of image sequences so as to compute enhanced pictures of the overall capillary network. Image registration is combined with image enhancement by fusing subsequent frames of a same region. To evaluate the attainable results, the signal-to-noise ratio was estimated before and after integration. Experimental results on synthetic images of vessel-like structures with different kind of Gaussian additive noise as well as on real fundus images are reported.

  5. Low autocorrelation binary sequences (United States)

    Packebusch, Tom; Mertens, Stephan


    Binary sequences with minimal autocorrelations have applications in communication engineering, mathematics and computer science. In statistical physics they appear as groundstates of the Bernasconi model. Finding these sequences is a notoriously hard problem, that so far can be solved only by exhaustive search. We review recent algorithms and present a new algorithm that finds optimal sequences of length N in time O(N {1.73}N). We computed all optimal sequences for N≤slant 66 and all optimal skewsymmetric sequences for N≤slant 119.

  6. Repdigits in -Lucas Sequences

    Indian Academy of Sciences (India)

    Jhon J J Bravo; Florian Luca


    For an integer ≥ 2, let $(L_n^{(k)})_n$ be the -Lucas sequence which starts with $0,\\ldots,0,2,1$ ( terms) and each term afterwards is the sum of the preceding terms. In 2000, Luca (Port. Math. 57(2) 2000 243-254) proved that 11 is the largest number with only one distinct digit (the so-called repdigit) in the sequence $(L_n^{(2)})_n$. In this paper, we address a similar problem in the family of -Lucas sequences. We also show that the -Lucas sequences have similar properties to those of -Fibonacci sequences and occur in formulae simultaneously with the latter.

  7. On Maximal Green Sequences

    CERN Document Server

    Brüstle, Thomas; Pérotin, Matthieu


    Maximal green sequences are particular sequences of quiver mutations which were introduced by Keller in the context of quantum dilogarithm identities and independently by Cecotti-Cordova-Vafa in the context of supersymmetric gauge theory. Our aim is to initiate a systematic study of these sequences from a combinatorial point of view. Interpreting maximal green sequences as paths in various natural posets arising in representation theory, we prove the finiteness of the number of maximal green sequences for cluster finite quivers, affine quivers and acyclic quivers with at most three vertices. We also give results concerning the possible numbers and lengths of these maximal green sequences. Finally we describe an algorithm for computing maximal green sequences for arbitrary valued quivers which we used to obtain numerous explicit examples that we present.

  8. Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features. (United States)

    Yáñez-Cuna, J Omar; Arnold, Cosmas D; Stampfel, Gerald; Boryń, Lukasz M; Gerlach, Daniel; Rath, Martina; Stark, Alexander


    Gene expression is determined by genomic elements called enhancers, which contain short motifs bound by different transcription factors (TFs). However, how enhancer sequences and TF motifs relate to enhancer activity is unknown, and general sequence requirements for enhancers or comprehensive sets of important enhancer sequence elements have remained elusive. Here, we computationally dissect thousands of functional enhancer sequences from three different Drosophila cell lines. We find that the enhancers display distinct cis-regulatory sequence signatures, which are predictive of the enhancers' cell type-specific or broad activities. These signatures contain transcription factor motifs and a novel class of enhancer sequence elements, dinucleotide repeat motifs (DRMs). DRMs are highly enriched in enhancers, particularly in enhancers that are broadly active across different cell types. We experimentally validate the importance of the identified TF motifs and DRMs for enhancer function and show that they can be sufficient to create an active enhancer de novo from a nonfunctional sequence. The function of DRMs as a novel class of general enhancer features that are also enriched in human regulatory regions might explain their implication in several diseases and provides important insights into gene regulation.

  9. Transcriptional enhancer from milk protein genes

    Energy Technology Data Exchange (ETDEWEB)

    Casperson, Gerald F. (Ballwin, MO); Schmidhauser, Christian T. (Berkeley, CA); Bissell, Mina J. (Berkeley, CA)


    The invention relates to novel enhancer nucleotide sequences which stimulate transcription of heterologous DNA in cells in culture. The enhancers are derived from major milk protein genes by the process of deletion mapping and functional analysis. The invention also relates to expression vectors containing the novel enhancers.

  10. Transcriptional enhancer from milk protein genes

    Energy Technology Data Exchange (ETDEWEB)

    Casperson, G.F.; Schmidhauser, C.T.; Bissell, M.J.


    The invention relates to novel enhancer nucleotide sequences which stimulate transcription of heterologous DNA in cells in culture. The enhancers are derived from major milk protein genes by the process of deletion mapping and functional analysis. The invention also relates to expression vectors containing the novel enhancers.

  11. Whole Genome Sequencing of Newly Established Pancreatic Cancer Lines Identifies Novel Somatic Mutation (c.2587G>A in Axon Guidance Receptor Plexin A1 as Enhancer of Proliferation and Invasion.

    Directory of Open Access Journals (Sweden)

    Rebecca Sorber

    Full Text Available The genetic profile of human pancreatic cancers harbors considerable heterogeneity, which suggests a possible explanation for the pronounced inefficacy of single therapies in this disease. This observation has led to a belief that custom therapies based on individual tumor profiles are necessary to more effectively treat pancreatic cancer. It has recently been discovered that axon guidance genes are affected by somatic structural variants in up to 25% of human pancreatic cancers. Thus far, however, some of these mutations have only been correlated to survival probability and no function has been assigned to these observed axon guidance gene mutations in pancreatic cancer. In this study we established three novel pancreatic cancer cell lines and performed whole genome sequencing to discover novel mutations in axon guidance genes that may contribute to the cancer phenotype of these cells. We discovered, among other novel somatic variants in axon guidance pathway genes, a novel mutation in the PLXNA1 receptor (c.2587G>A in newly established cell line SB.06 that mediates oncogenic cues of increased invasion and proliferation in SB.06 cells and increased invasion in 293T cells upon stimulation with the receptor's natural ligand semaphorin 3A compared to wild type PLXNA1 cells. Mutant PLXNA1 signaling was associated with increased Rho-GTPase and p42/p44 MAPK signaling activity and cytoskeletal expansion, but not changes in E-cadherin, vimentin, or metalloproteinase 9 expression levels. Pharmacologic inhibition of the Rho-GTPase family member CDC42 selectively abrogated PLXNA1 c.2587G>A-mediated increased invasion. These findings provide in-vitro confirmation that somatic mutations in axon guidance genes can provide oncogenic gain-of-function signals and may contribute to pancreatic cancer progression.

  12. Cosmetology: Scope and Sequence. (United States)

    Nashville - Davidson County Metropolitan Public Schools, TN.

    This scope and sequence guide, developed for a cosmetology vocational education program, represents an initial step in the development of a systemwide articulated curriculum sequence for all vocational programs within the Metropolitan Nashville Public School System. It was developed as a result of needs expressed by teachers, parents, and the…

  13. DNA sequencing by CE. (United States)

    Karger, Barry L; Guttman, András


    Sequencing of human and other genomes has been at the center of interest in the biomedical field over the past several decades and is now leading toward an era of personalized medicine. During this time, DNA-sequencing methods have evolved from the labor-intensive slab gel electrophoresis, through automated multiCE systems using fluorophore labeling with multispectral imaging, to the "next-generation" technologies of cyclic-array, hybridization based, nanopore and single molecule sequencing. Deciphering the genetic blueprint and follow-up confirmatory sequencing of Homo sapiens and other genomes were only possible with the advent of modern sequencing technologies that were a result of step-by-step advances with a contribution of academics, medical personnel and instrument companies. While next-generation sequencing is moving ahead at breakneck speed, the multicapillary electrophoretic systems played an essential role in the sequencing of the Human Genome, the foundation of the field of genomics. In this prospective, we wish to overview the role of CE in DNA sequencing based in part of several of our articles in this journal.

  14. Hardware bitstream sequence recognizer


    Karpin, Oleksandr; Sokil, Volodymyr


    This paper describes how to implement in hardware a bistream sequence recognizer using the PSoC Pseudo Random Sequence Generator (PRS) User Module. The PRS can be used in digital communication systems with the serial data interface for automatic preamble detection and extraction, control words selection, etc.

  15. Sequence Classification: 770169 [

    Lifescience Database Archive (English)

    Full Text Available Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|17555348|ref|NP_499459.1| presenili...n ENhancer (enhancer of sel-12 null) PEN-2, presenilin enhancer (pen-2) || ...

  16. Sequencing the maize genome. (United States)

    Martienssen, Robert A; Rabinowicz, Pablo D; O'Shaughnessy, Andrew; McCombie, W Richard


    Sequencing of complex genomes can be accomplished by enriching shotgun libraries for genes. In maize, gene-enrichment by copy-number normalization (high C(0)t) and methylation filtration (MF) have been used to generate up to two-fold coverage of the gene-space with less than 1 million sequencing reads. Simulations using sequenced bacterial artificial chromosome (BAC) clones predict that 5x coverage of gene-rich regions, accompanied by less than 1x coverage of subclones from BAC contigs, will generate high-quality mapped sequence that meets the needs of geneticists while accommodating unusually high levels of structural polymorphism. By sequencing several inbred strains, we propose a strategy for capturing this polymorphism to investigate hybrid vigor or heterosis.

  17. Fungal genome sequencing: basic biology to biotechnology. (United States)

    Sharma, Krishna Kant


    The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.

  18. Only correlated sequences that are actively processed contribute to implicit sequence learning. (United States)

    Meier, Beat; Weiermann, Brigitte; Cock, Josephine


    The purpose of the study was to investigate how implicit sequence learning is affected by the presence of secondary information that is correlated with the primary sequence but not necessarily relevant to performance. In a previous work, we have shown that correlation plays an important role but other prerequisites may also be involved. In Experiments 1 and 2, using a task sequence learning paradigm, we found that primary sequence learning was not affected by secondary information that was sequenced but irrelevant to performance, even though the two streams of information were correlated. In contrast, in Experiment 3, we found that sensitivity to the main sequence was greater with the provision of extra sequenced information that was relevant to performance in addition to being correlated. This suggests that sequence learning was enhanced through the integration of information. We conclude that information in secondary as well as primary sequences must be actively processed if it is to have a beneficial impact. By actively processed we mean information that is selectively attended and necessary for carrying out the tasks.

  19. RIKEN Integrated Sequence Analysis (RISA) System—384-Format Sequencing Pipeline with 384 Multicapillary Sequencer


    Shibata, Kazuhiro; Itoh, Masayoshi; Aizawa, Katsunori; Nagaoka, Sumiharu; Sasaki, Nobuya; Carninci, Piero; Konno, Hideaki; AKIYAMA, Junichi; Nishi, Katsuo; Kitsunai, Tokuji; Tashiro, Hideo; Itoh, Mari; Sumi, Noriko; Ishii, Yoshiyuki; Nakamura, Shin


    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto seque...

  20. Engineering an enhanced, thermostable, monomeric bacterial luciferase gene as a reporter in plant protoplasts. (United States)

    Cui, Boyu; Zhang, Lifeng; Song, Yunhong; Wei, Jinsong; Li, Changfu; Wang, Tietao; Wang, Yao; Zhao, Tianyong; Shen, Xihui


    The application of the luxCDABE operon of the bioluminescent bacterium Photorhabdus luminescens as a reporter has been published for bacteria, yeast and mammalian cells. We report here the optimization of fused luxAB (the bacterial luciferase heterodimeric enzyme) expression, quantum yield and its application as a reporter gene in plant protoplasts. The fused luxAB gene was mutated by error prone PCR or chemical mutagenesis and screened for enhanced luciferase activity utilizing decanal as substrate. Positive luxAB mutants with superior quantum yield were subsequently shuffled by DNase I digestion and PCR assembly for generation of recombinants with additional increases in luciferase activity in bacteria. The coding sequence of the best recombinant, called eluxAB, was then optimized further to conform to Arabidopsis (Arabidopsis thaliana) codon usage. A plant expression vector of the final, optimized eluxAB gene (opt-eluxAB) was constructed and transformed into protoplasts of Arabidopsis and maize (Zea mays). Luciferase activity was dramatically increased for opt-eluxAB compared to the original luxAB in Arabidopsis and maize cells. The opt-eluxAB driven by two copies of the 35S promoter expresses significantly higher than that driven by a single copy. These results indicate that the eluxAB gene can be used as a reporter in plant protoplasts. To our knowledge, this is the first report to engineer the bacterium Photorhabdus luminescens luciferase luxAB as a reporter by directed evolution which paved the way for further improving the luxAB reporter in the future.

  1. The"minimum information about an environmental sequence" (MIENS) specification

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, P.; Kottmann, R.; Field, D.; Knight, R.; Cole, J.R.; Amaral-Zettler, L.; Gilbert, J.A.; Karsch-Mizrachi, I.; Johnston, A.; Cochrane, G.; Vaughan, R.; Hunter, C.; Park, J.; Morrison, N.; Rocca-Serra, P.; Sterk, P.; Arumugam, M.; Baumgartner, L.; Birren, B.W.; Blaser, M.J.; Bonazzi, V.; Bork, P.; Buttigieg, P. L.; Chain, P.; Costello, E.K.; Huot-Creasy, H.; Dawyndt, P.; DeSantis, T.; Fierer, N.; Fuhrman, J.; Gallery, R.E.; Gibbs, R.A.; Giglio, M.G.; Gil, I. San; Gonzalez, A.; Gordon, J.I.; Guralnick, R.; Hankeln, W.; Highlander, S.; Hugenholtz, P.; Jansson, J.; Kennedy, J.; Knights, D.; Koren, O.; Kuczynski, J.; Kyrpides, N.; Larsen, R.; Lauber, C.L.; Legg, T.; Ley, R.E.; Lozupone, C.A.; Ludwig, W.; Lyons, D.; Maguire, E.; Methe, B.A.; Meyer, F.; Nakieny, S.; Nelson, K.E.; Nemergut, D.; Neufeld, J.D.; Pace, N.R.; Palanisamy, G.; Peplies, J.; Peterson, J.; Petrosino, J.; Proctor, L.; Raes, J.; Ratnasingham, S.; Ravel, J.; Relman, D.A.; Assunta-Sansone, S.; Schriml, L.; Sodergren, E.; Spor, A.; Stombaugh, J.; Tiedje, J.M.; Ward, D.V.; Weinstock, G.M.; Wendel, D.; White, O.; Wikle, A.; Wortman, J.R.; Glockner, F.O.; Bushman, F.D.; Charlson, E.; Gevers, D.; Kelley, S.T.; Neubold, L.K.; Oliver, A.E.; Pruesse, E.; Quast, C.; Schloss, P.D.; Sinha, R.; Whitely, A.


    We present the Genomic Standards Consortium's (GSC) 'Minimum Information about an ENvironmental Sequence' (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

  2. Single-Spin Magnetometry with Multipulse Sensing Sequences

    NARCIS (Netherlands)

    De Lange, G.; Ristè, D.; Dobrovitski, V.V.; Hanson, R.


    We experimentally demonstrate single-spin magnetometry with multipulse sensing sequences. The use of multipulse sequences can greatly increase the sensing time per measurement shot, resulting in enhanced ac magnetic field sensitivity. We theoretically derive and experimentally verify the optimal num

  3. HIV Sequence Compendium 2015

    Energy Technology Data Exchange (ETDEWEB)

    Foley, Brian Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas Kenneth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Cristian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Pennsylvania, Philadelphia, PA (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette Tina Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    This compendium is an annual printed summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2015. Hence, though it is published in 2015 and called the 2015 Compendium, its contents correspond to the 2014 curated alignments on our website. The number of sequences in the HIV database is still increasing. In total, at the end of 2014, there were 624,121 sequences in the HIV Sequence Database, an increase of 7% since the previous year. This is the first year that the number of new sequences added to the database has decreased compared to the previous year. The number of near complete genomes (>7000 nucleotides) increased to 5834 by end of 2014. However, as in previous years, the compendium alignments contain only a fraction of these. A more complete version of all alignments is available on our website, content/sequence/NEWALIGN/align.html As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to

  4. Phylogenetic Trees From Sequences (United States)

    Ryvkin, Paul; Wang, Li-San

    In this chapter, we review important concepts and approaches for phylogeny reconstruction from sequence data.We first cover some basic definitions and properties of phylogenetics, and briefly explain how scientists model sequence evolution and measure sequence divergence. We then discuss three major approaches for phylogenetic reconstruction: distance-based phylogenetic reconstruction, maximum parsimony, and maximum likelihood. In the third part of the chapter, we review how multiple phylogenies are compared by consensus methods and how to assess confidence using bootstrapping. At the end of the chapter are two sections that list popular software packages and additional reading.

  5. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold


    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  6. In Favor of Sequencing?

    NARCIS (Netherlands)

    van der Borgh, G.J.C.


    This short article is a contribution to an online discussion about political sequencing and stability. It argues that despite all the risks of democratization in fragile states,a more gradual approach should be preferred.

  7. Scope and Sequence. (United States)

    Callison, Daniel


    Discusses scope and sequence plans for curriculum coordination in elementary and secondary education related to school libraries. Highlights include library skills; levels of learning objectives; technology skills; media literacy skills; and information inquiry skills across disciplines by grade level. (LRW)

  8. Pierre Robin sequence (United States)

    Pierre Robin syndrome; Pierre Robin complex; Pierre Robin anomaly ... The exact causes of Pierre Robin sequence are unknown. It may be part of many genetic syndromes. The lower jaw develops slowly before birth, but may grow ...

  9. HIV Sequence Compendium 2010

    Energy Technology Data Exchange (ETDEWEB)

    Kuiken, Carla [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Foley, Brian [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Leitner, Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Apetrei, Christian [Univ. of Pittsburgh, PA (United States); Hahn, Beatrice [Univ. of Alabama, Tuscaloosa, AL (United States); Mizrachi, Ilene [National Center for Biotechnology Information, Bethesda, MD (United States); Mullins, James [Univ. of Washington, Seattle, WA (United States); Rambaut, Andrew [Univ. of Edinburgh, Scotland (United Kingdom); Wolinsky, Steven [Northwestern Univ., Evanston, IL (United States); Korber, Bette [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)


    This compendium is an annual printed summary of the data contained in the HIV sequence database. In these compendia we try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus. This compendium contains sequences published before January 1, 2010. Hence, though it is called the 2010 Compendium, its contents correspond to the 2009 curated alignments on our website. The number of sequences in the HIV database is still increasing exponentially. In total, at the time of printing, there were 339,306 sequences in the HIV Sequence Database, an increase of 45% since last year. The number of near complete genomes (>7000 nucleotides) increased to 2576 by end of 2009, reflecting a smaller increase than in previous years. However, as in previous years, the compendium alignments contain only a small fraction of these. Included in the alignments are a small number of sequences representing each of the subtypes and the more prevalent circulating recombinant forms (CRFs) such as 01 and 02, as well as a few outgroup sequences (group O and N and SIV-CPZ). Of the rarer CRFs we included one representative each. A more complete version of all alignments is available on our website, Reprints are available from our website in the form of both HTML and PDF files. As always, we are open to complaints and suggestions for improvement. Inquiries and comments regarding the compendium should be addressed to

  10. Biological sequence analysis

    DEFF Research Database (Denmark)

    Durbin, Richard; Eddy, Sean; Krogh, Anders Stærmose

    This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis, and phylogene......This book provides an up-to-date and tutorial-level overview of sequence analysis methods, with particular emphasis on probabilistic modelling. Discussed methods include pairwise alignment, hidden Markov models, multiple alignment, profile searches, RNA secondary structure analysis...

  11. Text Mining: (Asynchronous Sequences

    Directory of Open Access Journals (Sweden)

    Sheema Khan


    Full Text Available In this paper we tried to correlate text sequences those provides common topics for semantic clues. We propose a two step method for asynchronous text mining. Step one check for the common topics in the sequences and isolates these with their timestamps. Step two takes the topic and tries to give the timestamp of the text document. After multiple repetitions of step two, we could give optimum result.

  12. Gene and translation initiation site prediction in metagenomic sequences

    Energy Technology Data Exchange (ETDEWEB)

    Hyatt, Philip Douglas [ORNL; LoCascio, Philip F [ORNL; Hauser, Loren John [ORNL; Uberbacher, Edward C [ORNL


    Gene prediction in metagenomic sequences remains a difficult problem. Current sequencing technologies do not achieve sufficient coverage to assemble the individual genomes in a typical sample; consequently, sequencing runs produce a large number of short sequences whose exact origin is unknown. Since these sequences are usually smaller than the average length of a gene, algorithms must make predictions based on very little data. We present MetaProdigal, a metagenomic version of the gene prediction program Prodigal, that can identify genes in short, anonymous coding sequences with a high degree of accuracy. The novel value of the method consists of enhanced translation initiation site identification, ability to identify sequences that use alternate genetic codes and confidence values for each gene call. We compare the results of MetaProdigal with other methods and conclude with a discussion of future improvements.

  13. Next-generation sequencing strategies for characterizing the turkey genome. (United States)

    Dalloul, Rami A; Zimin, Aleksey V; Settlage, Robert E; Kim, Sungwon; Reed, Kent M


    The turkey genome sequencing project was initiated in 2008 and has relied primarily on next-generation sequencing (NGS) technologies. Our first efforts used a synergistic combination of 2 NGS platforms (Roche/454 and Illumina GAII), detailed bacterial artificial chromosome (BAC) maps, and unique assembly tools to sequence and assemble the genome of the domesticated turkey, Meleagris gallopavo. Since the first release in 2010, efforts to improve the genome assembly, gene annotation, and genomic analyses continue. The initial assembly build (2.01) represented about 89% of the genome sequence with 17X coverage depth (931 Mb). Sequence contigs were assigned to 30 of the 40 chromosomes with approximately 10% of the assembled sequence corresponding to unassigned chromosomes (ChrUn). The sequence has been refined through both genome-wide and area-focused sequencing, including shotgun and paired-end sequencing, and targeted sequencing of chromosomal regions with low or incomplete coverage. These additional efforts have improved the sequence assembly resulting in 2 subsequent genome builds of higher genome coverage (25X/Build3.0 and 30X/Build4.0) with a current sequence totaling 1,010 Mb. Further, BAC with end sequences assigned to the Z/W and MG18 (MHC) chromosomes, ChrUn, or not placed in the previous build were isolated, deeply sequenced (Hi-Seq), and incorporated into the latest build (5.0). To aid in the annotation and to generate a gene expression atlas of major tissues, a comprehensive set of RNA samples was collected at various developmental stages of female and male turkeys. Transcriptome sequencing data (using Illumina Hi-Seq) will provide information to enhance the final assembly and ultimately improve sequence annotation. The most current sequence covers more than 95% of the turkey genome and should yield a much improved gene level of annotation, making it a valuable resource for studying genetic variations underlying economically important traits in poultry.

  14. GATA: a graphic alignment tool for comparative sequence analysis

    Directory of Open Access Journals (Sweden)

    Nix David A


    Full Text Available Abstract Background Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dot plot analysis is often used to estimate non-coding sequence relatedness. Yet dot plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments. Results To address some of these issues, we created a stand alone, platform independent, graphic alignment tool for comparative sequence analysis (GATA GATA uses the NCBI-BLASTN program and extensive post-processing to identify all small sub-alignments above a low cut-off score. These are graphed as two shaded boxes, one for each sequence, connected by a line using the coordinate system of their parent sequence. Shading and colour are used to indicate score and orientation. A variety of options exist for querying, modifying and retrieving conserved sequence elements. Extensive gene annotation can be added to both sequences using a standardized General Feature Format (GFF file. Conclusions GATA uses the NCBI-BLASTN program in conjunction with post-processing to exhaustively align two DNA

  15. Adaptive Processing for Sequence Alignment

    KAUST Repository

    Zidan, Mohammed Affan


    Disclosed are various embodiments for adaptive processing for sequence alignment. In one embodiment, among others, a method includes obtaining a query sequence and a plurality of database sequences. A first portion of the plurality of database sequences is distributed to a central processing unit (CPU) and a second portion of the plurality of database sequences is distributed to a graphical processing unit (GPU) based upon a predetermined splitting ratio associated with the plurality of database sequences, where the database sequences of the first portion are shorter than the database sequences of the second portion. A first alignment score for the query sequence is determined with the CPU based upon the first portion of the plurality of database sequences and a second alignment score for the query sequence is determined with the GPU based upon the second portion of the plurality of database sequences.

  16. Propeller liver acquisition with volume acceleration sequence in diagnosis of small enhancing nodular of chronic liver disease in arterial phase with contrast-enhanced dynamic MRI%Propeller肝脏三维容积内插快速序列诊断慢性肝病动脉期强化小结节

    Institute of Scientific and Technical Information of China (English)

    秦海燕; 王丹; 刘芳; 曹绍东; 薛美娜; 申宝忠; 方芳; 韩东; 刘学佳


    目的 评价Propeller LAVA序列MR动态增强对慢性肝病背景下动脉期强化小结节(≤3.0 cm)的诊断价值.方法 回顾分析132例经组织学和(或)临床实验室检查证实的慢性肝病者Propeller LAVA增强检查资料,观察动脉期强化小结节的血供特点、强化规律及程度.结果 所有患者中,89例153个结节(0.5~3.0 cm)符合本组纳入要求,其中<2.0 cm圆形或卵圆形结节62个,≥2.0 cm 55个,其他形状36个.90个肝细胞癌结节中,与邻近肝实质比较,62个在门静脉期和延迟期表现为低信号结节,21个略低于邻近肝实质,7个信号强度近似于邻近肝实质.肝血管瘤20个,15个T2WI信号强度类似于脑脊液,5个略低于脑脊液;动脉期10个边缘结节状强化,8个均匀强化,2个周边见楔状高信号;门静脉期和延迟期均表现为稍高于或等于邻近肝实质的强化结节.动脉门静脉分流40个,动脉期位于肝脏中心或周边部分的卵圆形、楔形或三角形强化影,随时间延迟与邻近肝实质信号强度一致.局灶结节增生3个,动脉期强化程度近似于同层面腹主动脉,门静脉期和延迟期与邻近肝实质信号强度近似.结论 Propeller LAVA序列可准确显示慢性肝病患者动脉期强化小结节的血供特点、形态、边缘及其组织学性质.%Objective To evaluate Propeller liver acquisition with volume acceleration(LAVA) dynamic enhanced MR in diagnosing small enhancing nodular of chronic liver disease. Methods Propeller LAVA examination data of 132 patients with chronic hepatic disease confirmed by histological and (or) laboratory were analyzed retrospectively. The features of small enhancing nodular, including blood supplying, contrast enhanced regulation and degree and lesions were observed.Results Totally 89 cases (153 nodulars 0. 5-3. 0 cm) were included, 117 (62 nodulars<2.0 cm and 55 nodulars≥2.0 cm) nodulars were round or oval, 36 were other shape. Compared with adjacent

  17. Controlled processing during sequencing

    Directory of Open Access Journals (Sweden)

    Malathi eThothathiri


    Full Text Available Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6 in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex (ACC. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region’s activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  18. Controlled processing during sequencing. (United States)

    Thothathiri, Malathi; Rattinger, Michelle


    Longstanding evidence has identified a role for the frontal cortex in sequencing within both linguistic and non-linguistic domains. More recently, neuropsychological studies have suggested a specific role for the left premotor-prefrontal junction (BA 44/6) in selection between competing alternatives during sequencing. In this study, we used neuroimaging with healthy adults to confirm and extend knowledge about the neural correlates of sequencing. Participants reproduced visually presented sequences of syllables and words using manual button presses. Items in the sequence were presented either consecutively or concurrently. Concurrent presentation is known to trigger the planning of multiple responses, which might compete with one another. Therefore, we hypothesized that regions involved in controlled processing would show greater recruitment during the concurrent than the consecutive condition. Whole-brain analysis showed concurrent > consecutive activation in sensory, motor and somatosensory cortices and notably also in rostral-dorsal anterior cingulate cortex. Region of interest analyses showed increased activation within left BA 44/6 and correlation between this region's activation and behavioral response times. Functional connectivity analysis revealed increased connectivity between left BA 44/6 and the posterior lobe of the cerebellum during the concurrent than the consecutive condition. These results corroborate recent evidence and demonstrate the involvement of BA 44/6 and other control regions when ordering co-activated representations.

  19. 肝硬化患者肝门静脉三维对比增强磁共振成像--THRIVE_BH序列与CE_MRA_ABD序列应用比较%Three-dimensional contrast-enhanced MRI of portal vein in cirrhosis-comparison of THRIVE_BH and CE_MRA_ABD sequences

    Institute of Scientific and Technical Information of China (English)

    周围; 胡秋根; 岑玉坚; 陆涛


      目的探讨磁共振肝脏动态增强与肝门静脉三维成像一站式检查代替单纯三维对比增强腹部血管成像检查评估肝门静脉的可能性和可靠性,为“一站式检查”的序列设计提供参考依据。方法选择100例病历资料完整、临床确诊肝硬化的住院患者,其中50例行应用THRIVE_BH序列的磁共振肝脏动态增强与肝门静脉三维成像一站式检查,为A组;另外50例行应用CE_MRA_ABD序列的单纯的三维对比增强腹部血管成像检查,为B组。对两组肝门静脉图像分别进行单盲分析并评分,结果使用SPSS 13.0软件进行统计分析。结果肝门静脉的肝外部分:A组肠系膜下静脉干显示率低于B组(P<0.05);肝门静脉的肝内部分:A、B组间无统计学差异(P>0.05)。结论应用THRIVE_BH序列的磁共振肝脏动态增强与肝门静脉三维成像一站式检查替代应用CE_MRA_ABD序列的单纯的三维对比增强腹部血管成像检查评估肝门静脉是可行的,可作为肝硬化患者随访的重要手段。%  Objective To compare 3-D contrast-enhanced abdominal MR angiography(MRA)with dynamic contrast-enhanced MRI and 3-D MRI of portal vein.Methods One hundred in-patients with clinical diagnosis of cirrhosis and complete medical records were divided randomly into two groups of 50 patients. One group underwent one-stop MRI including dynamic contrast-enhanced MRI and 3-D MRI of the portal vein using the THRIVE_BH sequence.The other group underwent 3-D contrast-enhanced abdominal MRA.The image quality of the portal vein using the two methods was compared.Results The inferior mesenteric venous branch of the extra-hepatic portal vein was less well seen on dynamic contrast-enhanced and 3-D THRIVE_BH MRI than 3-D contrast-enhanced MRA(P0.05).Conclusions One-stop examination including dynamic contrast-enhanced and 3-D THRIVE_BH MRI of portal vein can be useful for monitoring cirrhosis.

  20. Two genome sequences of the same bacterial strain, Gluconacetobacter diazotrophicus PAl 5, suggest a new standard in genome sequence submission. (United States)

    Giongo, Adriana; Tyler, Heather L; Zipperer, Ursula N; Triplett, Eric W


    Gluconacetobacter diazotrophicus PAl 5 is of agricultural significance due to its ability to provide fixed nitrogen to plants. Consequently, its genome sequence has been eagerly anticipated to enhance understanding of endophytic nitrogen fixation. Two groups have sequenced the PAl 5 genome from the same source (ATCC 49037), though the resulting sequences contain a surprisingly high number of differences. Therefore, an optical map of PAl 5 was constructed in order to determine which genome assembly more closely resembles the chromosomal DNA by aligning each sequence against a physical map of the genome. While one sequence aligned very well, over 98% of the second sequence contained numerous rearrangements. The many differences observed between these two genome sequences could be owing to either assembly errors or rapid evolutionary divergence. The extent of the differences derived from sequence assembly errors could be assessed if the raw sequencing reads were provided by both genome centers at the time of genome sequence submission. Hence, a new genome sequence standard is proposed whereby the investigator supplies the raw reads along with the closed sequence so that the community can make more accurate judgments on whether differences observed in a single stain may be of biological origin or are simply caused by differences in genome assembly procedures.

  1. Program Synthesizes UML Sequence Diagrams (United States)

    Barry, Matthew R.; Osborne, Richard N.


    A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

  2. Tip enhancement

    CERN Document Server

    Kawata, Satoshi


    This book discusses the recent advances in the area of near-field Raman scattering, mainly focusing on tip-enhanced and surface-enhanced Raman scattering. Some of the key features covered here are the optical structuring and manipulations, single molecule sensitivity, analysis of single-walled carbon nanotubes, and analytic applications in chemistry, biology and material sciences. This book also discusses the plasmonic materials for better enhancement, and optical antennas. Further, near-field microscopy based on second harmonic generation is also discussed. Chapters have been written by some of the leading scientists in this field, who present some of their recent work in this field.·Near-field Raman scattering·Tip-enhanced Raman spectroscopy·Surface-enhanced Raman spectroscopy·Nano-photonics·Nanoanalysis of Physical, chemical and biological materials beyond the diffraction limits·Single molecule detection

  3. Sequencing BPS Spectra

    CERN Document Server

    Gukov, Sergei; Saberi, Ingmar; Stosic, Marko; Sulkowski, Piotr


    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincar\\'e polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular $S$-matrix. This leads to the identifi...

  4. The 16 April 2015 M w 6.0 offshore eastern Crete earthquake and its aftershock sequence: implications for local/regional seismotectonics (United States)

    Görgün, Ethem; Kekovalı, Kıvanç; Kalafat, Doğan


    We examine the 16 April 2015 M w 6.0 offshore eastern Crete earthquake and its aftershock sequence in southern Aegean Sea. Centroid moment tensors for 45 earthquakes with moment magnitudes (M w) between 3.3 and 6.0 are determined by applying a waveform inversion method. The mainshock is shallow focus thrust event with a strike-slip component at a depth of 30 km. The seismic moment (M o) of the mainshock is estimated as 1.33 × 1018 Nm, and rupture duration of the mainshock is 3.5 s. The focal mechanisms of aftershocks are mainly thrust faulting with a strike-slip component. The geometry of the moment tensors (M w ≥ 3.3) reveals a thrust-faulting regime with NE-SW-trending direction of T axis in the entire activated region. According to high-resolution hypocenter relocation of the eastern Crete earthquake sequence, one main cluster consisting of 352 events is revealed. The aftershock activity in the observation period between 5 January 2015 and 7 July 2015 extends from N to S direction. Seismic cross sections indicate a complex pattern of the hypocenter distribution with the activation of three segments. The subduction interface is clearly revealed with high-resolution hypocenter relocation and moment tensor solution. The best constrained focal depths indicate that the aftershock sequence is mainly confined in the upper plate (depth <40 km) and are ranging from about 4.5 to 39 km depth. A stress tensor inversion of focal mechanism data is performed to obtain a more precise picture of the offshore eastern Crete stress field. The stress tensor inversion results indicate a predominant thrust stress regime with a NW-SE-oriented maximum horizontal compressive stress (S H). According to variance of the stress tensor inversion, to first order, the Crete region is characterized by a homogeneous interplate stress field. We also investigate the Coulomb stress change associated with the mainshock to evaluate any significant enhancement of stresses along Crete and surrounding

  5. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    DEFF Research Database (Denmark)

    Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn


    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environmental...... present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere....

  6. Sequence Classification: 893726 [

    Lifescience Database Archive (English)

    Full Text Available se, responsible for arginine degradation, expression responds to both induction by arginine and nitrogen catabolite repression; disru...ption enhances freeze tolerance; Car1p || ...

  7. Sequence Classification: 774115 [

    Lifescience Database Archive (English)

    Full Text Available phila Enhancer of zeste/polycombeotic homolog essential for viability of the germline, Maternal Effect Sterile MES-2 (88.7 kD) (mes-2) || ...

  8. Twin anemia polycythemia sequence

    NARCIS (Netherlands)

    Slaghekke, Femke


    In this thesis we describe that Twin Anemia Polycythemia Sequence (TAPS) is a form of chronic feto-fetal transfusion in monochorionic (identical) twins based on a small amount of blood transfusion through very small anastomoses. For the antenatal diagnosis of TAPS, Middle Cerebral Artery – Peak Syst

  9. Family Sequencing and Cooperation

    NARCIS (Netherlands)

    Grundel, S.; Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.


    To analyze the allocation problem of the maximal cost savings of the whole group of jobs, we define and analyze a so-called corresponding cooperative family sequencing game which explicitly takes into account the maximal cost savings for any coalition of jobs. Using nonstandard techniques we prove t

  10. Image encryption using random sequence generated from generalized information domain (United States)

    Xia-Yan, Zhang; Guo-Ji, Zhang; Xuan, Li; Ya-Zhou, Ren; Jie-Hua, Wu


    A novel image encryption method based on the random sequence generated from the generalized information domain and permutation-diffusion architecture is proposed. The random sequence is generated by reconstruction from the generalized information file and discrete trajectory extraction from the data stream. The trajectory address sequence is used to generate a P-box to shuffle the plain image while random sequences are treated as keystreams. A new factor called drift factor is employed to accelerate and enhance the performance of the random sequence generator. An initial value is introduced to make the encryption method an approximately one-time pad. Experimental results show that the random sequences pass the NIST statistical test with a high ratio and extensive analysis demonstrates that the new encryption scheme has superior security.

  11. Role of intron-mediated enhancement on accumulation of an Arabidopsis NB-LRR class R-protein that confers resistance to Cucumber mosaic virus.

    Directory of Open Access Journals (Sweden)

    Yukiyo Sato

    Full Text Available The accumulation of RCY1 protein, which is encoded by RESISTANCE TO CMV(Y (RCY1, a CC-NB-LRR class R-gene, is tightly correlated with the strength of the resistance to a yellow strain of Cucumber mosaic virus [CMV(Y] in Arabidopsis thaliana. In order to enhance resistance to CMV by overexpression of RCY1, A. thaliana was transformed with intron-less RCY1 cDNA construct under the control of strong CaMV35S promoter. Remarkably, a relative amount of RCY1 protein accumulation in the transformants was much lower than that in plants expressing genomic RCY1 under the control of its native promoter. To identify a regulatory element of RCY1 that could cause such differential levels of RCY1 accumulation, a series of RCY1 cDNA and genomic RCY1 constructs were transiently expressed in Nicotiana benthamiana leaves by the Agrobacterium-mediated infiltration method. Comparative analysis of the level of RCY1 accumulation in the leaf tissues transiently expressing each construct indicated that the intron located in the RCY1-coding region of genomic RCY1, but not the native RCY1 genomic promoter or the 5'-and 3'-untranslated regions of RCY1, was indispensable for high level RCY1 accumulation. The increased levels of RCY1 accelerated plant disease defense reactions. Interestingly, such intron-mediated enhancement of RCY1 accumulation depended neither on the abundance of the RCY1 transcript nor on the RCY1 specific-intron sequence. Taken together, intron-mediated RCY1 expression seems to play a key role in the expression of complete resistance to CMV(Y by maintaining RCY1 accumulation at high levels.

  12. What are super-enhancers? (United States)

    Pott, Sebastian; Lieb, Jason D


    The term 'super-enhancer' has been used to describe groups of putative enhancers in close genomic proximity with unusually high levels of Mediator binding, as measured by chromatin immunoprecipitation and sequencing (ChIP-seq). Here we review the identification and composition of super-enhancers, describe links between super-enhancers, gene regulation and disease, and discuss the functional significance of enhancer clustering. We also provide our perspective regarding the proposition that super-enhancers are a regulatory entity conceptually distinct from what was known before the introduction of the term. Our opinion is that there is not yet strong evidence that super-enhancers are a novel paradigm in gene regulation and that use of the term in this context is not currently justified. However, the term likely identifies strong enhancers that exhibit behaviors consistent with previous models and concepts of transcriptional regulation. In this respect, the super-enhancer definition is useful in identifying regulatory elements likely to control genes important for cell type specification.

  13. Chromatin domains and prediction of MAR sequences. (United States)

    Boulikas, T


    Polynuceosomes are constrained into loops or domains and are insulated from the effects of chromatin structure and torsional strain from flanking domains by the cross-complexation of matrix-attached regions (MARs) and matrix proteins. MARs or SARs have an average size of 500 bp, are spaced about every 30 kb, and are control elements maintaining independent realms of gene activity. A fraction of MARs may cohabit with core origin replication (ORIs) and another fraction might cohabit with transcriptional enhancers. DNA replication, transcription, repair, splicing, and recombination seem to take place on the nuclear matrix. Classical AT-rich MARs have been proposed to anchor the core enhancers and core origins complexed with low abundancy transcription factors to the nuclear matrix via the cooperative binding to MARs of abundant classical matrix proteins (topoisomerase II, histone H1, lamins, SP120, ARBP, SATB1); this creates a unique nuclear microenvironment rich in regulatory proteins able to sustain transcription, replication, repair, and recombination. Theoretical searches and experimental data strongly support a model of activation of MARs and ORIs by transcription factors. A set of 21 characteristics are deduced or proposed for MAR/ORI sequences including their enrichment in inverted repeats, AT tracts, DNA unwinding elements, replication initiator protein sites, homooligonucleotide repeats (i.e., AAA, TTT, CCC), curved DNA, DNase I-hypersensitive sites, nucleosome-free stretches, polypurine stretches, and motifs with a potential for left-handed and triplex structures. We are establishing Banks of ORI and MAR sequences and have undertaken a large project of sequencing a large number of MARs in an effort to determine classes of DNA sequences in these regulatory elements and to understand their role at the origins of replication and transcriptional enhancers.

  14. Development of an efficient bi-directional promoter with tripartite enhancer employing three viral promoters. (United States)

    Patro, Sunita; Maiti, Indu B; Dey, Nrisingha


    We have developed a novel bi-directional promoter (FsFfCBD) by placing two heterogeneous core-promoters from the Figwort mosaic virus sub-genomic transcript promoter (FsCP, -69 to +31) and Cauliflower mosaic virus 35S promoter (CCP, -89 to +1) respectively on upstream (5') and downstream (3') ends of a tri-hybrid enhancer (FsEFfECE), in reverse orientation. The FsEFfECE domain encompasses three heterologous enhancer fragments from Figwort mosaic virus sub-genomic transcript promoter (FsE, 101 bp, -70 to -170), Figwort mosaic virus full-length transcript promoter (FfE, 196 bp, -249 to -54) and Cauliflower mosaic virus 35S promoter (CE, 254 bp, -343 to -90). The bi-directional nature of the FsFfCBD promoter (coupled to GFP and GUS) was established both in transient systems (onion epidermal cells and tobacco protoplasts) and transgenic plant (Nicotiana tabacum samsun NN) by monitoring the simultaneous expression of GFP and GUS employing fluorescence (for GFP) and biochemical (for GUS) based assays. In transgenic plants, the FsFfCBD promoter was found to be 6.8 and 2.5 times stronger than two parent promoters; Fs and FfC respectively. The bi-directional compound promoter FsFfCBD, composed of three heterologous enhancers with enhanced activity could become a valuable additional tool for efficient plant metabolic engineering and molecular pharming.

  15. Next-generation sequencing

    DEFF Research Database (Denmark)

    Rieneck, Klaus; Bak, Mads; Jønson, Lars


    , Illumina); several millions of PCR sequences were analyzed. RESULTS: The results demonstrated the feasibility of diagnosing the fetal KEL1 or KEL2 blood group from cell-free DNA purified from maternal plasma. CONCLUSION: This method requires only one primer pair, and the large amount of sequence......BACKGROUND: Maternal immunization against KEL1 of the Kell blood group system can have serious adverse consequences for the fetus as well as the newborn baby. Therefore, it is important to determine the phenotype of the fetus to predict whether it is at risk. We present data that show...... information obtained allows well for statistical analysis of the data. This general approach can be integrated into current laboratory practice and has numerous applications. Besides DNA-based predictions of blood group phenotypes, platelet phenotypes, or sickle cell anemia, and the determination of zygosity...

  16. Rapid-Sequence Intubation

    Directory of Open Access Journals (Sweden)

    Evangelina Dávila Cabo de Villa


    Full Text Available In medical practice there are several situations that require immediate intervention of the airway in some patients, in order to ensure proper entrance and exit of gases into and out of the lungs and prevent aspiration. Rapid-sequence intubation has been considered as the administration of a hypnotic agent and a neuromuscular relaxant consecutively (virtually simultaneously to facilitate orotracheal intubation in critically ill patients and minimize the risk of aspiration. This paper aims to collect elements that promote a successful medical management according to the situation presented, since there is no single way of proceeding in case of rapid-sequence intubation. The elements to consider include: knowing the anatomy of the upper respiratory tract, having a group of drugs to choose from, receiving adequate training and having an alternative plan for the difficulties that may arise.

  17. Sequencing of aromatase inhibitors



    Since the development of the third-generation aromatase inhibitors (AIs), anastrozole, letrozole and exemestane, these agents have been the subject of intensive research to determine their optimal use in advanced breast cancer. Not only have they replaced progestins in second-line therapy and challenged the role of tamoxifen in first-line, but there is also evidence for a lack of cross-resistance between the steroidal and nonsteroidal AIs, meaning that they may be used in sequence to obtain p...

  18. Learning Sequence Neighbourhood Metrics

    CERN Document Server

    Bayer, Justin; van der Smagt, Patrick


    Recurrent neural networks (RNNs) in combination with a pooling operator and the neighbourhood components analysis (NCA) objective function are able to detect the characterizing dynamics of sequences and embed them into a fixed-length vector space of arbitrary dimensionality. Subsequently, the resulting features are meaningful and can be used for visualization or nearest neighbour classification in linear time. This kind of metric learning for sequential data enables the use of algorithms tailored towards fixed length vector spaces such as R^n.

  19. Sequence Classification: 885394 [

    Lifescience Database Archive (English)

    Full Text Available 703); The expression pattern of this gene is described in PMID:12000842; possible frameshift detected when compare...Non-TMB TMH Non-TMB Non-TMB Non-TMB Non-TMB >gi|23619146|ref|NP_705108.1| Slight difference exist when to the published sequence of EBL-1 from Dd2 strain of P. falciparum (PMID:10613

  20. Properties of Semijoin Sequences

    Institute of Scientific and Technical Information of China (English)

    BengC.Ooi; B.Srinivasan


    The problem of finding optimum semijoin sequ4ence of an arbitrary query under linear cost function for the transmission cost is NP.hard.Hence heuristic algorithms with desirable properties are explored.In this paper four properties of semijoin programs for distributed query processing are identified,The use of these properties in constructing semijoin sequence is justified.An existing algorithm is modified incorporating these properties.Empirical comparison with existing algorithms shows the superiority of the proposed algorithm.

  1. Image sequence analysis

    CERN Document Server


    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  2. Sequencing BPS spectra (United States)

    Gukov, Sergei; Nawata, Satoshi; Saberi, Ingmar; Stošić, Marko; Sułkowski, Piotr


    This paper provides both a detailed study of color-dependence of link homologies, as realized in physics as certain spaces of BPS states, and a broad study of the behavior of BPS states in general. We consider how the spectrum of BPS states varies as continuous parameters of a theory are perturbed. This question can be posed in a wide variety of physical contexts, and we answer it by proposing that the relationship between unperturbed and perturbed BPS spectra is described by a spectral sequence. These general considerations unify previous applications of spectral sequence techniques to physics, and explain from a physical standpoint the appearance of many spectral sequences relating various link homology theories to one another. We also study structural properties of colored HOMFLY homology for links and evaluate Poincaré polynomials in numerous examples. Among these structural properties is a novel "sliding" property, which can be explained by using (refined) modular S-matrix. This leads to the identification of modular transformations in Chern-Simons theory and 3d {N}=2 theory via the 3d/3d correspondence. Lastly, we introduce the notion of associated varieties as classical limits of recursion relations of colored superpolynomials of links, and study their properties.

  3. The Galaxy End Sequence (United States)

    Eales, Stephen; de Vis, Pieter; Smith, Matthew W. L.; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon


    A common assumption is that galaxies fall in two distinct regions of a plot of specific star formation rate (SSFR) versus galaxy stellar mass: a star-forming galaxy main sequence (GMS) and a separate region of 'passive' or 'red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus representing the end-point of ≃12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the 'red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather than implying a distinct population of galaxies. Herschel observations, which show at least half of early-type galaxies contain a cool interstellar medium, also imply continuity between early-type and late-type galaxies. This picture of a unitary population of galaxies requires more gradual evolutionary processes than the rapid quenching process needed to explain two distinct populations. We challenge theorists to predict quantitatively the properties of this 'Galaxy End Sequence'.

  4. Telemetry-Enhancing Scripts (United States)

    Maimone, Mark W.


    Scripts Providing a Cool Kit of Telemetry Enhancing Tools (SPACKLE) is a set of software tools that fill gaps in capabilities of other software used in processing downlinked data in the Mars Exploration Rovers (MER) flight and test-bed operations. SPACKLE tools have helped to accelerate the automatic processing and interpretation of MER mission data, enabling non-experts to understand and/or use MER query and data product command simulation software tools more effectively. SPACKLE has greatly accelerated some operations and provides new capabilities. The tools of SPACKLE are written, variously, in Perl or the C or C++ language. They perform a variety of search and shortcut functions that include the following: Generating text-only, Event Report-annotated, and Web-enhanced views of command sequences; Labeling integer enumerations with their symbolic meanings in text messages and engineering channels; Systematic detecting of corruption within data products; Generating text-only displays of data-product catalogs including downlink status; Validating and labeling of commands related to data products; Performing of convenient searches of detailed engineering data spanning multiple Martian solar days; Generating tables of initial conditions pertaining to engineering, health, and accountability data; Simplified construction and simulation of command sequences; and Fast time format conversions and sorting.

  5. Information Theory of DNA Sequencing

    CERN Document Server

    Motahari, Abolfazl; Tse, David


    DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are assembled to reconstruct the original sequence. By drawing an analogy between the DNA sequencing problem and the classic communication problem, we define an information theoretic notion of sequencing capacity. This is the maximum number of DNA base pairs that can be resolved reliably per read, and provides a fundamental limit to the performance that can be achieved by any assembly algorithm. We compute the sequencing capacity explicitly for a simple statistical model of the DNA sequence and the read process. Using this framework, we also study the impact of noise in the read process on the sequencing capacity.

  6. PN Sequence Preestimator Scheme for DS-SS Signal Acquisition Using Block Sequence Estimation

    Directory of Open Access Journals (Sweden)

    Sang Kyu Park


    Full Text Available An m-sequence (PN sequence preestimator scheme for direct-sequence spread spectrum (DS-SS signal acquisition by using block sequence estimation (BSE is proposed and analyzed. The proposed scheme consists of an estimator and a verifier which work according to the PN sequence chip clock, and provides not only the enhanced chip estimates with a threshold decision logic and one-chip error correction among the first m received chips, but also the reliability check of the estimates with additional decision logic. The probabilities of the estimator and verifier operations are calculated. With these results, the detection, the false alarm, and the missing probabilities of the proposed scheme are derived. In addition, using a signal flow graph, the average acquisition time is calculated. The proposed scheme can be used as a preestimator and easily implemented by changing the internal signal path of a generally used digital matched filter (DMF correlator or any other correlator that has a lot of sampling data memories for sampled PN sequence. The numerical results show rapid acquisition performance in a relatively good CNR.

  7. Foreign DNA sequences are received by a wild-type strain of Aspergillus niger after co-culture with transgenic higher plants. (United States)

    Hoffmann, T; Golz, C; Schieder, O


    Different transgenic plants of Brassica napus, Brassica nigra, Datura innoxia and Vicia narbonensis expressing the hph gene under the control of the 35s promoter were co-cultivated with mycelial material of Aspergillus niger in microcosms under sterile conditions. A significantly higher number of hygromycin B-resistant colonies of re-isolated fungi was obtained if compared with co-cultures with non-transgenic plants. The hph gene and other foreign sequences could be detected in some of the resistant strains only for a short time after selection, indicating a rapid loss of foreign DNA. A more stable transgenic strain was obtained after co-culture with transgenic plants of D. innoxia including a high number of hph copies in their genome. DNA with detected pUC sequences was prepared to transform E. coli DH5 alpha. One of the recovered plasmids is shown to include pieces of the plant-transforming vector and a foreign sequence. The 35s-regulated expression of genes is studied in A. niger.

  8. Speech enhancement

    CERN Document Server

    Benesty, Jacob; Chen, Jingdong


    We live in a noisy world! In all applications (telecommunications, hands-free communications, recording, human-machine interfaces, etc.) that require at least one microphone, the signal of interest is usually contaminated by noise and reverberation. As a result, the microphone signal has to be ""cleaned"" with digital signal processing tools before it is played out, transmitted, or stored.This book is about speech enhancement. Different well-known and state-of-the-art methods for noise reduction, with one or multiple microphones, are discussed. By speech enhancement, we mean not only noise red

  9. A vision for ubiquitous sequencing. (United States)

    Erlich, Yaniv


    Genomics has recently celebrated reaching the $1000 genome milestone, making affordable DNA sequencing a reality. With this goal successfully completed, the next goal of the sequencing revolution can be sequencing sensors--miniaturized sequencing devices that are manufactured for real-time applications and deployed in large quantities at low costs. The first part of this manuscript envisions applications that will benefit from moving the sequencers to the samples in a range of domains. In the second part, the manuscript outlines the critical barriers that need to be addressed in order to reach the goal of ubiquitous sequencing sensors.

  10. Psychoacoustic Properties of Fibonacci Sequences

    Directory of Open Access Journals (Sweden)

    J. Sokoll


    Full Text Available 1202, Fibonacci set up one of the most interesting sequences in number theory. This sequence can be represented by so-called Fibonacci Numbers, and by a binary sequence of zeros and ones. If such a binary Fibonacci Sequence is played back as an audio file, a very dissonant sound results. This is caused by the “almost-periodic”, “self-similar” property of the binary sequence. The ratio of zeros and ones converges to the golden ratio, as do the primary and secondary spectral components intheir frequencies and amplitudes. These Fibonacci Sequences will be characterized using listening tests and psychoacoustic analyses. 

  11. Tracking of Individuals in Very Long Video Sequences

    DEFF Research Database (Denmark)

    Fihl, Preben; Corlin, Rasmus; Park, Sangho


    In this paper we present an approach for automatically detecting and tracking humans in very long video sequences. The detection is based on background subtraction using a multi-mode Codeword method. We enhance this method both in terms of representation and in terms of automatically updating...... the background allowing for handling gradual and rapid changes. Tracking is conducted by building appearance-based models and matching these over time. Tests show promising detection and tracking results in a ten hour video sequence....

  12. Overexpression of gibberellin 20-oxidase1 from Pinus densiflora results in enhanced wood formation with gelatinous fiber development in a transgenic hybrid poplar. (United States)

    Park, Eung-Jun; Kim, Hyun-Tae; Choi, Young-Im; Lee, Chanhui; Nguyen, Van Phap; Jeon, Hyung-Woo; Cho, Jin-Seong; Funada, Ryo; Pharis, Richard P; Kurepin, Leonid V; Ko, Jae-Heung


    Gibberellins (GAs) are important regulators of plant shoot biomass growth, and GA 20-oxidase (GA20ox) is one of the major regulatory enzymes in the GA biosynthetic pathway. Previously, we showed that the expression levels of a putative GA20ox1 (i.e., PdGA20ox1) in stem tissue of 3-month-old seedlings of 12 families of Pinus densiflora were positively correlated with stem diameter growth across those same families growing in an even-aged 32-year-old pine forest (Park EJ, Lee WY, Kurepin LV, Zhang R, Janzen L, Pharis RP (2015) Plant hormone-assisted early family selection in Pinus densiflora via a retrospective approach. Tree Physiol 35:86-94). To further investigate the molecular function of this gene in the stem wood growth of forest trees, we produced transgenic poplar lines expressing PdGA20ox1 under the control of the 35S promoter (designated as 35S::PdGA20ox1). By age 3 months, most of the 35S::PdGA20ox1 poplar trees were showing an exceptional enhancement of stem wood growth, i.e., up to fourfold increases in stem dry weight, compared with the nontransformed control poplar plants. Significant increases in endogenous GA1, its immediate precursor (GA20) and its catabolite (GA8) in elongating internode tissue accompanied the increased stem growth in the transgenic lines. Additionally, the development of gelatinous fibers occurred in vertically grown stems of the 35S::PdGA20ox1 poplars. An analysis of the cell wall monosaccharide composition of the 35S::PdGA20ox1 poplars showed significant increases in xylose and glucose contents, indicating a qualitative increase in secondary wall depositions. Microarray analyses led us to find a total of 276 probe sets that were upregulated (using threefold as a threshold) in the stem tissues of 35S::PdGA20ox1 poplars relative to the controls. 'Cell organization or biogenesis'- and 'cell wall'-related genes were overrepresented, including many of genes that are involved in cell wall modification. Several transcriptional

  13. Learning the sequence determinants of alternative splicing from millions of random sequences. (United States)

    Rosenberg, Alexander B; Patwardhan, Rupali P; Shendure, Jay; Seelig, Georg


    Most human transcripts are alternatively spliced, and many disease-causing mutations affect RNA splicing. Toward better modeling the sequence determinants of alternative splicing, we measured the splicing patterns of over two million (M) synthetic mini-genes, which include degenerate subsequences totaling over 100 M bases of variation. The massive size of these training data allowed us to improve upon current models of splicing, as well as to gain new mechanistic insights. Our results show that the vast majority of hexamer sequence motifs measurably influence splice site selection when positioned within alternative exons, with multiple motifs acting additively rather than cooperatively. Intriguingly, motifs that enhance (suppress) exon inclusion in alternative 5' splicing also enhance (suppress) exon inclusion in alternative 3' or cassette exon splicing, suggesting a universal mechanism for alternative exon recognition. Finally, our empirically trained models are highly predictive of the effects of naturally occurring variants on alternative splicing in vivo.

  14. Infinite sequences and series

    CERN Document Server

    Knopp, Konrad


    One of the finest expositors in the field of modern mathematics, Dr. Konrad Knopp here concentrates on a topic that is of particular interest to 20th-century mathematicians and students. He develops the theory of infinite sequences and series from its beginnings to a point where the reader will be in a position to investigate more advanced stages on his own. The foundations of the theory are therefore presented with special care, while the developmental aspects are limited by the scope and purpose of the book. All definitions are clearly stated; all theorems are proved with enough detail to ma

  15. Tools for integrated sequence-structure analysis with UCSF Chimera

    Directory of Open Access Journals (Sweden)

    Huang Conrad C


    Full Text Available Abstract Background Comparing related structures and viewing the structures in the context of sequence alignments are important tasks in protein structure-function research. While many programs exist for individual aspects of such work, there is a need for interactive visualization tools that: (a provide a deep integration of sequence and structure, far beyond mapping where a sequence region falls in the structure and vice versa; (b facilitate changing data of one type based on the other (for example, using only sequence-conserved residues to match structures, or adjusting a sequence alignment based on spatial fit; (c can be used with a researcher's own data, including arbitrary sequence alignments and annotations, closely or distantly related sets of proteins, etc.; and (d interoperate with each other and with a full complement of molecular graphics features. We describe enhancements to UCSF Chimera to achieve these goals. Results The molecular graphics program UCSF Chimera includes a suite of tools for interactive analyses of sequences and structures. Structures automatically associate with sequences in imported alignments, allowing many kinds of crosstalk. A novel method is provided to superimpose structures in the absence of a pre-existing sequence alignment. The method uses both sequence and secondary structure, and can match even structures with very low sequence identity. Another tool constructs structure-based sequence alignments from superpositions of two or more proteins. Chimera is designed to be extensible, and mechanisms for incorporating user-specific data without Chimera code development are also provided. Conclusion The tools described here apply to many problems involving comparison and analysis of protein structures and their sequences. Chimera includes complete documentation and is intended for use by a wide range of scientists, not just those in the computational disciplines. UCSF Chimera is free for non-commercial use and is

  16. Stress Responsive Zinc-finger Protein Gene of Populus euphratica in Tobacco Enhances Salt Tolerance

    Institute of Scientific and Technical Information of China (English)


    The Populus euphratica stress responsive zinc-finger protein gene PSTZ, which encodes a protein including typical Cys2/His2 zinc finger structure, was isolated by reverse transcription-polymerase chain reaction from P. euphratica.Northern hybridization revealed that its expression was induced under drought and salt stress conditions. To examine its function, cDNA of the PSTZ gene, driven by the cauliflower mosaic virus 35S promoter, was cloned into a plant expression vector pBin438 and introduced into tobacco plants. Transgenic tobacco showed an enhanced salt tolerance, suggesting that PSTZ may play a role in plant responsiveness to salt stress.

  17. Allele Re-sequencing Technologies

    DEFF Research Database (Denmark)

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


    The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large and com...... alternative to whole genome re-sequencing to identify causative genetic variations in plants. One challenge, however, will be efficient bioinformatics strategies for data handling and analysis from the increasing amount of sequence information.......The development of next-generation sequencing technologies has made sequencing an affordable approach for detection of genetic variations associated with various traits. However, the cost of whole genome re-sequencing still remains too high to be feasible for many plant species with large...

  18. Spaces of Ideal Convergent Sequences

    Directory of Open Access Journals (Sweden)

    M. Mursaleen


    Full Text Available In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ=Mk. We also examine some topological properties of the resulting sequence spaces.

  19. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard


    The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl...

  20. Rapid Polymer Sequencer (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)


    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  1. The Galaxy End Sequence

    CERN Document Server

    Eales, Stephen; Smith, Matthew; Appah, Kiran; Ciesla, Laure; Duffield, Chris; Schofield, Simon


    A common assumption is that galaxies fall in two distinct regions on a plot of specific star-formation rate (SSFR) versus galaxy stellar mass: a star-forming Galaxy Main Sequence (GMS) and a separate region of `passive' or `red and dead galaxies'. Starting from a volume-limited sample of nearby galaxies designed to contain most of the stellar mass in this volume, and thus being a fair representation of the Universe at the end of 12 billion years of galaxy evolution, we investigate the distribution of galaxies in this diagram today. We show that galaxies follow a strongly curved extended GMS with a steep negative slope at high galaxy stellar masses. There is a gradual change in the morphologies of the galaxies along this distribution, but there is no clear break between early-type and late-type galaxies. Examining the other evidence that there are two distinct populations, we argue that the `red sequence' is the result of the colours of galaxies changing very little below a critical value of the SSFR, rather t...

  2. Translational genomics for plant breeding with the genome sequence explosion. (United States)

    Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha


    The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

  3. New chaos-based encryption scheme for digital sequence

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhengwei; Fan Yangyu; Zeng Li


    To enhance the anti-breaking performance of privacy information, this article proposes a new encryption method utilizing the leaping peculiarity of the periodic orbits of chaos systems. This method maps the secret sequence to several chaos periodic orbits, and a short sequence obtained by evolving the system parameters of the periodic orbits in another nonlinear system will be the key to reconstruct these periodic orbits. In the decryption end, the shadowing method of chaos trajectory based on the modified Newton-Raphson algorithm is adopted to restore these system parameters. Through deciding which orbit each pair coordinate falls on, the original digital sequence can be decrypted.

  4. Image-based temporal alignment of echocardiographic sequences (United States)

    Danudibroto, Adriyana; Bersvendsen, Jørn; Mirea, Oana; Gerard, Olivier; D'hooge, Jan; Samset, Eigil


    Temporal alignment of echocardiographic sequences enables fair comparisons of multiple cardiac sequences by showing corresponding frames at given time points in the cardiac cycle. It is also essential for spatial registration of echo volumes where several acquisitions are combined for enhancement of image quality or forming larger field of view. In this study, three different image-based temporal alignment methods were investigated. First, a method based on dynamic time warping (DTW). Second, a spline-based method that optimized the similarity between temporal characteristic curves of the cardiac cycle using 1D cubic B-spline interpolation. Third, a method based on the spline-based method with piecewise modification. These methods were tested on in-vivo data sets of 19 echo sequences. For each sequence, the mitral valve opening (MVO) time was manually annotated. The results showed that the average MVO timing error for all methods are well under the time resolution of the sequences.

  5. Novel sequences propel familiar folds. (United States)

    Jawad, Zahra; Paoli, Massimo


    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  6. Speech Enhancement

    DEFF Research Database (Denmark)

    Benesty, Jacob; Jensen, Jesper Rindom; Christensen, Mads Græsbøll;

    of methods and have been introduced in somewhat different contexts. Linear filtering methods originate in stochastic processes, while subspace methods have largely been based on developments in numerical linear algebra and matrix approximation theory. This book bridges the gap between these two classes......Speech enhancement is a classical problem in signal processing, yet still largely unsolved. Two of the conventional approaches for solving this problem are linear filtering, like the classical Wiener filter, and subspace methods. These approaches have traditionally been treated as different classes...... of methods by showing how the ideas behind subspace methods can be incorporated into traditional linear filtering. In the context of subspace methods, the enhancement problem can then be seen as a classical linear filter design problem. This means that various solutions can more easily be compared...

  7. RIKEN integrated sequence analysis (RISA) system--384-format sequencing pipeline with 384 multicapillary sequencer. (United States)

    Shibata, K; Itoh, M; Aizawa, K; Nagaoka, S; Sasaki, N; Carninci, P; Konno, H; Akiyama, J; Nishi, K; Kitsunai, T; Tashiro, H; Itoh, M; Sumi, N; Ishii, Y; Nakamura, S; Hazama, M; Nishine, T; Harada, A; Yamamoto, R; Matsumoto, H; Sakaguchi, S; Ikegami, T; Kashiwagi, K; Fujiwake, S; Inoue, K; Togawa, Y


    The RIKEN high-throughput 384-format sequencing pipeline (RISA system) including a 384-multicapillary sequencer (the so-called RISA sequencer) was developed for the RIKEN mouse encyclopedia project. The RISA system consists of colony picking, template preparation, sequencing reaction, and the sequencing process. A novel high-throughput 384-format capillary sequencer system (RISA sequencer system) was developed for the sequencing process. This system consists of a 384-multicapillary auto sequencer (RISA sequencer), a 384-multicapillary array assembler (CAS), and a 384-multicapillary casting device. The RISA sequencer can simultaneously analyze 384 independent sequencing products. The optical system is a scanning system chosen after careful comparison with an image detection system for the simultaneous detection of the 384-capillary array. This scanning system can be used with any fluorescent-labeled sequencing reaction (chain termination reaction), including transcriptional sequencing based on RNA polymerase, which was originally developed by us, and cycle sequencing based on thermostable DNA polymerase. For long-read sequencing, 380 out of 384 sequences (99.2%) were successfully analyzed and the average read length, with more than 99% accuracy, was 654.4 bp. A single RISA sequencer can analyze 216 kb with >99% accuracy in 2.7 h (90 kb/h). For short-read sequencing to cluster the 3' end and 5' end sequencing by reading 350 bp, 384 samples can be analyzed in 1.5 h. We have also developed a RISA inoculator, RISA filtrator and densitometer, RISA plasmid preparator which can handle throughput of 40,000 samples in 17.5 h, and a high-throughput RISA thermal cycler which has four 384-well sites. The combination of these technologies allowed us to construct the RISA system consisting of 16 RISA sequencers, which can process 50,000 DNA samples per day. One haploid genome shotgun sequence of a higher organism, such as human, mouse, rat, domestic animals, and plants, can be

  8. Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

    Directory of Open Access Journals (Sweden)

    Yan Wei Lim


    Full Text Available Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

  9. Sequencing genes in silico using single nucleotide polymorphisms

    Directory of Open Access Journals (Sweden)

    Zhang Xinyi


    Full Text Available Abstract Background The advent of high throughput sequencing technology has enabled the 1000 Genomes Project Pilot 3 to generate complete sequence data for more than 906 genes and 8,140 exons representing 697 subjects. The 1000 Genomes database provides a critical opportunity for further interpreting disease associations with single nucleotide polymorphisms (SNPs discovered from genetic association studies. Currently, direct sequencing of candidate genes or regions on a large number of subjects remains both cost- and time-prohibitive. Results To accelerate the translation from discovery to functional studies, we propose an in silico gene sequencing method (ISS, which predicts phased sequences of intragenic regions, using SNPs. The key underlying idea of our method is to infer diploid sequences (a pair of phased sequences/alleles at every functional locus utilizing the deep sequencing data from the 1000 Genomes Project and SNP data from the HapMap Project, and to build prediction models using flanking SNPs. Using this method, we have developed a database of prediction models for 611 known genes. Sequence prediction accuracy for these genes is 96.26% on average (ranges 79%-100%. This database of prediction models can be enhanced and scaled up to include new genes as the 1000 Genomes Project sequences additional genes on additional individuals. Applying our predictive model for the KCNJ11 gene to the Wellcome Trust Case Control Consortium (WTCCC Type 2 diabetes cohort, we demonstrate how the prediction of phased sequences inferred from GWAS SNP genotype data can be used to facilitate interpretation and identify a probable functional mechanism such as protein changes. Conclusions Prior to the general availability of routine sequencing of all subjects, the ISS method proposed here provides a time- and cost-effective approach to broadening the characterization of disease associated SNPs and regions, and facilitating the prioritization of candidate

  10. Expression Analysis of Hairpin RNA Carrying Sugarcane mosaic virus (SCMV) Derived Sequences and Transgenic Resistance Development in a Model Rice Plant (United States)

    Akbar, Sehrish; Wang, Ming-Bo; Liu, Qing


    Developing transgenic resistance in monocotyledonous crops against pathogens remains a challenging area of research. Sugarcane mosaic virus (SCMV) is a serious pathogen of many monocotyledonous crops including sugarcane. The objective of present study was to analyze transgenic expression of hairpin RNA (hpRNA), targeting simultaneously CP (Coat Protein) and Hc-Pro (helper component-proteinase) genes of SCMV, in a model rice plant. Conserved nucleotide sequences, exclusive for DAG (Aspartic acid-Alanine-Glycine) and KITC (Lycine-Isoleucine-Threonine-Cysteine) motifs, derived from SCMV CP and Hc-Pro genes, respectively, were fused together and assembled into the hpRNA cassette under maize ubiquitin promoter to form Ubi-hpCP:Hc-Pro construct. The same CP:Hc-Pro sequence was fused with the β-glucuronidase gene (GUS) at the 3′ end under CaMV 35S promoter to develop 35S-GUS:CP:Hc-Pro served as a target reporter gene construct. When delivered into rice callus tissues by particle bombardment, the Ubi-hpCP:Hc-Pro construct induced strong silencing of 35S-GUS:CP:Hc-Pro. Transgenic rice plants, containing Ubi-hpCP:Hc-Pro construct, expressed high level of 21–24 nt small interfering RNAs, which induced specific suppression against GUS:CP:Hc-Pro delivered by particle bombardment and conferred strong resistance to mechanically inoculated SCMV. It is concluded that fusion hpRNA approach is an affordable method for developing resistance against SCMV in model rice plant and it could confer SCMV resistance when transformed into sugarcane. PMID:28255554

  11. Finding and Improving the Key-Frames of Long Video Sequences for Face Recognition

    DEFF Research Database (Denmark)

    Nasrollahi, Kamal; Moeslund, Thomas B.


    Face recognition systems are very sensitive to the quality and resolution of their input face images. This makes such systems unreliable when working with long surveillance video sequences without employing some selection and enhancement algorithms. On the other hand, processing all the frames...... of such video sequences by any enhancement or even face recognition algorithm is demanding. Thus, there is a need for a mechanism to summarize the input video sequence to a set of key-frames and then applying an enhancement algorithm to this subset. This paper presents a system doing exactly this. The system...... uses face quality assessment to select the key-frames and a hybrid super-resolution to enhance the face image quality. The suggested system that employs a linear associator face recognizer to evaluate the enhanced results has been tested on real surveillance video sequences and the experimental results...

  12. Solid phase sequencing of biopolymers

    Energy Technology Data Exchange (ETDEWEB)

    Cantor, Charles (Del Mar, CA); Koster, Hubert (La Jolla, CA)


    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  13. Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome. (United States)

    Kolano, B; Gardunia, B W; Michalska, M; Bonifacio, A; Fairbanks, D; Maughan, P J; Coleman, C E; Stevens, M R; Jellen, E N; Maluszynska, J


    The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.

  14. Infectivity and complete nucleotide sequence of cucumber fruit mottle mosaic virus isolate Cm cDNA. (United States)

    Rhee, Sun-Ju; Hong, Jin-Sung; Lee, Gung Pyo


    Three isolates of cucumber fruit mottle mosaic virus (CFMMV) were collected from melon, cucumber, and pumpkin plants in Korea. A full-length cDNA clone of CFMMV-Cm (melon isolate) was produced and evaluated for infectivity after T7 transcription in vitro (pT7CF-Cmflc). The complete CFMMV genome sequence of the infectious clone pT7CF-Cmflc was determined. The genome of CFMMV-Cm consisted of 6,571 nucleotides and shared high nucleotide sequence identity (98.8 %) with the Israel isolate of CFMMV. Based on the infectious clone pT7CF-Cmflc, a CaMV 35S-promoter driven cDNA clone (p35SCF-Cmflc) was subsequently constructed and sequenced. Mechanical inoculation with RNA transcripts of pT7CF-Cmflc and agro-inoculation with p35SCF-Cmflc resulted in systemic infection of cucumber and melon, producing symptoms similar to those produced by CFMMV-Cm. Progeny virus in infected plants was detected by RT-PCR, western blot assay, and transmission electron microscopy.

  15. Sequence determinants in human polyadenylation site selection

    Directory of Open Access Journals (Sweden)

    Gautheret Daniel


    Full Text Available Abstract Background Differential polyadenylation is a widespread mechanism in higher eukaryotes producing mRNAs with different 3' ends in different contexts. This involves several alternative polyadenylation sites in the 3' UTR, each with its specific strength. Here, we analyze the vicinity of human polyadenylation signals in search of patterns that would help discriminate strong and weak polyadenylation sites, or true sites from randomly occurring signals. Results We used human genomic sequences to retrieve the region downstream of polyadenylation signals, usually absent from cDNA or mRNA databases. Analyzing 4956 EST-validated polyadenylation sites and their -300/+300 nt flanking regions, we clearly visualized the upstream (USE and downstream (DSE sequence elements, both characterized by U-rich (not GU-rich segments. The presence of a USE and a DSE is the main feature distinguishing true polyadenylation sites from randomly occurring A(A/UUAAA hexamers. While USEs are indifferently associated with strong and weak poly(A sites, DSEs are more conspicuous near strong poly(A sites. We then used the region encompassing the hexamer and DSE as a training set for poly(A site identification by the ERPIN program and achieved a prediction specificity of 69 to 85% for a sensitivity of 56%. Conclusion The availability of complete genomes and large EST sequence databases now permit large-scale observation of polyadenylation sites. Both U-rich sequences flanking both sides of poly(A signals contribute to the definition of "true" sites. However, the downstream U-rich sequences may also play an enhancing role. Based on this information, poly(A site prediction accuracy was moderately but consistently improved compared to the best previously available algorithm.

  16. Intra-species sequence comparisons for annotating genomes

    Energy Technology Data Exchange (ETDEWEB)

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.


    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  17. Enhanced drought and heat stress tolerance of tobacco plants with ectopically enhanced cytokinin oxidase/dehydrogenase gene expression. (United States)

    Macková, Hana; Hronková, Marie; Dobrá, Jana; Turečková, Veronika; Novák, Ondřej; Lubovská, Zuzana; Motyka, Václav; Haisel, Daniel; Hájek, Tomáš; Prášil, Ilja Tom; Gaudinová, Alena; Štorchová, Helena; Ge, Eva; Werner, Tomáš; Schmülling, Thomas; Vanková, Radomíra


    Responses to drought, heat, and combined stress were compared in tobacco (Nicotiana tabacum L.) plants ectopically expressing the cytokinin oxidase/dehydrogenase CKX1 gene of Arabidopsis thaliana L. under the control of either the predominantly root-expressed WRKY6 promoter or the constitutive 35S promoter, and in the wild type. WRKY6:CKX1 plants exhibited high CKX activity in the roots under control conditions. Under stress, the activity of the WRKY6 promoter was down-regulated and the concomitantly reduced cytokinin degradation coincided with raised bioactive cytokinin levels during the early phase of the stress response, which might contribute to enhanced stress tolerance of this genotype. Constitutive expression of CKX1 resulted in an enlarged root system, a stunted, dwarf shoot phenotype, and a low basal level of expression of the dehydration marker gene ERD10B. The high drought tolerance of this genotype was associated with a relatively moderate drop in leaf water potential and a significant decrease in leaf osmotic potential. Basal expression of the proline biosynthetic gene P5CSA was raised. Both wild-type and WRKY6:CKX1 plants responded to heat stress by transient elevation of stomatal conductance, which correlated with an enhanced abscisic acid catabolism. 35S:CKX1 transgenic plants exhibited a small and delayed stomatal response. Nevertheless, they maintained a lower leaf temperature than the other genotypes. Heat shock applied to drought-stressed plants exaggerated the negative stress effects, probably due to the additional water loss caused by a transient stimulation of transpiration. The results indicate that modulation of cytokinin levels may positively affect plant responses to abiotic stress through a variety of physiological mechanisms.

  18. Hoxc8 early enhancer of the Indonesian coelacanth, Latimeria menadoensis. (United States)

    Shashikant, Cooduvalli; Bolanowski, Stacey A; Danke, Joshua; Amemiya, Chris T


    Hoxc8 early enhancer controls the initiation and establishment phase of Hoxc8 expression in the mouse. Comparative studies indicate the presence of Hoxc8 early enhancer sequences in different vertebrate clades including mammals, birds and fish. Previous studies have shown differences between teleost and mammalian Hoxc8 early enhancers with respect to sequence and organization of protein binding elements. This raises the question of when the Hoxc8 early enhancer arose and how it has become modified in different vertebrate lineages. Here, we describe Hoxc8 early enhancer from the Indonesian coelacanth, Latimeria menadoensis. Coelacanths are the only extant lobefinned fish whose genome is tractable to genome analysis. The Latimeria Hoxc8 early enhancer sequence more closely resembles that of the mouse than that of Fugu or zebrafish. When assayed for enhancer activity by reporter gene analysis in transgenic mouse embryos, Latimeria Hoxc8 early enhancer directs expression to the posterior neural tube and mesoderm similar to that of the mouse enhancer. These observations support a close relationship between coelacanths and tetrapods and place the origin of a common Hoxc8 early enhancer sequence within the sarcopterygian lineage. The divergence of teleost (actinopterygii) Hoxc8 early enhancer may reflect a case of relaxed selection or other forms of instability induced by genome duplication events.

  19. The MsPRP2 promoter enables strong heterologous gene expression in a root-specific manner and is enhanced by overexpression of Alfin 1. (United States)

    Winicov, Ilga; Valliyodan, Babu; Xue, Lingru; Hoober, J Kenneth


    Promoter specificity and efficiency of utilization are essential for endogenous and transgene expression. Selective root expression remains to be defined in terms of both promoter elements and transcription factors that provide high levels of ubiquitous expression. We characterized expression from the MsPRP2 promoter with the green fluorescent protein (GFP) reporter transgene in alfalfa (Medicago sativa) and found that a promoter fragment (+1 to -652 bp) retained the root and callus specificity of the endogenous MsPRP2 gene and hence this promoter fragment contains elements necessary for root-specific expression. The strong ubiquitous expression obtained from this promoter was comparable to that of the CaMV 35S promoter in roots and was enhanced by transgenic overexpression of Alfin 1, a root- and callus-specific transcription factor in alfalfa. No transgenic expression was obtained in leaves with this promoter in the presence or absence of Alfin 1. The increased expression of GFP in alfalfa containing the Alfin 1 transgene confirms the function of Alfin 1 binding sites in the MsPRP2 promoter fragment and also indicates that Alfin 1 concentrations are limiting for maximal expression in calli and roots. These findings characterize the MsPRP2 promoter as a novel root- and callus-specific promoter of plant origin that can be used as an effective tool for strong root-directed gene expression. In addition, we have demonstrated that the signal sequence of MsPRP2 can be used for efficient secretion of transgene products from callus and roots.

  20. Complete Genome Sequence of Bacillus megaterium Siphophage Silence


    Solis, Jonathan A.; Farmer, Nicholas G.; Cahill, Jesse L.; Rasche, Eric S.; Kuty Everett, Gabriel F.


    Silence is a newly isolated siphophage that infects Bacillus megaterium, a soil bacterium that is used readily in research and commercial applications. A study of B. megaterium phage Silence will enhance our knowledge of the diversity of Bacillus phages. Here, we describe the complete genome sequence and annotated features of Silence.

  1. PseudoRandomSequencesPy Library v 1.0.


    Cipriano, Marcelo; Arzubi, Alejandro Arroyo; Ballesteros, Hugo


    An open source library in Python language is developed for academic use. It can also be applied in software development. The library allows users to implement applications using relevant stream ciphers, to evaluate pseudorandom sequences and their robustness in cryptographic applications. Its use may enhance teaching techniques, improve software readability, and save encoding times at the developmental stage.

  2. EDITORIAL: Enhancing nanolithography Enhancing nanolithography (United States)

    Demming, Anna


    Lithography was invented in late 18th century Bavaria by an ambitious young playwright named Alois Senefelder. Senefelder experimented with stone, wax, water and ink in the hope of finding a way of reproducing text so that he might financially gain from a wider distribution of his already successful scripts. His discovery not only facilitated the profitability of his plays, but also provided the world with an affordable printing press that would ultimately democratize the dissemination of art, knowledge and literature. Since Senefelder, experiments in lithography have continued with a range of innovations including the use of electron beams and UV that allow increasingly higher-resolution features [1, 2]. Applications for this have now breached the limits of paper printing into the realms of semiconductor and microelectronic mechanical systems technology. In this issue, researchers demonstrate a technique for fabricating periodic features in poly(3,4-ethylene dioxythiophene)-poly(styrenesulfonate) (PEDOT-PSS) [3]. Their method combines field enhancements from silica nanospheres with laser-interference lithography to provide a means of patterning a polymer that has the potential to open the market of low-end, high-volume microelectronics. Laser-interference lithography has already been used successfully in patterning. Researchers in Korea used laser-interference lithography to generate stamps for imprinting a two-dimensional photonic crystal structure into green light emitting diodes (LEDs) [4]. The imprinted patterns comprised depressions 100 nm deep and 180 nm wide with a periodicity of 295 nm. In comparison with unpatterned LEDs, the intensity of photoluminescence was enhanced by a factor of seven in the LEDs that had the photonic crystal structures imprinted in them. The potential of exploiting field enhancements around nanostructures for new technologies has also attracted a great deal of attention. Researchers in the USA and Australia have used the field

  3. Graphene nanodevices for DNA sequencing (United States)

    Heerema, Stephanie J.; Dekker, Cees


    Fast, cheap, and reliable DNA sequencing could be one of the most disruptive innovations of this decade, as it will pave the way for personalized medicine. In pursuit of such technology, a variety of nanotechnology-based approaches have been explored and established, including sequencing with nanopores. Owing to its unique structure and properties, graphene provides interesting opportunities for the development of a new sequencing technology. In recent years, a wide range of creative ideas for graphene sequencers have been theoretically proposed and the first experimental demonstrations have begun to appear. Here, we review the different approaches to using graphene nanodevices for DNA sequencing, which involve DNA passing through graphene nanopores, nanogaps, and nanoribbons, and the physisorption of DNA on graphene nanostructures. We discuss the advantages and problems of each of these key techniques, and provide a perspective on the use of graphene in future DNA sequencing technology.

  4. Solid phase sequencing of biopolymers (United States)

    Cantor, Charles R.; Hubert, Koster


    This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Probes may be affixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

  5. Effect of Initial pH on Enhanced Biological Phosphorus Removal in Sequencing Batch Reactor (SBR)%起始 pH 值对序批式反应器中强化生物除磷系统的影响研究

    Institute of Scientific and Technical Information of China (English)

    李亚静; 谭静亮


      通过3个序批式反应器(SBR)的连续运行,研究了污水不同起始 pH 值对强化生物除磷系统(EBPR)的影响(SBR1:pH=6.5;SBR2:pH=7.0;SBR3:pH=7.5).结果表明:随着 pH 值的提高,厌氧释磷量和好氧吸磷量都逐渐增加,释磷速率和吸磷速率也在增加;除磷效率分别为82.69%、93.87%和98.50%.运用荧光原位杂交技术(FISH)鉴定 EBPR 中的功能菌为聚磷菌(PAO)并计算出其含量,即 SBR3>SBR2>SBR1,得到在一定的 pH 值范围内 pH 值越高聚磷菌的含量越高.比较不同 pH 值下 EBPR 系统中脱氢酶活性的变化规律,在 pH=6.5~7.5范围内,脱氢酶的活性随着 pH 的增加而线性增加,表明较高的 pH 有利于 PAO 的生长和提高 PAO 的活性,从而提高了除磷效率.因此,通过控制污水起始 pH 值的方法可以达到显著提高强化生物除磷效果的目的.%Three laboratory-scale sequencing batch reactors (SBRs) were operated continuously to investigate the influence of wastewater initial pH on enhanced biological phosphorus removal (SBR1: pH=6.5; SBR2: pH=7.0; SBR3: pH=7.5). Re-sults showed that the soluble ortho-phosphorus (SOP) release and uptake were increased, while the pH value was increased. And the SOP removal efficiency of the three reactors reached 82.69%、93.87% and 98.50% respectively. The proportion of phosphorus accumulating bacteria (PAO) in the three SBRs was calculated by FISH technology, namely SBR3 > SBR2 >SBR1, The proportion of PAO increased with the increase of the pH value. In the range of pH 6.5~7.5,the activity of dehy-drogenase increased linearly with pH value,The results indicated that a higher pH value was beneficial to the growth and the activity of PAO,which led to an improved phosphorus removal performance. Thus, the efficiency of enhanced biological phosphorus removal can be significantly improved by controlling the initial pH of wastewater.

  6. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna


    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  7. Biosensors for DNA sequence detection (United States)

    Vercoutere, Wenonah; Akeson, Mark


    DNA biosensors are being developed as alternatives to conventional DNA microarrays. These devices couple signal transduction directly to sequence recognition. Some of the most sensitive and functional technologies use fibre optics or electrochemical sensors in combination with DNA hybridization. In a shift from sequence recognition by hybridization, two emerging single-molecule techniques read sequence composition using zero-mode waveguides or electrical impedance in nanoscale pores.

  8. Nonlinear analysis of biological sequences

    Energy Technology Data Exchange (ETDEWEB)

    Torney, D.C.; Bruno, W.; Detours, V. [and others


    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The main objectives of this project involved deriving new capabilities for analyzing biological sequences. The authors focused on tabulating the statistical properties exhibited by Human coding DNA sequences and on techniques of inferring the phylogenetic relationships among protein sequences related by descent.

  9. Nitrogen chronology of massive main sequence stars

    CERN Document Server

    Köhler, K; Brott, I; Langer, N; de Koter, A


    Rotational mixing in massive main sequence stars is predicted to monotonically increase their surface nitrogen abundance with time. We use this effect to design a method for constraining the age and the inclination angle of massive main sequence stars, given their observed luminosity, effective temperature, projected rotational velocity and surface nitrogen abundance. This method relies on stellar evolution models for different metallicities, masses and rotation rates. We use the population synthesis code STARMAKER to show the range of applicability of our method. We apply this method to 79 early B-type main sequence stars near the LMC clusters NGC 2004 and N 11 and the SMC clusters NGC 330 and NGC 346. From all stars within the sample, 17 were found to be suitable for an age analysis. For ten of them, which are rapidly rotating stars without a strong nitrogen enhancement, it has been previously concluded that they did not evolve as rotationally mixed single stars. This is confirmed by our analysis, which fla...

  10. Agaricus bisporus genome sequence: a commentary. (United States)

    Kerrigan, Richard W; Challen, Michael P; Burton, Kerry S


    The genomes of two isolates of Agaricus bisporus have been sequenced recently. This soil-inhabiting fungus has a wide geographical distribution in nature and it is also cultivated in an industrialized indoor process ($4.7bn annual worldwide value) to produce edible mushrooms. Previously this lignocellulosic fungus has resisted precise econutritional classification, i.e. into white- or brown-rot decomposers. The generation of the genome sequence and transcriptomic analyses has revealed a new classification, 'humicolous', for species adapted to grow in humic-rich, partially decomposed leaf material. The Agaricus biporus genomes contain a collection of polysaccharide and lignin-degrading genes and more interestingly an expanded number of genes (relative to other lignocellulosic fungi) that enhance degradation of lignin derivatives, i.e. heme-thiolate peroxidases and β-etherases. A motif that is hypothesized to be a promoter element in the humicolous adaptation suite is present in a large number of genes specifically up-regulated when the mycelium is grown on humic-rich substrate. The genome sequence of A. bisporus offers a platform to explore fungal biology in carbon-rich soil environments and terrestrial cycling of carbon, nitrogen, phosphorus and potassium.

  11. Assembly sequencing with toleranced parts

    Energy Technology Data Exchange (ETDEWEB)

    Latombe, J.C. [Stanford Univ., CA (United States). Robotics Lab.; Wilson, R.H. [Sandia National Labs., Albuquerque, NM (United States). Intelligent Systems and Robotics Center


    The goal of assembly sequencing is to plan a feasible series of operations to construct a product from its individual parts. Previous research has thoroughly investigated assembly sequencing under the assumption that parts have nominal geometry. This paper considers the case where parts have toleranced geometry. Its main contribution is an efficient procedure that decides if a product admits an assembly sequence with infinite translations that is feasible for all possible instances of the components within the specified tolerances. If the product admits one such sequence, the procedure can also generate it. For the cases where there exists no such assembly sequence, another procedure is proposed which generates assembly sequences that are feasible only for some values of the toleranced dimensions. If this procedure produces no such sequence, then no instance of the product is assemblable. Finally, this paper analyzes the relation between assembly and disassembly sequences in the presence of toleranced parts. This work assumes a simple, but non-trivial tolerance language that falls short of capturing all imperfections of a manufacturing process. Hence, it is only one step toward assembly sequencing with toleranced parts.

  12. SNMR pulse sequence phase cycling (United States)

    Walsh, David O; Grunewald, Elliot D


    Technologies applicable to SNMR pulse sequence phase cycling are disclosed, including SNMR acquisition apparatus and methods, SNMR processing apparatus and methods, and combinations thereof. SNMR acquisition may include transmitting two or more SNMR pulse sequences and applying a phase shift to a pulse in at least one of the pulse sequences, according to any of a variety cycling techniques. SNMR processing may include combining SNMR from a plurality of pulse sequences comprising pulses of different phases, so that desired signals are preserved and indesired signals are canceled.

  13. Blazar Sequence in Fermi Era

    Indian Academy of Sciences (India)

    Liang Chen


    In this paper, we review the latest research results on the topic of blazar sequence. It seems that the blazar sequence is phenomenally ruled out, while the theoretical blazar sequence still holds. We point out that black hole mass is a dominated parameter accounting for high-power-high-synchrotron-peaked and low-power-low-sychrotron-peaked blazars. Because most blazars have similar size of emission region, theoretical blazar sequence implies that the break of Spectral Energy Distribution (SED) is a cooling break in nature.

  14. Sequence Algebra, Sequence Decision Diagrams and Dynamic Fault Trees

    Energy Technology Data Exchange (ETDEWEB)

    Rauzy, Antoine B., E-mail: Antoine.Rauzy@lix.polytechnique.f [LIX-CNRS, Computer Science, Ecole Polytechnique, 91128 Palaiseau Cedex (France)


    A large attention has been focused on the Dynamic Fault Trees in the past few years. By adding new gates to static (regular) Fault Trees, Dynamic Fault Trees aim to take into account dependencies among events. Merle et al. proposed recently an algebraic framework to give a formal interpretation to these gates. In this article, we extend Merle et al.'s work by adopting a slightly different perspective. We introduce Sequence Algebras that can be seen as Algebras of Basic Events, representing failures of non-repairable components. We show how to interpret Dynamic Fault Trees within this framework. Finally, we propose a new data structure to encode sets of sequences of Basic Events: Sequence Decision Diagrams. Sequence Decision Diagrams are very much inspired from Minato's Zero-Suppressed Binary Decision Diagrams. We show that all operations of Sequence Algebras can be performed on this data structure.

  15. Characterization of human chromosomal DNA sequences which replicate autonomously in Saccharomyces cerevisiae. (United States)

    Montiel, J F; Norbury, C J; Tuite, M F; Dobson, M J; Mills, J S; Kingsman, A J; Kingsman, S M


    We have characterised two restriction fragments, isolated from a "shotgun" collection of human DNA, which function as autonomously replicating sequences (ARSs) in Saccharomyces cerevisiae. Functional domains of these fragments have been defined by subcloning and exonuclease (BAL 31) deletion analysis. Both fragments contain two spatially distinct domains. One is essential for high frequency transformation and is termed the Replication Sequence (RS) domain, the other, termed the Replication Enhancer (RE) domain, has no inherent replication competence but is essential for ensuring maximum function of the RS domain. The nucleotide sequence of these domains reveals several conserved sequences one of which is strikingly similar to the yeast ARS consensus sequence. PMID:6320114

  16. Expression of Cryptogein in tobacco plants exhibits enhanced disease resistance and tolerance to salt stress

    Institute of Scientific and Technical Information of China (English)

    JIANG Donghua; CHEN Xujun; WU Kunlu; GUO Zejian


    Cryptogein (Crypt), an elicitin secreted from Phytophthora cryptogea, was used for genetic engineering of biotic and abiotic resistance plants. We generated transgenic tobacco plants harboring a rice phenylalanine ammonia-lyase (PAL) promoter and Crypt fusion gene (PAL::Crypt) or the mutated Crypt (mutation of the lysine at the position 13 to valine) under the control CaMV35S promoter (CaMV35S::CryK13V). T2 progeny of the transgenic plants showed significantly enhanced disease resistance to pathogens of fungal Phytophthora parasitica var nicotiana (Ppn) and Alternaria alternata, and bacterial Pseudomonas syringae pv tabaci. The amount of mRNA accumulation of Crypt and CryK13V was quite low in the transgenic lines analyzed by Northern blot, and was detected by a reverse transcription PCR method. Plants harboring PAL::Crypt construct showed faster and stronger induction of PR-1a gene after Ppn inoculation than that in the wild-type plants. The results suggested that the inducible PAL promoter could rapidly respond to pathogen attack and efficiently suppress the pathogen infection. Furthermore, the enhanced tolerance to salt stress in both of the Crypt and CryK13V expressing tobacco plants was also observed compared with that in the control plants. The constitutive expression of PR and transcription factor genes in the transformants was probably associated with the salt tolerance. The above observations suggested that a cross-talk between biotic and abiotic stresses existed in tobacco plants.

  17. Unsupervised statistical clustering of environmental shotgun sequences

    Directory of Open Access Journals (Sweden)

    Bhatnagar Srijak


    Full Text Available Abstract Background The development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. While previous methods have focused primarily on supervised learning involving extrinsic data, a first-principles statistical model combined with a self-training fitting method has not yet been developed. Results We derive an unsupervised, maximum-likelihood formalism for clustering short sequences by their taxonomic origin on the basis of their k-mer distributions. The formalism is implemented using a Markov Chain Monte Carlo approach in a k-mer feature space. We introduce a space transformation that reduces the dimensionality of the feature space and a genomic fragment divergence measure that strongly correlates with the method's performance. Pairwise analysis of over 1000 completely sequenced genomes reveals that the vast majority of genomes have sufficient genomic fragment divergence to be amenable for binning using the present formalism. Using a high-performance implementation, the binner is able to classify fragments as short as 400 nt with accuracy over 90% in simulations of low-complexity communities of 2 to 10 species, given sufficient genomic fragment divergence. The method is available as an open source package called LikelyBin. Conclusion An unsupervised binning method based on statistical signatures of short environmental sequences is a viable stand-alone binning method for low complexity samples. For medium and high complexity samples, we discuss the possibility of combining the current method with other methods as part of an iterative process to enhance the resolving power of sorting reads into taxonomic and/or functional bins.

  18. Bayesian analysis of binary sequences (United States)

    Torney, David C.


    This manuscript details Bayesian methodology for "learning by example", with binary n-sequences encoding the objects under consideration. Priors prove influential; conformable priors are described. Laplace approximation of Bayes integrals yields posterior likelihoods for all n-sequences. This involves the optimization of a definite function over a convex domain--efficiently effectuated by the sequential application of the quadratic program.

  19. Gambling strategies for random sequences


    George Davie


    There is a general consensus that it is not possible to gamble successfully against a random se-quence. This consensus is based on results from probability theory that all gambling systems arein some sense futile and the idea that at any stage of the sequence, the next outcome is entirelyunpredictable.

  20. DNA Sequencing Sensors: An Overview

    Directory of Open Access Journals (Sweden)

    Jose Antonio Garrido-Cardenas


    Full Text Available The first sequencing of a complete genome was published forty years ago by the double Nobel Prize in Chemistry winner Frederick Sanger. That corresponded to the small sized genome of a bacteriophage, but since then there have been many complex organisms whose DNA have been sequenced. This was possible thanks to continuous advances in the fields of biochemistry and molecular genetics, but also in other areas such as nanotechnology and computing. Nowadays, sequencing sensors based on genetic material have little to do with those used by Sanger. The emergence of mass sequencing sensors, or new generation sequencing (NGS meant a quantitative leap both in the volume of genetic material that was able to be sequenced in each trial, as well as in the time per run and its cost. One can envisage that incoming technologies, already known as fourth generation sequencing, will continue to cheapen the trials by increasing DNA reading lengths in each run. All of this would be impossible without sensors and detection systems becoming smaller and more precise. This article provides a comprehensive overview on sensors for DNA sequencing developed within the last 40 years.


    Institute of Scientific and Technical Information of China (English)

    XuChengqian; ZhaoXiaoqun


    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP)is proposed .A new class of block design-Difference Family Pair (DFP)is also proposed .The relationship between PCSP and DFP,the properties and exising conditions of PCSP and the recursive constructions for PCSP are given.


    Institute of Scientific and Technical Information of China (English)

    Xu Chengqian; Zhao Xiaoqun


    A new set of binary sequences-Periodic Complementary Binary Sequence Pair (PCSP) is proposed. A new class of block design-Difference Family Pair (DFP) is also proposed.The relationship between PCSP and DFP, the properties and existing conditions of PCSP and the recursive constructions for PCSP are given.

  3. Sequence conserved for subcellular localization (United States)

    Nair, Rajesh; Rost, Burkhard


    The more proteins diverged in sequence, the more difficult it becomes for bioinformatics to infer similarities of protein function and structure from sequence. The precise thresholds used in automated genome annotations depend on the particular aspect of protein function transferred by homology. Here, we presented the first large-scale analysis of the relation between sequence similarity and identity in subcellular localization. Three results stood out: (1) The subcellular compartment is generally more conserved than what might have been expected given that short sequence motifs like nuclear localization signals can alter the native compartment; (2) the sequence conservation of localization is similar between different compartments; and (3) it is similar to the conservation of structure and enzymatic activity. In particular, we found the transition between the regions of conserved and nonconserved localization to be very sharp, although the thresholds for conservation were less well defined than for structure and enzymatic activity. We found that a simple measure for sequence similarity accounting for pairwise sequence identity and alignment length, the HSSP distance, distinguished accurately between protein pairs of identical and different localizations. In fact, BLAST expectation values outperformed the HSSP distance only for alignments in the subtwilight zone. We succeeded in slightly improving the accuracy of inferring localization through homology by fine tuning the thresholds. Finally, we applied our results to the entire SWISS-PROT database and five entirely sequenced eukaryotes. PMID:12441382

  4. Optimization of CPMG sequences for NMR borehole measurements

    Directory of Open Access Journals (Sweden)

    M. Ronczka


    Full Text Available Nuklear Magnetic Resonance (NMR can provide key information such as porosity and permeability for hydrological characterization of geological material. Especially the NMR transverse relaxation time T2 is used to estimate permeability since it reflects a pore-size dependent relaxation process. The measurement sequence (CPMG usually used consists of several thousands of electromagnetic pulses to densely record the relaxation process. These pulses are equidistantly spaced by a time constant τ. In NMR borehole applications the use of CPMG sequences for measuring the transverse relaxation time T2 is limited due to requirements on energy consumption. It is state of the art to conduct at least two sequences with different echo spacings (τ for recording fast and slow relaxing processes that correspond to different pore-sizes. For the purpose to reduce the amount of energy used for conducting CPMG sequences and to obtain both, slow and fast, decaying components within one sequence we tested the usage of CPMG sequences with an increasing τ and a decreasing number of pulses. A synthetic study as well as laboratory measurements on samples of glass beads and granulate of different grain size spectra were conducted to evaluate the effects of of an increasing τ spacing, e.g. an enhanced relaxation due to diffusion processes. The results are showing broadened T2 distributions if the number of pulses is decreasing and the mean grain size is increasing, which is mostly an effect of a significantly shortened acquisition time. The shift of T2 distributions to small decay times in dependence of the τ spacing and the mean grain size distribution is observable. We found that it is possible to conduct CPMG sequences with an increased τ spacing. According to the acquisition time and enhanced diffusion the sequence parameters (number of pulses and τmax has to be chosen carefully. Otherwise the underestimated relaxation time (T2 will lead to misinterpretations.

  5. Quantum Exchangeable Sequences of Algebras

    CERN Document Server

    Curran, Stephen


    We extend the notion of quantum exchangeability, introduced by K\\"ostler and Speicher in arXiv:0807.0677, to sequences (\\rho_1,\\rho_2,...c) of homomorphisms from an algebra C into a noncommutative probability space (A,\\phi), and prove a free de Finetti theorem: an infinite quantum exchangeable sequence (\\rho_1,\\rho_2,...c) is freely independent and identically distributed with respect to a conditional expectation. As a corollary we obtain a free analogue of the Hewitt Savage zero-one law. As in the classical case, the theorem fails for finite sequences. We give a characterization of finite quantum exchangeable sequences, which can be viewed as a noncommutative analogue of sampling without replacement. We then give an approximation to how far a finite quantum exchangeable sequence is from being freely independent with amalgamation.

  6. Protein sequence classification with improved extreme learning machine algorithms. (United States)

    Cao, Jiuwen; Xiong, Lianglin


    Precisely classifying a protein sequence from a large biological protein sequences database plays an important role for developing competitive pharmacological products. Comparing the unseen sequence with all the identified protein sequences and returning the category index with the highest similarity scored protein, conventional methods are usually time-consuming. Therefore, it is urgent and necessary to build an efficient protein sequence classification system. In this paper, we study the performance of protein sequence classification using SLFNs. The recent efficient extreme learning machine (ELM) and its invariants are utilized as the training algorithms. The optimal pruned ELM is first employed for protein sequence classification in this paper. To further enhance the performance, the ensemble based SLFNs structure is constructed where multiple SLFNs with the same number of hidden nodes and the same activation function are used as ensembles. For each ensemble, the same training algorithm is adopted. The final category index is derived using the majority voting method. Two approaches, namely, the basic ELM and the OP-ELM, are adopted for the ensemble based SLFNs. The performance is analyzed and compared with several existing methods using datasets obtained from the Protein Information Resource center. The experimental results show the priority of the proposed algorithms.

  7. Inference of splicing regulatory activities by sequence neighborhood analysis.

    Directory of Open Access Journals (Sweden)

    Michael B Stadler


    Full Text Available Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI that predicts sequences with activity in regulating a biochemical process based on the local density of known sites in sequence space. Applied to the problem of RNA splicing regulation, NI was used to predict hundreds of new exonic splicing enhancer (ESE and silencer (ESS hexanucleotides from known human ESEs and ESSs. These predictions were supported by cross-validation analysis, by analysis of published splicing regulatory activity data, by sequence-conservation analysis, and by measurement of the splicing regulatory activity of 24 novel predicted ESEs, ESSs, and neutral sequences using an in vivo splicing reporter assay. These results demonstrate the ability of NI to accurately predict splicing regulatory activity and show that the scope of exonic splicing regulatory elements is substantially larger than previously anticipated. Analysis of orthologous exons in four mammals showed that the NI score of ESEs, a measure of function, is much more highly conserved above background than ESE primary sequence. This observation indicates a high degree of selection for ESE activity in mammalian exons, with surprisingly frequent interchangeability between ESE sequences.

  8. SeqControl: process control for DNA sequencing. (United States)

    Chong, Lauren C; Albuquerque, Marco A; Harding, Nicholas J; Caloian, Cristian; Chan-Seng-Yue, Michelle; de Borja, Richard; Fraser, Michael; Denroche, Robert E; Beck, Timothy A; van der Kwast, Theodorus; Bristow, Robert G; McPherson, John D; Boutros, Paul C


    As high-throughput sequencing continues to increase in speed and throughput, routine clinical and industrial application draws closer. These 'production' settings will require enhanced quality monitoring and quality control to optimize output and reduce costs. We developed SeqControl, a framework for predicting sequencing quality and coverage using a set of 15 metrics describing overall coverage, coverage distribution, basewise coverage and basewise quality. Using whole-genome sequences of 27 prostate cancers and 26 normal references, we derived multivariate models that predict sequencing quality and depth. SeqControl robustly predicted how much sequencing was required to reach a given coverage depth (area under the curve (AUC) = 0.993), accurately classified clinically relevant formalin-fixed, paraffin-embedded samples, and made predictions from as little as one-eighth of a sequencing lane (AUC = 0.967). These techniques can be immediately incorporated into existing sequencing pipelines to monitor data quality in real time. SeqControl is available at

  9. Rapid multi-locus sequence typing using microfluidic biochips.

    Directory of Open Access Journals (Sweden)

    Timothy D Read

    Full Text Available BACKGROUND: Multiple locus sequence typing (MLST has become a central genotyping strategy for analysis of bacterial populations. The scheme involves de novo sequencing of 6-8 housekeeping loci to assign unique sequence types. In this work we adapted MLST to a rapid microfluidics platform in order to enhance speed and reduce laboratory labor time. METHODOLOGY/PRINCIPAL FINDINGS: Using two integrated microfluidic devices, DNA was purified from 100 Bacillus cereus soil isolates, used as a template for multiplex amplification of 7 loci and sequenced on forward and reverse strands. The time on instrument from loading genomic DNA to generation of electropherograms was only 1.5 hours. We obtained full-length sequence of all seven MLST alleles from 84 representing 46 different Sequence Types. At least one allele could be sequenced from a further 15 strains. The nucleotide diversity of B. cereus isolated in this study from one location in Rockville, Maryland (0.04 substitutions per site was found to be as great as the global collection of isolates. CONCLUSIONS/SIGNIFICANCE: Biogeographical investigation of pathogens is only one of a panoply of possible applications of microfluidics based MLST; others include microbiologic forensics, biothreat identification, and rapid characterization of human clinical samples.

  10. The Parallel Maximal Cliques Algorithm for Protein Sequence Clustering

    Directory of Open Access Journals (Sweden)

    Khalid Jaber


    Full Text Available Problem statement: Protein sequence clustering is a method used to discover relations between proteins. This method groups the proteins based on their common features. It is a core process in protein sequence classification. Graph theory has been used in protein sequence clustering as a means of partitioning the data into groups, where each group constitutes a cluster. Mohseni-Zadeh introduced a maximal cliques algorithm for protein clustering. Approach: In this study we adapted the maximal cliques algorithm of Mohseni-Zadeh to find cliques in protein sequences and we then parallelized the algorithm to improve computation times and allowed large protein databases to be processed. We used the N-Gram Hirschberg approach proposed by Abdul Rashid to calculate the distance between protein sequences. The task farming parallel program model was used to parallelize the enhanced cliques algorithm. Results: Our parallel maximal cliques algorithm was implemented on the stealth cluster using the C programming language and a hybrid approach that includes both the Message Passing Interface (MPI library and POSIX threads (PThread to accelerate protein sequence clustering. Conclusion: Our results showed a good speedup over sequential algorithms for cliques in protein sequences.

  11. Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria

    DEFF Research Database (Denmark)

    Larsen, Mette Voldby; Cosentino, Salvatore; Rasmussen, Simon


    Accurate strain identification is essential for anyone working with bacteria. For many species, multilocus sequence typing (MLST) is considered the "gold standard" of typing, but it is traditionally performed in an expensive and time-consuming manner. As the costs of whole-genome sequencing (WGS......) continue to decline, it becomes increasingly available to scientists and routine diagnostic laboratories. Currently, the cost is below that of traditional MLST. The new challenges will be how to extract the relevant information from the large amount of data so as to allow for comparison over time...... and between laboratories. Ideally, this information should also allow for comparison to historical data. We developed a Web-based method for MLST of 66 bacterial species based on WGS data. As input, the method uses short sequence reads from four sequencing platforms or preassembled genomes. Updates from...

  12. Ossification sequence heterochrony among amphibians. (United States)

    Harrington, Sean M; Harrison, Luke B; Sheil, Christopher A


    Heterochrony is an important mechanism in the evolution of amphibians. Although studies have centered on the relationship between size and shape and the rates of development, ossification sequence heterochrony also may have been important. Rigorous, phylogenetic methods for assessing sequence heterochrony are relatively new, and a comprehensive study of the relative timing of ossification of skeletal elements has not been used to identify instances of sequence heterochrony across Amphibia. In this study, a new version of the program Parsimov-based genetic inference (PGi) was used to identify shifts in ossification sequences across all extant orders of amphibians, for all major structural units of the skeleton. PGi identified a number of heterochronic sequence shifts in all analyses, the most interesting of which seem to be tied to differences in metamorphic patterns among major clades. Early ossification of the vomer, premaxilla, and dentary is retained by Apateon caducus and members of Gymnophiona and Urodela, which lack the strongly biphasic development seen in anurans. In contrast, bones associated with the jaws and face were identified as shifting late in the ancestor of Anura. The bones that do not shift late, and thereby occupy the earliest positions in the anuran cranial sequence, are those in regions of the skull that undergo the least restructuring throughout anuran metamorphosis. Additionally, within Anura, bones of the hind limb and pelvic girdle were also identified as shifting early in the sequence of ossification, which may be a result of functional constraints imposed by the drastic metamorphosis of most anurans.


    Directory of Open Access Journals (Sweden)

    Ahmed Mohamed El-Shehawi


    Full Text Available Isoflavones are large group of secondary metabolites produced in legumes such as soybeans. They have essential biological functions as nutraceutical and health functions for human. They are involved in plant resistance to biotic and abiotic stresses, symbiotic relationship with nitrogen-fixing organisms and plant competition (allelopathy. In this report, isoflavonoids were expressed in wheat (Triticum aestivum via introducing the key enzymes Isoflavone Synthase (IFS. Transgenic callli induced from wheat immature embryos were propagated and prepared for bombardment. Five gene constructs were prepared; the binary vector (plasmid pAHC25, 35S-CRC, 35S-IFS, Oleocin-IFS, Oleocin-IFS-CHI and were used for wheat calli transformation. Putative transgenic calli were used to regenerate transgenic wheat plants. Evaluation of recovered transgenic plants was carried out using PCR, southern bloting of PCR products and IFS-specific probe and HPLC analysis of transgenic plant tissue extracts. Genistein and naranigenin were detected in transgenic plants carrying IFS gene, indicating that the introduced IFS was able to use the endogenous substrate from wheat. IFS showed activity under 35S promoter as well as oleocin promoter. The activity of oleocin promoter in monocots provides a good tool to use plant promoters to drive plant gene expression in plants. This also represents promoter compatibility that the cis acting elements of the oleocin promoter represent binding targets for trans acting elements of wheat. Engineering the isoflavone pathway in wheat would lead to enhancement of nutraceutical value of wheat grains and improvement of wheat resistance to diseases.

  14. Jmol-Enhanced Biochemistry Research Projects (United States)

    Saderholm, Matthew; Reynolds, Anthony


    We developed a protein research project for a one-semester biochemistry lecture class to enhance learning and more effectively train students to understand protein structure and function. During this semester-long process, students select a protein with known structure and then research its structure, sequence, and function. This project…

  15. A Criterion for Regular Sequences

    Indian Academy of Sciences (India)

    D P Patil; U Storch; J Stückrad


    Let be a commutative noetherian ring and $f_1,\\ldots,f_r \\in R$. In this article we give (cf. the Theorem in $\\mathcal{x}$2) a criterion for $f_1,\\ldots,f_r$ to be regular sequence for a finitely generated module over which strengthens and generalises a result in [2]. As an immediate consequence we deduce that if $V(g_1,\\ldots,g_r) \\subseteq V(f_1,\\ldots,f_r)$ in Spec and if $f_1,\\ldots,f_r$ is a regular sequence in , then $g_1,\\ldots,g_r$ is also a regular sequence in .

  16. Weak disorder in Fibonacci sequences

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Naim, E [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Krapivsky, P L [Department of Physics and Center for Molecular Cybernetics, Boston University, Boston, MA 02215 (United States)


    We study how weak disorder affects the growth of the Fibonacci series. We introduce a family of stochastic sequences that grow by the normal Fibonacci recursion with probability 1 - {epsilon}, but follow a different recursion rule with a small probability {epsilon}. We focus on the weak disorder limit and obtain the Lyapunov exponent that characterizes the typical growth of the sequence elements, using perturbation theory. The limiting distribution for the ratio of consecutive sequence elements is obtained as well. A number of variations to the basic Fibonacci recursion including shift, doubling and copying are considered. (letter to the editor)

  17. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

    Energy Technology Data Exchange (ETDEWEB)

    Clum, Alicia; Nolan, Matt; Lang, Elke; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Goker, Markus; Spring, Stefan; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla


    Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger


    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  19. Classification of Base Sequences (+1,

    Directory of Open Access Journals (Sweden)

    Dragomir Ž. Ðoković


    Full Text Available Base sequences BS(+1, are quadruples of {±1}-sequences (;;;, with A and B of length +1 and C and D of length n, such that the sum of their nonperiodic autocor-relation functions is a -function. The base sequence conjecture, asserting that BS(+1, exist for all n, is stronger than the famous Hadamard matrix conjecture. We introduce a new definition of equivalence for base sequences BS(+1, and construct a canonical form. By using this canonical form, we have enumerated the equivalence classes of BS(+1, for ≤30. As the number of equivalence classes grows rapidly (but not monotonically with n, the tables in the paper cover only the cases ≤13.

  20. Molecular beacon sequence design algorithm. (United States)

    Monroe, W Todd; Haselton, Frederick R


    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  1. Pythagorean Triples from Harmonic Sequences. (United States)

    DiDomenico, Angelo S.; Tanner, Randy J.


    Shows how all primitive Pythagorean triples can be generated from harmonic sequences. Use inductive and deductive reasoning to explore how Pythagorean triples are connected with another area of mathematics. (KHR)

  2. ISIS Individualized Support In Sequencing

    NARCIS (Netherlands)

    Drachsler, Hendrik; Hummel, Hans


    Drachsler, H., & Hummel, H. G. K. (2007). ISIS Individualized Support In Sequencing. Presentation given during the PIP meeting on March 22, 2007. Open University of the Netherlands: Heerlen, The Netherlands.

  3. Overview of Sequence Data Formats. (United States)

    Zhang, Hongen


    Next-generation sequencing experiment can generate billions of short reads for each sample and processing of the raw reads will add more information. Various file formats have been introduced/developed in order to store and manipulate this information. This chapter presents an overview of the file formats including FASTQ, FASTA, SAM/BAM, GFF/GTF, BED, and VCF that are commonly used in analysis of next-generation sequencing data.

  4. Many human accelerated regions are developmental enhancers. (United States)

    Capra, John A; Erwin, Genevieve D; McKinsey, Gabriel; Rubenstein, John L R; Pollard, Katherine S


    The genetic changes underlying the dramatic differences in form and function between humans and other primates are largely unknown, although it is clear that gene regulatory changes play an important role. To identify regulatory sequences with potentially human-specific functions, we and others used comparative genomics to find non-coding regions conserved across mammals that have acquired many sequence changes in humans since divergence from chimpanzees. These regions are good candidates for performing human-specific regulatory functions. Here, we analysed the DNA sequence, evolutionary history, histone modifications, chromatin state and transcription factor (TF) binding sites of a combined set of 2649 non-coding human accelerated regions (ncHARs) and predicted that at least 30% of them function as developmental enhancers. We prioritized the predicted ncHAR enhancers using analysis of TF binding site gain and loss, along with the functional annotations and expression patterns of nearby genes. We then tested both the human and chimpanzee sequence for 29 ncHARs in transgenic mice, and found 24 novel developmental enhancers active in both species, 17 of which had very consistent patterns of activity in specific embryonic tissues. Of these ncHAR enhancers, five drove expression patterns suggestive of different activity for the human and chimpanzee sequence at embryonic day 11.5. The changes to human non-coding DNA in these ncHAR enhancers may modify the complex patterns of gene expression necessary for proper development in a human-specific manner and are thus promising candidates for understanding the genetic basis of human-specific biology.

  5. Enhancement in Sport, and Enhancement outside Sport. (United States)

    Douglas, Thomas


    Sport is one of the first areas in which enhancement has become commonplace. It is also one of the first areas in which the use of enhancement technologies has been heavily regulated. Some have thus seen sport as a testing ground for arguments about whether to permit enhancement. However, I argue that there are fairness-based objections to enhancement in sport that do not apply as strongly in some other areas of human activity. Thus, I claim that there will often be a stronger case for permitting enhancement outside of sport than for permitting enhancement in sport. I end by considering some methodological implications of this conclusion.

  6. Enhancing chaoticity of spatiotemporal chaos. (United States)

    Li, Xiaowen; Zhang, Heqiao; Xue, Yu; Hu, Gang


    In some practical situations strong chaos is needed. This introduces the task of chaos control with enhancing chaoticity rather than suppressing chaoticity. In this paper a simple method of linear amplifications incorporating modulo operations is suggested to make spatiotemporal systems, which may be originally chaotic or nonchaotic, strongly chaotic. Specifically, this control can eliminate periodic windows, increase the values and the number of positive Lyapunov exponents, make the probability distributions of the output chaotic sequences more homogeneous, and reduce the correlations of chaotic outputs for different times and different space units. The applicability of the method to practical tasks, in particular to random number generators and secure communications, is briefly discussed.

  7. Genome Sequence of Canine Herpesvirus.

    Directory of Open Access Journals (Sweden)

    Konstantinos V Papageorgiou

    Full Text Available Canine herpesvirus is a widespread alphaherpesvirus that causes a fatal haemorrhagic disease of neonatal puppies. We have used high-throughput methods to determine the genome sequences of three viral strains (0194, V777 and V1154 isolated in the United Kingdom between 1985 and 2000. The sequences are very closely related to each other. The canine herpesvirus genome is estimated to be 125 kbp in size and consists of a unique long sequence (97.5 kbp and a unique short sequence (7.7 kbp that are each flanked by terminal and internal inverted repeats (38 bp and 10.0 kbp, respectively. The overall nucleotide composition is 31.6% G+C, which is the lowest among the completely sequenced alphaherpesviruses. The genome contains 76 open reading frames predicted to encode functional proteins, all of which have counterparts in other alphaherpesviruses. The availability of the sequences will facilitate future research on the diagnosis and treatment of canine herpesvirus-associated disease.

  8. Inflammation-sensitive super enhancers form domains of coordinately regulated enhancer RNAs. (United States)

    Hah, Nasun; Benner, Chris; Chong, Ling-Wa; Yu, Ruth T; Downes, Michael; Evans, Ronald M


    Enhancers are critical genomic elements that define cellular and functional identity through the spatial and temporal regulation of gene expression. Recent studies suggest that key genes regulating cell type-specific functions reside in enhancer-dense genomic regions (i.e., super enhancers, stretch enhancers). Here we report that enhancer RNAs (eRNAs) identified by global nuclear run-on sequencing are extensively transcribed within super enhancers and are dynamically regulated in response to cellular signaling. Using Toll-like receptor 4 (TLR4) signaling in macrophages as a model system, we find that transcription of super enhancer-associated eRNAs is dynamically induced at most of the key genes driving innate immunity and inflammation. Unexpectedly, genes repressed by TLR4 signaling are also associated with super enhancer domains and accompanied by massive repression of eRNA transcription. Furthermore, we find each super enhancer acts as a single regulatory unit within which eRNA and genic transcripts are coordinately regulated. The key regulatory activity of these domains is further supported by the finding that super enhancer-associated transcription factor binding is twice as likely to be conserved between human and mouse than typical enhancer sites. Our study suggests that transcriptional activities at super enhancers are critical components to understand the dynamic gene regulatory network.

  9. Rational Design of Biobetters with Enhanced Stability. (United States)

    Courtois, Fabienne; Schneider, Curtiss P; Agrawal, Neeraj J; Trout, Bernhardt L


    Biotherapeutics are the fastest growing class of pharmaceutical with a rapidly evolving market facing the rise of biosimilar and biobetter products. In contrast to a biosimilar, which is derived from the same gene sequence as the innovator product, a biobetter has enhanced properties, such as enhanced efficacy or reduced immunogenicity. Little work has been carried out so far to increase the intrinsic stability of biotherapeutics via sequence changes, even though, aggregation, the primary degradation pathway of proteins, leads to issues ranging from manufacturing failure to immunological response and to loss of therapeutic activity. Using our spatial aggregation propensity tool as a first step to a rational design approach to identify aggregation-prone regions, biobetters of rituximab have been produced with enhanced stability by introducing site-specific mutations. Significant stabilization against aggregation was achieved for rituximab with no decrease in its binding affinity to the antigen.

  10. Long-range barcode labeling-sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Feng; Zhang, Tao; Singh, Kanwar K.; Pennacchio, Len A.; Froula, Jeff L.; Eng, Kevin S.


    Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

  11. Pig genome sequence - analysis and publication strategy

    NARCIS (Netherlands)

    Archibald, A.L.; Bolund, L.; Churcher, C.; Fredholm, M.; Groenen, M.A.M.; Harlizius, B.


    Background - The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. Results - Assemblies of the B

  12. Sequencing and comparative analysis of the gorilla MHC genomic sequence. (United States)

    Wilming, Laurens G; Hart, Elizabeth A; Coggill, Penny C; Horton, Roger; Gilbert, James G R; Clee, Chris; Jones, Matt; Lloyd, Christine; Palmer, Sophie; Sims, Sarah; Whitehead, Siobhan; Wiley, David; Beck, Stephan; Harrow, Jennifer L


    Major histocompatibility complex (MHC) genes play a critical role in vertebrate immune response and because the MHC is linked to a significant number of auto-immune and other diseases it is of great medical interest. Here we describe the clone-based sequencing and subsequent annotation of the MHC region of the gorilla genome. Because the MHC is subject to extensive variation, both structural and sequence-wise, it is not readily amenable to study in whole genome shotgun sequence such as the recently published gorilla genome. The variation of the MHC also makes it of evolutionary interest and therefore we analyse the sequence in the context of human and chimpanzee. In our comparisons with human and re-annotated chimpanzee MHC sequence we find that gorilla has a trimodular RCCX cluster, versus the reference human bimodular cluster, and additional copies of Class I (pseudo)genes between Gogo-K and Gogo-A (the orthologues of HLA-K and -A). We also find that Gogo-H (and Patr-H) is coding versus the HLA-H pseudogene and, conversely, there is a Gogo-DQB2 pseudogene versus the HLA-DQB2 coding gene. Our analysis, which is freely available through the VEGA genome browser, provides the research community with a comprehensive dataset for comparative and evolutionary research of the MHC.


    Directory of Open Access Journals (Sweden)

    Guillermo eBorragán


    Full Text Available Enhanced procedural learning has been evidenced in conditions where cognitive control is diminished, including hypnosis, disruption of prefrontal activity and non-optimal time of the day. Another condition depleting the availability of controlled resources is cognitive fatigue. We tested the hypothesis that cognitive fatigue, eventually leading to diminished cognitive control, facilitates procedural sequence learning. In a two-day experiment, twenty-three young healthy adults were administered a serial reaction time task (SRTT following the induction of high or low levels of cognitive fatigue, in a counterbalanced order. Cognitive fatigue was induced using the Time load Dual-back (TloadDback paradigm, a dual working memory task that allows tailoring cognitive load levels to the individual's optimal performance capacity. In line with our hypothesis, reaction times in the SRTT were faster in the high- than in the low-level fatigue condition, and performance improvement showed more of a benefit from the sequential components than from motor. Altogether, our results suggest a paradoxical, facilitating impact of cognitive fatigue on procedural motor sequence learning. We propose that facilitated learning in the high-level fatigue condition stems from a reduction in the cognitive resources devoted to cognitive control processes that normally oppose automatic procedural acquisition mechanisms.

  14. Depositional sequence evolution, Paleozoic and early Mesozoic of the central Saharan platform, North Africa

    Energy Technology Data Exchange (ETDEWEB)

    Sprague, A.R.G. (Exxon Production Research Co., Houston, TX (United States))


    Over 30 depositional sequences have been identified in the Paleozoic and lower Mesozoic of the Ghadames basin of eastern Algeria, southern Tunisia, and western Libya. Well logs and lithologic information from more than 500 wells were used to correlate the 30 sequences throughout the basin (total area more than 1 million km{sup 2}). Based on systematic change in the log response of strata in successively younger sequences, five groups of sequences with distinctive characteristics have been identified: Cambro-Ordivician, Upper Silurian-Middle Devonian, Upper Devonian, Carboniferous, and Middle Triassic-Middle Jurassic. Each sequence group is terminated by a major, tectonically enhanced sequence boundary that is immediately overlain (except for the Carboniferous) by a shale-prone interval deposited in response to basin-wide flooding. The four Paleozoic sequence groups were deposited on the Saharan platform, a north facing, clastic-dominated shelf that covered most of North Africa during the Paleozoic. The sequence boundary at the top of the Carboniferous sequence group is one of several Permian-Carboniferous angular unconformities in North Africa related to the Hercynian orogeny. The youngest sequence group (Middle Triassic to Middle Jurassic) is a clastic-evaporite package that onlaps southward onto the top of Paleozoic sequence boundary. The progressive changes from the Cambrian to the Jurassic, in the nature of the Ghadames basin sequences is a reflection of the interplay between basin morphology and tectonics, vegetation, eustasy, climate, and sediment supply.

  15. Quantitative modeling of a gene's expression from its intergenic sequence.

    Directory of Open Access Journals (Sweden)

    Md Abul Hassan Samee


    Full Text Available Modeling a gene's expression from its intergenic locus and trans-regulatory context is a fundamental goal in computational biology. Owing to the distributed nature of cis-regulatory information and the poorly understood mechanisms that integrate such information, gene locus modeling is a more challenging task than modeling individual enhancers. Here we report the first quantitative model of a gene's expression pattern as a function of its locus. We model the expression readout of a locus in two tiers: 1 combinatorial regulation by transcription factors bound to each enhancer is predicted by a thermodynamics-based model and 2 independent contributions from multiple enhancers are linearly combined to fit the gene expression pattern. The model does not require any prior knowledge about enhancers contributing toward a gene's expression. We demonstrate that the model captures the complex multi-domain expression patterns of anterior-posterior patterning genes in the early Drosophila embryo. Altogether, we model the expression patterns of 27 genes; these include several gap genes, pair-rule genes, and anterior, posterior, trunk, and terminal genes. We find that the model-selected enhancers for each gene overlap strongly with its experimentally characterized enhancers. Our findings also suggest the presence of sequence-segments in the locus that would contribute ectopic expression patterns and hence were "shut down" by the model. We applied our model to identify the transcription factors responsible for forming the stripe boundaries of the studied genes. The resulting network of regulatory interactions exhibits a high level of agreement with known regulatory influences on the target genes. Finally, we analyzed whether and why our assumption of enhancer independence was necessary for the genes we studied. We found a deterioration of expression when binding sites in one enhancer were allowed to influence the readout of another enhancer. Thus, interference

  16. ChIP-seq Identification of Weakly Conserved Heart Enhancers

    Energy Technology Data Exchange (ETDEWEB)

    Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.


    Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type.

  17. Shadow enhancers enable Hunchback bifunctionality in the Drosophila embryo. (United States)

    Staller, Max V; Vincent, Ben J; Bragdon, Meghan D J; Lydiard-Martin, Tara; Wunderlich, Zeba; Estrada, Javier; DePace, Angela H


    Hunchback (Hb) is a bifunctional transcription factor that activates and represses distinct enhancers. Here, we investigate the hypothesis that Hb can activate and repress the same enhancer. Computational models predicted that Hb bifunctionally regulates the even-skipped (eve) stripe 3+7 enhancer (eve3+7) in Drosophila blastoderm embryos. We measured and modeled eve expression at cellular resolution under multiple genetic perturbations and found that the eve3+7 enhancer could not explain endogenous eve stripe 7 behavior. Instead, we found that eve stripe 7 is controlled by two enhancers: the canonical eve3+7 and a sequence encompassing the minimal eve stripe 2 enhancer (eve2+7). Hb bifunctionally regulates eve stripe 7, but it executes these two activities on different pieces of regulatory DNA--it activates the eve2+7 enhancer and represses the eve3+7 enhancer. These two "shadow enhancers" use different regulatory logic to create the same pattern.

  18. ARC Code TI: sequenceMiner (United States)

    National Aeronautics and Space Administration — The sequenceMiner was developed to address the problem of detecting and describing anomalies in large sets of high-dimensional symbol sequences. sequenceMiner works...

  19. Sequence-dependent nucleosome positioning. (United States)

    Chung, Ho-Ryun; Vingron, Martin


    Eukaryotic DNA is organized into a macromolecular structure called chromatin. The basic repeating unit of chromatin is the nucleosome, which consists of two copies of each of the four core histones and DNA. The nucleosomal organization and the positions of nucleosomes have profound effects on all DNA-dependent processes. Understanding the factors that influence nucleosome positioning is therefore of general interest. Among the many determinants of nucleosome positioning, the DNA sequence has been proposed to have a major role. Here, we analyzed more than 860,000 nucleosomal DNA sequences to identify sequence features that guide the formation of nucleosomes in vivo. We found that both a periodic enrichment of AT base pairs and an out-of-phase oscillating enrichment of GC base pairs as well as the overall preference for GC base pairs are determinants of nucleosome positioning. The preference for GC pairs can be related to a lower energetic cost required for deformation of the DNA to wrap around the histones. In line with this idea, we found that only incorporation of both signal components into a sequence model for nucleosome formation results in maximal predictive performance on a genome-wide scale. In this manner, one achieves greater predictive power than published approaches. Our results confirm the hypothesis that the DNA sequence has a major role in nucleosome positioning in vivo.

  20. Sequencing Needs for Viral Diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Lam, M; Mulakken, N J; Torres, C L; Smith, J R; Slezak, T


    We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''near neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.

  1. Identification of DVA interneuron regulatory sequences in Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Carmie Puckett Robinson

    Full Text Available BACKGROUND: The identity of each neuron is determined by the expression of a distinct group of genes comprising its terminal gene battery. The regulatory sequences that control the expression of such terminal gene batteries in individual neurons is largely unknown. The existence of a complete genome sequence for C. elegans and draft genomes of other nematodes let us use comparative genomics to identify regulatory sequences directing expression in the DVA interneuron. METHODOLOGY/PRINCIPAL FINDINGS: Using phylogenetic comparisons of multiple Caenorhabditis species, we identified conserved non-coding sequences in 3 of 10 genes (fax-1, nmr-1, and twk-16 that direct expression of reporter transgenes in DVA and other neurons. The conserved region and flanking sequences in an 85-bp intronic region of the twk-16 gene directs highly restricted expression in DVA. Mutagenesis of this 85 bp region shows that it has at least four regions. The central 53 bp region contains a 29 bp region that represses expression and a 24 bp region that drives broad neuronal expression. Two short flanking regions restrict expression of the twk-16 gene to DVA. A shared GA-rich motif was identified in three of these genes but had opposite effects on expression when mutated in the nmr-1 and twk-16 DVA regulatory elements. CONCLUSIONS/SIGNIFICANCE: We identified by multi-species conservation regulatory regions within three genes that direct expression in the DVA neuron. We identified four contiguous regions of sequence of the twk-16 gene enhancer with positive and negative effects on expression, which combined to restrict expression to the DVA neuron. For this neuron a single binding site may thus not achieve sufficient specificity for cell specific expression. One of the positive elements, an 8-bp sequence required for expression was identified in silico by sequence comparisons of seven nematode species, demonstrating the potential resolution of expanded multi

  2. The Star-Forming Main Sequence at Low Galaxy Mass (United States)

    Stierwalt, Sabrina; Johnson, Kelsey E.; Patton, David R.; Besla, Gurtina; Kallivayalil, Nitya; Liss, Sandra; Pearson, Sarah; Privon, George C.; Putman, Mary E.


    We present an investigation of the star-forming main sequence at the low mass end. The relation between galaxy stellar mass and star formation rate has been well-studied in the recent literature for a range of redshifts and galaxy type, but almost all of these studies are limited to galaxies with stellar masses above the dwarf galaxy range ( 109 Msun ). Our work, based on the panchromatic TiNy Titans survey of interacting dwarf galaxies, shows that dwarf galaxies extend the well-established main sequence at z=0 down to lower masses. Furthermore, like their more massive counterparts, dwarf mergers appear on an elevated main sequence with higher star formation rates for a given stellar mass. Finally we show that star formation is enhanced to a greater extent in low mass galaxy mergers than for higher mass systems.

  3. S-sequence patterned illumination iterative photoacoustic tomography. (United States)

    Harrison, Tyler; Shao, Peng; Zemp, Roger J


    Quantitatively reconstructing optical absorption using photoacoustic imaging is nontrivial. Theoretical hurdles, such as nonuniqueness and numerical instability, can be mitigated by using multiple illuminations. However, even with multiple illuminations, using ANSI-safety-limited fluence for practical imaging may result in poor performance owing to limited signal-to-noise ratio (SNR). We demonstrate the use of S-sequence coded patterned illumination to boost SNR while preserving the enhanced stability of multiple-illumination iterative techniques.

  4. Origin and evolution of developmental enhancers in the mammalian neocortex. (United States)

    Emera, Deena; Yin, Jun; Reilly, Steven K; Gockley, Jake; Noonan, James P


    Morphological innovations such as the mammalian neocortex may involve the evolution of novel regulatory sequences. However, de novo birth of regulatory elements active during morphogenesis has not been extensively studied in mammals. Here, we use H3K27ac-defined regulatory elements active during human and mouse corticogenesis to identify enhancers that were likely active in the ancient mammalian forebrain. We infer the phylogenetic origins of these enhancers and find that ∼20% arose in the mammalian stem lineage, coincident with the emergence of the neocortex. Implementing a permutation strategy that controls for the nonrandom variation in the ages of background genomic sequences, we find that mammal-specific enhancers are overrepresented near genes involved in cell migration, cell signaling, and axon guidance. Mammal-specific enhancers are also overrepresented in modules of coexpressed genes in the cortex that are associated with these pathways, notably ephrin and semaphorin signaling. Our results also provide insight into the mechanisms of regulatory innovation in mammals. We find that most neocortical enhancers did not originate by en bloc exaptation of transposons. Young neocortical enhancers exhibit smaller H3K27ac footprints and weaker evolutionary constraint in eutherian mammals than older neocortical enhancers. Based on these observations, we present a model of the enhancer life cycle in which neocortical enhancers initially emerge from genomic background as short, weakly constrained "proto-enhancers." Many proto-enhancers are likely lost, but some may serve as nucleation points for complex enhancers to evolve.

  5. Eukaryotic enhancers: common features, regulation, and participation in diseases. (United States)

    Erokhin, Maksim; Vassetzky, Yegor; Georgiev, Pavel; Chetverina, Darya


    Enhancers are positive DNA regulatory sequences controlling temporal and tissue-specific gene expression. These elements act independently of their orientation and distance relative to the promoters of target genes. Enhancers act through a variety of transcription factors that ensure their correct match with target promoters and consequent gene activation. There is a growing body of evidence on association of enhancers with transcription factors, co-activators, histone chromatin marks, and lncRNAs. Alterations in enhancers lead to misregulation of gene expression, causing a number of human diseases. In this review, we focus on the common characteristics of enhancers required for transcription stimulation.

  6. Sequence Patterns of Identity Authentication Protocols

    Institute of Scientific and Technical Information of China (English)

    Tao Hongcai; He Dake


    From the viewpoint of protocol sequence, analyses are made of the sequence patterns of possible identity authentication protocol under two cases: with or without the trusted third party (TTP). Ten feasible sequence patterns of authentication protocol with TTP and 5 sequence patterns without TTP are gained. These gained sequence patterns meet the requirements for identity authentication,and basically cover almost all the authentication protocols with TTP and without TTP at present. All of the sequence patterns gained are classified into unilateral or bilateral authentication. Then , according to the sequence symmetry, several good sequence patterns with TTP are evaluated. The accompolished results can provide a reference to design of new identity authentication protocols.

  7. Comparative analysis of sequences from PT 2013

    DEFF Research Database (Denmark)

    Mikkelsen, Susie Sommer

    . All but one sequence mapped to the MCP gene while the last sequence mapped to the Neurofilament gene. Approx. half of the sequences contained no errors while the rest differed with 88-99 percent similarity with most having 99% similarity. One sequence, when BLASTed, showed most similarity to European...... Sheatfish and not EHNV. Generally, mistakes occurred at the ends of the sequences. This can be due to several factors. One is that the sequence has not been trimmed of the sequence primer sites. Another is the lack of quality control of the chromatogram. Finally, sequencing in just one direction can result...

  8. On the base sequence conjecture

    CERN Document Server

    Djokovic, Dragomir Z


    Let BS(m,n) denote the set of base sequences (A;B;C;D), with A and B of length m and C and D of length n. The base sequence conjecture (BSC) asserts that BS(n+1,n) exist (i.e., are non-empty) for all n. This is known to be true for n <= 36 and when n is a Golay number. We show that it is also true for n=37 and n=38. It is worth pointing out that BSC is stronger than the famous Hadamard matrix conjecture. In order to demonstrate the abundance of base sequences, we have previously attached to BS(n+1,n) a graph Gamma_n and computed the Gamma_n for n <= 27. We now extend these computations and determine the Gamma_n for n=28,...,35. We also propose a conjecture describing these graphs in general.

  9. Explaining the harmonic sequence paradox. (United States)

    Schmidt, Ulrich; Zimper, Alexander


    According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced.

  10. Transgressive Surface as Sequence Boundary

    Institute of Scientific and Technical Information of China (English)


    Analysis of the four cases of the sequence boundary (SB)-transgressive surface (TS) relation in nature shows that applying transgressive surfaces as sequence boundaries has the following merits: it improves the methodology of stratigraphic subdivision; the position of transgressive surface in a sea level curve is relatively fixed; the transgressive surface is a transforming surface of the stratal structure; in platforms or ramps, the transgressive surface is the only choice for determining the sequence boundary; the transgressive surface is a readily recognized physical surface reflected by seismic records in seismostratigraphy. The paper reaches a conclusion that to delineate a SB in terms of the TS is theoretically and practically better than to delineate it between highstand and lowstand sediments as has been done traditionally.

  11. Primate-Specific Evolution of an LDLR Enhancer

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qian-fei; Prabhakar, Shyam; Wang, Qianben; Moses, Alan M.; Chanan, Sumita; Brown, Myles; Eisen, Michael B.; Cheng, Jan-Fang; Rubin,Edward M.; Boffelli, Dario


    Sequence changes in regulatory regions have often beeninvoked to explain phenotypic divergence among species, but molecularexamples of this have been difficult to obtain. In this study, weidentified an anthropoid primate specific sequence element thatcontributed to the regulatory evolution of the LDL receptor. Using acombination of close and distant species genomic sequence comparisonscoupled with in vivo and in vitro studies, we show that a functionalcholesterol-sensing sequence motif arose and was fixed within apre-existing enhancer in the common ancestor of anthropoid primates. Ourstudy demonstrates one molecular mechanism by which ancestral mammalianregulatory elements can evolve to perform new functions in the primatelineage leading to human.

  12. Enhanced MRI of breast cancer smaller than 3 cm

    Energy Technology Data Exchange (ETDEWEB)

    Ikeda, Yukio; Yoshida, Shouji (Hyogo Medical Center for Adults (Japan)); Narabayashi, Isamu (and others)


    Twenty-two patients with breast cancers were studied using magnetic resonance (MR) imaging with a cylindrical surface coil at 1.5 Tesla. All were examined with the FE sequence and Gd-DTPA as a contrast medium. These images were compared with micrographs of the specimens. All cancers were enhanced clearly, and demarcated margins or spiculations of the tumors were seen as clearly on MR images as on micrographs of the specimens. In 12 patients (9 carcinomas, 2 fibroadenomas and 1 benign phyllodes tumor), dynamic studies were performed after the intravenous injection of Gd-DTPA. All nine carcinomas showed enhancement characterized by a sudden increase in signal intensity on the order of 100% or more with the first 2 minutes after injection. Two fibroadenomas were enhanced slowly. Thirteen patients with breast cancers were examined with several sequences (FE, T{sub 1}-weighted SE, T{sub 2}-weighted SE and STIR) with or without Gd-DTPA. The most clearly delineated images of the tumors were those of FE images with Gd-DTPA enhancement. A phantom constituted of various concentrations of Gd-DTPA in 20% albumin solution was measured by signal intensities with T{sub 1}-weighted SE sequence and FE sequence. The ratio of enhancement of the 20% albumin solution relative to the Gd-DTPA concentration was higher with the FE sequence than with the SE sequence. The sensitivity of the FE sequence to Gd-DTPA enhancement was 1.5 times that of the SE sequence under the usual concentration of Gd-DTPA. (author).

  13. Sequences and series involving the sequence of composite numbers

    Directory of Open Access Journals (Sweden)

    Panayiotis Vlamos


    Full Text Available Denoting by pn and cn the nth prime number and the nth composite number, respectively, we prove that both the sequence (xnn≥1, defined by xn=∑k=1n (ck+1−ck / k−pn / n, and the series ∑n=1∞ (pcn−cpn / npn are convergent.


    Institute of Scientific and Technical Information of China (English)

    Yuke HUANG; Zhiying WEN


    In this paper, we investigate the factor properties and gap sequence of the Tri-bonacci sequence, the fixed point of the substitution σ(a, b, c) = (ab, ac, a). Let ωp be the p-th occurrence of ω and Gp(ω) be the gap between ωp and ωp+1. We introduce a notion of kernel for each factor ω, and then give the decomposition of the factor ω with respect to its kernel. Using the kernel and the decomposition, we prove the main result of this paper:for each factorω, the gap sequence{Gp(ω)}p≥1 is the Tribonacci sequence over the alphabet{G1(ω), G2(ω), G4(ω)}, and the expressions of gaps are determined completely. As an appli-cation, for each factorω and p∈N, we determine the position ofωp. Finally we introduce a notion of spectrum for studying some typical combinatorial properties, such as power, overlap and separate of factors.

  15. Convergence of Fuzzy Set Sequences

    Institute of Scientific and Technical Information of China (English)

    FENG Yu-hu


    There are more than one mode of convergence with respect to the fuzzy set sequences. In this paper,common six modes of convergence and their relationships are discussed. These six modes are convergence in uniform metric D, convergence in separable metric Dp or D*p, 1 ≤ p <∞, convergence in level set, strong convergence in level set and weak convergence. Suitable counterexamples are given. The necessary and sufficient conditions of convergence in uniform metric D are described. Some comme nts on the convergence of LRfuzzy number sequences are represented.

  16. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P


    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  17. DNA Sequencing Using capillary Electrophoresis

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Barry Karger


    The overall goal of this program was to develop capillary electrophoresis as the tool to be used to sequence for the first time the Human Genome. Our program was part of the Human Genome Project. In this work, we were highly successful and the replaceable polymer we developed, linear polyacrylamide, was used by the DOE sequencing lab in California to sequence a significant portion of the human genome using the MegaBase multiple capillary array electrophoresis instrument. In this final report, we summarize our efforts and success. We began our work by separating by capillary electrophoresis double strand oligonucleotides using cross-linked polyacrylamide gels in fused silica capillaries. This work showed the potential of the methodology. However, preparation of such cross-linked gel capillaries was difficult with poor reproducibility, and even more important, the columns were not very stable. We improved stability by using non-cross linked linear polyacrylamide. Here, the entangled linear chains could move when osmotic pressure (e.g. sample injection) was imposed on the polymer matrix. This relaxation of the polymer dissipated the stress in the column. Our next advance was to use significantly lower concentrations of the linear polyacrylamide that the polymer could be automatically blown out after each run and replaced with fresh linear polymer solution. In this way, a new column was available for each analytical run. Finally, while testing many linear polymers, we selected linear polyacrylamide as the best matrix as it was the most hydrophilic polymer available. Under our DOE program, we demonstrated initially the success of the linear polyacrylamide to separate double strand DNA. We note that the method is used even today to assay purity of double stranded DNA fragments. Our focus, of course, was on the separation of single stranded DNA for sequencing purposes. In one paper, we demonstrated the success of our approach in sequencing up to 500 bases. Other

  18. Network motifs in music sequences

    CERN Document Server

    Zanette, Damian H


    In this note, I summarize ongoing research on motif distribution in networks built up out of symbolic sequences of Western musical origin. Their motif significance profiles exhibit remarkable consistency over different styles and periods, and define a class that cannot be identified with any of the four "superfamilies" to which most real networks seem to belong. Networks from music sequences possess an unusual abundance of bidirectional connections, due to the inherent reversibility of short musical note patterns. This property contributes to motif significance from both local and large-scale features of musical structure.

  19. Comparison of Southern blot analysis with isotopic and nonisotopic in situ hybridization for the detection of human papillomavirus sequences in invasive carcinoma of the uterine cervix. (United States)

    D'Amato, L; Pilotti, S; Rotola, A; Di Luca, D; Cassai, E; Rilke, F


    To compare the efficiency of hybridization methods for the detection of HPV genome, 22 cases of invasive squamous cell carcinoma of the uterine cervix were analyzed by Southern blot analysis and in situ hybridization carried out with 35S- and biotin-labeled probes. These cases contained from less than one to as many as 50 copies per cell of HPV 16 and 18 types. To increase the sensitivity of biotinylated probes, a silver enhancement procedure of the peroxidase reaction product was applied. Results showed that in situ hybridization performed with isotopic probes is as sensitive as Southern blot analysis and is more sensitive than that performed with biotin-labeled probe. However, the application of the silver enhancement procedure increases the percentage of HPV-positive cases from 27 to 50%.

  20. Anchored pseudo-de novo assembly of human genomes identifies extensive sequence variation from unmapped sequence reads. (United States)

    Faber-Hammond, Joshua J; Brown, Kim H


    The human genome reference (HGR) completion marked the genomics era beginning, yet despite its utility universal application is limited by the small number of individuals used in its development. This is highlighted by the presence of high-quality sequence reads failing to map within the HGR. Sequences failing to map generally represent 2-5 % of total reads, which may harbor regions that would enhance our understanding of population variation, evolution, and disease. Alternatively, complete de novo assemblies can be created, but these effectively ignore the groundwork of the HGR. In an effort to find a middle ground, we developed a bioinformatic pipeline that maps paired-end reads to the HGR as separate single reads, exports unmappable reads, de novo assembles these reads per individual and then combines assemblies into a secondary reference assembly used for comparative analysis. Using 45 diverse 1000 Genomes Project individuals, we identified 351,361 contigs covering 195.5 Mb of sequence unincorporated in GRCh38. 30,879 contigs are represented in multiple individuals with ~40 % showing high sequence complexity. Genomic coordinates were generated for 99.9 %, with 52.5 % exhibiting high-quality mapping scores. Comparative genomic analyses with archaic humans and primates revealed significant sequence alignments and comparisons with model organism RefSeq gene datasets identified novel human genes. If incorporated, these sequences will expand the HGR, but more importantly our data highlight that with this method low coverage (~10-20×) next-generation sequencing can still be used to identify novel unmapped sequences to explore biological functions contributing to human phenotypic variation, disease and functionality for personal genomic medicine.

  1. An efficient strategy for large-scale high-throughput transposon-mediated sequencing of cDNA clones (United States)

    Butterfield, Yaron S. N.; Marra, Marco A.; Asano, Jennifer K.; Chan, Susanna Y.; Guin, Ranabir; Krzywinski, Martin I.; Lee, Soo Sen; MacDonald, Kim W. K.; Mathewson, Carrie A.; Olson, Teika E.; Pandoh, Pawan K.; Prabhu, Anna-Liisa; Schnerch, Angelique; Skalska, Ursula; Smailus, Duane E.; Stott, Jeff M.; Tsai, Miranda I.; Yang, George S.; Zuyderduyn, Scott D.; Schein, Jacqueline E.; Jones, Steven J. M.


    We describe an efficient high-throughput method for accurate DNA sequencing of entire cDNA clones. Developed as part of our involvement in the Mammalian Gene Collection full-length cDNA sequencing initiative, the method has been used and refined in our laboratory since September 2000. Amenable to large scale projects, we have used the method to generate >7 Mb of accurate sequence from 3695 candidate full-length cDNAs. Sequencing is accomplished through the insertion of Mu transposon into cDNAs, followed by sequencing reactions primed with Mu-specific sequencing primers. Transposon insertion reactions are not performed with individual cDNAs but rather on pools of up to 96 clones. This pooling strategy reduces the number of transposon insertion sequencing libraries that would otherwise be required, reducing the costs and enhancing the efficiency of the transposon library construction procedure. Sequences generated using transposon-specific sequencing primers are assembled to yield the full-length cDNA sequence, with sequence editing and other sequence finishing activities performed as required to resolve sequence ambiguities. Although analysis of the many thousands (22 785) of sequenced Mu transposon insertion events revealed a weak sequence preference for Mu insertion, we observed insertion of the Mu transposon into 1015 of the possible 1024 5mer candidate insertion sites. PMID:12034834

  2. The origin of biased sequence depth in sequence-independent nucleic acid amplification and optimization for efficient massive parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Toon Rosseel

    Full Text Available Sequence Independent Single Primer Amplification is one of the most widely used random amplification approaches in virology for sequencing template preparation. This technique relies on oligonucleotides consisting of a 3' random part used to prime complementary DNA synthesis and a 5' defined tag sequence for subsequent amplification. Recently, this amplification method was combined with next generation sequencing to obtain viral sequences. However, these studies showed a biased distribution of the resulting sequence reads over the analyzed genomes. The aim of this study was to elucidate the mechanisms that lead to biased sequence depth when using random amplification. Avian paramyxovirus type 8 was used as a model RNA virus to investigate these mechanisms. We showed, based on in silico analysis of the sequence depth in relation to GC-content, predicted RNA secondary structure and sequence complementarity to the 3' part of the tag sequence, that the tag sequence has the main contribution to the observed bias in sequence depth. We confirmed this finding experimentally using both fragmented and non-fragmented viral RNAs as well as primers differing in random oligomer length (6 or 12 nucleotides and in the sequence of the amplification tag. The observed oligonucleotide annealing bias can be reduced by extending the random oligomer sequence and by in silico combining sequence data from SISPA experiments using different 5' defined tag sequences. These findings contribute to the optimization of random nucleic acid amplification protocols that are currently required for downstream applications such as viral metagenomics and microarray analysis.

  3. Intestinal lesions in pediatric Crohn disease: comparative detectability among pulse sequences at MR enterography

    Energy Technology Data Exchange (ETDEWEB)

    Sohn, Beomseok; Kim, Myung-Joon; Lee, Mi-Jung [Severance Children' s Hospital, Yonsei University, College of Medicine, Department of Radiology and Research Institute of Radiological Science, Seoul (Korea, Republic of); Koh, Hong [Severance Children' s Hospital, Department of Pediatrics, Seoul (Korea, Republic of); Han, Kyung Hwa [Yonsei University, College of Medicine, Biostatistics Collaboration Unit, Seoul (Korea, Republic of)


    Variable sequences can be used in MR enterography, and no consensus exists for the best protocol in children with Crohn disease. To compare the lesion detectability of various MR enterography sequences and to correlate the findings of these sequences with the Pediatric Crohn's Disease Activity Index (PCDAI) in children with Crohn disease. Children with clinically or pathologically confirmed Crohn disease underwent MR enterography, including a single-shot fast spin-echo (SSFSE) sequence, motility imaging (coronal 2-D balanced fast field echo), diffusion-weighted imaging (DWI), and dynamic contrast enhancement imaging (including arterial, portal and delayed phases). The lesion detectability of each sequence was graded 0-2 for each involved bowel segment. The lesion detectability and PCDAI result on different sequences were compared using the weighted least squares method and Student's t-test, respectively. Fifteen children (11 boys, 4 girls, mean age 13.7 ± 1.4 years) with a total of 41 lesions were included in this study. All lesions detected in more than two sequences were visible on the single-shot fast spin-echo (SSFSE) sequence. The relative lesion detection rate was 78.1% on motility imaging, 90.2% on DWI, and 92.7% on arterial, 95.1% on portal and 95.1% on delayed phase imaging. Compared to the SSFSE sequence, motility imaging (P < 0.001) and DWI (P = 0.039) demonstrated lower detectability. The mean PCDAI result in the detected lesions was statistically higher only on dynamic enhancement imaging (P < 0.001). All MR enterography sequences were found to have relatively high lesion detectability in children with Crohn disease, while motility imaging showed the lowest lesion detectability. Lesions detected on dynamic enhancement imaging showed a higher PCDAI result, which suggests that this sequence is specific for active inflammation. (orig.)

  4. Sequences in language and text

    CERN Document Server

    Mikros, George K


    The aim of this volume is to present the diverse but highly interesting area of the quantitative analysis of the sequence of various linguistic structures. The collected articles present a wide spectrum of quantitative analyses of linguistic syntagmatic structures and explore novel sequential linguistic entities. This volume will be interesting to all researchers studying linguistics using quantitative methods.

  5. Farey Sequences and Resistor Networks

    Indian Academy of Sciences (India)

    Sameen Ahmed Khan


    In this article, we employ the Farey sequence and Fibonacci numbers to establish strict upper and lower bounds for the order of the set of equivalent resistances for a circuit constructed from equal resistors combined in series and in parallel. The method is applicable for networks involving bridge and non-planar circuits.

  6. Multifractal analyses of music sequences (United States)

    Su, Zhi-Yuan; Wu, Tzuyin


    Multifractal analysis is applied to study the fractal property of music. In this paper, a method is proposed to transform both the melody and rhythm of a music piece into individual sets of distributed points along a one-dimensional line. The structure of the musical composition is thus manifested and characterized by the local clustering pattern of these sequences of points. Specifically, the local Hölder exponent and the multifractal spectrum are calculated for the transformed music sequences according to the multifractal formalism. The observed fluctuations of the Hölder exponent along the music sequences confirm the non-uniformity feature in the structures of melodic and rhythmic motions of music. Our present result suggests that the shape and opening width of the multifractal spectrum plot can be used to distinguish different styles of music. In addition, a characteristic curve is constructed by mapping the point sequences converted from the melody and rhythm of a musical work into a two-dimensional graph. Each different pieces of music has its own unique characteristic curve. This characteristic curve, which also exhibits a fractal trait, unveils the intrinsic structure of music.

  7. Single-primer fluorescent sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Ruth, J.L.; Morgan, C.A.; Middendorf, L.R.; Grone, D.L.; Brumbaugh, J.A.


    Modified linker arm oligonucleotides complementary to standard M13 priming sites were synthesized, labelled with either one, two, or three fluoresceins, and purified by reverse-phase HPLC. When used as primers in standard dideoxy M13 sequencing with /sup 32/P-dNTPs, normal autoradiographic patterns were obtained. To eliminate the radioactivity, direct on-line fluorescence detection was achieved by the use of a scanning 10 mW Argon laser emitting 488 nm light. Fluorescent bands were detected directly in standard 0.2 or 0.35 mm thick polyacrylamide gels at a distance of 24 cm from the loading wells by a photomultiplier tube filtered at 520 nm. Horizontal and temporal location of each band was displayed by computer as a band in real time, providing visual appearance similar to normal 4-lane autoradiograms. Using a single primer labelled with two fluoresceins, sequences of between 500 and 600 bases have been read in a single loading with better than 98% accuracy; up to 400 bases can be read reproducibly with no errors. More than 50 sequences have been determined by this method. This approach requires only 1-2 ug of cloned template, and produces continuous sequence data at about one band per minute.

  8. Fractals in DNA sequence analysis

    Institute of Scientific and Technical Information of China (English)

    Yu Zu-Guo(喻祖国); Vo Anh; Gong Zhi-Min(龚志民); Long Shun-Chao(龙顺潮)


    Fractal methods have been successfully used to study many problems in physics, mathematics, engineering, finance,and even in biology. There has been an increasing interest in unravelling the mysteries of DNA; for example, how can we distinguish coding and noncoding sequences, and the problems of classification and evolution relationship of organisms are key problems in bioinformatics. Although much research has been carried out by taking into consideration the long-range correlations in DNA sequences, and the global fractal dimension has been used in these works by other people, the models and methods are somewhat rough and the results are not satisfactory. In recent years, our group has introduced a time series model (statistical point of view) and a visual representation (geometrical point of view)to DNA sequence analysis. We have also used fractal dimension, correlation dimension, the Hurst exponent and the dimension spectrum (multifractal analysis) to discuss problems in this field. In this paper, we introduce these fractal models and methods and the results of DNA sequence analysis.

  9. The consolidation of implicit sequence memory in obstructive sleep apnea.

    Directory of Open Access Journals (Sweden)

    Eszter Csabi

    Full Text Available Obstructive Sleep Apnea (OSA Syndrome is a relatively frequent sleep disorder characterized by disrupted sleep patterns. It is a well-established fact that sleep has beneficial effect on memory consolidation by enhancing neural plasticity. Implicit sequence learning is a prominent component of skill learning. However, the formation and consolidation of this fundamental learning mechanism remains poorly understood in OSA. In the present study we examined the consolidation of different aspects of implicit sequence learning in patients with OSA. We used the Alternating Serial Reaction Time task to measure general skill learning and sequence-specific learning. There were two sessions: a learning phase and a testing phase, separated by a 10-hour offline period with sleep. Our data showed differences in offline changes of general skill learning between the OSA and control group. The control group demonstrated offline improvement from evening to morning, while the OSA group did not. In contrast, we did not observe differences between the groups in offline changes in sequence-specific learning. Our findings suggest that disrupted sleep in OSA differently affects neural circuits involved in the consolidation of sequence learning.

  10. Enhancer activity-based identification of functional enhancers using zebrafish embryos. (United States)

    Taminato, Tomohito; Yokota, Daisuke; Araki, Soh; Ovara, Hiroki; Yamasu, Kyo; Kawamura, Akinori


    Chromatin immunoprecipitation (ChIP) against enhancer-associated marks with massive sequencing is a powerful approach to identify genome-wide distributions of putative enhancers. However, functional in vivo analysis is required to elucidate the activities of predicted enhancers. Using zebrafish embryos, we established a ChIP-Injection method that enables identification of functional enhancers based on their enhancer activities in embryos. Each reporter gene possessing the enhancer-associated genomic region enriched by ChIP was injected into zebrafish embryos to analyze the activity of putative enhancers. By using the ChIP-Injection, we identified 32 distinct putative enhancers that drove specific expression. Additionally, we generated transgenic lines that exhibit distributions of the EGFP signal as was observed in the screening. Furthermore, the expression pattern driven by the identified somite-specific enhancer resembled that of the gene acta2. The results indicate that ChIP-Injection provides an efficient approach for identification of active enhancers in a potentially wide variety of developmental tissues and stages.

  11. Enhancer evolution across 20 mammalian species

    DEFF Research Database (Denmark)

    Villar, Diego; Berthelot, Camille; Aldridge, Sarah;


    The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders...... by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements....... In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences...

  12. Consolidating the effects of waking and sleep on motor-sequence learning. (United States)

    Brawn, Timothy P; Fenn, Kimberly M; Nusbaum, Howard C; Margoliash, Daniel


    Sleep is widely believed to play a critical role in memory consolidation. Sleep-dependent consolidation has been studied extensively in humans using an explicit motor-sequence learning paradigm. In this task, performance has been reported to remain stable across wakefulness and improve significantly after sleep, making motor-sequence learning the definitive example of sleep-dependent enhancement. Recent work, however, has shown that enhancement disappears when the task is modified to reduce task-related inhibition that develops over a training session, thus questioning whether sleep actively consolidates motor learning. Here we use the same motor-sequence task to demonstrate sleep-dependent consolidation for motor-sequence learning and explain the discrepancies in results across studies. We show that when training begins in the morning, motor-sequence performance deteriorates across wakefulness and recovers after sleep, whereas performance remains stable across both sleep and subsequent waking with evening training. This pattern of results challenges an influential model of memory consolidation defined by a time-dependent stabilization phase and a sleep-dependent enhancement phase. Moreover, the present results support a new account of the behavioral effects of waking and sleep on explicit motor-sequence learning that is consistent across a wide range of tasks. These observations indicate that current theories of memory consolidation that have been formulated to explain sleep-dependent performance enhancements are insufficient to explain the range of behavioral changes associated with sleep.

  13. The Toothpick Sequence and Other Sequences from Cellular Automata

    CERN Document Server

    Applegate, David; Sloane, N J A


    A two-dimensional arrangement of toothpicks is constructed by the following iterative procedure. At stage 1, place a single toothpick of length 1 on a square grid, aligned with the y-axis. At each subsequent stage, for every exposed toothpick end, place an orthogonal toothpick centered at that end. The resulting structure has a fractal-like appearance. We will analyze the toothpick sequence, which gives the total number of toothpicks after n steps. We also study several related sequences that arise from enumerating active cells in cellular automata. Some unusual recurrences appear: a typical example is that instead of the Fibonacci recurrence, which we may write as a(2+i) = a(i) + a(i+1), we set n = 2^k+i (0 = 0} (1+x^{2^k-1}+2x^{2^k}) and variations thereof.

  14. Enhancement in Sport, and Enhancement outside Sport


    Douglas, Thomas


    Sport is one of the first areas in which enhancement has become commonplace. It is also one of the first areas in which the use of enhancement technologies has been heavily regulated. Some have thus seen sport as a testing ground for arguments about whether to permit enhancement. However, I argue that there are fairness-based objections to enhancement in sport that do not apply as strongly in some other areas of human activity. Thus, I claim that there will often be a stronger case for permit...

  15. Pig genome sequence - analysis and publication strategy

    DEFF Research Database (Denmark)

    Archibald, Alan L.; Bolund, Lars; Churcher, Carol;


    BACKGROUND: The pig genome is being sequenced and characterised under the auspices of the Swine Genome Sequencing Consortium. The sequencing strategy followed a hybrid approach combining hierarchical shotgun sequencing of BAC clones and whole genome shotgun sequencing. RESULTS: Assemblies......) is under construction and will incorporate whole genome shotgun sequence (WGS) data providing > 30x genome coverage. The WGS sequence, most of which comprise short Illumina/Solexa reads, were generated from DNA from the same single Duroc sow as the source of the BAC library from which clones were...

  16. Stream cipher based on GSS sequences

    Institute of Scientific and Technical Information of China (English)

    HU Yupu; XIAO Guozhen


    Generalized self-shrinking sequences, simply named the GSS sequences,are novel periodic sequences that have many advantages in cryptography. In this paper,we give several results about GSS sequence's application to cryptography. First, we give a simple method for selecting those GSS sequences whose least periods reach the maximum. Second, we give a method for describing and computing the auto-correlation coefficients of GSS sequences. Finally, we point out that some GSS sequences, when used as stream ciphers, have a security weakness.

  17. Sequence-structure relations of biopolymers

    CERN Document Server

    Barrett, Christopher; Reidys, Christian M


    Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as structural semantics of sequence data that allows for a different interpretation than conventional sequence alignment. Structural semantics could enable us to identify more general embedded "patterns" in DNA and RNA sequences. Results: We compute the partition function of sequences with respect to a fixed structure and connect this computation to the mutual information of a sequence-structure pair for RNA secondary structures. We present a Boltzmann sampler and obtain the a priori probability of specific sequence patterns. We present a detailed analysis for the three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA). We localize specific sequence patterns, contrast the energy spectrum of the Boltzmann sampled sequences versus those sequences that refold ...

  18. Expressing stochastic filters via number sequences


    Capponi, A.; Farina, A; Pilotto, C.


    We generalize the results presented in [1] regarding the relation between the Kalman filter and the Fibonacci sequence. We consider more general filtering models and relate the finite dimensional Kalman and Benes filters to the Fibonacci sequence and to the Golden Section. We also prove that Fibonacci numbers may be expressed as the convolution of the Fibonacci and Padovan sequence, thus extending the connection between stochastic filtering and Fibonacci sequence to the Padovan sequence.

  19. Next-generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation.

    NARCIS (Netherlands)

    Guryev, V.; Cuppen, E.


    Rapid advances in DNA sequencing improve existing techniques and enable new approaches in genetics and functional genomics, bringing about unprecedented coverage, resolution and sensitivity. Enhanced toolsets can facilitate the untangling of connections between genomic variation, environmental facto

  20. Next-generation sequencing approaches in genetic rodent model systems to study functional effects of human genetic variation

    NARCIS (Netherlands)

    Guryev, Victor; Cuppen, Edwin


    Rapid advances in DNA sequencing improve existing techniques and enable new approaches in genetics and functional genomics, bringing about unprecedented coverage, resolution and sensitivity. Enhanced toolsets can facilitate the untangling of connections between genomic variation, environmental facto

  1. Nonparametric Inference for Periodic Sequences

    KAUST Repository

    Sun, Ying


    This article proposes a nonparametric method for estimating the period and values of a periodic sequence when the data are evenly spaced in time. The period is estimated by a "leave-out-one-cycle" version of cross-validation (CV) and complements the periodogram, a widely used tool for period estimation. The CV method is computationally simple and implicitly penalizes multiples of the smallest period, leading to a "virtually" consistent estimator of integer periods. This estimator is investigated both theoretically and by simulation.We also propose a nonparametric test of the null hypothesis that the data have constantmean against the alternative that the sequence of means is periodic. Finally, our methodology is demonstrated on three well-known time series: the sunspots and lynx trapping data, and the El Niño series of sea surface temperatures. © 2012 American Statistical Association and the American Society for Quality.

  2. Genome Sequence of Mycobacteriophage Momo. (United States)

    Pope, Welkin H; Bina, Elizabeth A; Brahme, Indraneel S; Hill, Amy B; Himmelstein, Philip H; Hunsicker, Sara M; Ish, Amanda R; Le, Tinh S; Martin, Mary M; Moscinski, Catherine N; Shetty, Sameer A; Swierzewski, Tomasz; Iyengar, Varun B; Kim, Hannah; Schafer, Claire E; Grubb, Sarah R; Warner, Marcie H; Bowman, Charles A; Russell, Daniel A; Hatfull, Graham F


    Momo is a newly discovered phage of Mycobacterium smegmatis mc(2)155. Momo has a double-stranded DNA genome 154,553 bp in length, with 233 predicted protein-encoding genes, 34 tRNA genes, and one transfer-messenger RNA (tmRNA) gene. Momo has a myoviral morphology and shares extensive nucleotide sequence similarity with subcluster C1 mycobacteriophages.

  3. Multiplicative LSTM for sequence modelling


    Krause, Ben; Lu, Liang; Murray, Iain; Renals, Steve


    This paper introduces multiplicative LSTM, a novel hybrid recurrent neural network architecture for sequence modelling that combines the long short-term memory (LSTM) and multiplicative recurrent neural network architectures. Multiplicative LSTM is motivated by its flexibility to have very different recurrent transition functions for each possible input, which we argue helps make it more expressive in autoregressive density estimation. We show empirically that multiplicative LSTM outperforms ...

  4. Mining the NCBI Influenza Sequence Database: adaptive grouping of BLAST results using precalculated neighbor indexing. (United States)

    Zaslavsky, Leonid; Tatusova, Tatiana


    The Influenza Virus Resource and other Virus Variation Resources at NCBI provide enhanced visualization web tools for exploratory analysis for influenza sequence data. Despite the improvements in data analysis, the initial data retrieval remains unsophisticated, frequently producing huge and imbalanced datasets due to the large number of identical and nearly-identical sequences in the database.We propose a data mining algorithm to organize reported sequences into groups based on their relatedness to the query sequence and to each other. The algorithm uses BLAST to find database sequences related to the query. Neighbor lists precalculated from pairwise BLAST alignments between database sequences are used to organize results in groups of nearly-identical and strongly related sequences. We propose to use a non-symmetric dissimilarity measure well crafted for dealing with sequences of different length (fragments).A balanced and representative data set produced by this tool can be used for further analysis, i.e. multiple sequence alignment and phylogenetic trees. The algorithm is implemented for protein coding sequences and is being integrated with the NCBI Influenza Virus Resource.

  5. Targeted amplicon sequencing (TAS): a scalable next-gen approach to multilocus, multitaxa phylogenetics. (United States)

    Bybee, Seth M; Bracken-Grissom, Heather; Haynes, Benjamin D; Hermansen, Russell A; Byers, Robert L; Clement, Mark J; Udall, Joshua A; Wilcox, Edward R; Crandall, Keith A


    Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach.

  6. Functional analysis of limb transcriptional enhancers in the mouse. (United States)

    Nolte, Mark J; Wang, Ying; Deng, Jian Min; Swinton, Paul G; Wei, Caimiao; Guindani, Michele; Schwartz, Robert J; Behringer, Richard R


    Transcriptional enhancers are genomic sequences bound by transcription factors that act together with basal transcriptional machinery to regulate gene transcription. Several high-throughput methods have generated large datasets of tissue-specific enhancer sequences with putative roles in developmental processes. However, few enhancers have been deleted from the genome to determine their roles in development. To understand the roles of two enhancers active in the mouse embryonic limb bud we deleted them from the genome. Although the genes regulated by these enhancers are unknown, they were selected because they were identified in a screen for putative limb bud-specific enhancers associated with p300, an acetyltransferase that participates in protein complexes that promote active transcription, and because the orthologous human enhancers (H1442 and H280) drive distinct lacZ expression patterns in limb buds of embryonic day (E) 11.5 transgenic mice. We show that the orthologous mouse sequences, M1442 and M280, regulate dynamic expression in the developing limb. Although significant transcriptional differences in enhancer-proximal genes in embryonic limb buds accompany the deletion of M1442 and M280 no gross limb malformations during embryonic development were observed, demonstrating that M1442 and M280 are not required for mouse limb development. However, M280 is required for the development and/or maintenance of body size; M280 mice are significantly smaller than controls. M280 also harbors an "ultraconserved" sequence that is identical between human, rat, and mouse. This is the first report of a phenotype resulting from the deletion of an ultraconserved element. These studies highlight the importance of determining enhancer regulatory function by experiments that manipulate them in situ and suggest that some of an enhancer's regulatory capacities may be developmentally tolerated rather than developmentally required.

  7. 快速自旋回波与快速小角度激发抑脂序列在颈部增强扫描中的应用%Application of Fast Turbo Spin Echo and Low Angle Shot Fat Saturation Sequences in Cervical Enhanced Scanning

    Institute of Scientific and Technical Information of China (English)

    肖建明; 彭涛; 陈志凡


    目的:探讨快速自旋回波(TSE)抑脂序列与快速小角度激发(FLASH)抑脂序列在颈部增强扫描中的应用价值。方法采用Siemens Avanto 1.5T磁共振扫描仪对30名受检者行颈部增强扫描,分别采用T1加权快速自旋回波抑脂序列(T1-TSE-FS)、T1加权快速小角度激发抑脂序列(T1-FLASH-FS)。由两名高年资医师对两种序列的成像效果进行评分,采用秩和检验分析评分结果。结果30名受检者均完成T1-TSE-FS和T1-FLASH-FS序列的横轴位、冠状位、矢状位扫描。横、冠、矢三方位的总扫描时间:T1-FLASH-FS比T1-TSE-FS快2 min 55 s。运动伪影:横、冠、矢三方位上,T1-FLASH-FS的运动伪影数目均少于T1-TSE-FS,两者评分的差异均有统计学意义(P0.05)。脂肪抑制效果:横、冠、矢三方位上,T1-FLASH-FS的脂肪抑制效果均优于T1-TSE-FS,两者评分的差异均有统计学意义(P0.05). As for fat saturation effect, in all the transverse and coronal as well as sagittal orientations, it was better on T1-FLASH-FS sequence than the T1-TSE-FS with statistical signiifcant differences between the two scores (P<0.05). Conclusion With shorter acquisition time, less motion artifacts and pulsatility artifacts as well as better fat suppression effect, T1-FLASH-FS sequence could better meet the diagnostic requirements in comparison with T1-TSE-FS sequence in cervical CE-MRI scanning.

  8. Multineuronal Spike Sequences Repeat with Millisecond Precision

    Directory of Open Access Journals (Sweden)

    Koki eMatsumoto


    Full Text Available Cortical microcircuits are nonrandomly wired by neurons. As a natural consequence, spikes emitted by microcircuits are also nonrandomly patterned in time and space. One of the prominent spike organizations is a repetition of fixed patterns of spike series across multiple neurons. However, several questions remain unsolved, including how precisely spike sequences repeat, how the sequences are spatially organized, how many neurons participate in sequences, and how different sequences are functionally linked. To address these questions, we monitored spontaneous spikes of hippocampal CA3 neurons ex vivo using a high-speed functional multineuron calcium imaging technique that allowed us to monitor spikes with millisecond resolution and to record the location of spiking and nonspiking neurons. Multineuronal spike sequences were overrepresented in spontaneous activity compared to the statistical chance level. Approximately 75% of neurons participated in at least one sequence during our observation period. The participants were sparsely dispersed and did not show specific spatial organization. The number of sequences relative to the chance level decreased when larger time frames were used to detect sequences. Thus, sequences were precise at the millisecond level. Sequences often shared common spikes with other sequences; parts of sequences were subsequently relayed by following sequences, generating complex chains of multiple sequences.

  9. Method and apparatus for biological sequence comparison (United States)

    Marr, T.G.; Chang, W.I.


    A method and apparatus are disclosed for comparing biological sequences from a known source of sequences, with a subject (query) sequence. The apparatus takes as input a set of target similarity levels (such as evolutionary distances in units of PAM), and finds all fragments of known sequences that are similar to the subject sequence at each target similarity level, and are long enough to be statistically significant. The invention device filters out fragments from the known sequences that are too short, or have a lower average similarity to the subject sequence than is required by each target similarity level. The subject sequence is then compared only to the remaining known sequences to find the best matches. The filtering member divides the subject sequence into overlapping blocks, each block being sufficiently large to contain a minimum-length alignment from a known sequence. For each block, the filter member compares the block with every possible short fragment in the known sequences and determines a best match for each comparison. The determined set of short fragment best matches for the block provide an upper threshold on alignment values. Regions of a certain length from the known sequences that have a mean alignment value upper threshold greater than a target unit score are concatenated to form a union. The current block is compared to the union and provides an indication of best local alignment with the subject sequence. 5 figs.

  10. SU-E-J-240: Development of a Novel 4D MRI Sequence for Real-Time Liver Tumor Tracking During Radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Zhuang, L; Burmeister, J [Department of Oncology, Wayne State Univ School of Medicine, Detroit, MI (United States); Ye, Y [Department of Radiology, Wayne State Univ School of Medicine, Detroit, MI (United States)


    Purpose: To develop a Novel 4D MRI Technique that is feasible for realtime liver tumor tracking during radiotherapy. Methods: A volunteer underwent an abdominal 2D fast EPI coronal scan on a 3.0T MRI scanner (Siemens Inc., Germany). An optimal set of parameters was determined based on image quality and scan time. A total of 23 slices were scanned to cover the whole liver in the test scan. For each scan position, the 2D images were retrospectively sorted into multiple phases based on breathing signal extracted from the images. Consequently the 2D slices with same phase numbers were stacked to form one 3D image. Multiple phases of 3D images formed the 4D MRI sequence representing one breathing cycle. Results: The optimal set of scan parameters were: TR= 57ms, TE= 19ms, FOV read= 320mm and flip angle= 30°, which resulted in a total scan time of 14s for 200 frames (FMs) per slice and image resolution of (2.5mm,2.5mm,5.0mm) in three directions. Ten phases of 3D images were generated, each of which had 23 slices. Based on our test scan, only 100FMs were necessary for the phase sorting process which may lower the scan time to 7s/100FMs/slice. For example, only 5 slices/35s are necessary for a 4D MRI scan to cover liver tumor size ≤ 2cm leading to the possibility of tumor trajectory tracking every 35s during treatment. Conclusion: The novel 4D MRI technique we developed can reconstruct a 4D liver MRI sequence representing one breathing cycle (7s/ slice) without an external monitor. This technique can potentially be used for real-time liver tumor tracking during radiotherapy.

  11. The complete mitochondrial genome of Haliotis laevigata (Gastropoda: Haliotidae) using MiSeq and HiSeq sequencing. (United States)

    Robinson, Nick A; Hall, Nathan E; Ross, Elizabeth M; Cooke, Ira R; Shiel, Brett P; Robinson, Andrew J; Strugnell, Jan M


    The mitochondrial genome of greenlip abalone, Haliotis laevigata, is reported. MiSeq and HiSeq sequencing of one individual was assembled to yield a single 16,545 bp contig. The sequence shares 92% identity to the H. rubra mitochondrial genome (a closely related species that hybridize with H. laevigata in the wild). The sequence will be useful for determining the maternal contribution to hybrid populations, for investigating population structure and stock-enhancement effectiveness.

  12. An Investigation on the Accuracy of Truncated DKLT Representation for Speaker Identification With Short Sequences of Speech Frames. (United States)

    Biagetti, Giorgio; Crippa, Paolo; Falaschetti, Laura; Orcioni, Simone; Turchetti, Claudio


    Speaker identification plays a crucial role in biometric person identification as systems based on human speech are increasingly used for the recognition of people. Mel frequency cepstral coefficients (MFCCs) have been widely adopted for decades in speech processing to capture the speech-specific characteristics with a reduced dimensionality. However, although their ability to decorrelate the vocal source and the vocal tract filter make them suitable for speech recognition, they greatly mitigate the speaker variability, a specific characteristic that distinguishes different speakers. This paper presents a theoretical framework and an experimental evaluation showing that reducing the dimension of features by applying the discrete Karhunen-Loève transform (DKLT) to the log-spectrum of the speech signal guarantees better performance compared to conventional MFCC features. In particular with short sequences of speech frames, with typical duration of less than 2 s, the performance of truncated DKLT representation achieved for the identification of five speakers are always better than those achieved with the MFCCs for the experiments we performed. Additionally, the framework was tested on up to 100 TIMIT speakers with sequences of less than 3.5 s showing very good recognition capabilities.

  13. Genome-wide analysis of functional and evolutionary features of tele-enhancers. (United States)

    Huang, Di; Ovcharenko, Ivan


    We investigated sequence features of enhancers separated from their target gene by at least one intermediate gene/exon (named tele-enhancers in this study) and enhancers residing inside their target gene locus. In this study, we used whole genome enhancer maps and gene expression profiles to establish a large panel of tele-enhancers. By contrasting tele-enhancers to proximal enhancers targeting heart genes, we observed that heart tele-enhancers use unique regulatory mechanisms based on the cardiac transcription factors SRF, TEAD, and NKX-2.5, whereas proximal heart enhancers rely on GATA4 instead. A functional analysis showed that tele-enhancers preferentially regulate house-keeping genes and genes with a metabolic role during heart development. In addition, tele-enhancers are significantly more conserved than their proximal counterparts. Similar trends have been observed for non-heart tissues and cell types, suggesting that our findings represent general characteristics of tele-enhancers.

  14. Static multiplicities in heterogeneous azeotropic distillation sequences

    DEFF Research Database (Denmark)

    Esbjerg, Klavs; Andersen, Torben Ravn; Jørgensen, Sten Bay;


    In this paper the results of a bifurcation analysis on heterogeneous azeotropic distillation sequences are given. Two sequences suitable for ethanol dehydration are compared: The 'direct' and the 'indirect' sequence. It is shown, that the two sequences, despite their similarities, exhibit very...... performances are compared for minimal impurities in both products, where the direct sequence exhibits output multiplicity, while the indirect sequence exhibits state multiplicity. The latter multiplicity may be avoided by accepting a slightly increased impurity in the ethanol product. Copyright (C) 1998 IFAC....

  15. On Inclusion Relations between Some Sequence Spaces

    Directory of Open Access Journals (Sweden)

    R. Çolak


    Full Text Available We determine the relations between the classes S^λ of almost λ-statistically convergent sequences and the relations between the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ, μ in the class Λ. Furthermore we also give the relations between the classes S^λ of almost λ-statistically convergent sequences and the classes V^,λ of strongly almost V,λ-summable sequences for various sequences λ,μ∈Λ.

  16. Bernoulli measure of complex admissible kneading sequences

    CERN Document Server

    Bruin, Henk


    Iterated quadratic polynomials give rise to a rich collection of different dynamical systems that are parametrized by a simple complex parameter $c$. The different dynamical features are encoded by the \\emph{kneading sequence} which is an infinite sequence over $\\{0,\\1\\}$. Not every such sequence actually occurs in complex dynamics. The set of admissible kneading sequences was described by Milnor and Thurston for real quadratic polynomials, and by the authors in the complex case. We prove that the set of admissible kneading sequences has positive Bernoulli measure within the set of sequences over $\\{0,\\1\\}$.

  17. Dynamic encoding of natural luminance sequences by LGN bursts.

    Directory of Open Access Journals (Sweden)

    Nicholas A Lesica


    Full Text Available In the lateral geniculate nucleus (LGN of the thalamus, visual stimulation produces two distinct types of responses known as tonic and burst. Due to the dynamics of the T-type Ca(2+ channels involved in burst generation, the type of response evoked by a particular stimulus depends on the resting membrane potential, which is controlled by a network of modulatory connections from other brain areas. In this study, we use simulated responses to natural scene movies to describe how modulatory and stimulus-driven changes in LGN membrane potential interact to determine the luminance sequences that trigger burst responses. We find that at low resting potentials, when the T channels are de-inactivated and bursts are relatively frequent, an excitatory stimulus transient alone is sufficient to evoke a burst. However, to evoke a burst at high resting potentials, when the T channels are inactivated and bursts are relatively rare, prolonged inhibitory stimulation followed by an excitatory transient is required. We also observe evidence of these effects in vivo, where analysis of experimental recordings demonstrates that the luminance sequences that trigger bursts can vary dramatically with the overall burst percentage of the response. To characterize the functional consequences of the effects of resting potential on burst generation, we simulate LGN responses to different luminance sequences at a range of resting potentials with and without a mechanism for generating bursts. Using analysis based on signal detection theory, we show that bursts enhance detection of specific luminance sequences, ranging from the onset of excitatory sequences at low resting potentials to the offset of inhibitory sequences at high resting potentials. These results suggest a dynamic role for burst responses during visual processing that may change according to behavioral state.

  18. Triggered Swarms and Induced Aftershock Sequences in Geothermal Systems (United States)

    Shcherbakov, R.; Turcotte, D. L.; Yikilmaz, M. B.; Kellogg, L. H.; Rundle, J. B.


    Natural geothermal systems, which are used for energy generation, are usually associated with high seismic activity. This can be related to the large-scale injection and extraction of fluids to enhance geothermal recovery. This results in the changes of the pore pressure and pore-elastic stress field and can stimulate the occurrence of earthquakes. These systems are also prone to triggering of seismicity by the passage of seismic waves generated by large distant main shocks. In this study, we analyze clustering and triggering of seismicity at several geothermal fields in California. Particularly, we consider the seismicity at the Geysers, Coso, and Salton Sea geothermal fields. We analyze aftershock sequences generated by local large events with magnitudes greater than 4.0 and earthquake swarms generated by several significant long distant main shocks. We show that the rate of the aftershock sequences generated by the local large events in the two days before and two days after the reference event can be modelled reasonably well by the time dependent Epidemic Type Aftershock Sequence (ETAS) model. On the other hand, the swarms of activity triggered by large distant earthquakes cannot be described by the ETAS model. To model the increase in the rate of seismicity associated with triggering by large distant main shocks we introduce an additional time-dependent triggering mechanism into the ETAS model. In almost all cases the frequency-magnitude statistics of triggered sequences follow Gutenberg-Richter scaling to a good approximation. The analysis indicates that the seismicity triggered by relatively large local events can initiate sequences similar to regular aftershock sequences. In contrast, the distant main shocks trigger swarm like activity with faster decaying rates.

  19. Modified Genetic Algorithm for DNA Sequence Assembly by Shotgun and Hybridization Sequencing Techniques

    Directory of Open Access Journals (Sweden)

    Prof.Narayan Kumar Sahu


    Full Text Available Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pair wise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing by hybridization (SBH, infers a DNA sequence given the set of oligomers that represents all sub words of some fixed length, k. In this paper, we propose a new computer algorithm for DNA sequence assembly that combines in a novel way the techniques of both shotgun and SBH methods. Based on our preliminary investigations, the algorithm promises- to be very fast and practical for DNA sequence assembly [1].

  20. Biomolecule Sequencer: Nanopore Sequencing Technology for In-Situ Environmental Monitoring and Astrobiology (United States)

    John, K. K.; Botkin, D. J.; Burton, A. S.; Castro-Wallace, S. L.; Chaput, J. D.; Dworkin, J. P.; Lupisella, M. L.; Mason, C. E.; Rubins, K. H.; Smith, D. J.; Stahl, S.; Switzer, C.


    Biomolecule Sequencer will demonstrate, for the first time, that DNA sequencing is feasible as a tool for in-situ environmental monitoring and astrobiology. A space-based sequencer could identify microbes, diseases, and help detect DNA-based life.

  1. In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer

    Energy Technology Data Exchange (ETDEWEB)

    Poulin, Francis; Nobrega, Marcelo A.; Plajzer-Frick, Ingrid; Holt, Amy; Afzal, Veena; Rubin, Edward M.; Pennacchio, Len


    Genomic sequence comparisons between human, mouse and pufferfish (Takifugu rubripes (Fugu))have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change in order to retain in vivo functionality, such elements have been minimally explored experimentally. In this study, we describe the in-depth characterization of an ancient conserved enhancer, Dc2 located near the dachshund gene, which displays a human-Fugu identity of 84 percent over 424 basepairs (bp). In addition to this large overall conservation, we find that Dc2 is characterized by the presence of a large block of sequence (144 bp) that is completely identical between human, mouse, chicken, zebrafish and Fugu. Through the testing of reporter vector constructs in transgenic mice, we observed that the 424 bp Dc2 conserved element is necessary and sufficient for brain tissue enhancer activity. In vivo analyses also revealed that the 144 bp 100 percent conserved sequence is necessary, but not sufficient, to replicate Dc2 enhancer function. However, the introduction of two separate 16 bp insertions into the highly conserved enhancer core did not cause any detectable modification of its in vivo activity. Our observations indicate that the 144 bp 100 percent conserved element is tolerant of change at least at the resolution of this transgenic mouse assay and suggest that purifying selection on Dc2 sequence might not be as strong as we predicted or that some unknown property also constrains this highly conserved enhancer sequence.

  2. What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual (United States)

    BACKGROUND: Next-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain u...

  3. Oxygen-enhanced combustion

    CERN Document Server

    Baukal, Charles E


    Combustion technology has traditionally been dominated by air/fuel combustion. However, two developments have increased the significance of oxygen-enhanced combustion-new technologies that produce oxygen less expensively and the increased importance of environmental regulations. Advantages of oxygen-enhanced combustion include less pollutant emissions as well as increased energy efficiency and productivity. Oxygen-Enhanced Combustion, Second Edition compiles information about using oxygen to enhance industrial heating and melting processes. It integrates fundamental principles, applications, a

  4. Discrete low-discrepancy sequences

    CERN Document Server

    Angel, Omer; Martin, James B; Propp, James


    Holroyd and Propp used Hall's marriage theorem to show that, given a probability distribution pi on a finite set S, there exists an infinite sequence s_1,s_2,... in S such that for all integers k >= 1 and all s in S, the number of i in [1,k] with s_i = s differs from k pi(s) by at most 1. We prove a generalization of this result using a simple explicit algorithm. A special case of this algorithm yields an extension of Holroyd and Propp's result to the case of discrete probability distributions on infinite sets.

  5. Infinite matrices and sequence spaces

    CERN Document Server

    Cooke, Richard G


    This clear and correct summation of basic results from a specialized field focuses on the behavior of infinite matrices in general, rather than on properties of special matrices. Three introductory chapters guide students to the manipulation of infinite matrices, covering definitions and preliminary ideas, reciprocals of infinite matrices, and linear equations involving infinite matrices.From the fourth chapter onward, the author treats the application of infinite matrices to the summability of divergent sequences and series from various points of view. Topics include consistency, mutual consi

  6. Asymptotics of Lagged Fibonacci Sequences

    CERN Document Server

    Mertens, Stephan


    Consider "lagged" Fibonacci sequences $a(n) = a(n-1)+a(\\lfloor n/k\\rfloor)$ for $k > 1$. We show that $\\lim_{n\\to\\infty} a(kn)/a(n)\\cdot\\ln n/n = k\\ln k$ and we demonstrate the slow numerical convergence to this limit and how to deal with this slow convergence. We also discuss the connection between two classical results of N.G. de Bruijn and K. Mahler on the asymptotics of $a(n)$.

  7. Contextual information-aided kidney segmentation in CT sequences (United States)

    Zhao, Enwei; Liang, Yanmei; Fan, Hailun


    Based on the continuity of adjacent slices in a medical image sequence, a slice-based 3-D segmentation framework is constructed to extract the intact kidney by processing all slices automatically in the whole sequence. The framework includes four sections: initial segmentation, selection of the most reliable initial segmentation, location and modification of leakage. The crucial section of the proposed framework is selecting the most reliable initial segmentation image, which will be regarded as the reference image to evaluate the continuity of the following slice. Leakage location is carried out based on the contextual features, and the local iterative thresholding (LIT) is used to modify the leakage. As test examples of the framework, abdominal computed tomography (CT) images in enhanced phases are processed to segment kidney automatically. The total of 392 CT images in 7 sequences from 3 patients are selected as training images to determine the parameters in the database, and other 898 CT images in 21 sequences from 7 patients are used as test images to evaluate the effectiveness of the method. An average of three dimensional Dice similarity coefficient (3-D DSC) of 94.7% and average symmetric surface distance (ASSD) of 0.91 mm are obtained, which indicate that the intact kidney can be perfectly extracted with hardly any leakage automatically.

  8. Pulse sequences for uniform perfluorocarbon droplet vaporization and ultrasound imaging. (United States)

    Puett, C; Sheeran, P S; Rojas, J D; Dayton, P A


    Phase-change contrast agents (PCCAs) consist of liquid perfluorocarbon droplets that can be vaporized into gas-filled microbubbles by pulsed ultrasound waves at diagnostic pressures and frequencies. These activatable contrast agents provide benefits of longer circulating times and smaller sizes relative to conventional microbubble contrast agents. However, optimizing ultrasound-induced activation of these agents requires coordinated pulse sequences not found on current clinical systems, in order to both initiate droplet vaporization and image the resulting microbubble population. Specifically, the activation process must provide a spatially uniform distribution of microbubbles and needs to occur quickly enough to image the vaporized agents before they migrate out of the imaging field of view. The development and evaluation of protocols for PCCA-enhanced ultrasound imaging using a commercial array transducer are described. The developed pulse sequences consist of three states: (1) initial imaging at sub-activation pressures, (2) activating droplets within a selected region of interest, and (3) imaging the resulting microbubbles. Bubble clouds produced by the vaporization of decafluorobutane and octafluoropropane droplets were characterized as a function of focused pulse parameters and acoustic field location. Pulse sequences were designed to manipulate the geometries of discrete microbubble clouds using electronic steering, and cloud spacing was tailored to build a uniform vaporization field. The complete pulse sequence was demonstrated in the water bath and then in vivo in a rodent kidney. The resulting contrast provided a significant increase (>15 dB) in signal intensity.

  9. Prediction of transposable element derived enhancers using chromatin modification profiles.

    Directory of Open Access Journals (Sweden)

    Ahsan Huda

    Full Text Available Experimentally characterized enhancer regions have previously been shown to display specific patterns of enrichment for several different histone modifications. We modelled these enhancer chromatin profiles in the human genome and used them to guide the search for novel enhancers derived from transposable element (TE sequences. To do this, a computational approach was taken to analyze the genome-wide histone modification landscape characterized by the ENCODE project in two human hematopoietic cell types, GM12878 and K562. We predicted the locations of 2,107 and 1,448 TE-derived enhancers in the GM12878 and K562 cell lines respectively. A vast majority of these putative enhancers are unique to each cell line; only 3.5% of the TE-derived enhancers are shared between the two. We evaluated the functional effect of TE-derived enhancers by associating them with the cell-type specific expression of nearby genes, and found that the number of TE-derived enhancers is strongly positively correlated with the expression of nearby genes in each cell line. Furthermore, genes that are differentially expressed between the two cell lines also possess a divergent number of TE-derived enhancers in their vicinity. As such, genes that are up-regulated in the GM12878 cell line and down-regulated in K562 have significantly more TE-derived enhancers in their vicinity in the GM12878 cell line and vice versa. These data indicate that human TE-derived sequences are likely to be involved in regulating cell-type specific gene expression on a broad scale and suggest that the enhancer activity of TE-derived sequences is mediated by epigenetic regulatory mechanisms.

  10. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿


    Brown, Pamela J.B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V


    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  11. Genome sequences of eight morphologically diverse Alphaproteobacteria. (United States)

    Brown, Pamela J B; Kysela, David T; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V


    The Alphaproteobacteria comprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium.

  12. Genome Sequences of Eight Morphologically Diverse Alphaproteobacteria▿ (United States)

    Brown, Pamela J. B.; Kysela, David T.; Buechlein, Aaron; Hemmerich, Chris; Brun, Yves V.


    The Alphaproteobacteriacomprise morphologically diverse bacteria, including many species of stalked bacteria. Here we announce the genome sequences of eight alphaproteobacteria, including the first genome sequences of species belonging to the genera Asticcacaulis, Hirschia, Hyphomicrobium, and Rhodomicrobium. PMID:21705585

  13. On topological spaces possessing uniformly distributed sequences

    CERN Document Server

    Bogachev, V I


    Two classes of topological spaces are introduced on which every probability Radon measure possesses a uniformly distributed sequence or a uniformly tight uniformly distributed sequence. It is shown that these classes are stable under multiplication by completely regular Souslin spaces

  14. The Art of Gymnastics: Creating Sequences. (United States)

    Rovegno, Inez


    Offering students opportunities for creating movement sequences in gymnastics allows them to understand the essence of gymnastics, have creative experiences, and learn about themselves. The process of creating sequences is described. (MT)

  15. FOGSAA: Fast Optimal Global Sequence Alignment Algorithm (United States)

    Chakraborty, Angana; Bandyopadhyay, Sanghamitra


    In this article we propose a Fast Optimal Global Sequence Alignment Algorithm, FOGSAA, which aligns a pair of nucleotide/protein sequences faster than any optimal global alignment method including the widely used Needleman-Wunsch (NW) algorithm. FOGSAA is applicable for all types of sequences, with any scoring scheme, and with or without affine gap penalty. Compared to NW, FOGSAA achieves a time gain of (70-90)% for highly similar nucleotide sequences (> 80% similarity), and (54-70)% for sequences having (30-80)% similarity. For other sequences, it terminates with an approximate score. For protein sequences, the average time gain is between (25-40)%. Compared to three heuristic global alignment methods, the quality of alignment is improved by about 23%-53%. FOGSAA is, in general, suitable for aligning any two sequences defined over a finite alphabet set, where the quality of the global alignment is of supreme importance.

  16. On Paranorm Zweier -Convergent Sequence Spaces

    Directory of Open Access Journals (Sweden)

    Vakeel A. Khan


    Full Text Available In this paper, we introduce the paranorm Zweier -convergent sequence spaces , , and , a sequence of positive real numbers. We study some topological properties, prove the decomposition theorem, and study some inclusion relations on these spaces.

  17. On General Fibonacci Sequences in Groups


    Özkan, Engin


    In this paper, we have constituted 3-step general Fibonacci sequences in a nilpotent group with exponent p (p is a prime number) and nilpotency class 4 and given formulas to find the a term of the sequence.

  18. Ultraconservation identifies a small subset of extremely constrained developmental enhancers

    Energy Technology Data Exchange (ETDEWEB)

    Pennacchio, Len A.; Visel, Axel; Prabhakar, Shyam; Akiyama, Jennifer A.; Shoukry, Malak; Lewis, Keith D.; Holt, Amy; Plajzer-Frick, Ingrid; Afzal, Veena; Rubin, Edward M.; Pennacchio, Len A.


    While experimental studies have suggested that non-coding ultraconserved DNA elements are central nodes in the regulatory circuitry that specifies mammalian embryonic development, the possible functional relevance of their>200bp of perfect sequence conservation between human-mouse-rat remains obscure 1,2. Here we have compared the in vivo enhancer activity of a genome-wide set of 231 non-exonic sequences with ultraconserved cores to that of 206 sequences that are under equivalently severe human-rodent constraint (ultra-like), but lack perfect sequence conservation. In transgenic mouse assays, 50percent of the ultraconserved and 50percent of the ultra-like conserved elements reproducibly functioned as tissue-specific enhancers at embryonic day 11.5. In this in vivo assay, we observed that ultraconserved enhancers and constrained non-ultraconserved enhancers targeted expression to a similar spectrum of tissues with a particular enrichment in the developing central nervous system. A human genome-wide comparative screen uncovered ~;;2,600 non-coding elements that evolved under ultra-like human-rodent constraint and are similarly enriched near transcriptional regulators and developmental genes as the much smaller number of ultraconserved elements. These data indicate that ultraconserved elements possessing absolute human-rodent sequence conservation are not distinct from other non-coding elements that are under comparable purifying selection in mammals and suggest they are principal constituents of the cis-regulatory framework of mammalian development.

  19. Cross-correlation properties of cyclotomic sequences

    CERN Document Server

    Cai, Kai; Zheng, Zhiming


    Sequences with good correlation properties are widely used in engineering applications, especially in the area of communications. Among the known sequences, cyclotomic families have the optimal autocorrelation property. In this paper, we decide the cross-correlation function of the known cyclotomic sequences completely. Moreover, to get our results, the relations between the multiplier group and the decimations of the characteristic sequence are also established for an arbitrary difference set.

  20. Information Analysis of DNA Sequences

    CERN Document Server

    Mohammed, Riyazuddin


    The problem of differentiating the informational content of coding (exons) and non-coding (introns) regions of a DNA sequence is one of the central problems of genomics. The introns are estimated to be nearly 95% of the DNA and since they do not seem to participate in the process of transcription of amino-acids, they have been termed "junk DNA." Although it is believed that the non-coding regions in genomes have no role in cell growth and evolution, demonstration that these regions carry useful information would tend to falsify this belief. In this paper, we consider entropy as a measure of information by modifying the entropy expression to take into account the varying length of these sequences. Exons are usually much shorter in length than introns; therefore the comparison of the entropy values needs to be normalized. A length correction strategy was employed using randomly generated nucleonic base strings built out of the alphabet of the same size as the exons under question. Our analysis shows that intron...

  1. Strong sequences and independent sets

    Directory of Open Access Journals (Sweden)

    Joanna Jureczko


    Full Text Available A family $\\mathcal{S} \\in \\mathcal{P}(\\omega$ is \\textit{an independent family} if for each pair $\\mathcal{A, B}$ of disjoint finite subsets of $\\mathcal{S}$ the set $\\bigcap \\mathcal{A} \\cap (\\omega \\setminus \\bigcup \\mathcal{B}$ is nonempty. The fact that there is an independent family on $\\omega$ of size continuum was proved by Fichtenholz and Kantorowicz in \\cite{FK}. If we substitute $\\mathcal{P}(\\omega$ by a set $(X, r$ with arbitrary relation \\textit{r} it is natural question about existence and length of an independent set on $(X, r$. In this paper special assumptions of such existence will be considered. On the other hand in 60s' of the last century the strong sequences method was introduced by Efimov. He used it for proving some famous theorems in dyadic spaces like: Marczewski theorem on cellularity, Shanin theorem on a calibre, Esenin-Volpin theorem and others. In this paper there will be considered: length of strong sequences, the length of independent sets and other well known cardinal invariants and there will be examined inequalities among them.

  2. Sequence Analysis in Demographic Research

    Directory of Open Access Journals (Sweden)

    Billari, Francesco C.


    Full Text Available EnglishThis paper examines the salient features of sequence analysis in demogrpahicresearch. The new approach allows a holistic perspective on life course analysis and is based on arepresentation of lives as sequences of states. Some of the methods for analyzing such data aresketched, from complex description to optimal matching ot monoethetic divisive algorithms. Afer ashort ilustration of a demographically-relevant example, the needs in terms of data collection and theopportunities of applying the same aproach to synthetic data are discussed.FrenchOn examine ici les principaux éléments de l’analyse par séquence endémographie. Cette nouvelle technique permet une perspective unifiée del’analyse du cours de la vie, en représentant la vie comme une série d’états.Certaines des méthodes pour de telles analyses sont décrites, en commençant parla description complexe, pour considérer ensuite les alignements optimales, etles algorithmes de division. Après un court exemple en démographie, onconsidère les besoins en données et les possibilités d’application aux donnéessynthétique.

  3. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

    Energy Technology Data Exchange (ETDEWEB)

    Clum, Alicia [U.S. Department of Energy, Joint Genome Institute; Nolan, Matt [U.S. Department of Energy, Joint Genome Institute; Lang, Elke [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Glavina Del Rio, Tijana [U.S. Department of Energy, Joint Genome Institute; Tice, Hope [U.S. Department of Energy, Joint Genome Institute; Copeland, A [U.S. Department of Energy, Joint Genome Institute; Cheng, Jan-Fang [U.S. Department of Energy, Joint Genome Institute; Lucas, Susan [U.S. Department of Energy, Joint Genome Institute; Chen, Feng [U.S. Department of Energy, Joint Genome Institute; Bruce, David [U.S. Department of Energy, Joint Genome Institute; Goodwin, Lynne A. [Los Alamos National Laboratory (LANL); Pitluck, Sam [U.S. Department of Energy, Joint Genome Institute; Ivanova, N [U.S. Department of Energy, Joint Genome Institute; Mavromatis, K [U.S. Department of Energy, Joint Genome Institute; Mikhailova, Natalia [U.S. Department of Energy, Joint Genome Institute; Pati, Amrita [U.S. Department of Energy, Joint Genome Institute; Chen, Amy [U.S. Department of Energy, Joint Genome Institute; Palaniappan, Krishna [U.S. Department of Energy, Joint Genome Institute; Goker, Markus [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Spring, Stefan [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Chang, Yun-Juan [ORNL; Jeffries, Cynthia [Oak Ridge National Laboratory (ORNL); Chain, Patrick S. G. [Lawrence Livermore National Laboratory (LLNL); Bristow, James [U.S. Department of Energy, Joint Genome Institute; Eisen, Jonathan [U.S. Department of Energy, Joint Genome Institute; Markowitz, Victor [U.S. Department of Energy, Joint Genome Institute; Hugenholtz, Philip [U.S. Department of Energy, Joint Genome Institute; Kyrpides, Nikos C [U.S. Department of Energy, Joint Genome Institute; Klenk, Hans-Peter [DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany; Lapidus, Alla L. [U.S. Department of Energy, Joint Genome Institute


    Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the ge-nus, which until recently was the only genus within the actinobacterial family Acidimicrobia-ceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome se-quence, and annotation. This is the first complete genome sequence of the order Acidomi-crobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. Whole genome sequencing in clinical and public health microbiology. (United States)

    Kwong, J C; McCallum, N; Sintchenko, V; Howden, B P


    Genomics and whole genome sequencing (WGS) have the capacity to greatly enhance knowledge and understanding of infectious diseases and clinical microbiology.The growth and availability of bench-top WGS analysers has facilitated the feasibility of genomics in clinical and public health microbiology.Given current resource and infrastructure limitations, WGS is most applicable to use in public health laboratories, reference laboratories, and hospital infection control-affiliated laboratories.As WGS represents the pinnacle for strain characterisation and epidemiological analyses, it is likely to replace traditional typing methods, resistance gene detection and other sequence-based investigations (e.g., 16S rDNA PCR) in the near future.Although genomic technologies are rapidly evolving, widespread implementation in clinical and public health microbiology laboratories is limited by the need for effective semi-automated pipelines, standardised quality control and data interpretation, bioinformatics expertise, and infrastructure.

  5. Super-Resolution for Traditional and Omnidirectional Image Sequences

    Directory of Open Access Journals (Sweden)

    Attila Nagy


    Full Text Available This article presents a simple method on how to implement a super-resolutionbased video enhancement technique in .NET using the functions of the OpenCV library.First, we outline the goal of this project and after that, a short review of the steps of superresolutiontechnique is given. As a part of the discussion about the implementation itself,the general design aspects are detailed in short. Then, the different optical flow algorithmsare analyzed and the super-resolution calculation of omnidirectional image sequences isdiscussed. After all that, the achieved results can be seen and finally, a short generalconclusion can be read. This paper is a revision of our previous work [1]. In this edition,we focus on the super-resolution of omnidirectional image sequences rather than thetechnological issues that were discussed in our previous article. Further information aboutthe implementation and wrapper development can be found in [1 and 12].

  6. 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.

  7. A rapid method for detection of genetically modified organisms based on magnetic separation and surface-enhanced Raman scattering. (United States)

    Guven, Burcu; Boyacı, İsmail Hakkı; Tamer, Ugur; Çalık, Pınar


    In this study, a new method combining magnetic separation (MS) and surface-enhanced Raman scattering (SERS) was developed to detect genetically modified organisms (GMOs). An oligonucleotide probe which is specific for 35 S DNA target was immobilized onto gold coated magnetic nanospheres to form oligonucleotide-coated nanoparticles. A self assembled monolayer was formed on gold nanorods using 5,5'-dithiobis (2-nitrobenzoic acid) (DTNB) and the second probe of the 35 S DNA target was immobilized on the activated nanorod surfaces. Probes on the nanoparticles were hybridized with the target oligonucleotide. Optimization parameters for hybridization were investigated by high performance liquid chromatography. Optimum hybridization parameters were determined as: 4 μM probe concentration, 20 min immobilization time, 30 min hybridization time, 55 °C hybridization temperature, 750 mM buffer salt concentration and pH: 7.4. Quantification of the target concentration was performed via SERS spectra of DTNB on the nanorods. The correlation between the target concentration and the SERS signal was found to be linear within the range of 25-100 nM. The analyses were performed with only one hybridization step in 40 min. Real sample analysis was conducted using Bt-176 maize sample. The results showed that the developed MS-SERS assay is capable of detecting GMOs in a rapid and selective manner.

  8. Genome sequencing - the ultimate answer to global real time genotyping and surveillance?

    DEFF Research Database (Denmark)

    Hendriksen, Rene S.


    of the complete human genome sequence in 2003, whole genome sequencing (WGS) has greatly increased our ability to in a rapid and more reliable way distinguish between epidemiologically unrelated isolates from the same bacterial species and thereby enhance our capacity to detect outbreaks, conduct surveillance...... and understand or elucidate the epidemiology of certain types or clones. Methods: Today, several WGS platforms are available on the market, however, all have in common that they determine the nucleotide sequences of millions of DNA stretches present in a sample and combine those into almost complete genomes...

  9. Cluster-Based Multipolling Sequencing Algorithm for Collecting RFID Data in Wireless LANs (United States)

    Choi, Woo-Yong; Chatterjee, Mainak


    With the growing use of RFID (Radio Frequency Identification), it is becoming important to devise ways to read RFID tags in real time. Access points (APs) of IEEE 802.11-based wireless Local Area Networks (LANs) are being integrated with RFID networks that can efficiently collect real-time RFID data. Several schemes, such as multipolling methods based on the dynamic search algorithm and random sequencing, have been proposed. However, as the number of RFID readers associated with an AP increases, it becomes difficult for the dynamic search algorithm to derive the multipolling sequence in real time. Though multipolling methods can eliminate the polling overhead, we still need to enhance the performance of the multipolling methods based on random sequencing. To that extent, we propose a real-time cluster-based multipolling sequencing algorithm that drastically eliminates more than 90% of the polling overhead, particularly so when the dynamic search algorithm fails to derive the multipolling sequence in real time.

  10. Hardware Acceleration of Bioinformatics Sequence Alignment Applications

    NARCIS (Netherlands)

    Hasan, L.


    Biological sequence alignment is an important and challenging task in bioinformatics. Alignment may be defined as an arrangement of two or more DNA or protein sequences to highlight the regions of their similarity. Sequence alignment is used to infer the evolutionary relationship between a set of pr

  11. Incidental Sequence Learning across the Lifespan (United States)

    Weiermann, Brigitte; Meier, Beat


    The purpose of the present study was to investigate incidental sequence learning across the lifespan. We tested 50 children (aged 7-16), 50 young adults (aged 20-30), and 50 older adults (aged >65) with a sequence learning paradigm that involved both a task and a response sequence. After several blocks of practice, all age groups slowed down…

  12. Comparative genomics beyond sequence-based alignments

    DEFF Research Database (Denmark)

    Þórarinsson, Elfar; Yao, Zizhen; Wiklund, Eric D.;


    Recent computational scans for non-coding RNAs (ncRNAs) in multiple organisms have relied on existing multiple sequence alignments. However, as sequence similarity drops, a key signal of RNA structure--frequent compensating base changes--is increasingly likely to cause sequence-based alignment me...

  13. PacBio Sequencing and Its Applications

    Institute of Scientific and Technical Information of China (English)

    Anthony Rhoads; Kin Fai Au


    Single-molecule, real-time sequencing developed by Pacific BioSciences offers longer read lengths than the second-generation sequencing (SGS) technologies, making it well-suited for unsolved problems in genome, transcriptome, and epigenetics research. The highly-contiguous de novo assemblies using PacBio sequencing can close gaps in current reference assemblies and characterize structural variation (SV) in personal genomes. With longer reads, we can sequence through extended repetitive regions and detect mutations, many of which are associated with dis-eases. Moreover, PacBio transcriptome sequencing is advantageous for the identification of gene isoforms and facilitates reliable discoveries of novel genes and novel isoforms of annotated genes, due to its ability to sequence full-length transcripts or fragments with significant lengths. Addition-ally, PacBio’s sequencing technique provides information that is useful for the direct detection of base modifications, such as methylation. In addition to using PacBio sequencing alone, many hybrid sequencing strategies have been developed to make use of more accurate short reads in conjunction with PacBio long reads. In general, hybrid sequencing strategies are more affordable and scalable especially for small-size laboratories than using PacBio Sequencing alone. The advent of PacBio sequencing has made available much information that could not be obtained via SGS alone.

  14. The recurrence sequence via the Fibonacci groups (United States)

    Aküzüm, Yeşim; Deveci, Ömür


    This work develops properties of the recurrence sequence defined by the aid of the relation matrix of the Fibonacci groups. The study of this sequence modulo m yields cyclic groups and semigroups from generating matrix. Finally, we extend the sequence defined to groups and then, we obtain its period in the Fibonacci groups.

  15. RNAome sequencing delineates the complete RNA landscape

    NARCIS (Netherlands)

    K.W.J. Derks (Kasper); J. Pothof (Joris)


    textabstractStandard RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species. For example, small and large RNAs from the same sample cannot be sequenced in a single sequence run. We designed RNAome sequencing, which is a strand-specif

  16. Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.

    Directory of Open Access Journals (Sweden)

    Leho Tedersoo

    Full Text Available Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE ( for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA;, the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  17. The role of 3D volumetric MR sequences in diagnosing intraventricular neurocysticercosis: preliminar results

    Directory of Open Access Journals (Sweden)

    Francisco Edward Frota Mont'Alverne Filho


    Full Text Available OBJECTIVE: The purpose of this paper was to investigate the role of two three-dimensional magnetic resonance (MRI sequences: enhanced spoiled gradient recalled echo (SPGR, and fast imaging employing steady-state acquisition (FIESTA in the evaluation of intraventricular neurocysticercosis cysts and scolices. METHOD: Seven neurocysticercosis patients suspected of presenting intraventricular lesions were evaluated by magnetic resonance imaging using enhanced SPGR, and FIESTA. RESULTS: Enhanced SPGR detected eight cystic lesions, with scolices in four. Contrast enhancement was observed in three cysts. FIESTA also detected eight cystic lesions with the presence of scolices in seven of those cystic lesions. Four patients presented parenchymal involvement, while the remaining three presented the racemose form. CONCLUSION: FIESTA and SPGR are sequences that can detect intraventricular cysts of neurocysticercosis, and FIESTA also is good for the detection of the scolex. Considering this information we suggest that FIESTA and SPGR should be included in the MRI protocol for the investigation of intraventricular neurocysticercosis.

  18. Surfactant enhanced volumetric sweep efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Harwell, J.H.; Scamehorn, J.F.


    Surfactant-enhanced waterflooding is a novel EOR method aimed to improve the volumetric sweep efficiencies in reservoirs. The technique depends upon the ability to induce phase changes in surfactant solutions by mixing with surfactants of opposite charge or with salts of appropriate type. One surfactant or salt solution is injected into the reservoir. It is followed later by injection of another surfactant or salt solution. The sequence of injections is arranged so that the two solutions do not mix until they are into the permeable regions well away from the well bore. When they mix at this point, by design they form a precipitate or gel-like coacervate phase, plugging this permeable region, forcing flow through less permeable regions of the reservoir, improving sweep efficiency. The selectivity of the plugging process is demonstrated by achieving permeability reductions in the high permeable regions of Berea sandstone cores. Strategies were set to obtain a better control over the plug placement and the stability of plugs. A numerical simulator has been developed to investigate the potential increases in oil production of model systems. Furthermore, the hardness tolerance of anionic surfactant solutions is shown to be enhanced by addition of monovalent electrolyte or nonionic surfactants. 34 refs., 32 figs., 8 tabs.

  19. Exome sequencing: what clinicians need to know

    Directory of Open Access Journals (Sweden)

    Sastre L


    Full Text Available Leandro SastreInstituto de Investigaciones Biomédicas, CSIC/UAM, C/Arturo Duperier 4, Madrid, Spain; Terapias Experimentales y Biomarcadores en Cáncer, IdiPaz, Madrid, Spain; CIBER de Enfermedades Raras, CIBERER, Valencia, SpainAbstract: The recent development of high throughput methods of deoxyribonucleic acid (DNA sequencing has made it possible to determine individual genome sequences and their specific variations. A region of particular interest is the protein-coding part of the genome, or exome, which is composed of gene exons. The principles of exome purification and sequencing will be described in this review, as well as analyses of the data generated. Results will be discussed in terms of their possible functional and clinical significance. The advantages and limitations of exome sequencing will be compared to those of other massive sequencing approaches such as whole-genome sequencing, ribonucleic acid sequencing or selected DNA sequencing. Exome sequencing has been used recently in the study of various diseases. Monogenic diseases with Mendelian inheritance are among these, but studies have also been carried out on genetic variations that represent risk factors for complex diseases. Cancer is another intensive area for exome sequencing studies. Several examples of the use of exome sequencing in the diagnosis, prognosis, and treatment of these diseases will be described. Finally, remaining challenges and some practical and ethical considerations for the clinical application of exome sequencing will be discussed.Keywords: massively parallel sequencing, RNA sequencing, whole-genome sequencing, genetic variants, molecular diagnosis, pharmacogenomics, personalized medicine, NGS, SGS, SNP, SNV

  20. Discovering motifs in ranked lists of DNA sequences.

    Directory of Open Access Journals (Sweden)

    Eran Eden


    Full Text Available Computational methods for discovery of sequence elements that are enriched in a target set compared with a background set are fundamental in molecular biology research. One example is the discovery of transcription factor binding motifs that are inferred from ChIP-chip (chromatin immuno-precipitation on a microarray measurements. Several major challenges in sequence motif discovery still require consideration: (i the need for a principled approach to partitioning the data into target and background sets; (ii the lack of rigorous models and of an exact p-value for measuring motif enrichment; (iii the need for an appropriate framework for accounting for motif multiplicity; (iv the tendency, in many of the existing methods, to report presumably significant motifs even when applied to randomly generated data. In this paper we present a statistical framework for discovering enriched sequence elements in ranked lists that resolves these four issues. We demonstrate the implementation of this framework in a software application, termed DRIM (discovery of rank imbalanced motifs, which identifies sequence motifs in lists of ranked DNA sequences. We applied DRIM to ChIP-chip and CpG methylation data and obtained the following results. (i Identification of 50 novel putative transcription factor (TF binding sites in yeast ChIP-chip data. The biological function of some of them was further investigated to gain new insights on transcription regulation networks in yeast. For example, our discoveries enable the elucidation of the network of the TF ARO80. Another finding concerns a systematic TF binding enhancement to sequences containing CA repeats. (ii Discovery of novel motifs in human cancer CpG methylation data. Remarkably, most of these motifs are similar to DNA sequence elements bound by the Polycomb complex that promotes histone methylation. Our findings thus support a model in which histone methylation and CpG methylation are mechanistically linked

  1. Hyperrecombination at a specific DNA sequence in pneumococcal transformation.


    Lefèvre, J C; Gasc, A M; Burger, A C; Mostachfi, P; Sicard, A M


    In pneumococcal transformation, recombination frequency between point mutations is usually proportional to physical distances. We have identified an aberrant marker belonging to the amiA locus that appeared to markedly enhance recombination frequency when crossed with any other markers of this gene. This mutation results from the C-to-A transversion in the sequence A-T-T-C-A-T----A-T-T-A-A-T. This effect is especially apparent for short distances as small as 27 base pairs. The hyperrecombinat...

  2. Value of a newly sequenced bacterial genome

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj;


    Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also...... in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome...

  3. MatrixPlot: visualizing sequence constraints

    DEFF Research Database (Denmark)

    Gorodkin, Jan; Stærfeldt, Hans Henrik; Lund, Ole


    MatrixPlot: visualizing sequence constraints. Sub-title Abstract Summary : MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information...... about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. Availability : MatrixPlot can be obtained on request, and can also be accessed online at http://www. Contact :

  4. Chip-based sequencing nucleic acids (United States)

    Beer, Neil Reginald


    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  5. Permutation Entropy for Random Binary Sequences

    Directory of Open Access Journals (Sweden)

    Lingfeng Liu


    Full Text Available In this paper, we generalize the permutation entropy (PE measure to binary sequences, which is based on Shannon’s entropy, and theoretically analyze this measure for random binary sequences. We deduce the theoretical value of PE for random binary sequences, which can be used to measure the randomness of binary sequences. We also reveal the relationship between this PE measure with other randomness measures, such as Shannon’s entropy and Lempel–Ziv complexity. The results show that PE is consistent with these two measures. Furthermore, we use PE as one of the randomness measures to evaluate the randomness of chaotic binary sequences.

  6. Computing with Hereditarily Finite Sequences

    CERN Document Server

    Tarau, Paul


    e use Prolog as a flexible meta-language to provide executable specifications of some fundamental mathematical objects and their transformations. In the process, isomorphisms are unraveled between natural numbers and combinatorial objects (rooted ordered trees representing hereditarily finite sequences and rooted ordered binary trees representing G\\"odel's System {\\bf T} types). This paper focuses on an application that can be seen as an unexpected "paradigm shift": we provide recursive definitions showing that the resulting representations are directly usable to perform symbolically arbitrary-length integer computations. Besides the theoretically interesting fact of "breaking the arithmetic/symbolic barrier", the arithmetic operations performed with symbolic objects like trees or types turn out to be genuinely efficient -- we derive implementations with asymptotic performance comparable to ordinary bitstring implementations of arbitrary-length integer arithmetic. The source code of the paper, organized as a ...

  7. An Attempt to Enhance the Class Efficiency with a Task-centered Instructional Strategy:An Instruction Redesign with Educational Components Sequence in Business English Interpreting Training%面向完整任务提高教学效能的一项课改尝试--以重构商务英语口译教学任务排序为例

    Institute of Scientific and Technical Information of China (English)

    戴黎鹂; 盛群力


    First Principles of Instruction advocates a task⁃centered instructional strategy with the content components of knowledge objects as contrasted with the topic⁃by⁃topic approach that typifies more traditional curriculum approaches. This paper discusses and attempts to apply First Principles of Instruction to reform in⁃structional design of Business English Interpreting Training for English majors. The business English interpre⁃ting class is task⁃centered and breaks down with educational components sequence in the real world. Instructors support learners in the form of scaffolding,learner guidance,or coaching,until learners can completely accom⁃plish the tasks,which may help learners facilitate their application of newly acquired knowledge and skills.%首要教学原理提倡在教学过程中面向现实社会中的完整任务设计教学,教学内容的设计转向聚焦任务序列。在商务英语口译教学实践中,尝试运用该原理来重新设计课堂教学,将以任务为中心的教学内容排序替代传统的以主题为中心的教学模式,教师从扶到放,使学习者在任务或者问题情境中掌握知识技能,在融会贯通的基础上实现学习迁移,这些为探寻优质教学之路提供了一种借鉴。

  8. Smart Image Enhancement Process (United States)

    Jobson, Daniel J. (Inventor); Rahman, Zia-ur (Inventor); Woodell, Glenn A. (Inventor)


    Contrast and lightness measures are used to first classify the image as being one of non-turbid and turbid. If turbid, the original image is enhanced to generate a first enhanced image. If non-turbid, the original image is classified in terms of a merged contrast/lightness score based on the contrast and lightness measures. The non-turbid image is enhanced to generate a second enhanced image when a poor contrast/lightness score is associated therewith. When the second enhanced image has a poor contrast/lightness score associated therewith, this image is enhanced to generate a third enhanced image. A sharpness measure is computed for one image that is selected from (i) the non-turbid image, (ii) the first enhanced image, (iii) the second enhanced image when a good contrast/lightness score is associated therewith, and (iv) the third enhanced image. If the selected image is not-sharp, it is sharpened to generate a sharpened image. The final image is selected from the selected image and the sharpened image.

  9. [DNA sequencing technology and automatization of it]. (United States)

    Kraev, A S


    Precise manipulations with genetic material, typical for modern experiments in molecular biology and in new biotechnology, require a capability to determine DNA base sequence. This capability enables today to exploit specific genetic knowledge for the dissection of complex cell processes and for modulation of cell metabolism in transgenic organisms. The review focuses on such DNA sequencing technologies that are widespread in general laboratory practice. They can safely be called, with the availability of commercial reagents, industrial techniques. Modern DNA sequencing requires recurrent breakdown of large genomic DNA into smaller pieces, that are then amplified, sequenced and the initial long stretch reconstructed via overlap of small pieces. The DNA sequencing process has several steps: a DNA fragment is obtained in sufficient quantity and purity, it is converted to a form suitable for a particular sequencing method, a sequencing reaction is performed and its products fractionated; and finally the resultant data are interpreted (i.e. an autoradiograph is read into a computer memory) and a long sequence in reconstructed via overlap of short stretches. These steps are considered in separate parts; an accent is made on sequencing strategies with respect to their biological task. In the last part, possibilities for automation of sequencing experiment are considered, followed by a discussion of domestic problems in DNA sequencing.

  10. Design of Digital Hybrid Chaotic Sequence Generator

    Institute of Scientific and Technical Information of China (English)

    RAO Nini; ZENG Dong


    The feasibility of the hybrid chaotic sequences as the spreading codes in code divided multiple access(CDMA) system is analyzed.The design and realization of the digital hybrid chaotic sequence generator by very high speed integrated circuit hardware description language(VHDL) are described.A valid hazard canceledl method is presented.Computer simulations show that the stable digital sequence waveforms can be produced.The correlations of the digital hybrid chaotic sequences are compared with those of m-sequences.The results show that the correlations of the digital hybrid chaotic sequences are almost as good as those of m-sequences.The works in this paper explored a road for the practical applications of chaos.

  11. The Idefix enhancer-blocking insulator also harbors barrier activity. (United States)

    Brasset, E; Hermant, C; Jensen, S; Vaury, C


    Chromatin insulators are cis-regulatory sequences participating in the regulation of gene expression. Their presence within the genome is associated with two main functions. One of them is an enhancer-blocking function that blocks enhancer-promoter communication when the insulator is located in between. The second is a boundary or barrier function that insulates independent units of transcription. This latter is observed when two insulators flanking a gene and its regulatory sequences block the regulatory influences of surrounding chromatin. Some years ago, we reported the presence of an insulator within the retrotransposon Idefix from Drosophila melanogaster. This insulator displays an enhancer-blocking activity toward an enhancer located within a second retrotransposon called ZAM. Here, we show that this insulator is not specific to the ZAM enhancer but has the capacity to interfere in the communication established between a broad range of cis-regulatory enhancer and a promoter. Furthermore, we show that, if it is placed on both sides of a transgene, this insulator acts as a barrier able to isolate the transgene from its repressive or enhancing environment. Thus, the Idefix insulator carries both an enhancer-blocking and a barrier activity. According to these properties, the Idefix insulator might prove to be a useful tool to isolate artificial transgenes from positive or negative influences from their integration sites.

  12. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbach, Dana J.; Gasch, Audrey P.


    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  13. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbach, Dana J.; Gasch, Audrey P.


    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  14. Genes related to xylose fermentation and methods of using same for enhanced biofuel production (United States)

    Wohlbach, Dana J.; Gasch, Audrey P.


    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  15. Enhancing human capacities

    CERN Document Server

    Savulescu, Julian; Kahane, Guy


    Enhancing Human Capacities is the first to review the very latest scientific developments in human enhancement. It is unique in its examination of the ethical and policy implications of these technologies from a broad range of perspectives. Presents a rich range of perspectives on enhancement from world leading ethicists and scientists from Europe and North America The most comprehensive volume yet on the science and ethics of human enhancement Unique in providing a detailed overview of current and expected scientific advances in this area Discusses both general conceptual and ethical issues

  16. Highly conserved non-coding sequences are associated with vertebrate development.

    Directory of Open Access Journals (Sweden)

    Adam Woolfe


    Full Text Available In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH, in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development

  17. Assembly Sequence Planning for Mechanical Products

    Institute of Scientific and Technical Information of China (English)


    A method for assembly sequence planning is proposed in this paper. First, two methods for assembly sequence planning are compared, which are indirect method and direct method. Then, the limits of the previous assembly planning system are pointed out. On the basis of indirect method, an improved method for assembly sequence planning is put forward. This method is composed of four parts, which are assembly modeling for products, assembly sequence representing, assembly sequence planning, and evaluation and optimization. The assembly model is established by human machine interaction, and the assembly model contains components' information and the assembly relation among the components. The assembly sequence planning is based on the breaking up of the assembly model. And/or graph is used to represent assembly sequence set. Every component which satisfies the disassembly condition is recorded as a node of an and/or graph. After the disassembly sequence and/or graph is generated, heuristic algorithm - AO* algorithm is used to search the disassembly sequence and/or graph, and the optimum assembly sequence planning is realized. This method is proved to be effective in a prototype system which is a sub-project of a state 863/CIMS research project of China - ‘Concurrent Engineering’.

  18. Randomness in Sequence Evolution Increases over Time.

    Directory of Open Access Journals (Sweden)

    Guangyu Wang

    Full Text Available The second law of thermodynamics states that entropy, as a measure of randomness in a system, increases over time. Although studies have investigated biological sequence randomness from different aspects, it remains unknown whether sequence randomness changes over time and whether this change consists with the second law of thermodynamics. To capture the dynamics of randomness in molecular sequence evolution, here we detect sequence randomness based on a collection of eight statistical random tests and investigate the randomness variation of coding sequences with an application to Escherichia coli. Given that core/essential genes are more ancient than specific/non-essential genes, our results clearly show that core/essential genes are more random than specific/non-essential genes and accordingly indicate that sequence randomness indeed increases over time, consistent well with the second law of thermodynamics. We further find that an increase in sequence randomness leads to increasing randomness of GC content and longer sequence length. Taken together, our study presents an important finding, for the first time, that sequence randomness increases over time, which may provide profound insights for unveiling the underlying mechanisms of molecular sequence evolution.

  19. A human cellular sequence implicated in trk oncogene activation is DNA damage inducible

    Energy Technology Data Exchange (ETDEWEB)

    Ben-Ishai, R.; Scharf, R.; Sharon, R.; Kapten, I. (Technion-Israel Institute of Technology, Haifa (Israel))


    Xeroderma pigmentosum cells, which are deficient in the repair of UV light-induced DNA damage, have been used to clone DNA-damage-inducible transcripts in human cells. The cDNA clone designated pC-5 hybridizes on RNA gel blots to a 1-kilobase transcript, which is moderately abundant in nontreated cells and whose synthesis is enhanced in human cells following UV irradiation or treatment with several other DNA-damaging agents. UV-enhanced transcription of C-5 RNA is transient and occurs at lower fluences and to a greater extent in DNA-repair-deficient than in DNA-repair-proficient cells. Southern blot analysis indicates that the C-5 gene belongs to a multigene family. A cDNA clone containing the complete coding sequence of C-5 was isolated. Sequence analysis revealed that it is homologous to a human cellular sequence encoding the amino-terminal activating sequence of the trk-2h chimeric oncogene. The presence of DNA-damage-responsive sequences at the 5' end of a chimeric oncogene could result in enhanced expression of the oncogene in response to carcinogens.

  20. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer. (United States)

    Wu, Tsai-Chin; Vasudev, Milana; Dutta, Mitra; Stroscio, Michael A


    Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.