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Sample records for rapid homology search

  1. Chromosome movements promoted by the mitochondrial protein SPD-3 are required for homology search during Caenorhabditis elegans meiosis.

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    Leticia Labrador

    2013-05-01

    Full Text Available Pairing of homologous chromosomes during early meiosis is essential to prevent the formation of aneuploid gametes. Chromosome pairing includes a step of homology search followed by the stabilization of homolog interactions by the synaptonemal complex (SC. These events coincide with dramatic changes in nuclear organization and rapid chromosome movements that depend on cytoskeletal motors and are mediated by SUN-domain proteins on the nuclear envelope, but how chromosome mobility contributes to the pairing process remains poorly understood. We show that defects in the mitochondria-localizing protein SPD-3 cause a defect in homolog pairing without impairing nuclear reorganization or SC assembly, which results in promiscuous installation of the SC between non-homologous chromosomes. Preventing SC assembly in spd-3 mutants does not improve homolog pairing, demonstrating that SPD-3 is required for homology search at the start of meiosis. Pairing center regions localize to SUN-1 aggregates at meiosis onset in spd-3 mutants; and pairing-promoting proteins, including cytoskeletal motors and polo-like kinase 2, are normally recruited to the nuclear envelope. However, quantitative analysis of SUN-1 aggregate movement in spd-3 mutants demonstrates a clear reduction in mobility, although this defect is not as severe as that seen in sun-1(jf18 mutants, which also show a stronger pairing defect, suggesting a correlation between chromosome-end mobility and the efficiency of pairing. SUN-1 aggregate movement is also impaired following inhibition of mitochondrial respiration or dynein knockdown, suggesting that mitochondrial function is required for motor-driven SUN-1 movement. The reduced chromosome-end mobility of spd-3 mutants impairs coupling of SC assembly to homology recognition and causes a delay in meiotic progression mediated by HORMA-domain protein HTP-1. Our work reveals how chromosome mobility impacts the different early meiotic events that promote

  2. Rapid and accurate identification of microorganisms contaminating cosmetic products based on DNA sequence homology.

    Science.gov (United States)

    Fujita, Y; Shibayama, H; Suzuki, Y; Karita, S; Takamatsu, S

    2005-12-01

    The aim of this study was to develop rapid and accurate procedures to identify microorganisms contaminating cosmetic products, based on the identity of the nucleotide sequences of the internal transcribed spacer (ITS) region of the ribosomal RNA coding DNA (rDNA). Five types of microorganisms were isolated from the inner portion of lotion bottle caps, skin care lotions, and cleansing gels. The rDNA ITS region of microorganisms was amplified through the use of colony-direct PCR or ordinal PCR using DNA extracts as templates. The nucleotide sequences of the amplified DNA were determined and subjected to homology search of a publicly available DNA database. Thereby, we obtained DNA sequences possessing high similarity with the query sequences from the databases of all the five organisms analyzed. The traditional identification procedure requires expert skills, and a time period of approximately 1 month to identify the microorganisms. On the contrary, 3-7 days were sufficient to complete all the procedures employed in the current method, including isolation and cultivation of organisms, DNA sequencing, and the database homology search. Moreover, it was possible to develop the skills necessary to perform the molecular techniques required for the identification procedures within 1 week. Consequently, the current method is useful for rapid and accurate identification of microorganisms, contaminating cosmetics.

  3. genBlastG: using BLAST searches to build homologous gene models.

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    She, Rong; Chu, Jeffrey Shih-Chieh; Uyar, Bora; Wang, Jun; Wang, Ke; Chen, Nansheng

    2011-08-01

    BLAST users frequently expect to obtain homologous genes with certain similarity to their query genes. But what they get from BLAST searches are often collections of local alignments called high-scoring segment pairs (HSPs). On the other hand, most homology-based gene finders have been built using computation-intensive algorithms, without taking full advantage of BLAST searches that have been perfected over the last decades. Here we report an efficient algorithm, genBlastG that directly uses the HSPs reported by BLAST to define high-quality gene models. http://genome.sfu.ca/genblast/download.html

  4. Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology.

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    Li, W; Pio, F; Pawłowski, K; Godzik, A

    2000-12-01

    Two proteins can have a similar 3-dimensional structure and biological function, but have sequences sufficiently different that traditional protein sequence comparison algorithms do not identify their relationship. The desire to identify such relations has led to the development of more sensitive sequence alignment strategies. One such strategy is the Intermediate Sequence Search (ISS), which connects two proteins through one or more intermediate sequences. In its brute-force implementation, ISS is a strategy that repetitively uses the results of the previous query as new search seeds, making it time-consuming and difficult to analyze. Saturated BLAST is a package that performs ISS in an efficient and automated manner. It was developed using Perl and Perl/Tk and implemented on the LINUX operating system. Starting with a protein sequence, Saturated BLAST runs a BLAST search and identifies representative sequences for the next generation of searches. The procedure is run until convergence or until some predefined criteria are met. Saturated BLAST has a friendly graphic user interface, a built-in BLAST result parser, several multiple alignment tools, clustering algorithms and various filters for the elimination of false positives, thereby providing an easy way to edit, visualize, analyze, monitor and control the search. Besides detecting remote homologies, Saturated BLAST can be used to maintain protein family databases and to search for new genes in genomic databases.

  5. GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering.

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    Suzuki, Shuji; Kakuta, Masanori; Ishida, Takashi; Akiyama, Yutaka

    2016-01-01

    Sequence homology searches are used in various fields and require large amounts of computation time, especially for metagenomic analysis, owing to the large number of queries and the database size. To accelerate computing analyses, graphics processing units (GPUs) are widely used as a low-cost, high-performance computing platform. Therefore, we mapped the time-consuming steps involved in GHOSTZ, which is a state-of-the-art homology search algorithm for protein sequences, onto a GPU and implemented it as GHOSTZ-GPU. In addition, we optimized memory access for GPU calculations and for communication between the CPU and GPU. As per results of the evaluation test involving metagenomic data, GHOSTZ-GPU with 12 CPU threads and 1 GPU was approximately 3.0- to 4.1-fold faster than GHOSTZ with 12 CPU threads. Moreover, GHOSTZ-GPU with 12 CPU threads and 3 GPUs was approximately 5.8- to 7.7-fold faster than GHOSTZ with 12 CPU threads.

  6. Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA

    DEFF Research Database (Denmark)

    Freyhult, E.; Bollback, J. P.; Gardner, P. P.

    2006-01-01

    Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer, and Infer......Homology search is one of the most ubiquitous bioinformatic tasks, yet it is unknown how effective the currently available tools are for identifying noncoding RNAs (ncRNAs). In this work, we use reliable ncRNA data sets to assess the effectiveness of methods such as BLAST, FASTA, HMMer...

  7. An artificial functional family filter in homolog searching in next-generation sequencing metagenomics.

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    Ruofei Du

    Full Text Available In functional metagenomics, BLAST homology search is a common method to classify metagenomic reads into protein/domain sequence families such as Clusters of Orthologous Groups of proteins (COGs in order to quantify the abundance of each COG in the community. The resulting functional profile of the community is then used in downstream analysis to correlate the change in abundance to environmental perturbation, clinical variation, and so on. However, the short read length coupled with next-generation sequencing technologies poses a barrier in this approach, essentially because similarity significance cannot be discerned by searching with short reads. Consequently, artificial functional families are produced, in which those with a large number of reads assigned decreases the accuracy of functional profile dramatically. There is no method available to address this problem. We intended to fill this gap in this paper. We revealed that BLAST similarity scores of homologues for short reads from COG protein members coding sequences are distributed differently from the scores of those derived elsewhere. We showed that, by choosing an appropriate score cut-off, we are able to filter out most artificial families and simultaneously to preserve sufficient information in order to build the functional profile. We also showed that, by incorporated application of BLAST and RPS-BLAST, some artificial families with large read counts can be further identified after the score cutoff filtration. Evaluated on three experimental metagenomic datasets with different coverages, we found that the proposed method is robust against read coverage and consistently outperforms the other E-value cutoff methods currently used in literatures.

  8. Dynamics of rye chromosome 1R regions with high or low crossover frequency in homology search and synapsis development.

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    Nohelia T Valenzuela

    Full Text Available In many organisms, homologous pairing and synapsis depend on the meiotic recombination machinery that repairs double-strand DNA breaks (DSBs produced at the onset of meiosis. The culmination of recombination via crossover gives rise to chiasmata, which locate distally in many plant species such as rye, Secale cereale. Although, synapsis initiates close to the chromosome ends, a direct effect of regions with high crossover frequency on partner identification and synapsis initiation has not been demonstrated. Here, we analyze the dynamics of distal and proximal regions of a rye chromosome introgressed into wheat to define their role on meiotic homology search and synapsis. We have used lines with a pair of two-armed chromosome 1R of rye, or a pair of telocentrics of its long arm (1RL, which were homozygous for the standard 1RL structure, homozygous for an inversion of 1RL that changes chiasma location from distal to proximal, or heterozygous for the inversion. Physical mapping of recombination produced in the ditelocentric heterozygote (1RL/1RL(inv showed that 70% of crossovers in the arm were confined to a terminal segment representing 10% of the 1RL length. The dynamics of the arms 1RL and 1RL(inv during zygotene demonstrates that crossover-rich regions are more active in recognizing the homologous partner and developing synapsis than crossover-poor regions. When the crossover-rich regions are positioned in the vicinity of chromosome ends, their association is facilitated by telomere clustering; when they are positioned centrally in one of the two-armed chromosomes and distally in the homolog, their association is probably derived from chromosome elongation. On the other hand, chromosome movements that disassemble the bouquet may facilitate chromosome pairing correction by dissolution of improper chromosome associations. Taken together, these data support that repair of DSBs via crossover is essential in both the search of the homologous partner

  9. Searching remote homology with spectral clustering with symmetry in neighborhood cluster kernels.

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    Maulik, Ujjwal; Sarkar, Anasua

    2013-01-01

    Remote homology detection among proteins utilizing only the unlabelled sequences is a central problem in comparative genomics. The existing cluster kernel methods based on neighborhoods and profiles and the Markov clustering algorithms are currently the most popular methods for protein family recognition. The deviation from random walks with inflation or dependency on hard threshold in similarity measure in those methods requires an enhancement for homology detection among multi-domain proteins. We propose to combine spectral clustering with neighborhood kernels in Markov similarity for enhancing sensitivity in detecting homology independent of "recent" paralogs. The spectral clustering approach with new combined local alignment kernels more effectively exploits the unsupervised protein sequences globally reducing inter-cluster walks. When combined with the corrections based on modified symmetry based proximity norm deemphasizing outliers, the technique proposed in this article outperforms other state-of-the-art cluster kernels among all twelve implemented kernels. The comparison with the state-of-the-art string and mismatch kernels also show the superior performance scores provided by the proposed kernels. Similar performance improvement also is found over an existing large dataset. Therefore the proposed spectral clustering framework over combined local alignment kernels with modified symmetry based correction achieves superior performance for unsupervised remote homolog detection even in multi-domain and promiscuous domain proteins from Genolevures database families with better biological relevance. Source code available upon request. sarkar@labri.fr.

  10. Rapid generation of long tandem DNA repeat arrays by homologous recombination in yeast to study their function in mammalian genomes

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    Kouprina Natalay

    2011-10-01

    Full Text Available Abstract We describe here a method to rapidly convert any desirable DNA fragment, as small as 100 bp, into long tandem DNA arrays up to 140 kb in size that are inserted into a microbe vector. This method includes rolling-circle phi29 amplification (RCA of the sequence in vitro and assembly of the RCA products in vivo by homologous recombination in the yeast Saccharomyces cerevisiae. The method was successfully used for a functional analysis of centromeric and pericentromeric repeats and construction of new vehicles for gene delivery to mammalian cells. The method may have general application in elucidating the role of tandem repeats in chromosome organization and dynamics. Each cycle of the protocol takes ~ two weeks to complete.

  11. EST sequences and their annotation (amino acid sequence and results of homology search) - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available esource Project ( http://www.nbrp.jp/ ). The link to the National BioResource Pro...List Contact us Dicty_cDB EST sequences and their annotation (amino acid sequence and results of homology se...arch) Data detail Data name EST sequences and their annotation (amino acid sequence and results of homology ...search) DOI 10.18908/lsdba.nbdc00419-001 Description of data contents Sequences of cDNA clones of Dictyostelium discoideum and the...s (with target DBs: dicty EST-DB, DNA-DB and protein-DB)). Links to the Atlas database ( http://dictycdb.bio

  12. Cancer associated E17K mutation causes rapid conformational drift in AKT1 pleckstrin homology (PH domain.

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    Ambuj Kumar

    Full Text Available BACKGROUND: AKT1 (v-akt murine thymoma viral oncogene homologue 1 kinase is one of the most frequently activated proliferated and survival pathway of cancer. Recently it has been shown that E17K mutation in the Pleckstrin Homology (PH domain of AKT1 protein leads to cancer by amplifying the phosphorylation and membrane localization of protein. The mutant has shown resistance to AKT1/2 inhibitor VIII drug molecule. In this study we have demonstrated the detailed structural and molecular consequences associated with the activity regulation of mutant protein. METHODS: The docking score exhibited significant loss in the interaction affinity to AKT1/2 inhibitor VIII drug molecule. Furthermore, the molecular dynamics simulation studies presented an evidence of rapid conformational drift observed in mutant structure. RESULTS: There was no stability loss in mutant as compared to native structure and the major cation-π interactions were also shown to be retained. Moreover, the active residues involved in membrane localization of protein exhibited significant rise in NHbonds formation in mutant. The rise in NHbond formation in active residues accounts for the 4-fold increase in the membrane localization potential of protein. CONCLUSION: The overall result suggested that, although the mutation did not induce any stability loss in structure, the associated pathological consequences might have occurred due to the rapid conformational drifts observed in the mutant AKT1 PH domain. GENERAL SIGNIFICANCE: The methodology implemented and the results obtained in this work will facilitate in determining the core molecular mechanisms of cancer-associated mutations and in designing their potential drug inhibitors.

  13. An Improved Homologous Recombination Method for Rapid Cloning of the Antibody Heavy Chain Gene and Its Comparison with the Homologous Recombination and Traditional Cloning Methods

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    Masoumeh Hajirezaei

    2015-10-01

    Full Text Available Background: The homologous recombination (HR is one of the conventional cloning methods for the production of recombinant DNA. It is a quick method for in vivo DNA cloning without using the high cost restriction enzymes. A few modifications in the cloning procedure can increase the efficiency of this method.Materials and Methods: In this study, effect of heating on the rate of the IgG1 heavy chain gene cloning was investigated in the HR method and then it was compared with HR method without heating and traditional cloning method. For doing this comparison, three cloning methods including HR, HR with the heat treatment, and traditional cloning were used to clone the human IgG1 heavy chain into the pcDNA3.1(+ plasmid.Results: The results showed that adding heat in the HR method converts insert and vector from the double strand DNA to the single strand DNA. This allows them to copulate with each other better and faster than the two other methods. The heat addition also helps the cell enzyme system for a faster and easier recombination and moreover it increases the cloning efficiency of the HR method in case of in vitro processing.Conclusion: The results showed that giving heat in the HR method increases cloning rate 7.5% and this increase reaches 10% in comparison with the traditional method. 

  14. Searching for Rapid Orbital Decay of WASP-18b

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    Wilkins, Ashlee N.; Deming, Drake; Hamilton, Douglas [Department of Astronomy, University of Maryland, College Park, MD 20742-2421 (United States); Delrez, Laetitia [Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Barker, Adrian J. [Department of Applied Mathematics, School of Mathematics, University of Leeds, Leeds LS2 9JT (United Kingdom); Gillon, Michael; Jehin, Emmanuel, E-mail: awilkins@astro.umd.edu [Space Sciences, Technologies and Astrophysics Research (STAR) Institute, Université de Liège, allée du 6 Août 19C, B-4000 Lige (Belgium)

    2017-02-20

    The WASP-18 system, with its massive and extremely close-in planet, WASP-18b ( M{sub p} = 10.3 M{sub J}, a = 0.02 au, P = 22.6 hr), is one of the best-known exoplanet laboratories to directly measure Q ′, the modified tidal quality factor and proxy for efficiency of tidal dissipation, of the host star. Previous analysis predicted a rapid orbital decay of the planet toward its host star that should be measurable on the timescale of a few years, if the star is as dissipative as is inferred from the circularization of close-in solar-type binary stars. We have compiled published transit and secondary eclipse timing (as observed by WASP, TRAPPIST, and Spitzer ) with more recent unpublished light curves (as observed by TRAPPIST and Hubble Space Telescope ) with coverage spanning nine years. We find no signature of a rapid decay. We conclude that the absence of rapid orbital decay most likely derives from Q ′ being larger than was inferred from solar-type stars and find that Q ′ ≥ 1 × 10{sup 6}, at 95% confidence; this supports previous work suggesting that F stars, with their convective cores and thin convective envelopes, are significantly less tidally dissipative than solar-type stars, with radiative cores and large convective envelopes.

  15. Algorithm for Rapid Searching Among Star-Catalog Entries

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    Liebe, Carl Christian

    2006-01-01

    An algorithm searches a star catalog to identify guide stars within the field of view of a telescope or camera. The algorithm is fast: the number of computations needed to perform the search is approximately proportional to the logarithm of the number of stars in the catalog. The algorithm requires the prior organization of the star catalog into a hierarchy utilizing independent spherical coverings (see figure), such that each successively higher level contains fewer elements. In the lowest and most numerous level of the hierarchy, the elements are individual stars in the star catalog. The next higher level contains a spherical covering (a constellation of n points on a sphere that minimizes the maximum distance of any point on the sphere from the closest one of the n points), the next higher level contains a smaller spherical covering, and so forth, ending at the highest level, which contains one element representing the point of entry into the search structure. With necessary exceptions at the lowest and highest levels, each element at each level is labeled in terms of the element to which it is linked in the next higher level and the first element to which it is linked in the next lower level. Each element is also labeled in terms of (1) its coordinates on the celestial sphere and (2) the largest angular distance to any element in any lower level in the hierarchy. The elements at all levels of the hierarchy are numbered on a single list, such that the elements of each constellation at each level are numbered consecutively. The algorithm is recursive. The input required to start the algorithm comprises the coordinates of a point on the celestial sphere. Attention is then focused on individual elements of the hierarchy, starting from the topmost one, as follows: The angle between the input point and the element under consideration is calculated. If the calculated angle is larger than the sum of (1) the predetermined angle to the most distant element plus (2) the

  16. Highly Efficient CRISPR/Cas9-Mediated Homologous Recombination Promotes the Rapid Generation of Bacterial Artificial Chromosomes of Pseudorabies Virus.

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    Guo, Jin-Chao; Tang, Yan-Dong; Zhao, Kuan; Wang, Tong-Yun; Liu, Ji-Ting; Gao, Jia-Cong; Chang, Xiao-Bo; Cui, Hong-Yu; Tian, Zhi-Jun; Cai, Xue-Hui; An, Tong-Qing

    2016-01-01

    Bacterial artificial chromosomes (BACs) are powerful tools for the manipulation of the large genomes of DNA viruses, such as herpesviruses. However, the methods currently used to construct the recombinant viruses, an important intermediate link in the generation of BACs, involve the laborious process of multiple plaque purifications. Moreover, some fastidious viruses may be lost or damaged during these processes, making it impossible to generate BACs from these large-genome DNA viruses. Here, we introduce the CRISPR/Cas9 as a site-specific gene knock-in instrument that promotes the homologs recombination of a linearized transfer vector and the Pseudorabies virus genome through double incisions. The efficiency of recombination is as high as 86%. To our knowledge, this is the highest efficiency ever reported for Pseudorabies virus recombination. We also demonstrate that the positions and distances of the CRISPR/Cas9 single guide RNAs from the homology arms correlate with the efficiency of homologous recombination. Our work show a simple and fast cloning method of BACs with large genome inserted by greatly enhancing the HR efficiencies through CRISPR/Cas9-mediated homology-directed repair mechanism, and this method could be of helpful for manipulating large DNA viruses, and will provide a successful model for insertion of large DNA fragments into other viruses.

  17. A rapid search for the counterpart to an active magnetar

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    Levan, Andrew

    2016-10-01

    We propose to obtain a fast response observation of a magnetar undergoing an active period. Utilizing rapid, deep, diffraction limited observations with WFC3 we will maximize the chances of obtaining the IR detection of the magnetar. This in turn yields unique constraints on emission mechanisms, enables the measurement of dynamics (e.g. via proper motion) and can associate the magnetar with a given structure (e.g. young cluster or supernova remnant) in the galaxy. The association with a cluster provides means of measuring the stellar age, in turn informing the stellar properties (e.g. mass) of the magnetar progenitors. We have demonstrated the success of this approach with the detection of the counterpart of SGR 1935+2154 with a magnitude (during bursting activity) of F140W(AB) 25.5, a level extremely challenging to detect variability in from the ground, requiring multiple nights of adaptive optics imaging in typical conditions. Indeed, our observations will be senstive to counterparts significantly fainter than it is possible to detect from any ground based observatory. These observations will allow us to break through the observational barrier that has so far prevented us from detecting counterparts to more than two-thirds of magnetar candidates. With these observations we will construct a fuller picture of magnetars, the routes to their creation, and their role as cosmic engines across the Universe.

  18. Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile - Dicty_cDB | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available List Contact us Dicty_cDB Contig sequences and their annotation (amino acid sequence and results of homology... search), and expression profile Data detail Data name Contig sequences and their annotation (amino acid seq...f data contents Contig sequences of cDNA sequences of Dictyostelium discoideum and the...EST-3'EST-ligated sequence and full-length cDNA sequence by the assembly program ...Phrap ( http://www.phrap.org/index.html ). Link to the list of clones constituting the contig, the information on its mapping to the

  19. Simrank: Rapid and sensitive general-purpose k-mer search tool

    Energy Technology Data Exchange (ETDEWEB)

    DeSantis, T.Z.; Keller, K.; Karaoz, U.; Alekseyenko, A.V; Singh, N.N.S.; Brodie, E.L; Pei, Z.; Andersen, G.L; Larsen, N.

    2011-04-01

    Terabyte-scale collections of string-encoded data are expected from consortia efforts such as the Human Microbiome Project (http://nihroadmap.nih.gov/hmp). Intra- and inter-project data similarity searches are enabled by rapid k-mer matching strategies. Software applications for sequence database partitioning, guide tree estimation, molecular classification and alignment acceleration have benefited from embedded k-mer searches as sub-routines. However, a rapid, general-purpose, open-source, flexible, stand-alone k-mer tool has not been available. Here we present a stand-alone utility, Simrank, which allows users to rapidly identify database strings the most similar to query strings. Performance testing of Simrank and related tools against DNA, RNA, protein and human-languages found Simrank 10X to 928X faster depending on the dataset. Simrank provides molecular ecologists with a high-throughput, open source choice for comparing large sequence sets to find similarity.

  20. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches

    OpenAIRE

    Rognes, Torbjørn

    2001-01-01

    There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of th...

  1. THE RAPID PRODUCTION OF ACUTE DISSEMINATED ENCEPHALOMYELITIS IN RHESUS MONKEYS BY INJECTION OF HETEROLOGOUS AND HOMOLOGOUS BRAIN TISSUE WITH ADJUVANTS

    Science.gov (United States)

    Kabat, Elvin A.; Wolf, Abner; Bezer, Ada E.

    1947-01-01

    1. A picture resembling acute disseminated encephalomyelitis in the human being has been regularly and rapidly produced in rhesus monkeys by injection of emulsions of adult rabbit and monkey brain administered with adjuvants. 2. No lesions of the central nervous system resulted from injection of similar emulsions of fetal rabbit brain or adult rabbit lung. 3. A description of the gross and histological findings in the central nervous system is given and compared with features of human demyelinating disease. 4. The experimental findings are in accord with the hypothesis that antibody to the injected brain emulsion reacts with the tissues of the nervous system of the animal to produce the pathological changes. PMID:19871595

  2. Predicting Airport Screening Officers' Visual Search Competency With a Rapid Assessment.

    Science.gov (United States)

    Mitroff, Stephen R; Ericson, Justin M; Sharpe, Benjamin

    2017-11-01

    Objective The study's objective was to assess a new personnel selection and assessment tool for aviation security screeners. A mobile app was modified to create a tool, and the question was whether it could predict professional screeners' on-job performance. Background A variety of professions (airport security, radiology, the military, etc.) rely on visual search performance-being able to detect targets. Given the importance of such professions, it is necessary to maximize performance, and one means to do so is to select individuals who excel at visual search. A critical question is whether it is possible to predict search competency within a professional search environment. Method Professional searchers from the USA Transportation Security Administration (TSA) completed a rapid assessment on a tablet-based X-ray simulator (XRAY Screener, derived from the mobile technology app Airport Scanner; Kedlin Company). The assessment contained 72 trials that were simulated X-ray images of bags. Participants searched for prohibited items and tapped on them with their finger. Results Performance on the assessment significantly related to on-job performance measures for the TSA officers such that those who were better XRAY Screener performers were both more accurate and faster at the actual airport checkpoint. Conclusion XRAY Screener successfully predicted on-job performance for professional aviation security officers. While questions remain about the underlying cognitive mechanisms, this quick assessment was found to significantly predict on-job success for a task that relies on visual search performance. Application It may be possible to quickly assess an individual's visual search competency, which could help organizations select new hires and assess their current workforce.

  3. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

    Science.gov (United States)

    Rognes, T

    2001-04-01

    There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This approximate score is used to select the most interesting database sequences for a subsequent Smith-Waterman alignment, which is also parallelised. The resulting method represents a substantial improvement compared to existing heuristics. The sensitivity and specificity of ParAlign was found to be as good as Smith-Waterman implementations when the same method for computing the statistical significance of the matches was used. In terms of speed, only the significantly less sensitive NCBI BLAST 2 program was found to outperform the new approach. Online searches are available at http://dna.uio.no/search/

  4. Directed homology

    DEFF Research Database (Denmark)

    Fahrenberg, Uli

    2004-01-01

    We introduce a new notion of directed homology for semicubical sets. We show that it respects directed homotopy and is functorial, and that it appears to enjoy some good algebraic properties. Our work has applications to higher-dimensional automata.......We introduce a new notion of directed homology for semicubical sets. We show that it respects directed homotopy and is functorial, and that it appears to enjoy some good algebraic properties. Our work has applications to higher-dimensional automata....

  5. Caffeine suppresses homologous recombination through interference with RAD51-mediated joint molecule formation

    Science.gov (United States)

    Zelensky, Alex N.; Sanchez, Humberto; Ristic, Dejan; Vidic, Iztok; van Rossum-Fikkert, Sari E.; Essers, Jeroen; Wyman, Claire; Kanaar, Roland

    2013-01-01

    Caffeine is a widely used inhibitor of the protein kinases that play a central role in the DNA damage response. We used chemical inhibitors and genetically deficient mouse embryonic stem cell lines to study the role of DNA damage response in stable integration of the transfected DNA and found that caffeine rapidly, efficiently and reversibly inhibited homologous integration of the transfected DNA as measured by several homologous recombination-mediated gene-targeting assays. Biochemical and structural biology experiments revealed that caffeine interfered with a pivotal step in homologous recombination, homologous joint molecule formation, through increasing interactions of the RAD51 nucleoprotein filament with non-homologous DNA. Our results suggest that recombination pathways dependent on extensive homology search are caffeine-sensitive and stress the importance of considering direct checkpoint-independent mechanisms in the interpretation of the effects of caffeine on DNA repair. PMID:23666627

  6. Metagenomic gene annotation by a homology-independent approach

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    Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

    2011-06-02

    Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

  7. Internet search query analysis can be used to demonstrate the rapidly increasing public awareness of palliative care in the USA.

    Science.gov (United States)

    McLean, Sarah; Lennon, Paul; Glare, Paul

    2017-01-27

    A lack of public awareness of palliative care (PC) has been identified as one of the main barriers to appropriate PC access. Internet search query analysis is a novel methodology, which has been effectively used in surveillance of infectious diseases, and can be used to monitor public awareness of health-related topics. We aimed to demonstrate the utility of internet search query analysis to evaluate changes in public awareness of PC in the USA between 2005 and 2015. Google Trends provides a referenced score for the popularity of a search term, for defined regions over defined time periods. The popularity of the search term 'palliative care' was measured monthly between 1/1/2005 and 31/12/2015 in the USA and in the UK. Results were analysed using independent t-tests and joinpoint analysis. The mean monthly popularity of the search term increased between 2008-2009 (pquery surveillance is a novel methodology, it is freely accessible and has significant potential to monitor health-seeking behaviour among the public. PC is rapidly growing in the USA, and the rapidly increasing public awareness of PC as demonstrated in this study, in comparison with the UK, where PC is relatively well established is encouraging in increasingly ensuring appropriate PC access for all. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  8. Rapid broad area search and detection of Chinese surface-to-air missile sites using deep convolutional neural networks

    Science.gov (United States)

    Marcum, Richard A.; Davis, Curt H.; Scott, Grant J.; Nivin, Tyler W.

    2017-10-01

    We evaluated how deep convolutional neural networks (DCNN) could assist in the labor-intensive process of human visual searches for objects of interest in high-resolution imagery over large areas of the Earth's surface. Various DCNN were trained and tested using fewer than 100 positive training examples (China only) from a worldwide surface-to-air-missile (SAM) site dataset. A ResNet-101 DCNN achieved a 98.2% average accuracy for the China SAM site data. The ResNet-101 DCNN was used to process ˜19.6 M image chips over a large study area in southeastern China. DCNN chip detections (˜9300) were postprocessed with a spatial clustering algorithm to produce a ranked list of ˜2100 candidate SAM site locations. The combination of DCNN processing and spatial clustering effectively reduced the search area by ˜660X (0.15% of the DCNN-processed land area). An efficient web interface was used to facilitate a rapid serial human review of the candidate SAM sites in the China study area. Four novice imagery analysts with no prior imagery analysis experience were able to complete a DCNN-assisted SAM site search in an average time of ˜42 min. This search was ˜81X faster than a traditional visual search over an equivalent land area of ˜88,640 km2 while achieving nearly identical statistical accuracy (˜90% F1).

  9. Using KLSH to Rapidly Search Large Seismic Signal Archives on a Desktop Computer

    Science.gov (United States)

    Young, C. J.; Woodbridge, J.; Shaw, R.; Slinkard, M.

    2015-12-01

    The use of waveform correlation detection has become increasingly important in the last decade, and as the basic calculation is straightforward, and the online archives of past signals are ever-increasing, the use of technique should only become more widespread. Yet there is an inherent limitation in how widely the method can be applied due to the computational demands of searching large signal archives quickly. In this study, we investigate the applicability of Kernelized Locality-Sensitive Hashing (KLSH) to significantly decrease the computational requirements to the point that searches can be done on a commodity desktop computer. KLSH probabilistically interrogates the database such that much of the database is ignored when searching for closest matches, thereby dramatically reducing the number of correlations that need to be calculated. We evaluate KLSH using data from the IMS primary station MKAR. First we built a KLSH indexed archive using all associated signals from the IDC LEB catalog for 2002-2013 (~308,000 signals). We then tested the signal matching capability using the ~26,000 IDC-detected signals from 2014, including a variety of regional and teleseismic phases (56% are teleseismic P). We used the LEB phase assignments as ground-truth to score the results. Using a simple 0.60 correlation threshold, requiring at least two archive matches, and applying screening criteria based on consistency of metadata of archive matches, we were able to robustly identify 12% of the 2014 signals, including many teleseismic P phases from a variety of locations. Comparing KLSH against a full search, we established a recall rate of > 0.9, with search time on the order of 10 ms.

  10. Fat Content Modulates Rapid Detection of Food: A Visual Search Study Using Fast Food and Japanese Diet

    Directory of Open Access Journals (Sweden)

    Reiko Sawada

    2017-06-01

    Full Text Available Rapid detection of food is crucial for the survival of organisms. However, previous visual search studies have reported discrepant results regarding the detection speeds for food vs. non-food items; some experiments showed faster detection of food than non-food, whereas others reported null findings concerning any speed advantage for the detection of food vs. non-food. Moreover, although some previous studies showed that fat content can affect visual attention for food, the effect of fat content on the detection of food remains unclear. To investigate these issues, we measured reaction times (RTs during a visual search task in which participants with normal weight detected high-fat food (i.e., fast food, low-fat food (i.e., Japanese diet, and non-food (i.e., kitchen utensils targets within crowds of non-food distractors (i.e., cars. Results showed that RTs for food targets were shorter than those for non-food targets. Moreover, the RTs for high-fat food were shorter than those for low-fat food. These results suggest that food is more rapidly detected than non-food within the environment and that a higher fat content in food facilitates rapid detection.

  11. Fat Content Modulates Rapid Detection of Food: A Visual Search Study Using Fast Food and Japanese Diet

    Science.gov (United States)

    Sawada, Reiko; Sato, Wataru; Toichi, Motomi; Fushiki, Tohru

    2017-01-01

    Rapid detection of food is crucial for the survival of organisms. However, previous visual search studies have reported discrepant results regarding the detection speeds for food vs. non-food items; some experiments showed faster detection of food than non-food, whereas others reported null findings concerning any speed advantage for the detection of food vs. non-food. Moreover, although some previous studies showed that fat content can affect visual attention for food, the effect of fat content on the detection of food remains unclear. To investigate these issues, we measured reaction times (RTs) during a visual search task in which participants with normal weight detected high-fat food (i.e., fast food), low-fat food (i.e., Japanese diet), and non-food (i.e., kitchen utensils) targets within crowds of non-food distractors (i.e., cars). Results showed that RTs for food targets were shorter than those for non-food targets. Moreover, the RTs for high-fat food were shorter than those for low-fat food. These results suggest that food is more rapidly detected than non-food within the environment and that a higher fat content in food facilitates rapid detection. PMID:28690568

  12. Fat Content Modulates Rapid Detection of Food: A Visual Search Study Using Fast Food and Japanese Diet.

    Science.gov (United States)

    Sawada, Reiko; Sato, Wataru; Toichi, Motomi; Fushiki, Tohru

    2017-01-01

    Rapid detection of food is crucial for the survival of organisms. However, previous visual search studies have reported discrepant results regarding the detection speeds for food vs. non-food items; some experiments showed faster detection of food than non-food, whereas others reported null findings concerning any speed advantage for the detection of food vs. non-food. Moreover, although some previous studies showed that fat content can affect visual attention for food, the effect of fat content on the detection of food remains unclear. To investigate these issues, we measured reaction times (RTs) during a visual search task in which participants with normal weight detected high-fat food (i.e., fast food), low-fat food (i.e., Japanese diet), and non-food (i.e., kitchen utensils) targets within crowds of non-food distractors (i.e., cars). Results showed that RTs for food targets were shorter than those for non-food targets. Moreover, the RTs for high-fat food were shorter than those for low-fat food. These results suggest that food is more rapidly detected than non-food within the environment and that a higher fat content in food facilitates rapid detection.

  13. Homology, Analogy, and Ethology.

    Science.gov (United States)

    Beer, Colin G.

    1984-01-01

    Because the main criterion of structural homology (the principle of connections) does not exist for behavioral homology, the utility of the ethological concept of homology has been questioned. The confidence with which behavioral homologies can be claimed varies inversely with taxonomic distance. Thus, conjectures about long-range phylogenetic…

  14. Rapid Automatic Lighting Control of a Mixed Light Source for Image Acquisition using Derivative Optimum Search Methods

    Directory of Open Access Journals (Sweden)

    Kim HyungTae

    2015-01-01

    Full Text Available Automatic lighting (auto-lighting is a function that maximizes the image quality of a vision inspection system by adjusting the light intensity and color.In most inspection systems, a single color light source is used, and an equal step search is employed to determine the maximum image quality. However, when a mixed light source is used, the number of iterations becomes large, and therefore, a rapid search method must be applied to reduce their number. Derivative optimum search methods follow the tangential direction of a function and are usually faster than other methods. In this study, multi-dimensional forms of derivative optimum search methods are applied to obtain the maximum image quality considering a mixed-light source. The auto-lighting algorithms were derived from the steepest descent and conjugate gradient methods, which have N-size inputs of driving voltage and one output of image quality. Experiments in which the proposed algorithm was applied to semiconductor patterns showed that a reduced number of iterations is required to determine the locally maximized image quality.

  15. A SEARCH FOR RAPIDLY SPINNING PULSARS AND FAST TRANSIENTS IN UNIDENTIFIED RADIO SOURCES WITH THE NRAO 43 METER TELESCOPE

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Deborah; Crawford, Fronefield; Gilpin, Claire [Department of Physics and Astronomy, Franklin and Marshall College, P.O. Box 3003, Lancaster, PA 17604 (United States); Langston, Glen [National Radio Astronomy Observatory, P.O. Box 2, Green Bank, WV 24944 (United States)

    2013-04-15

    We have searched 75 unidentified radio sources selected from the NRAO VLA Sky Survey catalog for the presence of rapidly spinning pulsars and short, dispersed radio bursts. The sources are radio bright, have no identifications or optical source coincidences, are more than 5% linearly polarized, and are spatially unresolved in the catalog. If these sources are fast-spinning pulsars (e.g., sub-millisecond pulsars), previous large-scale pulsar surveys may have missed detection due to instrumental and computational limitations, eclipsing effects, or diffractive scintillation. The discovery of a sub-millisecond pulsar would significantly constrain the neutron star equation of state and would have implications for models predicting a rapid slowdown of highly recycled X-ray pulsars to millisecond periods from, e.g., accretion disk decoupling. These same sources were previously searched unsuccessfully for pulsations at 610 MHz with the Lovell Telescope at Jodrell Bank. This new search was conducted at a different epoch with a new 800 MHz backend on the NRAO 43 m Telescope at a center frequency of 1200 MHz. Our search was sensitive to sub-millisecond pulsars in highly accelerated binary systems and to short transient pulses. No periodic or transient signals were detected from any of the target sources. We conclude that diffractive scintillation, dispersive smearing, and binary acceleration are unlikely to have prevented detection of the large majority of the sources if they are pulsars, though we cannot rule out eclipsing, nulling or intermittent emission, or radio interference as possible factors for some non-detections. Other (speculative) possibilities for what these sources might include radio-emitting magnetic cataclysmic variables or older pulsars with aligned magnetic and spin axes.

  16. Expediting citation screening using PICo-based title-only screening for identifying studies in scoping searches and rapid reviews

    Directory of Open Access Journals (Sweden)

    John Rathbone

    2017-11-01

    Full Text Available Abstract Background Citation screening for scoping searches and rapid review is time-consuming and inefficient, often requiring days or sometimes months to complete. We examined the reliability of PICo-based title-only screening using keyword searches based on the PICo elements—Participants, Interventions, and Comparators, but not the Outcomes. Methods A convenience sample of 10 datasets, derived from the literature searches of completed systematic reviews, was used to test PICo-based title-only screening. Search terms for screening were generated from the inclusion criteria of each review, specifically the PICo elements—Participants, Interventions and Comparators. Synonyms for the PICo terms were sought, including alternatives for clinical conditions, trade names of generic drugs and abbreviations for clinical conditions, interventions and comparators. The MeSH database, Wikipedia, Google searches and online thesauri were used to assist generating terms. Title-only screening was performed by five reviewers independently in Endnote X7 reference management software using OR Boolean operator. Outcome measures were recall of included studies and the reduction in screening effort. Recall is the proportion of included studies retrieved using PICo title-only screening out of the total number of included studies in the original reviews. The percentage reduction in screening effort is the proportion of records not needing screening because the method eliminates them from the screen set. Results Across the 10 reviews, the reduction in screening effort ranged from 11 to 78% with a median reduction of 53%. In nine systematic reviews, the recall of included studies was 100%. In one review (oxygen therapy, four of five reviewers missed the same included study (median recall 67%. A post hoc analysis was performed on the dataset with the lowest reduction in screening effort (11%, and it was rescreened using only the intervention and comparator keywords and

  17. Expediting citation screening using PICo-based title-only screening for identifying studies in scoping searches and rapid reviews.

    Science.gov (United States)

    Rathbone, John; Albarqouni, Loai; Bakhit, Mina; Beller, Elaine; Byambasuren, Oyungerel; Hoffmann, Tammy; Scott, Anna Mae; Glasziou, Paul

    2017-11-25

    Citation screening for scoping searches and rapid review is time-consuming and inefficient, often requiring days or sometimes months to complete. We examined the reliability of PICo-based title-only screening using keyword searches based on the PICo elements-Participants, Interventions, and Comparators, but not the Outcomes. A convenience sample of 10 datasets, derived from the literature searches of completed systematic reviews, was used to test PICo-based title-only screening. Search terms for screening were generated from the inclusion criteria of each review, specifically the PICo elements-Participants, Interventions and Comparators. Synonyms for the PICo terms were sought, including alternatives for clinical conditions, trade names of generic drugs and abbreviations for clinical conditions, interventions and comparators. The MeSH database, Wikipedia, Google searches and online thesauri were used to assist generating terms. Title-only screening was performed by five reviewers independently in Endnote X7 reference management software using OR Boolean operator. Outcome measures were recall of included studies and the reduction in screening effort. Recall is the proportion of included studies retrieved using PICo title-only screening out of the total number of included studies in the original reviews. The percentage reduction in screening effort is the proportion of records not needing screening because the method eliminates them from the screen set. Across the 10 reviews, the reduction in screening effort ranged from 11 to 78% with a median reduction of 53%. In nine systematic reviews, the recall of included studies was 100%. In one review (oxygen therapy), four of five reviewers missed the same included study (median recall 67%). A post hoc analysis was performed on the dataset with the lowest reduction in screening effort (11%), and it was rescreened using only the intervention and comparator keywords and omitting keywords for participants. The reduction in

  18. Rapid photometry of EZ Canis Majoris - Searching for flare activity in Wolf-Rayet stars

    Science.gov (United States)

    Matthews, J. M.; Moffat, A. F. J.; Marchenko, S. V.

    1992-12-01

    EZ CMa was chosen for a trial run of high-speed photometry to search for flare activity in W-R stars. Data were collected during UT November 27-December 2, 1991 with the 1.0-telescope + ASCAP photometer and the 0.6-m telescope + manual photometer of the Cerro Tololo Inter-American Observatory. A period near 22.7 min was found. A brightness increase of about 1 percent, lasting for about 10 min in the otherwise smooth light curve, was observed. Fourier analysis of the data sets an upper limit of 0.0005 mag on any variations with periods less than about 10 min.

  19. Rapid search and quantitative analysis of gunshot residue particles in the SEM.

    Science.gov (United States)

    Lebiedzik, J; Johnson, D L

    2000-01-01

    Automated scanning electron microscopy coupled with image analysis and X-ray micro analysis was used to characterize a variety of gunshot residue (GSR) samples. More than 500 rounds of commercially available ammunition and six different types of hand gulls were used in the study of 17 GSR and 19 reference specimens. The individual particle X-ray composition was determined for 12 different elements. Elemental composition of GSR particles was highly variable but consistent with compounds mixed into or associated with a barium oxide matrix. When present in a specimen, GSR could be adequately characterized with automated procedures in less than an hour by restricting analyses to features larger than 2 microm. In "clean" samples, a higher resolution particle search was required to avoid reporting false negatives. Careful control of the back scattered electron signal strength threshold, by reference to a standard, was needed to ensure both time-efficient and accurate analyses. Samples collected from non-shooting subjects. active in a physical environment which contained firearms discharge residue were seen to be easily contaminated by sub-micron GSR particles.

  20. AKT (v-akt murine thymoma viral oncogene homolog 1) and N-Ras (neuroblastoma ras viral oncogene homolog) coactivation in the mouse liver promotes rapid carcinogenesis by way of mTOR (mammalian target of rapamycin complex 1), FOXM1 (forkhead box M1)/SKP2, and c-Myc pathways.

    Science.gov (United States)

    Ho, Coral; Wang, Chunmei; Mattu, Sandra; Destefanis, Giulia; Ladu, Sara; Delogu, Salvatore; Armbruster, Julia; Fan, Lingling; Lee, Susie A; Jiang, Lijie; Dombrowski, Frank; Evert, Matthias; Chen, Xin; Calvisi, Diego F

    2012-03-01

    Activation of v-akt murine thymoma viral oncogene homolog (AKT) and Ras pathways is often implicated in carcinogenesis. However, the oncogenic cooperation between these two cascades in relationship to hepatocellular carcinoma (HCC) development remains undetermined. To investigate this issue, we generated a mouse model characterized by combined overexpression of activated forms of AKT and neuroblastoma Ras viral oncogene homolog (N-Ras) protooncogenes in the liver by way of hydrodynamic gene transfer. The molecular mechanisms underlying crosstalk between AKT and N-Ras were assessed in the mouse model and further evaluated in human and murine HCC cell lines. We found that coexpression of AKT and N-Ras resulted in a dramatic acceleration of liver tumor development when compared with mice overexpressing AKT alone, whereas N-Ras alone did not lead to tumor formation. At the cellular level, concomitant up-regulation of AKT and N-Ras resulted in increased proliferation and microvascularization when compared with AKT-injected mice. Mechanistic studies suggested that accelerated hepatocarcinogenesis driven by AKT and N-Ras resulted from a strong activation of mammalian target of rapamycin complex 1 (mTORC1). Furthermore, elevated expression of FOXM1/SKP2 and c-Myc also contributed to rapid tumor growth in AKT/Ras mice, yet by way of mTORC1-independent mechanisms. The biological effects of coactivation of AKT and N-Ras were then recapitulated in vitro using HCC cell lines, which supports the functional significance of mTORC1, FOXM1/SKP2, and c-Myc signaling cascades in mediating AKT and N-Ras-induced liver tumor development. Our data demonstrate the in vivo crosstalk between the AKT and Ras pathways in promoting liver tumor development, and the pivotal role of mTORC1-dependent and independent pathways in mediating AKT and Ras induced hepatocarcinogenesis. Copyright © 2011 American Association for the Study of Liver Diseases.

  1. Improved approach for electric vehicle rapid charging station placement and sizing using Google maps and binary lightning search algorithm.

    Directory of Open Access Journals (Sweden)

    Md Mainul Islam

    Full Text Available The electric vehicle (EV is considered a premium solution to global warming and various types of pollution. Nonetheless, a key concern is the recharging of EV batteries. Therefore, this study proposes a novel approach that considers the costs of transportation loss, buildup, and substation energy loss and that incorporates harmonic power loss into optimal rapid charging station (RCS planning. A novel optimization technique, called binary lightning search algorithm (BLSA, is proposed to solve the optimization problem. BLSA is also applied to a conventional RCS planning method. A comprehensive analysis is conducted to assess the performance of the two RCS planning methods by using the IEEE 34-bus test system as the power grid. The comparative studies show that the proposed BLSA is better than other optimization techniques. The daily total cost in RCS planning of the proposed method, including harmonic power loss, decreases by 10% compared with that of the conventional method.

  2. Improved approach for electric vehicle rapid charging station placement and sizing using Google maps and binary lightning search algorithm.

    Science.gov (United States)

    Islam, Md Mainul; Shareef, Hussain; Mohamed, Azah

    2017-01-01

    The electric vehicle (EV) is considered a premium solution to global warming and various types of pollution. Nonetheless, a key concern is the recharging of EV batteries. Therefore, this study proposes a novel approach that considers the costs of transportation loss, buildup, and substation energy loss and that incorporates harmonic power loss into optimal rapid charging station (RCS) planning. A novel optimization technique, called binary lightning search algorithm (BLSA), is proposed to solve the optimization problem. BLSA is also applied to a conventional RCS planning method. A comprehensive analysis is conducted to assess the performance of the two RCS planning methods by using the IEEE 34-bus test system as the power grid. The comparative studies show that the proposed BLSA is better than other optimization techniques. The daily total cost in RCS planning of the proposed method, including harmonic power loss, decreases by 10% compared with that of the conventional method.

  3. Improved approach for electric vehicle rapid charging station placement and sizing using Google maps and binary lightning search algorithm

    Science.gov (United States)

    Shareef, Hussain; Mohamed, Azah

    2017-01-01

    The electric vehicle (EV) is considered a premium solution to global warming and various types of pollution. Nonetheless, a key concern is the recharging of EV batteries. Therefore, this study proposes a novel approach that considers the costs of transportation loss, buildup, and substation energy loss and that incorporates harmonic power loss into optimal rapid charging station (RCS) planning. A novel optimization technique, called binary lightning search algorithm (BLSA), is proposed to solve the optimization problem. BLSA is also applied to a conventional RCS planning method. A comprehensive analysis is conducted to assess the performance of the two RCS planning methods by using the IEEE 34-bus test system as the power grid. The comparative studies show that the proposed BLSA is better than other optimization techniques. The daily total cost in RCS planning of the proposed method, including harmonic power loss, decreases by 10% compared with that of the conventional method. PMID:29220396

  4. Identification of microRNAs in Macaca fascicularis (Cynomolgus Monkey by Homology Search and Experimental Validation by Small RNA-Seq and RT-qPCR Using Kidney Cortex Tissues.

    Directory of Open Access Journals (Sweden)

    Yaligara Veeranagouda

    Full Text Available MicroRNAs (miRNAs present in tissues and biofluids are emerging as sensitive and specific safety biomarkers. MiRNAs have not been thoroughly described in M. fascicularis, an animal model used in pharmaceutical industry especially in drug safety evaluation. Here we investigated the miRNAs in M. fascicularis. For Macaca mulatta, a closely related species of M. fascicularis, 619 stem-loop precursor miRNAs (pre-miRNAs and 914 mature miRNAs are available in miRBase version 21. Using M. mulatta miRNAs as a reference list and homology search tools, we identified 604 pre-miRNAs and 913 mature miRNAs in the genome of M. fascicularis. In order to validate the miRNAs identified by homology search we attempted to sequence miRNAs expressed in kidney cortex from M. fascicularis. MiRNAs expressed in kidney cortex may indeed be released in urine upon kidney cortex damage and be potentially used to monitor drug induced kidney injury. Hence small RNA sequencing libraries were prepared using kidney cortex tissues obtained from three naive M. fascicularis and sequenced. Analysis of sequencing data indicated that 432 out of 913 mature miRNAs were expressed in kidney cortex tissues. Assigning these 432 miRNAs to pre-miRNAs revealed that 273 were expressed from both the -5p and -3p arms of 150 pre-miRNAs and 159 miRNAs expressed from either the -5p or -3p arm of 176 pre-miRNAs. Mapping sequencing reads to pre-miRNAs also facilitated the detection of twenty-two new miRNAs. To substantiate miRNAs identified by small RNA sequencing, 313 miRNAs were examined by RT-qPCR. Expression of 262 miRNAs in kidney cortex tissues ware confirmed by TaqMan microRNA RT-qPCR assays. Analysis of kidney cortex miRNA targeted genes suggested that they play important role in kidney development and function. Data presented in this study may serve as a valuable resource to assess the renal safety biomarker potential of miRNAs in Cynomolgus monkeys.

  5. Lectures on functor homology

    CERN Document Server

    Touzé, Antoine

    2015-01-01

    This book features a series of lectures that explores three different fields in which functor homology (short for homological algebra in functor categories) has recently played a significant role. For each of these applications, the functor viewpoint provides both essential insights and new methods for tackling difficult mathematical problems. In the lectures by Aurélien Djament, polynomial functors appear as coefficients in the homology of infinite families of classical groups, e.g. general linear groups or symplectic groups, and their stabilization. Djament’s theorem states that this stable homology can be computed using only the homology with trivial coefficients and the manageable functor homology. The series includes an intriguing development of Scorichenko’s unpublished results. The lectures by Wilberd van der Kallen lead to the solution of the general cohomological finite generation problem, extending Hilbert’s fourteenth problem and its solution to the context of cohomology. The focus here is o...

  6. Real Topological Cyclic Homology

    DEFF Research Database (Denmark)

    Høgenhaven, Amalie

    , where O(2) is the semi-direct product of T, the multiplicative group of complex number of modulus 1, by the group G=Gal(C/R). We refer to this O(2)-spectrum as the real topological Hochschild homology. This generalization leads to a G-equivariant version of topological cyclic homology, which we call...... real topological cyclic homology. The first part of the thesis computes the G-equivariant homotopy type of the real topological cyclic homology of spherical group rings at a prime p with anti-involution induced by taking inverses in the group. The second part of the thesis investigates the derived G...

  7. Automatic and rapid identification of glycopeptides by nano-UPLC-LTQ-FT-MS and proteomic search engine.

    Science.gov (United States)

    Giménez, Estela; Gay, Marina; Vilaseca, Marta

    2017-01-30

    Here we demonstrate the potential of nano-UPLC-LTQ-FT-MS and the Byonic™ proteomic search engine for the separation, detection, and identification of N- and O-glycopeptide glycoforms in standard glycoproteins. The use of a BEH C18 nanoACQUITY column allowed the separation of the glycopeptides present in the glycoprotein digest and a baseline-resolution of the glycoforms of the same glycopeptide on the basis of the number of sialic acids. Moreover, we evaluated several acquisition strategies in order to improve the detection and characterization of glycopeptide glycoforms with the maximum number of identification percentages. The proposed strategy is simple to set up with the technology platforms commonly used in proteomic labs. The method allows the straightforward and rapid obtention of a general glycosylated map of a given protein, including glycosites and their corresponding glycosylated structures. The MS strategy selected in this work, based on a gas phase fractionation approach, led to 136 unique peptides from four standard proteins, which represented 78% of the total number of peptides identified. Moreover, the method does not require an extra glycopeptide enrichment step, thus preventing the bias that this step could cause towards certain glycopeptide species. Data are available via ProteomeXchange with identifier PXD003578. We propose a simple and high-throughput glycoproteomics-based methodology that allows the separation of glycopeptide glycoforms on the basis of the number of sialic acids, and their automatic and rapid identification without prior knowledge of protein glycosites or type and structure of the glycans. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. Towards alignment independent quantitative assessment of homology detection.

    Directory of Open Access Journals (Sweden)

    Avihay Apatoff

    Full Text Available Identification of homologous proteins provides a basis for protein annotation. Sequence alignment tools reliably identify homologs sharing high sequence similarity. However, identification of homologs that share low sequence similarity remains a challenge. Lowering the cutoff value could enable the identification of diverged homologs, but also introduces numerous false hits. Methods are being continuously developed to minimize this problem. Estimation of the fraction of homologs in a set of protein alignments can help in the assessment and development of such methods, and provides the users with intuitive quantitative assessment of protein alignment results. Herein, we present a computational approach that estimates the amount of homologs in a set of protein pairs. The method requires a prevalent and detectable protein feature that is conserved between homologs. By analyzing the feature prevalence in a set of pairwise protein alignments, the method can estimate the number of homolog pairs in the set independently of the alignments' quality. Using the HomoloGene database as a standard of truth, we implemented this approach in a proteome-wide analysis. The results revealed that this approach, which is independent of the alignments themselves, works well for estimating the number of homologous proteins in a wide range of homology values. In summary, the presented method can accompany homology searches and method development, provides validation to search results, and allows tuning of tools and methods.

  9. Homology, convergence and parallelism.

    Science.gov (United States)

    Ghiselin, Michael T

    2016-01-05

    Homology is a relation of correspondence between parts of parts of larger wholes. It is used when tracking objects of interest through space and time and in the context of explanatory historical narratives. Homologues can be traced through a genealogical nexus back to a common ancestral precursor. Homology being a transitive relation, homologues remain homologous however much they may come to differ. Analogy is a relationship of correspondence between parts of members of classes having no relationship of common ancestry. Although homology is often treated as an alternative to convergence, the latter is not a kind of correspondence: rather, it is one of a class of processes that also includes divergence and parallelism. These often give rise to misleading appearances (homoplasies). Parallelism can be particularly hard to detect, especially when not accompanied by divergences in some parts of the body. © 2015 The Author(s).

  10. RecA bundles mediate homology pairing between distant sisters during DNA break repair

    Science.gov (United States)

    Lesterlin, Christian; Ball, Graeme; Schermelleh, Lothar; Sherratt, David J.

    2014-02-01

    DNA double-strand break (DSB) repair by homologous recombination has evolved to maintain genetic integrity in all organisms. Although many reactions that occur during homologous recombination are known, it is unclear where, when and how they occur in cells. Here, by using conventional and super-resolution microscopy, we describe the progression of DSB repair in live Escherichia coli. Specifically, we investigate whether homologous recombination can occur efficiently between distant sister loci that have segregated to opposite halves of an E. coli cell. We show that a site-specific DSB in one sister can be repaired efficiently using distant sister homology. After RecBCD processing of the DSB, RecA is recruited to the cut locus, where it nucleates into a bundle that contains many more RecA molecules than can associate with the two single-stranded DNA regions that form at the DSB. Mature bundles extend along the long axis of the cell, in the space between the bulk nucleoid and the inner membrane. Bundle formation is followed by pairing, in which the two ends of the cut locus relocate at the periphery of the nucleoid and together move rapidly towards the homology of the uncut sister. After sister locus pairing, RecA bundles disassemble and proteins that act late in homologous recombination are recruited to give viable recombinants 1-2-generation-time equivalents after formation of the initial DSB. Mutated RecA proteins that do not form bundles are defective in sister pairing and in DSB-induced repair. This work reveals an unanticipated role of RecA bundles in channelling the movement of the DNA DSB ends, thereby facilitating the long-range homology search that occurs before the strand invasion and transfer reactions.

  11. Protein structural similarity search by Ramachandran codes

    Directory of Open Access Journals (Sweden)

    Chang Chih-Hung

    2007-08-01

    Full Text Available Abstract Background Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases. Results We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation. SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms. Conclusion As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.

  12. Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database

    Science.gov (United States)

    2007-01-01

    We present a novel protein structure database search tool, 3D-BLAST, that is useful for analyzing novel structures and can return a ranked list of alignments. This tool has the features of BLAST (for example, robust statistical basis, and effective and reliable search capabilities) and employs a kappa-alpha (κ, α) plot derived structural alphabet and a new substitution matrix. 3D-BLAST searches more than 12,000 protein structures in 1.2 s and yields good results in zones with low sequence similarity. PMID:17335583

  13. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases.

    Science.gov (United States)

    Floden, Evan W; Tommaso, Paolo D; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

    2016-07-08

    The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  14. Gorenstein homological dimensions

    DEFF Research Database (Denmark)

    Holm, Henrik Granau

    2004-01-01

    In basic homological algebra, the projective, injective and 2at dimensions of modules play an important and fundamental role. In this paper, the closely related Gorenstein projective, Gorenstein injective and Gorenstein 2at dimensions are studied. There is a variety of nice results about Gorenstein...

  15. A computer vision system for rapid search inspired by surface-based attention mechanisms from human perception.

    Science.gov (United States)

    Mohr, Johannes; Park, Jong-Han; Obermayer, Klaus

    2014-12-01

    Humans are highly efficient at visual search tasks by focusing selective attention on a small but relevant region of a visual scene. Recent results from biological vision suggest that surfaces of distinct physical objects form the basic units of this attentional process. The aim of this paper is to demonstrate how such surface-based attention mechanisms can speed up a computer vision system for visual search. The system uses fast perceptual grouping of depth cues to represent the visual world at the level of surfaces. This representation is stored in short-term memory and updated over time. A top-down guided attention mechanism sequentially selects one of the surfaces for detailed inspection by a recognition module. We show that the proposed attention framework requires little computational overhead (about 11 ms), but enables the system to operate in real-time and leads to a substantial increase in search efficiency. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. Algebra V homological algebra

    CERN Document Server

    Shafarevich, I

    1994-01-01

    This book, the first printing of which was published as volume 38 of the Encyclopaedia of Mathematical Sciences, presents a modern approach to homological algebra, based on the systematic use of the terminology and ideas of derived categories and derived functors. The book contains applications of homological algebra to the theory of sheaves on topological spaces, to Hodge theory, and to the theory of modules over rings of algebraic differential operators (algebraic D-modules). The authors Gelfand and Manin explain all the main ideas of the theory of derived categories. Both authors are well-known researchers and the second, Manin, is famous for his work in algebraic geometry and mathematical physics. The book is an excellent reference for graduate students and researchers in mathematics and also for physicists who use methods from algebraic geometry and algebraic topology.

  17. The search for city : between being and seeming in the rapid urbanisation of\\ud Doha, Qatar

    OpenAIRE

    Chomowicz, Peter

    2016-01-01

    This dissertation’s essential aim is to understand the collective nature of a rapidly evolving twenty-first-century city. Looking closely at Doha, Qatar - a city that can choose to be anything it desires - reveals a tension between the regime’s aspirations and the expectations of its (mostly foreign) constituents. Doha’s fundamental transformation from village to metropolis provides an interpretation of ‘city’ that discloses the possibilities and limitations of civic culture in the late twent...

  18. Tests of models of color reconnection and a search for glueballs using gluon jets with a rapidity gap

    CERN Document Server

    Abbiendi, G.; Akesson, P.F.; Alexander, G.; Allison, John; Amaral, P.; Anagnostou, G.; Anderson, K.J.; Arcelli, S.; Asai, S.; Axen, D.; Azuelos, G.; Bailey, I.; Barberio, E.; Barlow, R.J.; Batley, R.J.; Bechtle, P.; Behnke, T.; Bell, Kenneth Watson; Bell, P.J.; Bella, G.; Bellerive, A.; Benelli, G.; Bethke, S.; Biebel, O.; Boeriu, O.; Bock, P.; Boutemeur, M.; Braibant, S.; Brigliadori, L.; Brown, Robert M.; Buesser, K.; Burckhart, H.J.; Campana, S.; Carnegie, R.K.; Caron, B.; Carter, A.A.; Carter, J.R.; Chang, C.Y.; Charlton, David G.; Csilling, A.; Cuffiani, M.; Dado, S.; De Roeck, A.; De Wolf, E.A.; Desch, K.; Dienes, B.; Donkers, M.; Dubbert, J.; Duchovni, E.; Duckeck, G.; Duerdoth, I.P.; Etzion, E.; Fabbri, F.; Feld, L.; Ferrari, P.; Fiedler, F.; Fleck, I.; Ford, M.; Frey, A.; Furtjes, A.; Gagnon, P.; Gary, John William; Gaycken, G.; Geich-Gimbel, C.; Giacomelli, G.; Giacomelli, P.; Giunta, Marina; Goldberg, J.; Gross, E.; Grunhaus, J.; Gruwe, M.; Gunther, P.O.; Gupta, A.; Hajdu, C.; Hamann, M.; Hanson, G.G.; Harder, K.; Harel, A.; Harin-Dirac, M.; Hauschild, M.; Hawkes, C.M.; Hawkings, R.; Hemingway, R.J.; Hensel, C.; Herten, G.; Heuer, R.D.; Hill, J.C.; Hoffman, Kara Dion; Horvath, D.; Igo-Kemenes, P.; Ishii, K.; Jeremie, H.; Jovanovic, P.; Junk, T.R.; Kanaya, N.; Kanzaki, J.; Karapetian, G.; Karlen, D.; Kawagoe, K.; Kawamoto, T.; Keeler, R.K.; Kellogg, R.G.; Kennedy, B.W.; Kim, D.H.; Klein, K.; Klier, A.; Kluth, S.; Kobayashi, T.; Kobel, M.; Komamiya, S.; Kormos, Laura L.; Kramer, T.; Krieger, P.; von Krogh, J.; Kruger, K.; Kuhl, T.; Kupper, M.; Lafferty, G.D.; Landsman, H.; Lanske, D.; Layter, J.G.; Leins, A.; Lellouch, D.; Lettso, J.; Levinson, L.; Lillich, J.; Lloyd, S.L.; Loebinger, F.K.; Lu, J.; Ludwig, J.; Macpherson, A.; Mader, W.; Marcellini, S.; Martin, A.J.; Masetti, G.; Mashimo, T.; Mattig, Peter; McDonald, W.J.; McKenna, J.; McMahon, T.J.; McPherson, R.A.; Meijers, F.; Menges, W.; Merritt, F.S.; Mes, H.; Michelini, A.; Mihara, S.; Mikenberg, G.; Miller, D.J.; Moed, S.; Mohr, W.; Mori, T.; Mutter, A.; Nagai, K.; Nakamura, I.; Nanjo, H.; Neal, H.A.; Nisius, R.; O'Neale, S.W.; Oh, A.; Okpara, A.; Oreglia, M.J.; Orito, S.; Pahl, C.; Pasztor, G.; Pater, J.R.; Patrick, G.N.; Pilcher, J.E.; Pinfold, J.; Plane, David E.; Poli, B.; Polok, J.; Pooth, O.; Przybycien, M.; Quadt, A.; Rabbertz, K.; Rembser, C.; Renkel, P.; Roney, J.M.; Rosati, S.; Rozen, Y.; Runge, K.; Sachs, K.; Saeki, T.; Sarkisyan, E.K.G.; Schaile, A.D.; Schaile, O.; Scharff-Hansen, P.; Schieck, J.; Schoerner-Sadenius, Thomas; Schroder, Matthias; Schumacher, M.; Schwick, C.; Scott, W.G.; Seuster, R.; Shears, T.G.; Shen, B.C.; Sherwood, P.; Siroli, G.; Skuja, A.; Smith, A.M.; Sobie, R.; Soldner-Rembold, S.; Spano, F.; Stahl, A.; Stephens, K.; Strom, David M.; Strohmer, R.; Tarem, S.; Tasevsky, M.; Taylor, R.J.; Teuscher, R.; Thomson, M.A.; Torrence, E.; Toya, D.; Tran, P.; Trigger, I.; Trocsanyi, Z.; Tsur, E.; Turner-Watson, M.F.; Ueda, I.; Ujvari, B.; Vollmer, C.F.; Vannerem, P.; Vertesi, R.; Verzocchi, M.; Voss, H.; Vossebeld, J.; Waller, D.; Ward, C.P.; Ward, D.R.; Watkins, P.M.; Watson, A.T.; Watson, N.K.; Wells, P.S.; Wengler, T.; Wermes, N.; Wetterling, D.; Wilson, G.W.; Wilson, J.A.; Wolf, G.; Wyatt, T.R.; Yamashita, S.; Zer-Zion, D.; Zivkovic, Lidija

    2004-01-01

    Gluon jets with a mean energy of 22 GeV and purity of 95% are selected from hadronic Z0 decay events produced in e+e- annihilations. A subsample of these jets is identified which exhibits a large gap in the rapidity distribution of particles within the jet. After imposing the requirement of a rapidity gap, the gluon jet purity is 86%. These jets are observed to demonstrate a high degree of sensitivity to the presence of color reconnection, i.e. higher order QCD processes affecting the underlying color structure. We use our data to test three QCD models which include a simulation of color reconnection: one in the Ariadne Monte Carlo, one in the Herwig Monte Carlo, and the other by Rathsman in the Pythia Monte Carlo. We find the Rathsman and Ariadne color reconnection models can describe our gluon jet measurements only if very large values are used for the cutoff parameters which serve to terminate the parton showers, and that the description of inclusive Z0 data is significantly degraded in this case. We concl...

  19. Compositional Homology and Creative Thinking

    OpenAIRE

    Tedesco, S.

    2015-01-01

    The concept of homology is the most solid theoretical basis elaborated by the morphological thinking during its history. The enucleation of some general criteria for the interpretation of homology is today a fundamental tool for life sciences, and for restoring their own opening to the question of qualitative innovation that arose so powerfully in the original Darwinian project. The aim of this paper is to verify the possible uses of the concept of compositional homology in order to provide o...

  20. Grid diagrams and Khovanov homology

    DEFF Research Database (Denmark)

    Droz, Jean-Marie; Wagner, Emmanuel

    2009-01-01

    We explain how to compute the Jones polynomial of a link from one of its grid diagrams and we observe a connection between Bigelow’s homological definition of the Jones polynomial and Kauffman’s definition of the Jones polynomial. Consequently, we prove that the Maslov grading on the Seidel–Smith...... symplectic link invariant coincides with the difference between the homological grading on Khovanov homology and the Jones grading on Khovanov homology. We give some evidence for the truth of the Seidel–Smith conjecture....

  1. Rapid profiling of polymeric phenolic acids in Salvia miltiorrhiza by hybrid data-dependent/targeted multistage mass spectrometry acquisition based on expected compounds prediction and fragment ion searching.

    Science.gov (United States)

    Shen, Yao; Feng, Zijin; Yang, Min; Zhou, Zhe; Han, Sumei; Hou, Jinjun; Li, Zhenwei; Wu, Wanying; Guo, De-An

    2018-01-15

    Phenolic acids are the major water-soluble components in Salvia miltiorrhiza (> 5%). According to previous studies, many of them contribute to the cardiovascular effects and antioxidant effects of S. miltiorrhiza. Polymeric phenolic acids can be considered as the tanshinol derived metabolites, e.g., dimmers, trimers and tetramers. A strategy combined with tanshinol-based expected compounds prediction, total ion chromatogram filtering, Fragment Ion Searching and parent list-based multistage mass spectrometry acquisition by Linear Trap Quadropole-orbitrap Velos Mass Spectrometry was proposed to rapid profile polymeric phenolic acids in S. miltiorrhiza. More than 480 potential polymeric phenolic acids could be screened out by this strategy. Based on the fragment information obtained by parent list-activated data dependent multistage mass spectrometry acquisition, 190 polymeric phenolic acids were characterized by comparing their mass information with literature data, and 18 of them were firstly detected from S. miltiorrhiza. Seven potential compounds were tentatively characterized as new polymeric phenolic acids from S. miltiorrhiza. This strategy facilitates identification of polymeric phenolic acids in complex matrix with both selectivity and sensitivity, which could be expanded for rapid discovery and identification of compounds from complex matrix. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  2. Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

    Science.gov (United States)

    Rowe, Will; Baker, Kate S; Verner-Jeffreys, David; Baker-Austin, Craig; Ryan, Jim J; Maskell, Duncan; Pearce, Gareth

    2015-01-01

    Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR

  3. Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

    Directory of Open Access Journals (Sweden)

    Will Rowe

    Full Text Available Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring.Here we present the Search Engine for Antimicrobial Resistance (SEAR, a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei.We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we

  4. Language evolution: neural homologies and neuroinformatics.

    Science.gov (United States)

    Arbib, Michael; Bota, Mihail

    2003-11-01

    This paper contributes to neurolinguistics by grounding an evolutionary account of the readiness of the human brain for language in the search for homologies between different cortical areas in macaque and human. We consider two hypotheses for this grounding, that of Aboitiz and Garci;a [Brain Res. Rev. 25 (1997) 381] and the Mirror System Hypothesis of Rizzolatti and Arbib [Trends Neurosci. 21 (1998) 188] and note the promise of computational modeling of neural circuitry of the macaque and its linkage to analysis of human brain imaging data. In addition to the functional differences between the two hypotheses, problems arise because they are grounded in different cortical maps of the macaque brain. In order to address these divergences, we have developed several neuroinformatics tools included in an on-line knowledge management system, the NeuroHomology Database, which is equipped with inference engines both to relate and translate information across equivalent cortical maps and to evaluate degrees of homology for brain regions of interest in different species.

  5. PDBalert: automatic, recurrent remote homology tracking and protein structure prediction

    Directory of Open Access Journals (Sweden)

    Söding Johannes

    2008-11-01

    Full Text Available Abstract Background During the last years, methods for remote homology detection have grown more and more sensitive and reliable. Automatic structure prediction servers relying on these methods can generate useful 3D models even below 20% sequence identity between the protein of interest and the known structure (template. When no homologs can be found in the protein structure database (PDB, the user would need to rerun the same search at regular intervals in order to make timely use of a template once it becomes available. Results PDBalert is a web-based automatic system that sends an email alert as soon as a structure with homology to a protein in the user's watch list is released to the PDB database or appears among the sequences on hold. The mail contains links to the search results and to an automatically generated 3D homology model. The sequence search is performed with the same software as used by the very sensitive and reliable remote homology detection server HHpred, which is based on pairwise comparison of Hidden Markov models. Conclusion PDBalert will accelerate the information flow from the PDB database to all those who can profit from the newly released protein structures for predicting the 3D structure or function of their proteins of interest.

  6. Mod two homology and cohomology

    CERN Document Server

    Hausmann, Jean-Claude

    2014-01-01

    Cohomology and homology modulo 2 helps the reader grasp more readily the basics of a major tool in algebraic topology. Compared to a more general approach to (co)homology this refreshing approach has many pedagogical advantages: It leads more quickly to the essentials of the subject, An absence of signs and orientation considerations simplifies the theory, Computations and advanced applications can be presented at an earlier stage, Simple geometrical interpretations of (co)chains. Mod 2 (co)homology was developed in the first quarter of the twentieth century as an alternative to integral homology, before both became particular cases of (co)homology with arbitrary coefficients. The first chapters of this book may serve as a basis for a graduate-level introductory course to (co)homology. Simplicial and singular mod 2 (co)homology are introduced, with their products and Steenrod squares, as well as equivariant cohomology. Classical applications include Brouwer's fixed point theorem, Poincaré duality, Borsuk-Ula...

  7. Homology theory on algebraic varieties

    CERN Document Server

    Wallace, Andrew H

    1958-01-01

    Homology Theory on Algebraic Varieties, Volume 6 deals with the principles of homology theory in algebraic geometry and includes the main theorems first formulated by Lefschetz, one of which is interpreted in terms of relative homology and another concerns the Poincaré formula. The actual details of the proofs of these theorems are introduced by geometrical descriptions, sometimes aided with diagrams. This book is comprised of eight chapters and begins with a discussion on linear sections of an algebraic variety, with emphasis on the fibring of a variety defined over the complex numbers. The n

  8. Compositional Homology and Creative Thinking

    Directory of Open Access Journals (Sweden)

    Salvatore Tedesco

    2015-05-01

    Full Text Available The concept of homology is the most solid theoretical basis elaborated by the morphological thinking during its history. The enucleation of some general criteria for the interpretation of homology is today a fundamental tool for life sciences, and for restoring their own opening to the question of qualitative innovation that arose so powerfully in the original Darwinian project. The aim of this paper is to verify the possible uses of the concept of compositional homology in order to provide of an adequate understanding of the dynamics of creative thinking.

  9. Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations.

    Science.gov (United States)

    Lee, Aaron Y; Lee, Cecilia S; Van Gelder, Russell N

    2016-07-28

    Next generation sequencing technology has enabled characterization of metagenomics through massively parallel genomic DNA sequencing. The complexity and diversity of environmental samples such as the human gut microflora, combined with the sustained exponential growth in sequencing capacity, has led to the challenge of identifying microbial organisms by DNA sequence. We sought to validate a Scalable Metagenomics Alignment Research Tool (SMART), a novel searching heuristic for shotgun metagenomics sequencing results. After retrieving all genomic DNA sequences from the NCBI GenBank, over 1 × 10(11) base pairs of 3.3 × 10(6) sequences from 9.25 × 10(5) species were indexed using 4 base pair hashtable shards. A MapReduce searching strategy was used to distribute the search workload in a computing cluster environment. In addition, a one base pair permutation algorithm was used to account for single nucleotide polymorphisms and sequencing errors. Simulated datasets used to evaluate Kraken, a similar metagenomics classification tool, were used to measure and compare precision and accuracy. Finally using a same set of training sequences we compared Kraken, CLARK, and SMART within the same computing environment. Utilizing 12 computational nodes, we completed the classification of all datasets in under 10 min each using exact matching with an average throughput of over 1.95 × 10(6) reads classified per minute. With permutation matching, we achieved sensitivity greater than 83 % and precision greater than 94 % with simulated datasets at the species classification level. We demonstrated the application of this technique applied to conjunctival and gut microbiome metagenomics sequencing results. In our head to head comparison, SMART and CLARK had similar accuracy gains over Kraken at the species classification level, but SMART required approximately half the amount of RAM of CLARK. SMART is the first scalable, efficient, and rapid metagenomics classification algorithm

  10. Combining Evidence from Homologous Datasets

    National Research Council Canada - National Science Library

    Feng, Ao; Allan, James

    2006-01-01

    .... We argue that combining evidence from these "homologous" datasets can give us better representation of the original data, and our experiments show that a model combining all sources outperforms each...

  11. The tedious task of finding homologous noncoding RNA genes

    DEFF Research Database (Denmark)

    Menzel, Karl Peter; Gorodkin, Jan; Stadler, Peter F

    2009-01-01

    acknowledged. Here, we qualitatively describe a realistic scenario for what a "regular user" (i.e., a nonexpert in a particular RNA family) can do in practice, and what kind of results are likely to be achieved. Despite the indisputable advances in computational RNA biology, the conclusion is discouraging......: BLAST still works better or equally good as other methods unless extensive expert knowledge on the RNA family is included. However, when good curated data are available the recent development yields further improvements in finding remote homologs. Homology search beyond the reach of BLAST hence...... is not at all a routine task....

  12. FASTERp: A Feature Array Search Tool for Estimating Resemblance of Protein Sequences

    Energy Technology Data Exchange (ETDEWEB)

    Macklin, Derek; Egan, Rob; Wang, Zhong

    2014-03-14

    Metagenome sequencing efforts have provided a large pool of billions of genes for identifying enzymes with desirable biochemical traits. However, homology search with billions of genes in a rapidly growing database has become increasingly computationally impractical. Here we present our pilot efforts to develop a novel alignment-free algorithm for homology search. Specifically, we represent individual proteins as feature vectors that denote the presence or absence of short kmers in the protein sequence. Similarity between feature vectors is then computed using the Tanimoto score, a distance metric that can be rapidly computed on bit string representations of feature vectors. Preliminary results indicate good correlation with optimal alignment algorithms (Spearman r of 0.87, ~;;1,000,000 proteins from Pfam), as well as with heuristic algorithms such as BLAST (Spearman r of 0.86, ~;;1,000,000 proteins). Furthermore, a prototype of FASTERp implemented in Python runs approximately four times faster than BLAST on a small scale dataset (~;;1000 proteins). We are optimizing and scaling to improve FASTERp to enable rapid homology searches against billion-protein databases, thereby enabling more comprehensive gene annotation efforts.

  13. Homology groups for particles on one-connected graphs

    Science.gov (United States)

    MaciÄ Żek, Tomasz; Sawicki, Adam

    2017-06-01

    We present a mathematical framework for describing the topology of configuration spaces for particles on one-connected graphs. In particular, we compute the homology groups over integers for different classes of one-connected graphs. Our approach is based on some fundamental combinatorial properties of the configuration spaces, Mayer-Vietoris sequences for different parts of configuration spaces, and some limited use of discrete Morse theory. As one of the results, we derive the closed-form formulae for ranks of the homology groups for indistinguishable particles on tree graphs. We also give a detailed discussion of the second homology group of the configuration space of both distinguishable and indistinguishable particles. Our motivation is the search for new kinds of quantum statistics.

  14. Homological stability of diffeomorphism groups

    DEFF Research Database (Denmark)

    Berglund, Alexander; Madsen, Ib Henning

    2013-01-01

    In this paper we prove a stability theorem for block diffeomorphisms of 2d -dimensional manifolds that are connected sums of S d ×S d . Combining this with a recent theorem of S. Galatius and O. Randal-Williams and Morlet’s lemma of disjunction, we determine the homology of the classifying space ...

  15. Railway vehicle performance optimisation using virtual homologation

    Science.gov (United States)

    Magalhães, H.; Madeira, J. F. A.; Ambrósio, J.; Pombo, J.

    2016-09-01

    Unlike regular automotive vehicles, which are designed to travel in different types of roads, railway vehicles travel mostly in the same route during their life cycle. To accept the operation of a railway vehicle in a particular network, a homologation process is required according to local standard regulations. In Europe, the standards EN 14363 and UIC 518, which are used for railway vehicle acceptance, require on-track tests and/or numerical simulations. An important advantage of using virtual homologation is the reduction of the high costs associated with on-track tests by studying the railway vehicle performance in different operation conditions. This work proposes a methodology for the improvement of railway vehicle design with the objective of its operation in selected railway tracks by using optimisation. The analyses required for the vehicle improvement are performed under control of the optimisation method global and local optimisation using direct search. To quantify the performance of the vehicle, a new objective function is proposed, which includes: a Dynamic Performance Index, defined as a weighted sum of the indices obtained from the virtual homologation process; the non-compensated acceleration, which is related to the operational velocity; and a penalty associated with cases where the vehicle presents an unacceptable dynamic behaviour according to the standards. Thus, the optimisation process intends not only to improve the quality of the vehicle in terms of running safety and ride quality, but also to increase the vehicle availability via the reduction of the time for a journey while ensuring its operational acceptance under the standards. The design variables include the suspension characteristics and the operational velocity of the vehicle, which are allowed to vary in an acceptable range of variation. The results of the optimisation lead to a global minimum of the objective function in which the suspensions characteristics of the vehicle are

  16. Bloom DNA helicase facilitates homologous recombination between diverged homologous sequences.

    Science.gov (United States)

    Kikuchi, Koji; Abdel-Aziz, H Ismail; Taniguchi, Yoshihito; Yamazoe, Mitsuyoshi; Takeda, Shunichi; Hirota, Kouji

    2009-09-25

    Bloom syndrome caused by inactivation of the Bloom DNA helicase (Blm) is characterized by increases in the level of sister chromatid exchange, homologous recombination (HR) associated with cross-over. It is therefore believed that Blm works as an anti-recombinase. Meanwhile, in Drosophila, DmBlm is required specifically to promote the synthesis-dependent strand anneal (SDSA), a type of HR not associating with cross-over. However, conservation of Blm function in SDSA through higher eukaryotes has been a matter of debate. Here, we demonstrate the function of Blm in SDSA type HR in chicken DT40 B lymphocyte line, where Ig gene conversion diversifies the immunoglobulin V gene through intragenic HR between diverged homologous segments. This reaction is initiated by the activation-induced cytidine deaminase enzyme-mediated uracil formation at the V gene, which in turn converts into abasic site, presumably leading to a single strand gap. Ig gene conversion frequency was drastically reduced in BLM(-/-) cells. In addition, BLM(-/-) cells used limited donor segments harboring higher identity compared with other segments in Ig gene conversion event, suggesting that Blm can promote HR between diverged sequences. To further understand the role of Blm in HR between diverged homologous sequences, we measured the frequency of gene targeting induced by an I-SceI-endonuclease-mediated double-strand break. BLM(-/-) cells showed a severer defect in the gene targeting frequency as the number of heterologous sequences increased at the double-strand break site. Conversely, the overexpression of Blm, even an ATPase-defective mutant, strongly stimulated gene targeting. In summary, Blm promotes HR between diverged sequences through a novel ATPase-independent mechanism.

  17. Exceptional cosmetic surgeries on homology spheres

    OpenAIRE

    Ravelomanana, Huygens C.

    2016-01-01

    The cosmetic surgery conjecture is a longstanding conjecture in 3-manifold theory. We present a theorem about exceptional cosmetic surgery for homology spheres. Along the way we prove that if the surgery is not a small seifert $\\mathbb{Z}/2\\mathbb{Z}$-homology sphere or a toroidal irreducible non-Seifert surgery then there is at most one pair of exceptional truly cosmetic slope. We also prove that toroidal truly cosmetic surgeries on integer homology spheres must be integer homology spheres.

  18. Discrete homology theory for metric spaces

    NARCIS (Netherlands)

    H. Barcelo (Hélène); V. Capraro (Valerio); J. A. White; H. Barcelo (Hélène)

    2014-01-01

    htmlabstractWe define and study a notion of discrete homology theory for metric spaces. Instead of working with simplicial homology, our chain complexes are given by Lipschitz maps from an n n -dimensional cube to a fixed metric space. We prove that the resulting homology theory satisfies a

  19. Catching homologies by geometric entropy

    Science.gov (United States)

    Felice, Domenico; Franzosi, Roberto; Mancini, Stefano; Pettini, Marco

    2018-02-01

    A geometric entropy is defined in terms of the Riemannian volume of the parameter space of a statistical manifold associated with a given network. As such it can be a good candidate for measuring networks complexity. Here we investigate its ability to single out topological features of networks proceeding in a bottom-up manner: first we consider small size networks by analytical methods and then large size networks by numerical techniques. Two different classes of networks, the random graphs and the scale-free networks, are investigated computing their Betti numbers and then showing the capability of geometric entropy of detecting homologies.

  20. The Homological Nature of Entropy

    Directory of Open Access Journals (Sweden)

    Pierre Baudot

    2015-05-01

    Full Text Available We propose that entropy is a universal co-homological class in a theory associated to a family of observable quantities and a family of probability distributions. Three cases are presented: (1 classical probabilities and random variables; (2 quantum probabilities and observable operators; (3 dynamic probabilities and observation trees. This gives rise to a new kind of topology for information processes, that accounts for the main information functions: entropy, mutual-informations at all orders, and Kullback–Leibler divergence and generalizes them in several ways. The article is divided into two parts, that can be read independently. In the first part, the introduction, we provide an overview of the results, some open questions, future results and lines of research, and discuss briefly the application to complex data. In the second part we give the complete definitions and proofs of the theorems A, C and E in the introduction, which show why entropy is the first homological invariant of a structure of information in four contexts: static classical or quantum probability, dynamics of classical or quantum strategies of observation of a finite system.

  1. Conserved functional motifs and homology modelling to predict hidden moonlighting functional sites

    Directory of Open Access Journals (Sweden)

    Helen R Irving

    2015-06-01

    Full Text Available Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here we review how hidden moonlighting functional centers which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico which in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  2. Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites

    KAUST Repository

    Wong, Aloysius Tze

    2015-06-09

    Moonlighting functional centers within proteins can provide them with hitherto unrecognized functions. Here, we review how hidden moonlighting functional centers, which we define as binding sites that have catalytic activity or regulate protein function in a novel manner, can be identified using targeted bioinformatic searches. Functional motifs used in such searches include amino acid residues that are conserved across species and many of which have been assigned functional roles based on experimental evidence. Molecules that were identified in this manner seeking cyclic mononucleotide cyclases in plants are used as examples. The strength of this computational approach is enhanced when good homology models can be developed to test the functionality of the predicted centers in silico, which, in turn, increases confidence in the ability of the identified candidates to perform the predicted functions. Computational characterization of moonlighting functional centers is not diagnostic for catalysis but serves as a rapid screening method, and highlights testable targets from a potentially large pool of candidates for subsequent in vitro and in vivo experiments required to confirm the functionality of the predicted moonlighting centers.

  3. Equivariant ordinary homology and cohomology

    CERN Document Server

    Costenoble, Steven R

    2016-01-01

    Filling a gap in the literature, this book takes the reader to the frontiers of equivariant topology, the study of objects with specified symmetries. The discussion is motivated by reference to a list of instructive “toy” examples and calculations in what is a relatively unexplored field. The authors also provide a reading path for the first-time reader less interested in working through sophisticated machinery but still desiring a rigorous understanding of the main concepts. The subject’s classical counterparts, ordinary homology and cohomology, dating back to the work of Henri Poincaré in topology, are calculational and theoretical tools which are important in many parts of mathematics and theoretical physics, particularly in the study of manifolds. Similarly powerful tools have been lacking, however, in the context of equivariant topology. Aimed at advanced graduate students and researchers in algebraic topology and related fields, the book assumes knowledge of basic algebraic topology and group act...

  4. Homology and the nonlinear heat diffusion equation

    Science.gov (United States)

    Burgan, J. R.; Munier, A.; Feix, M. R.; Fijalkow, E.

    1984-02-01

    A theorem is presented which generalizes the concept of homology, introduced by Munier et al. (1981), to a large class of nonlinear diffusion coefficients. Possible changes in both initial and boundary conditions induced by self-homologous transformations are investigated. In order to be consistent with previously established definitions, generalized homology is expressed in terms of a Baecklund transformation, the only remaining process to overstep self-similar transformations.

  5. Homology in Electromagnetic Boundary Value Problems

    Directory of Open Access Journals (Sweden)

    Pellikka Matti

    2010-01-01

    Full Text Available We discuss how homology computation can be exploited in computational electromagnetism. We represent various cellular mesh reduction techniques, which enable the computation of generators of homology spaces in an acceptable time. Furthermore, we show how the generators can be used for setting up and analysis of an electromagnetic boundary value problem. The aim is to provide a rationale for homology computation in electromagnetic modeling software.

  6. Exploiting the potential of large databases of electronic health records for research using rapid search algorithms and an intuitive query interface.

    Science.gov (United States)

    Tate, A Rosemary; Beloff, Natalia; Al-Radwan, Balques; Wickson, Joss; Puri, Shivani; Williams, Timothy; Van Staa, Tjeerd; Bleach, Adrian

    2014-01-01

    UK primary care databases, which contain diagnostic, demographic and prescribing information for millions of patients geographically representative of the UK, represent a significant resource for health services and clinical research. They can be used to identify patients with a specified disease or condition (phenotyping) and to investigate patterns of diagnosis and symptoms. Currently, extracting such information manually is time-consuming and requires considerable expertise. In order to exploit more fully the potential of these large and complex databases, our interdisciplinary team developed generic methods allowing access to different types of user. Using the Clinical Practice Research Datalink database, we have developed an online user-focused system (TrialViz), which enables users interactively to select suitable medical general practices based on two criteria: suitability of the patient base for the intended study (phenotyping) and measures of data quality. An end-to-end system, underpinned by an innovative search algorithm, allows the user to extract information in near real-time via an intuitive query interface and to explore this information using interactive visualization tools. A usability evaluation of this system produced positive results. We present the challenges and results in the development of TrialViz and our plans for its extension for wider applications of clinical research. Our fast search algorithms and simple query algorithms represent a significant advance for users of clinical research databases.

  7. Combination of 2D/3D Ligand-Based Similarity Search in Rapid Virtual Screening from Multimillion Compound Repositories. Selection and Biological Evaluation of Potential PDE4 and PDE5 Inhibitors

    Directory of Open Access Journals (Sweden)

    Krisztina Dobi

    2014-05-01

    Full Text Available Rapid in silico selection of target focused libraries from commercial repositories is an attractive and cost effective approach. If structures of active compounds are available rapid 2D similarity search can be performed on multimillion compound databases but the generated library requires further focusing by various 2D/3D chemoinformatics tools. We report here a combination of the 2D approach with a ligand-based 3D method (Screen3D which applies flexible matching to align reference and target compounds in a dynamic manner and thus to assess their structural and conformational similarity. In the first case study we compared the 2D and 3D similarity scores on an existing dataset derived from the biological evaluation of a PDE5 focused library. Based on the obtained similarity metrices a fusion score was proposed. The fusion score was applied to refine the 2D similarity search in a second case study where we aimed at selecting and evaluating a PDE4B focused library. The application of this fused 2D/3D similarity measure led to an increase of the hit rate from 8.5% (1st round, 47% inhibition at 10 µM to 28.5% (2nd round at 50% inhibition at 10 µM and the best two hits had 53 nM inhibitory activities.

  8. Rapid screening and confirmation of drugs and toxic compounds in biological specimens using liquid chromatography/ion trap tandem mass spectrometry and automated library search.

    Science.gov (United States)

    Liu, Hsiu-Chuan; Liu, Ray H; Lin, Dong-Liang; Ho, Hsiu-O

    2010-01-01

    Recent advances in liquid chromatography/tandem mass spectrometry (LC/MS/MS) technology have provided an opportunity for the development of more specific approaches to achieve the 'screen' and 'confirmation' goals in a single analytical step. For this purpose, this study adapts the electrospray ionization ion trap LC/MS/MS instrumentation (LC/ESI-MS/MS) for the screening and confirmation of over 800 drugs and toxic compounds in biological specimens. Liquid-liquid and solid-phase extraction protocols were coupled to LC/ESI-MS/MS using a 1.8-microm particle size analytical column operated at 50 degrees C. Gradient elution of the analytes was conducted using a solvent system composed of methanol and water containing 0.1% formic acid. Positive-ion ESI-MS/MS spectra and retention times for each of the 800 drugs and toxic compounds were first established using 1-10 microg/mL standard solutions. This spectra and retention time information was then transferred to the library and searched by the identification algorithm for the confirmation of compounds found in test specimens - based on retention time matches and scores of fit, reverse fit, and purity resulting from the searching process. The established method was found highly effective when applied to the analyses of postmortem specimens (blood, urine, and hair) and external proficiency test samples provided by the College of American Pathology (CAP). The development of this approach has significantly improved the efficiency of our routine laboratory operation that was based on a two-step (immunoassay and GC/MS) approach in the past. Copyright 2009 John Wiley & Sons, Ltd.

  9. Stability of p53 homologs.

    Directory of Open Access Journals (Sweden)

    Tobias Brandt

    Full Text Available Most proteins have not evolved for maximal thermal stability. Some are only marginally stable, as for example, the DNA-binding domains of p53 and its homologs, whose kinetic and thermodynamic stabilities are strongly correlated. Here, we applied high-throughput methods using a real-time PCR thermocycler to study the stability of several full-length orthologs and paralogs of the p53 family of transcription factors, which have diverse functions, ranging from tumour suppression to control of developmental processes. From isothermal denaturation fluorimetry and differential scanning fluorimetry, we found that full-length proteins showed the same correlation between kinetic and thermodynamic stability as their isolated DNA-binding domains. The stabilities of the full-length p53 orthologs were marginal and correlated with the temperature of their organism, paralleling the stability of the isolated DNA-binding domains. Additionally, the paralogs p63 and p73 were significantly more stable and long-lived than p53. The short half-life of p53 orthologs and the greater persistence of the paralogs may be biologically relevant.

  10. Homotopic Chain Maps Have Equal s-Homology and d-Homology

    Directory of Open Access Journals (Sweden)

    M. Z. Kazemi-Baneh

    2016-01-01

    Full Text Available The homotopy of chain maps on preabelian categories is investigated and the equality of standard homologies and d-homologies of homotopic chain maps is established. As a special case, if X and Y are the same homotopy type, then their nth d-homology R-modules are isomorphic, and if X is a contractible space, then its nth d-homology R-modules for n≠0 are trivial.

  11. Homology Groups of a Pipeline Petri Net

    Directory of Open Access Journals (Sweden)

    A. A. Husainov

    2013-01-01

    Full Text Available Petri net is said to be elementary if every place can contain no more than one token. In this paper, it is studied topological properties of the elementary Petri net for a pipeline consisting of n functional devices. If the work of the functional devices is considered continuous, we can come to some topological space of “intermediate” states. In the paper, it is calculated the homology groups of this topological space. By induction on n, using the Addition Sequence for homology groups of semicubical sets, it is proved that in dimension 0 and 1 the integer homology groups of these nets are equal to the group of integers, and in the remaining dimensions are zero. Directed homology groups are studied. A connection of these groups with deadlocks and newsletters is found. This helps to prove that all directed homology groups of the pipeline elementary Petri nets are zeroth.

  12. PAR-TERRA directs homologous sex chromosome pairing.

    Science.gov (United States)

    Chu, Hsueh-Ping; Froberg, John E; Kesner, Barry; Oh, Hyun Jung; Ji, Fei; Sadreyev, Ruslan; Pinter, Stefan F; Lee, Jeannie T

    2017-08-01

    In mammals, homologous chromosomes rarely pair outside meiosis. One exception is the X chromosome, which transiently pairs during X-chromosome inactivation (XCI). How two chromosomes find each other in 3D space is not known. Here, we reveal a required interaction between the X-inactivation center (Xic) and the telomere in mouse embryonic stem (ES) cells. The subtelomeric, pseudoautosomal regions (PARs) of the two sex chromosomes (X and Y) also undergo pairing in both female and male cells. PARs transcribe a class of telomeric RNA, dubbed PAR-TERRA, which accounts for a vast majority of all TERRA transcripts. PAR-TERRA binds throughout the genome, including to the PAR and Xic. During X-chromosome pairing, PAR-TERRA anchors the Xic to the PAR, creating a 'tetrad' of pairwise homologous interactions (Xic-Xic, PAR-PAR, and Xic-PAR). Xic pairing occurs within the tetrad. Depleting PAR-TERRA abrogates pairing and blocks initiation of XCI, whereas autosomal PAR-TERRA induces ectopic pairing. We propose a 'constrained diffusion model' in which PAR-TERRA creates an interaction hub to guide Xic homology searching during XCI.

  13. Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

    NARCIS (Netherlands)

    Medema, Marnix H.; Takano, Eriko; Breitling, Rainer; Nowick, Katja

    The genes encoding many biomolecular systems and pathways are genomically organized in operons or gene clusters. With MultiGeneBlast, we provide a user-friendly and effective tool to perform homology searches with operons or gene clusters as basic units, instead of single genes. The

  14. Answering medical questions at the point of care: a cross-sectional study comparing rapid decisions based on PubMed and Epistemonikos searches with evidence-based recommendations developed with the GRADE approach.

    Science.gov (United States)

    Izcovich, Ariel; Criniti, Juan Martín; Popoff, Federico; Ragusa, Martín Alberto; Gigler, Cristel; Gonzalez Malla, Carlos; Clavijo, Manuela; Manzotti, Matias; Diaz, Martín; Catalano, Hugo Norberto; Neumann, Ignacio; Guyatt, Gordon

    2017-08-07

    Using the best current evidence to inform clinical decisions remains a challenge for clinicians. Given the scarcity of trustworthy clinical practice guidelines providing recommendations to answer clinicians' daily questions, clinical decision support systems (ie, assistance in question identification and answering) emerge as an attractive alternative. The trustworthiness of the recommendations achieved by such systems is unknown. To evaluate the trustworthiness of a question identification and answering system that delivers timely recommendations. Cross-sectional study. We compared the responses to 100 clinical questions related to inpatient management provided by two rapid response methods with 'Gold Standard' recommendations. One of the rapid methods was based on PubMed and the other on Epistemonikos database. We defined our 'Gold Standard' as trustworthy published evidence-based recommendations or, when unavailable, recommendations developed locally by a panel of six clinicians following the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Recommendations provided by the rapid strategies were classified as potentially misleading or reasonable. We also determined if the potentially misleading recommendations could have been avoided with the appropriate implementation of searching and evidence summary tools. We were able to answer all of the 100 questions with both rapid methods. Of the 200 recommendations obtained, 6.5% (95% CI 3% to 9.9%) were classified as potentially misleading and 93.5% (95% CI 90% to 96.9%) as reasonable. 6 of the 13 potentially misleading recommendations could have been avoided by the appropriate usage of the Epistemonikos matrix tool or by constructing summary of findings tables. No significant differences were observed between the evaluated rapid response methods. A question answering service based on the GRADE approach proved feasible to implement and provided appropriate guidance for most identified

  15. Dualities in Persistent (Co)Homology

    Energy Technology Data Exchange (ETDEWEB)

    de Silva, Vin; Morozov, Dmitriy; Vejdemo-Johansson, Mikael

    2011-09-16

    We consider sequences of absolute and relative homology and cohomology groups that arise naturally for a filtered cell complex. We establishalgebraic relationships between their persistence modules, and show that they contain equivalent information. We explain how one can use the existingalgorithm for persistent homology to process any of the four modules, and relate it to a recently introduced persistent cohomology algorithm. Wepresent experimental evidence for the practical efficiency of the latter algorithm.

  16. Investigating homology between proteins using energetic profiles.

    Directory of Open Access Journals (Sweden)

    James O Wrabl

    2010-03-01

    Full Text Available Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved

  17. Molecular evolution of an Avirulence Homolog (Avh) gene subfamily in Phytophthora ramorum

    Science.gov (United States)

    GossErica M.; Caroline M. Press; Niklaus J. Grünwald

    2008-01-01

    Pathogen effectors can serve a virulence function on behalf of the pathogen or trigger a rapid defense response in resistant hosts. Sequencing of the Phytophthora ramorum genome and subsequent analysis identified a diverse superfamily of approximately 350 genes that are homologous to the four known avirulence genes in plant pathogenic oomycetes and...

  18. On the hodological criterion for homology

    Directory of Open Access Journals (Sweden)

    Macarena eFaunes

    2015-06-01

    Full Text Available Owen’s pre-evolutionary definition of a homologue as the same organ in different animals under every variety of form and function and its redefinition after Darwin as the same trait in different lineages due to common ancestry entail the same heuristic problem: how to establish sameness. Although different criteria for homology often conflict, there is currently a generalized acceptance of gene expression as the best criterion. This gene-centered view of homology results from a reductionist and preformationist concept of living beings. Here, we adopt an alternative organismic-epigenetic viewpoint, and conceive living beings as systems whose identity is given by the dynamic interactions between their components at their multiple levels of composition. We posit that there cannot be an absolute homology criterion, and instead, homology should be inferred from comparisons at the levels and developmental stages where the delimitation of the compared trait lies. In this line, we argue that neural connectivity, i.e., the hodological criterion, should prevail in the determination of homologies between brain supra-cellular structures, such as the vertebrate pallium.

  19. Parallelism, deep homology, and evo-devo.

    Science.gov (United States)

    Hall, Brian K

    2012-01-01

    Parallelism has been the subject of a number of recent studies that have resulted in reassessment of the term and the process. Parallelism has been aligned with homology leaving convergence as the only case of homoplasy, regarded as a transition between homologous and convergent characters, and defined as the independent evolution of genetic traits. Another study advocates abolishing the term parallelism and treating all cases of the independent evolution of characters as convergence. With the sophistication of modern genomics and genetic analysis, parallelism of characters of the phenotype is being discovered to reflect parallel genetic evolution. Approaching parallelism from developmental and genetic perspectives enables us to tease out the degree to which the reuse of pathways represent deep homology and is a major task for evolutionary developmental biology in the coming decades. © 2012 Wiley Periodicals, Inc.

  20. Relative K-homology and normal operators

    DEFF Research Database (Denmark)

    Manuilov, Vladimir; Thomsen, Klaus

    2009-01-01

    -term exact sequence which generalizes the excision six-term exact sequence in the first variable of KK-theory. Subsequently we investigate the relative K-homology which arises from the group of relative extensions by specializing to abelian $C^*$-algebras. It turns out that this relative K-homology carries...... substantial information also in the operator theoretic setting from which the BDF theory was developed and we conclude the paper by extracting some of this information on approximation of normal operators....

  1. Search Patterns

    CERN Document Server

    Morville, Peter

    2010-01-01

    What people are saying about Search Patterns "Search Patterns is a delight to read -- very thoughtful and thought provoking. It's the most comprehensive survey of designing effective search experiences I've seen." --Irene Au, Director of User Experience, Google "I love this book! Thanks to Peter and Jeffery, I now know that search (yes, boring old yucky who cares search) is one of the coolest ways around of looking at the world." --Dan Roam, author, The Back of the Napkin (Portfolio Hardcover) "Search Patterns is a playful guide to the practical concerns of search interface design. It cont

  2. Overexpression of enhancer of zests homolog 2 in lymphoma.

    Science.gov (United States)

    Guo, Shan-Qi; Zhang, Yi-Zhuo

    2012-10-01

    This article aimed to review the biological characteristics of enhancer of zests homolog 2 (EZH2), and the transcriptional repression mechanism of action of EZH2 in tumors, particularly in the progression of lymphoma. The data cited in this review were mainly obtained from the articles listed in PubMed and HighWare that were published from March 2004 to April 2012. The search terms were "enhancer of zests homolog 2", "polycomb group", and "lymphoma". Articles regarding the mechanism of EZH2 in post-transcriptional modification, functions of polycomb group proteins, and the roles of EZH2 in lymphoma were selected. EZH2 acts as oncogene and involved in many kinds of tumors. Moreover, it plays an important role in tumorigenesis and lymphomagenesis by promoting the proliferation and aggressiveness of neoplastic cells, facilitating malignant tumor cell diffusion, and mediating transcriptional silencing. EZH2 mediated transcriptional repression through its methyltransferase activity at the chromatin level has certain influence on lymphoma, and there might exist a therapeutic window for the development of new agents and identification of novel diagnostic markers based on EZH2.

  3. Cell biology of homologous recombination in yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine Valerie; Rothstein, Rodney; Lisby, Michael

    2011-01-01

    Homologous recombination is an important pathway for error-free repair of DNA lesions, such as single- and double-strand breaks, and for rescue of collapsed replication forks. Here, we describe protocols for live cell imaging of single-lesion recombination events in the yeast Saccharomyces...

  4. GPCR Homology Model Generation for Lead Optimization.

    Science.gov (United States)

    Tautermann, Christofer S

    2018-01-01

    The vast increase of recently solved GPCR X-ray structures forms the basis for GPCR homology modeling to atomistic accuracy. Nowadays, homology models can be employed for GPCR-ligand optimization and have been reported as invaluable tools for drug design in the last few years. Elucidation of the complex GPCR pharmacology and the associated GPCR conformations made clear that different homology models have to be constructed for different activation states of the GPCRs. Therefore, templates have to be chosen accordingly to their sequence homology as well as to their activation state. The subsequent ligand placement is nontrivial, as some recent X-ray structures show very unusual ligand binding sites and solvent involvement, expanding the space of the putative ligand binding site from the generic retinal binding pocket to the whole receptor. In the present study, a workflow is presented starting from the selection of the target sequence, guiding through the GPCR modeling process, and finishing with ligand placement and pose validation.

  5. Homological stability for unordered configuration spaces

    DEFF Research Database (Denmark)

    Randal-Williams, Oscar

    2013-01-01

    This paper consists of two related parts. In the first part we give a self-contained proof of homological stability for the spaces C_n(M;X) of configurations of n unordered points in a connected open manifold M with labels in a path-connected space X, with the best possible integral stability ran...

  6. Homological algebra in n-abelian categories

    Indian Academy of Sciences (India)

    In this paper, we study the homological theory in n -abelian categories. First, we prove some useful properties of n -abelian categories, such as ( n + 2 ) × ( n + 2 ) -lemma, 5-lemma and n -Horseshoes lemma. Secondly, we introduce the notions of right(left) n -derived functors of left(right) n -exact functors, n -(co)resolutions, ...

  7. Threading homology through algebra selected patterns

    CERN Document Server

    Boffi, Giandomenico

    2006-01-01

    Aimed at graduate students and researchers in mathematics, this book takes homological themes, such as Koszul complexes and their generalizations, and shows how these can be used to clarify certain problems in selected parts of algebra, as well as their success in solving a number of them.

  8. Homology modeling of γ-aminobutyrateaminotransferase, a ...

    African Journals Online (AJOL)

    γ-Aminobutyrate aminotransferase (GABA-AT) is a pyridoxal phosphate dependent homodimeric enzyme of 50-kD subunits. It is a potential drug target against epilepsy. The three-dimensional structure of GABA-AT is not experimentally known, and we thus resorted to homology modelling to build a model based on x-ray ...

  9. Nash equilibria via duality and homological selection

    Indian Academy of Sciences (India)

    Keywords. Nash equilibria; Dold–Thom theorem; homological selection. 2010 Mathematics Subject Classification. Primary: 55M05, 55N45, 91A10. 1. Introduction. The main topological problem addressed in this paper is the following: Let X be a metric space and Subk(X) denote the collection of subsets of X with at most.

  10. On the homology length spectrum of surfaces

    OpenAIRE

    Massart, Daniel; Parlier, Hugo

    2014-01-01

    On a surface with a Finsler metric, we investigate the asymptotic growth of the number of closed geodesics of length less than L which minimize length among all geodesic multicurves in the same homology class. An important class of surfaces which are of interest to us are hyperbolic surfaces.

  11. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution.

    Science.gov (United States)

    Omelchenko, Marina V; Galperin, Michael Y; Wolf, Yuri I; Koonin, Eugene V

    2010-04-30

    Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC) numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted) to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (non)homologous relationships between proteins. We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE) that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. These results indicate that at least some of the non-homologous isofunctional enzymes were recruited relatively recently from enzyme families that are active against related substrates and are sufficiently flexible to accommodate changes in substrate specificity.

  12. Increasing coverage of transcription factor position weight matrices through domain-level homology.

    Directory of Open Access Journals (Sweden)

    Brady Bernard

    Full Text Available Transcription factor-DNA interactions, central to cellular regulation and control, are commonly described by position weight matrices (PWMs. These matrices are frequently used to predict transcription factor binding sites in regulatory regions of DNA to complement and guide further experimental investigation. The DNA sequence preferences of transcription factors, encoded in PWMs, are dictated primarily by select residues within the DNA binding domain(s that interact directly with DNA. Therefore, the DNA binding properties of homologous transcription factors with identical DNA binding domains may be characterized by PWMs derived from different species. Accordingly, we have implemented a fully automated domain-level homology searching method for identical DNA binding sequences.By applying the domain-level homology search to transcription factors with existing PWMs in the JASPAR and TRANSFAC databases, we were able to significantly increase coverage in terms of the total number of PWMs associated with a given species, assign PWMs to transcription factors that did not previously have any associations, and increase the number of represented species with PWMs over an order of magnitude. Additionally, using protein binding microarray (PBM data, we have validated the domain-level method by demonstrating that transcription factor pairs with matching DNA binding domains exhibit comparable DNA binding specificity predictions to transcription factor pairs with completely identical sequences.The increased coverage achieved herein demonstrates the potential for more thorough species-associated investigation of protein-DNA interactions using existing resources. The PWM scanning results highlight the challenging nature of transcription factors that contain multiple DNA binding domains, as well as the impact of motif discovery on the ability to predict DNA binding properties. The method is additionally suitable for identifying domain-level homology mappings to

  13. Personalized Search

    CERN Document Server

    AUTHOR|(SzGeCERN)749939

    2015-01-01

    As the volume of electronically available information grows, relevant items become harder to find. This work presents an approach to personalizing search results in scientific publication databases. This work focuses on re-ranking search results from existing search engines like Solr or ElasticSearch. This work also includes the development of Obelix, a new recommendation system used to re-rank search results. The project was proposed and performed at CERN, using the scientific publications available on the CERN Document Server (CDS). This work experiments with re-ranking using offline and online evaluation of users and documents in CDS. The experiments conclude that the personalized search result outperform both latest first and word similarity in terms of click position in the search result for global search in CDS.

  14. A rapid profiling of gallotannins and flavonoids of the aqueous extract of Rhus coriaria L. by flow injection analysis with high-resolution mass spectrometry assisted with database searching.

    Science.gov (United States)

    Regazzoni, Luca; Arlandini, Emanuele; Garzon, Davide; Santagati, Natale Alfredo; Beretta, Giangiacomo; Maffei Facino, Roberto

    2013-01-01

    Hydrolysable tannins appear to have some extremely important biological roles including antioxidant, antibacterial, anti-inflammatory, anti-hypoglycemic, anti-angiogenic, and anticancer activities. The aim of this work was to set up a flow injection high-resolution mass spectrometric approach combined with database searching to obtain rapidly a profiling of gallotannins and other phenolics in a crude extract from plant tissue. The flow injection analysis (FIA) takes place in an electrospray ionization source of an hybrid orbitrap high resolution mass spectrometry system (ESI-HR-MS/MS(2), resolution 100,000, negative ion mode) and polyphenols are tentatively identified by matching the monoisotopic masses of the spectra with those of polyphenols databases. This leads to the most probable molecular formulas and to the possible structures among those reported in the database. The structures confirmation occurs by the compliance of MS(2) fragments with those of a prediction fragment commercial database. With this method we identified in the aqueous extract of sumac leaves, with a maximum error of 1.7 ppm, a group of ten gallotannins from mono- to deca-galloyl glycosides of the class of hydrolysable tannins and a set of coextracted flavonoid derivatives including myricetin, quercetin-3-O-rhamnoside, myricetin-3-O-glucoside, myricetin-3-O-glucuronide, and myricetin-3-O-rhamnoglucoside. The separation of isomers of gallotannins and flavonoids present in the same extract occurred by high-performance liquid chromatography with electrospray ionization tandem mass spectrometry (HPLC/ESI-HR-MS(2)); this approach allowed the structure resolution of the isobaric flavonoids quercetin-3-O-glucoside and myricetin-3-O-rhamnoside. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Visual search

    NARCIS (Netherlands)

    Toet, A.; Bijl, P.

    2003-01-01

    Visual search, with or without the aid of optical or electro-optical instruments, plays a significant role in various types of military and civilian operations (e.g., reconnaissance, surveillance, and search and rescue). Advance knowledge of human visual search and target acquisition performance is

  16. Heterogeneous evolutionary rates of Pi2/9 homologs in rice

    Directory of Open Access Journals (Sweden)

    Wu Kejing

    2012-08-01

    Full Text Available Abstract Background The Pi2/9 locus contains multiple nucleotide binding site–leucine-rich repeat (NBS-LRR genes in the rice genome. Although three functional R-genes have been cloned from this locus, little is known about the origin and evolutionary history of these genes. Herein, an extensive genome-wide survey of Pi2/9 homologs in rice, sorghum, Brachypodium and Arabidopsis, was conducted to explore this theme. Results In our study, 1, 1, 5 and 156 Pi2/9 homologs were detected in Arabidopsis, Brachypodium, sorghum and rice genomes, respectively. Two distinct evolutionary patterns of Pi2/9 homologs, Type I and Type II, were observed in rice lines. Type I Pi2/9 homologs showed evidence of rapid gene diversification, including substantial copy number variations, obscured orthologous relationships, high levels of nucleotide diversity or/and divergence, frequent sequence exchanges and strong positive selection, whereas Type II Pi2/9 homologs exhibited a fairly slow evolutionary rate. Interestingly, the three cloned R-genes from the Pi2/9 locus all belonged to the Type I genes. Conclusions Our data show that the Pi2/9 locus had an ancient origin predating the common ancestor of gramineous species. The existence of two types of Pi2/9 homologs suggest that diversifying evolution should be an important strategy of rice to cope with different types of pathogens. The relationship of cloned Pi2/9 genes and Type I genes also suggests that rapid gene diversification might facilitate rice to adapt quickly to the changing spectrum of the fungal pathogen M. grisea. Based on these criteria, other potential candidate genes that might confer novel resistance specificities to rice blast could be predicted.

  17. Homological mirror symmetry and tropical geometry

    CERN Document Server

    Catanese, Fabrizio; Kontsevich, Maxim; Pantev, Tony; Soibelman, Yan; Zharkov, Ilia

    2014-01-01

    The relationship between Tropical Geometry and Mirror Symmetry goes back to the work of Kontsevich and Y. Soibelman (2000), who applied methods of non-archimedean geometry (in particular, tropical curves) to Homological Mirror Symmetry. In combination with the subsequent work of Mikhalkin on the “tropical” approach to Gromov-Witten theory, and the work of Gross and Siebert, Tropical Geometry has now become a powerful tool. Homological Mirror Symmetry is the area of mathematics concentrated around several categorical equivalences connecting symplectic and holomorphic (or algebraic) geometry. The central ideas first appeared in the work of Maxim Kontsevich (1993). Roughly speaking, the subject can be approached in two ways: either one uses Lagrangian torus fibrations of Calabi-Yau manifolds (the so-called Strominger-Yau-Zaslow picture, further developed by Kontsevich and Soibelman) or one uses Lefschetz fibrations of symplectic manifolds (suggested by Kontsevich and further developed by Seidel). Tropical Ge...

  18. Homological characterisation of Lambda-ranks

    OpenAIRE

    Howson, Susan

    1999-01-01

    If G is a pro-p, p-adic, Lie group and if $\\Lambda(G)$ denotes the Iwasawa algebra of G then we present a formula for determining the $\\Lambda(G)$-rank of a finitely generated $\\Lambda(G)$-module. This is given in terms of the G homology groups of the module. We explore some consequences of this for the structure of $\\Lambda(G)$-modules.

  19. Surfaces with pulleys and Khovanov homology

    OpenAIRE

    Audoux, Benjamin

    2011-01-01

    International audience; In this short note, we define surfaces with pulleys which are unions of 1 and 2-dimensional manifolds, glued together on a finite number of points of their interiors. Then, by seeing them as cobordisms, we give a refinment of Bar-Natan geometrical construction of Khovanov homology which can be applied to different notions of refined links as links in I-bundle or braid-like links.

  20. Whole genome analysis of CRISPR Cas9 sgRNA off-target homologies via an efficient computational algorithm.

    Science.gov (United States)

    Zhou, Hong; Zhou, Michael; Li, Daisy; Manthey, Joseph; Lioutikova, Ekaterina; Wang, Hong; Zeng, Xiao

    2017-11-17

    The beauty and power of the genome editing mechanism, CRISPR Cas9 endonuclease system, lies in the fact that it is RNA-programmable such that Cas9 can be guided to any genomic loci complementary to a 20-nt RNA, single guide RNA (sgRNA), to cleave double stranded DNA, allowing the introduction of wanted mutations. Unfortunately, it has been reported repeatedly that the sgRNA can also guide Cas9 to off-target sites where the DNA sequence is homologous to sgRNA. Using human genome and Streptococcus pyogenes Cas9 (SpCas9) as an example, this article mathematically analyzed the probabilities of off-target homologies of sgRNAs and discovered that for large genome size such as human genome, potential off-target homologies are inevitable for sgRNA selection. A highly efficient computationl algorithm was developed for whole genome sgRNA design and off-target homology searches. By means of a dynamically constructed sequence-indexed database and a simplified sequence alignment method, this algorithm achieves very high efficiency while guaranteeing the identification of all existing potential off-target homologies. Via this algorithm, 1,876,775 sgRNAs were designed for the 19,153 human mRNA genes and only two sgRNAs were found to be free of off-target homology. By means of the novel and efficient sgRNA homology search algorithm introduced in this article, genome wide sgRNA design and off-target analysis were conducted and the results confirmed the mathematical analysis that for a sgRNA sequence, it is almost impossible to escape potential off-target homologies. Future innovations on the CRISPR Cas9 gene editing technology need to focus on how to eliminate the Cas9 off-target activity.

  1. Clover calculus for homology 3-spheres via basic algebraic topology

    National Research Council Canada - National Science Library

    Auclair, Emmanuel; Lescop, Christine

    2005-01-01

    We present an alternative definition for the Goussarov--Habiro filtration of the Z-module freely generated by oriented integral homology 3-spheres, by means of Lagrangian-preserving homology handlebody replacements (LP-surgeries...

  2. BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins.

    Science.gov (United States)

    Kankainen, Matti; Ojala, Teija; Holm, Liisa

    2012-02-15

    Automated function prediction has played a central role in determining the biological functions of bacterial proteins. Typically, protein function annotation relies on homology, and function is inferred from other proteins with similar sequences. This approach has become popular in bacterial genomics because it is one of the few methods that is practical for large datasets and because it does not require additional functional genomics experiments. However, the existing solutions produce erroneous predictions in many cases, especially when query sequences have low levels of identity with the annotated source protein. This problem has created a pressing need for improvements in homology-based annotation. We present an automated method for the functional annotation of bacterial protein sequences. Based on sequence similarity searches, BLANNOTATOR accurately annotates query sequences with one-line summary descriptions of protein function. It groups sequences identified by BLAST into subsets according to their annotation and bases its prediction on a set of sequences with consistent functional information. We show the results of BLANNOTATOR's performance in sets of bacterial proteins with known functions. We simulated the annotation process for 3090 SWISS-PROT proteins using a database in its state preceding the functional characterisation of the query protein. For this dataset, our method outperformed the five others that we tested, and the improved performance was maintained even in the absence of highly related sequence hits. We further demonstrate the value of our tool by analysing the putative proteome of Lactobacillus crispatus strain ST1. BLANNOTATOR is an accurate method for bacterial protein function prediction. It is practical for genome-scale data and does not require pre-existing sequence clustering; thus, this method suits the needs of bacterial genome and metagenome researchers. The method and a web-server are available at http://ekhidna.biocenter.helsinki.fi/poxo/blannotator/.

  3. FLASH: a fast look-up algorithm for string homology.

    Science.gov (United States)

    Califano, A; Rigoutsos, I

    1993-01-01

    A key issue in managing today's large amounts of genetic data is the availability of efficient, accurate, and selective techniques for detecting homologies (similarities) between newly discovered and already stored sequences. A common characteristic of today's most advanced algorithms, such as FASTA, BLAST, and BLAZE is the need to scan the contents of the entire database, in order to find one or more matches. This design decision results in either excessively long search times or, as is the case of BLAST, in a sharp trade-off between the achieved accuracy and the required amount of computation. The homology detection algorithm presented in this paper, on the other hand, is based on a probabilistic indexing framework. The algorithm requires minimal access to the database in order to determine matches. This minimal requirement is achieved by using the sequences of interest to generate a highly redundant number of very descriptive tuples; these tuples are subsequently used as indices in a table look-up paradigm. In addition to the description of the algorithm, theoretical and experimental results on the sensitivity and accuracy of the suggested approach are provided. The storage and computational requirements are described and the probability of correct matches and false alarms is derived. Sensitivity and accuracy are shown to be close to those of dynamic programming techniques. A prototype system has been implemented using the described ideas. It contains the full Swiss-Prot database rel 25 (10 MR) and the genome of E. Coli (2 MR). The system is currently being expanded to include the complete Genbank database.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. GenBank blastn search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available 18908/lsdba.nbdc00120-007 Description of data contents Results of blastn searches against GenBank nucleotide...method Performed blastn searches against Genbank nucleotide sequences. Data analysis method Performed homology searches...5) using the blastn program (blast2.2.12). Sequences used in the searches were located in the following 10 o...search URL http://togodb.biosciencedbc.jp/togodb/view/kome_genbank_blastn_search_result#en Data acquisition

  5. GenBank blastx search result - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available 18908/lsdba.nbdc00120-008 Description of data contents Results of blastx searches against GenBank amino acid...method Performed blastx searches against Genbank amino acid sequences. Data analysis method Performed homology searches...5) using the blastx program (blast2.2.12). Sequences useed in the searches were located in the following 10 ...search URL http://togodb.biosciencedbc.jp/togodb/view/kome_genbank_blastx_search_result#en Data acquisition

  6. Physcomitrella patens has kinase-LRR R gene homologs and interacting proteins.

    Directory of Open Access Journals (Sweden)

    Yusuke Tanigaki

    Full Text Available Plant disease resistance gene (R gene-like sequences were screened from the Physcomitrella patens genome. We found 603 kinase-like, 475 Nucleotide Binding Site (NBS-like and 8594 Leucine Rich Repeat (LRR-like sequences by homology searching using the respective domains of PpC24 (Accession No. BAD38895, which is a candidate kinase-NBS-LRR (kinase-NL type R-like gene, as a reference. The positions of these domains in the genome were compared and 17 kinase-NLs were predicted. We also found four TIR-NBS-LRR (TIR-NL sequences with homology to Arabidopsis TIR-NL (NM_001125847, but three out of the four TIR-NLs had tetratricopeptide repeats or a zinc finger domain in their predicted C-terminus. We also searched for kinase-LRR (KLR type sequences by homology with rice OsXa21 and Arabidopsis thaliana FLS2. As a result, 16 KLRs with similarity to OsXa21 were found. In phylogenetic analysis of these 16 KLRs, PpKLR36, PpKLR39, PpKLR40, and PpKLR43 formed a cluster with OsXa21. These four PpKLRs had deduced transmembrane domain sequences and expression of all four was confirmed. We also found 14 homologs of rice OsXB3, which is known to interact with OsXa21 and is involved in signal transduction. Protein-protein interaction was observed between the four PpKLRs and at least two of the XB3 homologs in Y2H analysis.

  7. Non-homologous isofunctional enzymes: A systematic analysis of alternative solutions in enzyme evolution

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2010-04-01

    Full Text Available Abstract Background Evolutionarily unrelated proteins that catalyze the same biochemical reactions are often referred to as analogous - as opposed to homologous - enzymes. The existence of numerous alternative, non-homologous enzyme isoforms presents an interesting evolutionary problem; it also complicates genome-based reconstruction of the metabolic pathways in a variety of organisms. In 1998, a systematic search for analogous enzymes resulted in the identification of 105 Enzyme Commission (EC numbers that included two or more proteins without detectable sequence similarity to each other, including 34 EC nodes where proteins were known (or predicted to have distinct structural folds, indicating independent evolutionary origins. In the past 12 years, many putative non-homologous isofunctional enzymes were identified in newly sequenced genomes. In addition, efforts in structural genomics resulted in a vastly improved structural coverage of proteomes, providing for definitive assessment of (nonhomologous relationships between proteins. Results We report the results of a comprehensive search for non-homologous isofunctional enzymes (NISE that yielded 185 EC nodes with two or more experimentally characterized - or predicted - structurally unrelated proteins. Of these NISE sets, only 74 were from the original 1998 list. Structural assignments of the NISE show over-representation of proteins with the TIM barrel fold and the nucleotide-binding Rossmann fold. From the functional perspective, the set of NISE is enriched in hydrolases, particularly carbohydrate hydrolases, and in enzymes involved in defense against oxidative stress. Conclusions These results indicate that at least some of the non-homologous isofunctional enzymes were recruited relatively recently from enzyme families that are active against related substrates and are sufficiently flexible to accommodate changes in substrate specificity. Reviewers This article was reviewed by Andrei

  8. Faceted Search

    CERN Document Server

    Tunkelang, Daniel

    2009-01-01

    We live in an information age that requires us, more than ever, to represent, access, and use information. Over the last several decades, we have developed a modern science and technology for information retrieval, relentlessly pursuing the vision of a "memex" that Vannevar Bush proposed in his seminal article, "As We May Think." Faceted search plays a key role in this program. Faceted search addresses weaknesses of conventional search approaches and has emerged as a foundation for interactive information retrieval. User studies demonstrate that faceted search provides more

  9. A PHF8 homolog in C. elegans promotes DNA repair via homologous recombination.

    Directory of Open Access Journals (Sweden)

    Changrim Lee

    Full Text Available PHF8 is a JmjC domain-containing histone demethylase, defects in which are associated with X-linked mental retardation. In this study, we examined the roles of two PHF8 homologs, JMJD-1.1 and JMJD-1.2, in the model organism C. elegans in response to DNA damage. A deletion mutation in either of the genes led to hypersensitivity to interstrand DNA crosslinks (ICLs, while only mutation of jmjd-1.1 resulted in hypersensitivity to double-strand DNA breaks (DSBs. In response to ICLs, JMJD-1.1 did not affect the focus formation of FCD-2, a homolog of FANCD2, a key protein in the Fanconi anemia pathway. However, the dynamic behavior of RPA-1 and RAD-51 was affected by the mutation: the accumulations of both proteins at ICLs appeared normal, but their subsequent disappearance was retarded, suggesting that later steps of homologous recombination were defective. Similar changes in the dynamic behavior of RPA-1 and RAD-51 were seen in response to DSBs, supporting a role of JMJD-1.1 in homologous recombination. Such a role was also supported by our finding that the hypersensitivity of jmjd-1.1 worms to ICLs was rescued by knockdown of lig-4, a homolog of Ligase 4 active in nonhomologous end-joining. The hypersensitivity of jmjd-1.1 worms to ICLs was increased by rad-54 knockdown, suggesting that JMJD-1.1 acts in parallel with RAD-54 in modulating chromatin structure. Indeed, the level of histone H3 Lys9 tri-methylation, a marker of heterochromatin, was higher in jmjd-1.1 cells than in wild-type cells. We conclude that the histone demethylase JMJD-1.1 influences homologous recombination either by relaxing heterochromatin structure or by indirectly regulating the expression of multiple genes affecting DNA repair.

  10. Homological Perturbation Theory for Nonperturbative Integrals

    Science.gov (United States)

    Johnson-Freyd, Theo

    2015-11-01

    We use the homological perturbation lemma to produce explicit formulas computing the class in the twisted de Rham complex represented by an arbitrary polynomial. This is a non-asymptotic version of the method of Feynman diagrams. In particular, we explain that phenomena usually thought of as particular to asymptotic integrals in fact also occur exactly: integrals of the type appearing in quantum field theory can be reduced in a totally algebraic fashion to integrals over an Euler-Lagrange locus, provided this locus is understood in the scheme-theoretic sense, so that imaginary critical points and multiplicities of degenerate critical points contribute.

  11. Genetic Homologies Among Streptomyces violaceoruber Strains

    Science.gov (United States)

    Monson, A. M.; Bradley, S. G.; Enquist, L. W.; Cruces, Griselda

    1969-01-01

    Most of the genetic studies on streptomycetes have been done with cultures erroneously designated as Streptomyces coelicolor. To determine whether these cultures are genetically homologous with the S. violaceoruber nominifer, their deoxyribonucleic acids (DNA) were analyzed, and selected pairs of mutants were crossed. The four cultures used in genetic studies, and called S. coelicolor in the literature, were found to constitute a genospecies, based upon DNA hybridization and recombination tests. In addition, DNA from Actinopycnidium caeruleum formed extensive duplexes with S. violaceoruber DNA. S. violaceoruber cultures and A. caeruleum were distinctly different from the S. coelicolor nominifer. PMID:5370275

  12. Excluded volume effect enhances the homology pairing of model chromosomes

    Science.gov (United States)

    Takamiya, Kazunori; Yamamoto, Keisuke; Isami, Shuhei; Nishimori, Hiraku; Awazu, Akinori

    To investigate the structural dynamics of the homology pairing of polymers, we mod- eled the scenario of homologous chromosome pairings during meiosis in Schizosaccharomyces pombe, one of the simplest model organisms of eukaryotes. We consider a simple model consist- ing of pairs of homologous polymers with the same structures that are confined in a cylindrical container, which represents the local parts of chromosomes contained in an elongated nucleus of S. pombe. Brownian dynamics simulations of this model showed that the excluded volume effects among non-homological chromosomes and the transitional dynamics of nuclear shape serve to enhance the pairing of homologous chromosomes.

  13. DNA damage, homology-directed repair, and DNA methylation.

    Directory of Open Access Journals (Sweden)

    Concetta Cuozzo

    2007-07-01

    Full Text Available To explore the link between DNA damage and gene silencing, we induced a DNA double-strand break in the genome of Hela or mouse embryonic stem (ES cells using I-SceI restriction endonuclease. The I-SceI site lies within one copy of two inactivated tandem repeated green fluorescent protein (GFP genes (DR-GFP. A total of 2%-4% of the cells generated a functional GFP by homology-directed repair (HR and gene conversion. However, approximately 50% of these recombinants expressed GFP poorly. Silencing was rapid and associated with HR and DNA methylation of the recombinant gene, since it was prevented in Hela cells by 5-aza-2'-deoxycytidine. ES cells deficient in DNA methyl transferase 1 yielded as many recombinants as wild-type cells, but most of these recombinants expressed GFP robustly. Half of the HR DNA molecules were de novo methylated, principally downstream to the double-strand break, and half were undermethylated relative to the uncut DNA. Methylation of the repaired gene was independent of the methylation status of the converting template. The methylation pattern of recombinant molecules derived from pools of cells carrying DR-GFP at different loci, or from an individual clone carrying DR-GFP at a single locus, was comparable. ClustalW analysis of the sequenced GFP molecules in Hela and ES cells distinguished recombinant and nonrecombinant DNA solely on the basis of their methylation profile and indicated that HR superimposed novel methylation profiles on top of the old patterns. Chromatin immunoprecipitation and RNA analysis revealed that DNA methyl transferase 1 was bound specifically to HR GFP DNA and that methylation of the repaired segment contributed to the silencing of GFP expression. Taken together, our data support a mechanistic link between HR and DNA methylation and suggest that DNA methylation in eukaryotes marks homologous recombined segments.

  14. Advanced Search

    African Journals Online (AJOL)

    Items 151 - 200 of 500 ... Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more ...

  15. Search Results

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  16. Advanced Search

    African Journals Online (AJOL)

    Search tips: Search terms are case-insensitive; Common words are ignored; By default only articles containing all terms in the query are returned (i.e., AND is implied); Combine multiple words with OR to find articles containing either term; e.g., education OR research; Use parentheses to create more complex queries; e.g., ...

  17. Oral region homologies in paleozoic crinoids and other plesiomorphic pentaradial echinoderms.

    Directory of Open Access Journals (Sweden)

    Thomas W Kammer

    Full Text Available The phylogenetic relationships between major groups of plesiomorphic pentaradial echinoderms, the Paleozoic crinoids, blastozoans, and edrioasteroids, are poorly understood because of a lack of widely recognized homologies. Here, we present newly recognized oral region homologies, based on the Universal Elemental Homology model for skeletal plates, in a wide range of fossil taxa. The oral region of echinoderms is mainly composed of the axial, or ambulacral, skeleton, which apparently evolved more slowly than the extraxial skeleton that forms the majority of the body. Recent phylogenetic hypotheses have focused on characters of the extraxial skeleton, which may have evolved too rapidly to preserve obvious homologies across all these groups. The axial skeleton conserved homologous suites of characters shared between various edrioasteroids and specific blastozoans, and between other blastozoans and crinoids. Although individual plates can be inferred as homologous, no directly overlapping suites of characters are shared between edrioasteroids and crinoids. Six different systems of mouth (peristome plate organization (Peristomial Border Systems are defined. These include four different systems based on the arrangement of the interradially-positioned oral plates and their peristomial cover plates, where PBS A1 occurs only in plesiomorphic edrioasteroids, PBS A2 occurs in plesiomorphic edrioasteroids and blastozoans, and PBS A3 and PBS A4 occur in blastozoans and crinoids. The other two systems have radially-positioned uniserial oral frame plates in construction of the mouth frame. PBS B1 has both orals and uniserial oral frame plates and occurs in edrioasterid and possibly edrioblastoid edrioasteroids, whereas PBS B2 has exclusively uniserial oral frame plates and is found in isorophid edrioasteroids and imbricate and gogiid blastozoans. These different types of mouth frame construction offer potential synapomorphies to aid in parsimony

  18. Oral region homologies in paleozoic crinoids and other plesiomorphic pentaradial echinoderms.

    Science.gov (United States)

    Kammer, Thomas W; Sumrall, Colin D; Zamora, Samuel; Ausich, William I; Deline, Bradley

    2013-01-01

    The phylogenetic relationships between major groups of plesiomorphic pentaradial echinoderms, the Paleozoic crinoids, blastozoans, and edrioasteroids, are poorly understood because of a lack of widely recognized homologies. Here, we present newly recognized oral region homologies, based on the Universal Elemental Homology model for skeletal plates, in a wide range of fossil taxa. The oral region of echinoderms is mainly composed of the axial, or ambulacral, skeleton, which apparently evolved more slowly than the extraxial skeleton that forms the majority of the body. Recent phylogenetic hypotheses have focused on characters of the extraxial skeleton, which may have evolved too rapidly to preserve obvious homologies across all these groups. The axial skeleton conserved homologous suites of characters shared between various edrioasteroids and specific blastozoans, and between other blastozoans and crinoids. Although individual plates can be inferred as homologous, no directly overlapping suites of characters are shared between edrioasteroids and crinoids. Six different systems of mouth (peristome) plate organization (Peristomial Border Systems) are defined. These include four different systems based on the arrangement of the interradially-positioned oral plates and their peristomial cover plates, where PBS A1 occurs only in plesiomorphic edrioasteroids, PBS A2 occurs in plesiomorphic edrioasteroids and blastozoans, and PBS A3 and PBS A4 occur in blastozoans and crinoids. The other two systems have radially-positioned uniserial oral frame plates in construction of the mouth frame. PBS B1 has both orals and uniserial oral frame plates and occurs in edrioasterid and possibly edrioblastoid edrioasteroids, whereas PBS B2 has exclusively uniserial oral frame plates and is found in isorophid edrioasteroids and imbricate and gogiid blastozoans. These different types of mouth frame construction offer potential synapomorphies to aid in parsimony-based phylogenetics for

  19. Structure of the 40S ribosomal subunit of Plasmodium falciparum by homology and de novo modeling

    Directory of Open Access Journals (Sweden)

    Harrison Ndung'u Mwangi

    2017-01-01

    Full Text Available Generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. This is especially the case if a homologous crystal structure is already available. High-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of scientific discovery. In this study, homology modeling and structure prediction tools such as RNA123 and SWISS–MODEL were used to generate the 40S ribosomal subunit from Plasmodium falciparum. This structure was modeled using the published crystal structure from Tetrahymena thermophila, a homologous eukaryote. In the absence of the Plasmodium falciparum 40S ribosomal crystal structure, the model accurately depicts a global topology, secondary and tertiary connections, and gives an overall root mean square deviation (RMSD value of 3.9 Å relative to the template׳s crystal structure. Deviations are somewhat larger in areas with no homology between the templates. These results demonstrate that this approach has the power to identify motifs of interest in RNA and identify potential drug targets for macromolecules whose crystal structures are unknown. The results also show the utility of RNA homology modeling software for structure determination and lay the groundwork for applying this approach to larger and more complex eukaryotic ribosomes and other RNA-protein complexes. Structures generated from this study can be used in in silico screening experiments and lead to the determination of structures for targets/hit complexes.

  20. [Homologous amelogenin gene test of archaeological samples].

    Science.gov (United States)

    Zhang, Hu-Qin; Yang, Zhou-Qi; Liu, Fang-E; Zhang, Jin; Zhao, Wen-Ming

    2006-06-01

    Based on the sequence differences of Amelogenin homologous gene in the X and Y chromosomes, a pair of specific primers was designed to identify the sex of archaeological samples. Ancient DNA fragments were extracted from the bones and teeth of sacrificial slaves with an improved method that combines phenol-chloroform extraction, silicon dioxide adsorption with ultrafiltration concentration. The polyacrylamide gel electrophoresis (PAGE) was used to detect PCR products. Seven in sixteen samples from eight graves showed positive results and the targeted segments were visible: a male with two bands of 106bp (Amel-X) and 112 bp (Amel-Y), while a female with only one band of 106 bp (Amel-X). Ancient DNA analyzing results from tooth samples are more marked than that from bones. The improved extraction method is more effective for ancient DNA extraction, which reduced the PCR inhibitors and lowered experimental costs. The sex determination technology based on Amelogenin homologous gene is an important and feasible method in the molecular archaeological research.

  1. Productive homologous and non-homologous recombination of hepatitis C virus in cell culture

    DEFF Research Database (Denmark)

    Scheel, Troels K H; Galli, Andrea; Li, Yi-Ping

    2013-01-01

    -genotypic recombination could occur, but at a lower frequency than intra-genotypic recombination. Productive recombination of attenuated HCV genomes depended on expression of all HCV proteins and tolerated duplicated sequence. In general, no strong site specificity was observed. Non-homologous recombination was observed...

  2. Studies of Flerovium and Element 115 Homologs with Macrocyclic Extractants

    Energy Technology Data Exchange (ETDEWEB)

    Despotopulos, John D. [Univ. of Nevada, Las Vegas, NV (United States)

    2015-03-12

    Study of the chemistry of the heaviest elements, Z ≥ 104, poses a unique challenge due to their low production cross-sections and short half-lives. Chemistry also must be studied on the one-atom-at-a-time scale, requiring automated, fast, and very efficient chemical schemes. Recent studies of the chemical behavior of copernicium (Cn, element 112) and flerovium (Fl, element 114) together with the discovery of isotopes of these elements with half-lives suitable for chemical studies have spurred a renewed interest in the development of rapid systems designed to study the chemical properties of elements with Z ≥ 114. This dissertation explores both extraction chromatography and solvent extraction as methods for development of a rapid chemical separation scheme for the homologs of flerovium (Pb, Sn, Hg) and element 115 (Bi, Sb), with the goal of developing a chemical scheme that, in the future, can be applied to on-line chemistry of both Fl and element 115. Carrier-free radionuclides, used in these studies, of the homologs of Fl and element 115 were obtained by proton activation of high-purity metal foils at the Lawrence Livermore National Laboratory (LLNL) Center for Accelerator Mass Spectrometry (CAMS): natIn(p,n)113Sn, natSn(p,n)124Sb, and Au(p,n)197m,gHg. The carrier-free activity was separated from the foils by novel separation schemes based on ion exchange and extraction chromatography techniques. Carrier-free Pb and Bi isotopes were obtained from development of a novel generator based on cation exchange chromatography using the 232U parent to generate 212Pb and 212Bi. Macrocyclic extractants, specifically crown ethers and their derivatives, were chosen for these studies; crown ethers show high selectivity for metal ions. Finally. a potential chemical system for Fl was established based on the Eichrom Pb resin, and insight to an improved system based on thiacrown ethers is

  3. Autonomous search

    CERN Document Server

    Hamadi, Youssef; Saubion, Frédéric

    2012-01-01

    Autonomous combinatorial search (AS) represents a new field in combinatorial problem solving. Its major standpoint and originality is that it considers that problem solvers must be capable of self-improvement operations. This is the first book dedicated to AS.

  4. Clustering evolving proteins into homologous families.

    Science.gov (United States)

    Chan, Cheong Xin; Mahbob, Maisarah; Ragan, Mark A

    2013-04-08

    Clustering sequences into groups of putative homologs (families) is a critical first step in many areas of comparative biology and bioinformatics. The performance of clustering approaches in delineating biologically meaningful families depends strongly on characteristics of the data, including content bias and degree of divergence. New, highly scalable methods have recently been introduced to cluster the very large datasets being generated by next-generation sequencing technologies. However, there has been little systematic investigation of how characteristics of the data impact the performance of these approaches. Using clusters from a manually curated dataset as reference, we examined the performance of a widely used graph-based Markov clustering algorithm (MCL) and a greedy heuristic approach (UCLUST) in delineating protein families coded by three sets of bacterial genomes of different G+C content. Both MCL and UCLUST generated clusters that are comparable to the reference sets at specific parameter settings, although UCLUST tends to under-cluster compositionally biased sequences (G+C content 33% and 66%). Using simulated data, we sought to assess the individual effects of sequence divergence, rate heterogeneity, and underlying G+C content. Performance decreased with increasing sequence divergence, decreasing among-site rate variation, and increasing G+C bias. Two MCL-based methods recovered the simulated families more accurately than did UCLUST. MCL using local alignment distances is more robust across the investigated range of sequence features than are greedy heuristics using distances based on global alignment. Our results demonstrate that sequence divergence, rate heterogeneity and content bias can individually and in combination affect the accuracy with which MCL and UCLUST can recover homologous protein families. For application to data that are more divergent, and exhibit higher among-site rate variation and/or content bias, MCL may often be the better

  5. Modeling Non-homologous End Joining

    Science.gov (United States)

    Li, Yongfeng

    2013-01-01

    Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several NHEJ proteins such as Ku, DNA-PKcs, XRCC4, Ligase IV and so on. Once DSBs are generated, Ku is first recruited to the DNA end, followed by other NHEJ proteins for DNA end processing and ligation. Because of the direct ligation of break ends without the need for a homologous template, NHEJ turns out to be an error-prone but efficient repair pathway. Some mechanisms have been proposed of how the efficiency of NHEJ repair is affected. The type of DNA damage is an important factor of NHEJ repair. For instance, the length of DNA fragment may determine the recruitment efficiency of NHEJ protein such as Ku [1], or the complexity of the DNA breaks [2] is accounted for the choice of NHEJ proteins and subpathway of NHEJ repair. On the other hand, the chromatin structure also plays a role of the accessibility of NHEJ protein to the DNA damage site. In this talk, some mathematical models of NHEJ, that consist of series of biochemical reactions complying with the laws of chemical reaction (e.g. mass action, etc.), will be introduced. By mathematical and numerical analysis and parameter estimation, the models are able to capture the qualitative biological features and show good agreement with experimental data. As conclusions, from the viewpoint of modeling, how the NHEJ proteins are recruited will be first discussed for connection between the classical sequential model [4] and recently proposed two-phase model [5]. Then how the NHEJ repair pathway is affected, by the length of DNA fragment [6], the complexity of DNA damage [7] and the chromatin structure [8], will be addressed

  6. Inferring protein function from homology using the Princeton Protein Orthology Database (P-POD)

    Science.gov (United States)

    Livstone, Michael S.; Oughtred, Rose; Heinicke, Sven; Vernot, Benjamin; Huttenhower, Curtis; Durand, Dannie; Dolinski, Kara

    2011-01-01

    Inferring a protein’s function by homology is a powerful tool for biologists. The Princeton Protein Orthology Database (P-POD) offers a simple way to visualize and analyze the relationships between homologous proteins in order to infer function. P-POD contains computationally-generated analysis distinguishing orthologs from paralogs combined with curated published information on functional complementation and on human diseases. P-POD also features an applet, Notung, for users to explore and modify phylogenetic trees and generate their own ortholog/paralogs calls. This unit describes how to search P-POD for precomputed data, how to find and use the associated curated information from the literature, and how to use Notung to analyze and refine the results. PMID:21400696

  7. Computational identification of mutually homologous Zika virus ...

    African Journals Online (AJOL)

    Background Zika virus (ZIKV) has been associated with a variety of neuropathologies, including microcephaly. We hypothesize that ZIKV genes activate host microRNAs (miRNAs) causing dysfunctional development of human fetal brains. Objectives/methods A bioinformatics search for miRNA genome-wide binding sites in ...

  8. A geometric model for Hochschild homology of Soergel bimodules

    DEFF Research Database (Denmark)

    Webster, Ben; Williamson, Geordie

    2008-01-01

    An important step in the calculation of the triply graded link homology of Khovanov and Rozansky is the determination of the Hochschild homology of Soergel bimodules for SL(n). We present a geometric model for this Hochschild homology for any simple group G, as B–equivariant intersection cohomology...... of B×B–orbit closures in G. We show that, in type A, these orbit closures are equivariantly formal for the conjugation B–action. We use this fact to show that, in the case where the corresponding orbit closure is smooth, this Hochschild homology is an exterior algebra over a polynomial ring...

  9. $A$ searches

    CERN Document Server

    Beacham, James

    The Standard Model of particle physics encompasses three of the four known fundamental forces of nature, and has remarkably withstood all of the experimental tests of its predictions, a fact solidified by the discovery, in 2012, of the Higgs boson. However, it cannot be the complete picture. Many measurements have been made that hint at physics beyond the Standard Model, and the main task of the high- energy experimental physics community is to conduct searches for new physics in as many di↵erent places and regimes as possible. I present three searches for new phenomena in three di↵erent high-energy collider experiments, namely, a search for events with at least three photons in the final state, which is sensitive to an exotic decay of a Higgs boson into four photons via intermediate pseudoscalar particles, a, with ATLAS, at the Large Hadron Collider; a search for a dark photon, also known as an A0 , with APEX, at Thomas Je↵erson National Accelerator Facility; and a search for a Higgs decaying into four...

  10. Homologous Basal Ganglia Network Models in Physiological and Parkinsonian Conditions

    Directory of Open Access Journals (Sweden)

    Jyotika Bahuguna

    2017-08-01

    Full Text Available The classical model of basal ganglia has been refined in recent years with discoveries of subpopulations within a nucleus and previously unknown projections. One such discovery is the presence of subpopulations of arkypallidal and prototypical neurons in external globus pallidus, which was previously considered to be a primarily homogeneous nucleus. Developing a computational model of these multiple interconnected nuclei is challenging, because the strengths of the connections are largely unknown. We therefore use a genetic algorithm to search for the unknown connectivity parameters in a firing rate model. We apply a binary cost function derived from empirical firing rate and phase relationship data for the physiological and Parkinsonian conditions. Our approach generates ensembles of over 1,000 configurations, or homologies, for each condition, with broad distributions for many of the parameter values and overlap between the two conditions. However, the resulting effective weights of connections from or to prototypical and arkypallidal neurons are consistent with the experimental data. We investigate the significance of the weight variability by manipulating the parameters individually and cumulatively, and conclude that the correlation observed between the parameters is necessary for generating the dynamics of the two conditions. We then investigate the response of the networks to a transient cortical stimulus, and demonstrate that networks classified as physiological effectively suppress activity in the internal globus pallidus, and are not susceptible to oscillations, whereas parkinsonian networks show the opposite tendency. Thus, we conclude that the rates and phase relationships observed in the globus pallidus are predictive of experimentally observed higher level dynamical features of the physiological and parkinsonian basal ganglia, and that the multiplicity of solutions generated by our method may well be indicative of a natural

  11. Quantum theory-inspired search

    OpenAIRE

    Aerts, Diederik; Bruza, Peter; Hou, Yuexian; Jose, Joemon; Melucci, Massimo; Nie, Jian-Yun; Song, Dawei

    2011-01-01

    With the huge number and diversity of the users, the advertising products and services, the rapid growth of online multimedia resources, the context of information needs are even more broad and complex. Although research in search engine technology has led to various models over the past three decades, the investigation for effectively integrating the dimensions of context to deploy advanced search technology has been limited due to the lack of a unified modeling and evaluation framework. Qua...

  12. Genomic Tagging of AGO1 Using CRISPR/Cas9-Mediated Homologous Recombination.

    Science.gov (United States)

    Ghosh, Sanjay; Liu, Ji-Long

    2018-01-01

    Tagging of genes at the endogenous loci is a powerful strategy for the analysis of protein function. We have developed a homologous recombination-based approach for inserting epitope tag into Drosophila AGO1 locus by employing the CRISPR/Cas9 technology. The methodology involves co-expression of sgRNA (containing 20-nucleotide AGO1 targeting sequence) and Cas9 protein, together with a donor template that has HA-AGO1 cassette flanked by sequences homologous to the AGO1 locus. The integration is efficient and readily monitored by immunostaining of the transgenic cell line. This method facilitates rapid generation of stable cell lines and allows insertion of any tag sequence into endogenous loci, thus accelerating characterization of the tagged proteins.

  13. Targeting Homologous Recombination in Notch-Driven C. elegans Stem Cell and Human Tumors.

    Directory of Open Access Journals (Sweden)

    Xinzhu Deng

    Full Text Available Mammalian NOTCH1-4 receptors are all associated with human malignancy, although exact roles remain enigmatic. Here we employ glp-1(ar202, a temperature-sensitive gain-of-function C. elegans NOTCH mutant, to delineate NOTCH-driven tumor responses to radiotherapy. At ≤20°C, glp-1(ar202 is wild-type, whereas at 25°C it forms a germline stem cell⁄progenitor cell tumor reminiscent of human cancer. We identify a NOTCH tumor phenotype in which all tumor cells traffic rapidly to G2⁄M post-irradiation, attempt to repair DNA strand breaks exclusively via homology-driven repair, and when this fails die by mitotic death. Homology-driven repair inactivation is dramatically radiosensitizing. We show that these concepts translate directly to human cancer models.

  14. High-efficiency homologous recombination in the oil-producing alga Nannochloropsis sp.

    Science.gov (United States)

    Kilian, Oliver; Benemann, Christina S. E.; Niyogi, Krishna K.; Vick, Bertrand

    2011-01-01

    Algae have reemerged as potential next-generation feedstocks for biofuels, but strain improvement and progress in algal biology research have been limited by the lack of advanced molecular tools for most eukaryotic microalgae. Here we describe the development of an efficient transformation method for Nannochloropsis sp., a fast-growing, unicellular alga capable of accumulating large amounts of oil. Moreover, we provide additional evidence that Nannochloropsis is haploid, and we demonstrate that insertion of transformation constructs into the nuclear genome can occur by high-efficiency homologous recombination. As examples, we generated knockouts of the genes encoding nitrate reductase and nitrite reductase, resulting in strains that were unable to grow on nitrate and nitrate/nitrite, respectively. The application of homologous recombination in this industrially relevant alga has the potential to rapidly advance algal functional genomics and biotechnology. PMID:22123974

  15. A Survey On Meta Search Engine in Semantic Web

    OpenAIRE

    Prof. M.Surendra Prasad Babu; G.Sudeepthi

    2011-01-01

    The Search engines plays an important role in the success of the Web, Search engines helps any Internet user to rapidly find relevant information. But the unsolved problems of current search engines have led to the development of the Semantic Web. In the environment of Semantic Web, the search engines are more useful and efficient in searching the relevant web information., and our work shows how the fundamental elements of the meta search engine can be used in retriving the information resou...

  16. Induction of osteogenesis by demineralized homologous and xenograft bone matrix

    Directory of Open Access Journals (Sweden)

    Dall'Agnol Rosiris

    2003-01-01

    Full Text Available The osteogenesis induction by demineralized bone matrix grafts remains as a challenge in the reconstructions of the mandible through homologous and xenografts or in implants in abdominal muscle. PURPOSE: Observed the behaviour of implants of demineralized bone matrix at the mandible (right side with homologous graft and left side with xenograft of pig. METHODS: Experimental study with homologous and heterologous implants of demineralized bone matrix at the mandible and in ectopic muscle at the Center of Experimental Surgery of Heliopolis Hospital, Hosphel, São Paulo, Brazil. In 6 white New Zeland rabbits, 46 grafts were performed being 23 with homologous (rabbit and 23 with xenograft (pig. 12 homologous implants (6 at the right side of the mandible and 6 at abdominal muscle of the rabbit and 12 heterologous implants of pigs (6 at the left side of the mandible and 6 at abdominal muscle rabbit were performed with demineralized bone matrix. RESULTS: Osteogenesis was assessed through histologic features after 30 and 60 days. After 1 rabbit dead, osteogenesis (mandible were detected in 9 of 11 (82% rabbits that received homologous matrix, in spite of heterologous implants showed osteogenesis in 6 out of 11 (54% (p=0,18. The abdominal muscle showed induced osteogenesis in 3 out of 11(27% animals with homologous and 0% with heterologous implants (p=0,10. CONCLUSIONS: Osteogenesis induction through homologous grafts in rabbit mandible and abdominal muscle were more effective than xenografts.

  17. Efficacy of homologous peste des petits ruminants vaccine on sheep ...

    African Journals Online (AJOL)

    Efficacy of homologous peste des petits ruminants vaccine on sheep and goats at dengi, plateau state, Nigeria. ... Bulletin of Animal Health and Production in Africa ... The effect of homologous peste des petits ruminants vaccine (HPPRV) on flock size, morbidity and mortality in sheep and goats was determined in five ...

  18. CBH1 homologs and varian CBH1 cellulase

    Energy Technology Data Exchange (ETDEWEB)

    Goedegebuur, Frits; Gualfetti, Peter; Mitchinson, Colin; Neefe, Paulien

    2014-07-01

    Disclosed are a number of homologs and variants of Hypocrea jecorina Cel7A (formerly Trichoderma reesei cellobiohydrolase I or CBH1), nucleic acids encoding the same and methods for producing the same. The homologs and variant cellulases have the amino acid sequence of a glycosyl hydrolase of family 7A wherein one or more amino acid residues are substituted and/or deleted.

  19. Cloning and expression analysis of a LFY homologous gene in ...

    African Journals Online (AJOL)

    LEAFY (LFY) homologous genes are necessary for the transition from vegetative to reproductive development in flowering plants. The full-length cDNA of a LFY homolog was successfully isolated from floral buds of Chinese Jujube (Ziziphus jujube Mill.) by degenerate reverse transcriptase-polymerase chain reaction ...

  20. Regulation of homologous recombination at telomeres in budding yeast

    DEFF Research Database (Denmark)

    Eckert-Boulet, Nadine; Lisby, Michael

    2010-01-01

    Homologous recombination is suppressed at normal length telomere sequences. In contrast, telomere recombination is allowed when telomeres erode in the absence of telomerase activity or as a consequence of nucleolytic degradation or incomplete replication. Here, we review the mechanisms...... that contribute to regulating mitotic homologous recombination at telomeres and the role of these mechanisms in signalling short telomeres in the budding yeast Saccharomyces cerevisiae....

  1. Dynamic protein assemblies in homologous recombination with single DNA molecules

    NARCIS (Netherlands)

    van der Heijden, A.H.

    2007-01-01

    What happens when your DNA breaks? This thesis describes experimental work on the single-molecule level focusing on the interaction between DNA and DNA-repair proteins, in particular bacterial RecA and human Rad51, involved in homologous recombination. Homologous recombination and its central event

  2. Homology modelling and spectroscopy, a never-ending love story.

    NARCIS (Netherlands)

    Venselaar, H.; Joosten, R.P.; Vroling, B.; Baakman, C.A.; Hekkelman, M.L.; Krieger, E.; Vriend, G.

    2010-01-01

    Homology modelling is normally the technique of choice when experimental structure data are not available but three-dimensional coordinates are needed, for example, to aid with detailed interpretation of results of spectroscopic studies. Herein, the state of the art of homology modelling will be

  3. Statistical Inference for Porous Materials using Persistent Homology.

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Chul [Univ. of Georgia, Athens, GA (United States); Heath, Jason E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mitchell, Scott A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-12-01

    We propose a porous materials analysis pipeline using persistent homology. We rst compute persistent homology of binarized 3D images of sampled material subvolumes. For each image we compute sets of homology intervals, which are represented as summary graphics called persistence diagrams. We convert persistence diagrams into image vectors in order to analyze the similarity of the homology of the material images using the mature tools for image analysis. Each image is treated as a vector and we compute its principal components to extract features. We t a statistical model using the loadings of principal components to estimate material porosity, permeability, anisotropy, and tortuosity. We also propose an adaptive version of the structural similarity index (SSIM), a similarity metric for images, as a measure to determine the statistical representative elementary volumes (sREV) for persistence homology. Thus we provide a capability for making a statistical inference of the uid ow and transport properties of porous materials based on their geometry and connectivity.

  4. Descent with modification: the unity underlying homology and homoplasy as seen through an analysis of development and evolution.

    Science.gov (United States)

    Hall, Brian K

    2003-08-01

    identified in phylogenetic analyses. But seeing rudiments, reversals, vestiges, atavisms and parallelism as closer to homology than to homoplasy should guide us toward searching for the common elements underlying the formation of the phenotype (what some have called the deep homology of genetic and/or cellular mechanisms), rather than discussing features in terms of shared or independent evolution.

  5. Cloning, complementation, and characterization of an rfaE homolog from Neisseria gonorrhoeae.

    Science.gov (United States)

    Levin, J C; Stein, D C

    1996-08-01

    Neisseria gonorrhoeae WS1 is a spontaneous pyocin (a bacteriocin produced by Pseudomonas aeruginosa)-resistant mutant of N. gonorrhoeae FA19 that produces a truncated lipooligosaccharide (LOS) and is non-transformable. The LOS-specific mutation in WS1 was moved into a transformable background by transforming FA19 with chromosomal DNA from WS1 (generating strain JWS-1). A clone (pJCL2) capable of restoring JWS-1 to wild-type LOS expression, as detected by its acquisition of reactivity with monoclonal antibodies and by its complemented sodium dodecyl sulfate-polyacrylamide gel electrophoresis profile, was isolated. Sequential unidirectional deletion and DNA sequence analysis of pJCL2 identified an open reading frame, designated lsi-7, that could complement the defect in JWS-1. Homology searches against various databases indicated that lsi-7 bad homology with several Escherichia coli genes involved in the phosphorylation of sugars. lsi-7 is adjacent to the lsi-6 gene, another gene involved in LOS biosynthesis. Complementation studies using Salmonella typhimurium lipopolysaccharide mutants showed lsi-6 and lsi-7 to be gonococcal homologs of S. typhimurium rfaD and rfaE, respectively. Reverse transcriptase PCR analysis demonstrated that lsi-6 and lsi-7 are part of the same transcriptional unit.

  6. Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.

    Science.gov (United States)

    Asplund-Samuelsson, Johannes; Bergman, Birgitta; Larsson, John

    2012-01-01

    Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18%) were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota). Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  7. Internet Search Engines

    OpenAIRE

    Fatmaa El Zahraa Mohamed Abdou

    2004-01-01

    A general study about the internet search engines, the study deals main 7 points; the differance between search engines and search directories, components of search engines, the percentage of sites covered by search engines, cataloging of sites, the needed time for sites appearance in search engines, search capabilities, and types of search engines.

  8. Genetic probing of homologous recombination and non-homologous end joining during meiotic prophase in irradiated mouse spermatocytes.

    NARCIS (Netherlands)

    Ahmed, E.A.; Philippens, M.E.P.; Kal, H.B.; Rooij, D.G. de; Boer, P. de

    2010-01-01

    This study was designed to obtain a better insight into the relative contribution of homologous recombination (HR) and non-homologous end joining (NHEJ) to the repair of radiation-induced DNA double-strand breaks (DSBs) at first meiotic prophase. Early and late pachytene and early diplotene

  9. Efficient k-NN search on vertically decomposed data

    NARCIS (Netherlands)

    A.P. de Vries (Arjen); N. Mamoulis; N.J. Nes (Niels); M.L. Kersten (Martin)

    2002-01-01

    textabstractApplications like multimedia retrieval require efficient support for similarity search on large data collections. Yet, nearest neighbor search is a difficult problem in high dimensional spaces, rendering efficient applications hard to realize: index structures degrade rapidly with

  10. Rapid Prototyping

    Science.gov (United States)

    1999-01-01

    Javelin, a Lone Peak Engineering Inc. Company has introduced the SteamRoller(TM) System as a commercial product. The system was designed by Javelin during a Phase II NASA funded small commercial product. The purpose of the invention was to allow automated-feed of flexible ceramic tapes to the Laminated Object Manufacturing rapid prototyping equipment. The ceramic material that Javelin was working with during the Phase II project is silicon nitride. This engineered ceramic material is of interest for space-based component.

  11. A Bacterial Homolog of a Eukaryotic Inositol Phosphate Signaling Enzyme Mediates Cross-kingdom Dialog in the Mammalian Gut

    OpenAIRE

    Stentz, Régis; Osborne, Samantha; Horn, Nikki; Li, Arthur W.H.; Hautefort, Isabelle; Bongaerts, Roy; Rouyer, Marine; Bailey, Paul; Shears, Stephen B.; Hemmings, Andrew M.; Brearley, Charles A.; Carding, Simon R.

    2014-01-01

    Summary Dietary InsP6 can modulate eukaryotic cell proliferation and has complex nutritive consequences, but its metabolism in the mammalian gastrointestinal tract is poorly understood. Therefore, we performed phylogenetic analyses of the gastrointestinal microbiome in order to search for candidate InsP6 phosphatases. We determined that prominent gut bacteria express homologs of the mammalian InsP6 phosphatase (MINPP) and characterized the enzyme from Bacteroides thetaiotaomicron (BtMinpp). W...

  12. Click Models for Web Search

    NARCIS (Netherlands)

    Chuklin, A.; Markov, I.; de Rijke, M.

    2015-01-01

    With the rapid growth of web search in recent years the problem of modeling its users has started to attract more and more attention of the information retrieval community. This has several motivations. By building a model of user behavior we are essentially developing a better understanding of a

  13. Discovery of Entamoeba histolytica hexokinase 1 inhibitors through homology modeling and virtual screening.

    Science.gov (United States)

    Saucedo-Mendiola, María Leticia; Salas-Pacheco, José Manuel; Nájera, Hugo; Rojo-Domínguez, Arturo; Yépez-Mulia, Lilián; Avitia-Domínguez, Claudia; Téllez-Valencia, Alfredo

    2014-06-01

    Entamoeba histolytica, the parasite which causes amebiasis is responsible for 110,000 deaths a year. Entamoeba histolytica depends on glycolysis to obtain ATP for cellular work. According to metabolic flux studies, hexokinase exerts the highest flux control of this metabolic pathway; therefore, it is an excellent target in the search of new antiamebic drugs. To this end, a tridimensional model of E. histolytica hexokinase 1 (EhHK1) was constructed and validated by homology modeling. After virtual screening of 14,400 small molecules, the 100 with the best docking scores were selected, purchased and assessed in their inhibitory capacity. The results showed that three molecules (compounds 2921, 11275 and 2755) inhibited EhHK1 with an I50 of 48, 91 and 96 µM, respectively. Thus, we found the first inhibitors of EhHK1 that can be used in the search of new chemotherapeutic agents against amebiasis.

  14. Homologous recombination in bovine pestiviruses. Phylogenetic and statistic evidence.

    Science.gov (United States)

    Jones, Leandro Roberto; Weber, E Laura

    2004-12-01

    Bovine pestiviruses (Bovine Viral Diarrea Virus 1 (BVDV 1) and Bovine Viral Diarrea Virus 2 (BVDV 2)) belong to the genus Pestivirus (Flaviviridae), which is composed of positive stranded RNA viruses causing significant economic losses world-wide. We used phylogenetic and bootstrap analyses to systematically scan alignments of previously sequenced genomes in order to explore further the evolutionary mechanisms responsible for variation in the virus. Previously published data suggested that homologous crossover might be one of the mechanisms responsible for the genomic rearrangements observed in cytopathic (cp) strains of bovine pestiviruses. Nevertheless, homologous recombination involves not just homologous crossovers, but also replacement of a homologous region of the acceptor RNA. Furthermore, cytopathic strains represent dead paths in evolution, since they are isolated exclusively from the fatal cases of mucosal disease. Herein, we report evidence of homologous inter-genotype recombination in the genome of a non-cytopathic (ncp) strain of Bovine Viral Diarrea Virus 1, the type species of the genus Pestivirus. We also show that intra-genotype homologous recombination might be a common phenomenon in both species of Pestivirus. This evidence demonstrates that homologous recombination contribute to the diversification of bovine pestiviruses in nature. Implications for virus evolution, taxonomy and phylogenetics are discussed.

  15. The history of the homology concept and the "Phylogenetisches Symposium".

    Science.gov (United States)

    Hossfeld, Uwe; Olsson, Lennart

    2005-11-01

    The homology concept has had a long and varied history, starting out as a geometrical term in ancient Greece. Here we describe briefly how a typological use of homology to designate organs and body parts in the same position anatomically in different organisms was changed by Darwin's theory of evolution into a phylogenetic concept. We try to indicate the diversity of opinions on how to define and test for homology that has prevailed historically, before the important books by Hennig (1950. Grundzüge einer Theorie der Phylogenetischen Systematik. Deutscher Zentralverlag, Berlin) and Remane (1952. Die Grundlagen des Natürlichen Systems, der Vergleichenden Anatomie und der Phylogenetik. Geest & Portig, Leipzig) brought more rigor into both the debate on homology and into the usage of the term homology among systematists. Homology as a theme has recurred repeatedly throughout the history of the "Phylogenetisches Symposium" and we give a very brief overview of the different aspects of homology that have been discussed at specific symposia over the last 48 years. We also honour the fact that the 2004 symposium was held in Jena by pointing to the roles played by biologists active in Jena, such as Ernst Haeckel and Carl Gegenbaur, in starting the development towards a homology concept concordant with an evolutionary world view. As historians of biology, we emphasize the importance of major treatises on homology and its history that may be little read by systematists active today, and have sometimes also received less attention by historians of biology than they deserve. Prominent among these are the works of Dietrich Starck, who also happened to be both a student, and later a benefactor, of systematics at Jena University.

  16. Importing the homology concept from biology into developmental psychology.

    Science.gov (United States)

    Moore, David S

    2013-01-01

    To help introduce the idea of homology into developmental psychology, this article presents some of the concepts, distinctions, and guidelines biologists and philosophers of biology have devised to study homology. Some unresolved issues related to this idea are considered as well. Because homology reflects continuity across time, developmental scientists should find this concept to be useful in the study of psychological/behavioral development, just as biologists have found it essential in the study of the evolution and development of morphological and other characteristics. Copyright © 2012 Wiley Periodicals, Inc.

  17. Sequence of active site peptides from the penicillin-sensitive D-alanine carboxypeptidase of Bacillus subtilis. Mechanism of penicillin action and sequence homology to beta-lactamases.

    Science.gov (United States)

    Waxman, D J; Strominger, J L

    1980-05-10

    It has been proposed that penicillin and other beta-lactam antibiotics are substrate analogs which inactivate certain essential enzymes of bacterial cell wall biosynthesis by acylating a catalytic site amino acid residue (Tipper, D.J., and Strominger, J.L. (1965) Proc. Natl. Acad. Sci. U.S.A. 54, 1133-1141). A key prediction of this hypothesis, that the penicilloyl moiety and an acyl moiety derived from substrate both bind to the same active site residue, has been examined. D-Alanine carboxypeptidase, a penicillin-sensitive membrane enzyme, was purified from Bacillus subtilis and labeled covalently at the antibiotic binding site with [14C]penicillin G or with the cephalosporin [14C]cefoxitin. Alternatively, an acyl moiety derived from the depsipeptide substrate [14C]diacetyl L-Lys-D-Ala-D-lactate was trapped at the catalytic site in near-stoichiometric amounts by rapid denaturation of an acyl-enzyme intermediate. Radiolabeled peptides were purified from a pepsin digest of each of the 14C-labeled D-alanine carboxypeptidases and their amino acid sequences determined. Antibiotic- and substrate-labeled peptic peptides had the same sequence: Tyr-Ser-Lys-Asn-Ala-Asp-Lys-Arg-Leu-Pro-Ile-Ala-Ser-Met. Acyl moieties derived from antibiotic and from substrate were shown to be bound covalently in ester linkage to the identical amino acid residue, a serine at the penultimate position of the peptic peptide. These studies establish that beta-lactam antibiotics are indeed active site-directed acylating agents. Additional amino acid sequence data were obtained by isolating and sequencing [14C]penicilloyl peptides after digestion of [14C]penicilloyl D-alanine carboxypeptidase with either trypsin or cyanogen bromide and by NH2-terminal sequencing of the uncleaved protein. The sequence of the NH2-terminal 64 amino acids was thus determined and the active site serine then identified as residue 36. A computer search for homologous proteins indicated significant sequence homology between

  18. Aspergillus flavus whole genome and EST sequence releases and construction of homologous gene search blast server

    Science.gov (United States)

    Aflatoxins are toxic and carcinogenic secondary metabolites. These compounds, produced by Aspergillus flavus and A. parasiticus, contaminate pre-harvest agricultural crops in the field and post-harvest grains during storage. In order to reduce and eliminate aflatoxin contamination of food and feed...

  19. Comparative genomic survey, exon-intron annotation and phylogenetic analysis of NAT-homologous sequences in archaea, protists, fungi, viruses, and invertebrates

    Science.gov (United States)

    We have previously published extensive genomic surveys [1-3], reporting NAT-homologous sequences in hundreds of sequenced bacterial, fungal and vertebrate genomes. We present here the results of our latest search of 2445 genomes, representing 1532 (70 archaeal, 1210 bacterial, 43 protist, 97 fungal,...

  20. RecA: Regulation and Mechanism of a Molecular Search Engine.

    Science.gov (United States)

    Bell, Jason C; Kowalczykowski, Stephen C

    2016-06-01

    Homologous recombination maintains genomic integrity by repairing broken chromosomes. The broken chromosome is partially resected to produce single-stranded DNA (ssDNA) that is used to search for homologous double-stranded DNA (dsDNA). This homology driven 'search and rescue' is catalyzed by a class of DNA strand exchange proteins that are defined in relation to Escherichia coli RecA, which forms a filament on ssDNA. Here, we review the regulation of RecA filament assembly and the mechanism by which RecA quickly and efficiently searches for and identifies a unique homologous sequence among a vast excess of heterologous DNA. Given that RecA is the prototypic DNA strand exchange protein, its behavior affords insight into the actions of eukaryotic RAD51 orthologs and their regulators, BRCA2 and other tumor suppressors. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. A CRISPR-Cas9 Assisted Non-Homologous End-Joining Strategy for One-step Engineering of Bacterial Genome

    Science.gov (United States)

    Su, Tianyuan; Liu, Fapeng; Gu, Pengfei; Jin, Haiying; Chang, Yizhao; Wang, Qian; Liang, Quanfeng; Qi, Qingsheng

    2016-01-01

    Homologous recombination-mediated genome engineering has been broadly applied in prokaryotes with high efficiency and accuracy. However, this method is limited in realizing larger-scale genome editing with numerous genes or large DNA fragments because of the relatively complicated procedure for DNA editing template construction. Here, we describe a CRISPR-Cas9 assisted non-homologous end-joining (CA-NHEJ) strategy for the rapid and efficient inactivation of bacterial gene (s) in a homologous recombination-independent manner and without the use of selective marker. Our study show that CA-NHEJ can be used to delete large chromosomal DNA fragments in a single step that does not require homologous DNA template. It is thus a novel and powerful tool for bacterial genomes reducing and possesses the potential for accelerating the genome evolution. PMID:27883076

  2. ATR inhibition preferentially targets homologous recombination-deficient tumor cells

    NARCIS (Netherlands)

    Krajewska, M.; Fehrmann, R. S. N.; Schoonen, P. M.; Labib, S.; de Vries, E. G. E.; Franke, L.; van Vugt, M. A. T. M.

    Homologous recombination (HR) is required for faithful repair of double-strand DNA breaks. Defects in HR repair cause severe genomic instability and challenge cellular viability. Paradoxically, various cancers are HR defective and have apparently acquired characteristics to survive genomic

  3. Substrate and Cation Binding Mechanism of Glutamate Transporter Homologs

    NARCIS (Netherlands)

    Jensen, Sonja

    2017-01-01

    Glutamate transporters and their homologs are membrane proteins that transport glutamate and aspartate together with sodium ions and/or protons. Human glutamate transporters remove the neurotransmitter glutamate after signal transmission. Therefore, glutamate transporters play a great role in

  4. Homology of normal chains and cohomology of charges

    CERN Document Server

    Pauw, Th De; Pfeffer, W F

    2017-01-01

    The authors consider a category of pairs of compact metric spaces and Lipschitz maps where the pairs satisfy a linearly isoperimetric condition related to the solvability of the Plateau problem with partially free boundary. It includes properly all pairs of compact Lipschitz neighborhood retracts of a large class of Banach spaces. On this category the authors define homology and cohomology functors with real coefficients which satisfy the Eilenberg-Steenrod axioms, but reflect the metric properties of the underlying spaces. As an example they show that the zero-dimensional homology of a space in our category is trivial if and only if the space is path connected by arcs of finite length. The homology and cohomology of a pair are, respectively, locally convex and Banach spaces that are in duality. Ignoring the topological structures, the homology and cohomology extend to all pairs of compact metric spaces. For locally acyclic spaces, the authors establish a natural isomorphism between their cohomology and the �...

  5. Targeted recombination between homologous chromosomes for precise breeding in tomato

    OpenAIRE

    Filler Hayut, Shdema; Melamed Bessudo, Cathy; Levy, Avraham A

    2017-01-01

    Homologous recombination (HR) between parental chromosomes occurs stochastically. Here, we report on targeted recombination between homologous chromosomes upon somatic induction of DNA double-strand breaks (DSBs) via CRISPR-Cas9. We demonstrate this via a visual and molecular assay whereby DSB induction between two alleles carrying different mutations in the PHYTOENE SYNTHASE (PSY1) gene results in yellow fruits with wild type red sectors forming via HR-mediated DSB repair. We also show that ...

  6. The structure of information: from probability to homology

    OpenAIRE

    Vigneaux, Juan Pablo

    2017-01-01

    D. Bennequin and P. Baudot introduced a cohomological construction adapted to information theory, called "information cohomology" (see "The homological nature of Entropy", 2015). Our text serves as a detailed introduction to information cohomology, containing the necessary background in probability theory and homological algebra. It makes explicit the link with topos theory, as introduced by Grothendieck, Verdier and their collaborators in the SGA IV. It also contains several new construction...

  7. Urate-responsive MarR homologs from Burkholderia.

    Science.gov (United States)

    Grove, Anne

    2010-11-01

    The genus Burkholderia includes a large number of species, some of which are serious human pathogens. A genomic locus is conserved that consists of a gene encoding a member of the multiple antibiotic resistance regulator (MarR) family of transcriptional regulators and a divergently oriented gene encoding a major facilitator transport protein (MFTP), a predicted membrane efflux pump. Homology modeling shows that the MarR homolog conserves the location of four conserved amino acid residues previously shown to bind the ligand urate in the Deinococcus radiodurans-encoded MarR homolog HucR. Analysis of the B. thailandensis-encoded homolog shows that its specific DNA binding to two adjacent sites in the intergenic region between the genes encoding the transcription factor and the MFTP is attenuated by urate and to a lesser extent by xanthine and hypoxanthine, but not by adenine or the product of urate degradation, allantoin. These data suggest the existence of a four amino acid urate-binding signature in a subset of MarR homologs, and that homologs bearing this signature will respond to the ligand urate by attenuated DNA binding. The location of binding sites predicts regulation of the MFTP and prompts a proposal to name the cognate transcription factor MftR (major facilitator transport regulator).

  8. Molecular cloning and characterization of Saccharomyces cerevisiae RAD28, the yeast homolog of the human Cockayne syndrome A (CSA) gene.

    OpenAIRE

    P.K Bhatia; Verhage, R.A.; Brouwer, J; Friedberg, E C

    1996-01-01

    Cockayne syndrome patients exhibit severe developmental and neurological abnormalities. Cells derived from these patients are sensitive to killing by UV radiation and do not support the rapid repair of the transcribed strand of transcriptionally active genes observed in cells from normal individuals. We report the cloning of the Saccharomyces cerevisiae homolog of the Cockayne syndrome A (CSA) gene, which we designate as RAD28. A rad28 null mutant does not manifest increased sensitivity to ki...

  9. Studies of flerovium and element 115 homologs with macrocyclic extractants

    Science.gov (United States)

    Despotopulos, John Dustin

    Study of the chemistry of the heaviest elements, Z ? 104, poses a unique challenge due to their low production cross-sections and short half-lives. Chemistry also must be studied on the one-atom-at-a-time scale, requiring automated, fast, and very efficient chemical schemes. Recent studies of the chemical behavior of copernicium (Cn, element 112) and flerovium (Fl, element 114) together with the discovery of isotopes of these elements with half-lives suitable for chemical studies have spurred a renewed interest in the development of rapid systems designed to study the chemical properties of elements with Z ≥ 114. This dissertation explores both extraction chromatography and solvent extraction as methods for development of a rapid chemical separation scheme for the homologs of flerovium (Pb, Sn, Hg) and element 115 (Bi, Sb), with the goal of developing a chemical scheme that, in the future, can be applied to on-line chemistry of both Fl and element 115. Macrocyclic extractants, specifically crown ethers and their derivatives, were chosen for these studies. Carrier-free radionuclides, used in these studies, of the homologs of Fl and element 115 were obtained by proton activation of high purity metal foils at the Lawrence Livermore National Laboratory (LLNL) Center for Accelerator Mass Spectrometry (CAMS): natIn(p,n)113Sn, natSn(p,n)124Sb, and Au(p,n)197m,gHg. The carrier-free activity was separated from the foils by novel separation schemes based on ion exchange and extraction chromatography techniques. Carrier-free Pb and Bi isotopes were obtained from development of a novel generator based on cation exchange chromatography using the 232U parent to generate 212Pb and 212Bi. Crown ethers show high selectivity for metal ions based on their size compared to the negatively charged cavity of the ether. Extraction by crown ethers occur based on electrostatic ion-dipole interactions between the negatively charged ring atoms (oxygen, sulfur, etc.) and the positively

  10. Meta Search Engines.

    Science.gov (United States)

    Garman, Nancy

    1999-01-01

    Describes common options and features to consider in evaluating which meta search engine will best meet a searcher's needs. Discusses number and names of engines searched; other sources and specialty engines; search queries; other search options; and results options. (AEF)

  11. The Cost of Cache-Oblivious Searching

    DEFF Research Database (Denmark)

    Bender, Michael A.; Brodal, Gerth Stølting; Fagerberg, Rolf

    2011-01-01

    This paper gives tight bounds on the cost of cache-oblivious searching. The paper shows that no cache-oblivious search structure can guarantee a search performance of fewer than lg elog  B N memory transfers between any two levels of the memory hierarchy. This lower bound holds even if all...... increases. The expectation is taken over the random placement in memory of the first element of the structure. Because searching in the disk-access machine (DAM) model can be performed in log  B N+O(1) block transfers, this result establishes a separation between the (2-level) DAM model and cache......-oblivious model. The DAM model naturally extends to k levels. The paper also shows that as k grows, the search costs of the optimal k-level DAM search structure and the optimal cache-oblivious search structure rapidly converge. This result demonstrates that for a multilevel memory hierarchy, a simple cache...

  12. Automatic and rapid whole-body 3D shape measurement based on multinode 3D sensing and speckle projection.

    Science.gov (United States)

    Guo, Jiping; Peng, Xiang; Li, Ameng; Liu, Xiaoli; Yu, Jiping

    2017-11-01

    Automatic and rapid whole-body 3D shape measurement has attracted extensive attention in recent years and been widely used in many fields. Rapid 3D reconstruction, automatic 3D registration, and dedicated system layout are critical factors to enable an excellent 3D measurement system. In this paper, we present an automatic and rapid whole- body 3D measurement system that is based on multinode 3D sensors using speckle projection. A rapid algorithm for searching homologous point pairs is suggested, which takes advantage of the optimized projective rectification and simplified subpixel matching techniques, leading to an improved time efficiency of 3D reconstruction. Meanwhile, a low-cost automatic system with a flexible setup and an improved calibration strategy are proposed, where system parameters of each node sensor can be simultaneously estimated with the assistance of a cubic and a planar target. Furthermore, an automatic range data registration strategy by employing two aided cameras is investigated. Experiment results show that the presented approach can realize automatic whole-body 3D shape measurement with high efficiency and accuracy.

  13. Multiscale analysis of nonlinear systems using computational homology

    Energy Technology Data Exchange (ETDEWEB)

    Konstantin Mischaikow, Rutgers University/Georgia Institute of Technology, Michael Schatz, Georgia Institute of Technology, William Kalies, Florida Atlantic University, Thomas Wanner,George Mason University

    2010-05-19

    This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

  14. Multiscale analysis of nonlinear systems using computational homology

    Energy Technology Data Exchange (ETDEWEB)

    Konstantin Mischaikow; Michael Schatz; William Kalies; Thomas Wanner

    2010-05-24

    This is a collaborative project between the principal investigators. However, as is to be expected, different PIs have greater focus on different aspects of the project. This report lists these major directions of research which were pursued during the funding period: (1) Computational Homology in Fluids - For the computational homology effort in thermal convection, the focus of the work during the first two years of the funding period included: (1) A clear demonstration that homology can sensitively detect the presence or absence of an important flow symmetry, (2) An investigation of homology as a probe for flow dynamics, and (3) The construction of a new convection apparatus for probing the effects of large-aspect-ratio. (2) Computational Homology in Cardiac Dynamics - We have initiated an effort to test the use of homology in characterizing data from both laboratory experiments and numerical simulations of arrhythmia in the heart. Recently, the use of high speed, high sensitivity digital imaging in conjunction with voltage sensitive fluorescent dyes has enabled researchers to visualize electrical activity on the surface of cardiac tissue, both in vitro and in vivo. (3) Magnetohydrodynamics - A new research direction is to use computational homology to analyze results of large scale simulations of 2D turbulence in the presence of magnetic fields. Such simulations are relevant to the dynamics of black hole accretion disks. The complex flow patterns from simulations exhibit strong qualitative changes as a function of magnetic field strength. Efforts to characterize the pattern changes using Fourier methods and wavelet analysis have been unsuccessful. (4) Granular Flow - two experts in the area of granular media are studying 2D model experiments of earthquake dynamics where the stress fields can be measured; these stress fields from complex patterns of 'force chains' that may be amenable to analysis using computational homology. (5) Microstructure

  15. Heterozygous genome assembly via binary classification of homologous sequence.

    Science.gov (United States)

    Bodily, Paul M; Fujimoto, M; Ortega, Cameron; Okuda, Nozomu; Price, Jared C; Clement, Mark J; Snell, Quinn

    2015-01-01

    Genome assemblers to date have predominantly targeted haploid reference reconstruction from homozygous data. When applied to diploid genome assembly, these assemblers perform poorly, owing to the violation of assumptions during both the contigging and scaffolding phases. Effective tools to overcome these problems are in growing demand. Increasing parameter stringency during contigging is an effective solution to obtaining haplotype-specific contigs; however, effective algorithms for scaffolding such contigs are lacking. We present a stand-alone scaffolding algorithm, ScaffoldScaffolder, designed specifically for scaffolding diploid genomes. The algorithm identifies homologous sequences as found in "bubble" structures in scaffold graphs. Machine learning classification is used to then classify sequences in partial bubbles as homologous or non-homologous sequences prior to reconstructing haplotype-specific scaffolds. We define four new metrics for assessing diploid scaffolding accuracy: contig sequencing depth, contig homogeneity, phase group homogeneity, and heterogeneity between phase groups. We demonstrate the viability of using bubbles to identify heterozygous homologous contigs, which we term homolotigs. We show that machine learning classification trained on these homolotig pairs can be used effectively for identifying homologous sequences elsewhere in the data with high precision (assuming error-free reads). More work is required to comparatively analyze this approach on real data with various parameters and classifiers against other diploid genome assembly methods. However, the initial results of ScaffoldScaffolder supply validity to the idea of employing machine learning in the difficult task of diploid genome assembly. Software is available at http://bioresearch.byu.edu/scaffoldscaffolder.

  16. The OGCleaner: filtering false-positive homology clusters.

    Science.gov (United States)

    Fujimoto, M Stanley; Suvorov, Anton; Jensen, Nicholas O; Clement, Mark J; Snell, Quinn; Bybee, Seth M

    2017-01-01

    Detecting homologous sequences in organisms is an essential step in protein structure and function prediction, gene annotation and phylogenetic tree construction. Heuristic methods are often employed for quality control of putative homology clusters. These heuristics, however, usually only apply to pairwise sequence comparison and do not examine clusters as a whole. We present the Orthology Group Cleaner (the OGCleaner), a tool designed for filtering putative orthology groups as homology or non-homology clusters by considering all sequences in a cluster. The OGCleaner relies on high-quality orthologous groups identified in OrthoDB to train machine learning algorithms that are able to distinguish between true-positive and false-positive homology groups. This package aims to improve the quality of phylogenetic tree construction especially in instances of lower-quality transcriptome assemblies. https://github.com/byucsl/ogcleaner CONTACT: sfujimoto@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  17. Primary homologies of the circumorbital bones of snakes.

    Science.gov (United States)

    Palci, Alessandro; Caldwell, Michael W

    2013-09-01

    Some snakes have two circumorbital ossifications that in the current literature are usually referred to as the postorbital and supraorbital. We review the arguments that have been proposed to justify this interpretation and provide counter-arguments that reject those conjectures of primary homology based on the observation of 32 species of lizards and 81 species of snakes (both extant and fossil). We present similarity arguments, both topological and structural, for reinterpretation of the primary homologies of the dorsal and posterior orbital ossifications of snakes. Applying the test of similarity, we conclude that the posterior orbital ossification of snakes is topologically consistent as the homolog of the lacertilian jugal, and that the dorsal orbital ossification present in some snakes (e.g., pythons, Loxocemus, and Calabaria) is the homolog of the lacertilian postfrontal. We therefore propose that the terms postorbital and supraorbital should be abandoned as reference language for the circumorbital bones of snakes, and be replaced with the terms jugal and postfrontal, respectively. The primary homology claim for the snake "postorbital" fails the test of similarity, while the term "supraorbital" is an unnecessary and inaccurate application of the concept of a neomorphic ossification, for an element that passes the test of similarity as a postfrontal. This reinterpretation of the circumorbital bones of snakes is bound to have important repercussions for future phylogenetic analyses and consequently for our understanding of the origin and evolution of snakes. Copyright © 2013 Wiley Periodicals, Inc.

  18. Is searching full text more effective than searching abstracts?

    Directory of Open Access Journals (Sweden)

    Lin Jimmy

    2009-02-01

    Full Text Available Abstract Background With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata to directly access full-text content. Motivated by this emerging trend, I posed the following question: is searching full text more effective than searching abstracts? This question is answered by comparing text retrieval algorithms on MEDLINE® abstracts, full-text articles, and spans (paragraphs within full-text articles using data from the TREC 2007 genomics track evaluation. Two retrieval models are examined: bm25 and the ranking algorithm implemented in the open-source Lucene search engine. Results Experiments show that treating an entire article as an indexing unit does not consistently yield higher effectiveness compared to abstract-only search. However, retrieval based on spans, or paragraphs-sized segments of full-text articles, consistently outperforms abstract-only search. Results suggest that highest overall effectiveness may be achieved by combining evidence from spans and full articles. Conclusion Users searching full text are more likely to find relevant articles than searching only abstracts. This finding affirms the value of full text collections for text retrieval and provides a starting point for future work in exploring algorithms that take advantage of rapidly-growing digital archives. Experimental results also highlight the need to develop distributed text retrieval algorithms, since full-text articles are significantly longer than abstracts and may require the computational resources of multiple machines in a cluster. The MapReduce programming model provides a convenient framework for organizing such computations.

  19. Quantization of gauge fields, graph polynomials and graph homology

    Energy Technology Data Exchange (ETDEWEB)

    Kreimer, Dirk, E-mail: kreimer@physik.hu-berlin.de [Humboldt University, 10099 Berlin (Germany); Sars, Matthias [Humboldt University, 10099 Berlin (Germany); Suijlekom, Walter D. van [Radboud University Nijmegen, 6525 AJ Nijmegen (Netherlands)

    2013-09-15

    We review quantization of gauge fields using algebraic properties of 3-regular graphs. We derive the Feynman integrand at n loops for a non-abelian gauge theory quantized in a covariant gauge from scalar integrands for connected 3-regular graphs, obtained from the two Symanzik polynomials. The transition to the full gauge theory amplitude is obtained by the use of a third, new, graph polynomial, the corolla polynomial. This implies effectively a covariant quantization without ghosts, where all the relevant signs of the ghost sector are incorporated in a double complex furnished by the corolla polynomial–we call it cycle homology–and by graph homology. -- Highlights: •We derive gauge theory Feynman from scalar field theory with 3-valent vertices. •We clarify the role of graph homology and cycle homology. •We use parametric renormalization and the new corolla polynomial.

  20. Protein Remote Homology Detection Based on an Ensemble Learning Approach.

    Science.gov (United States)

    Chen, Junjie; Liu, Bingquan; Huang, Dong

    2016-01-01

    Protein remote homology detection is one of the central problems in bioinformatics. Although some computational methods have been proposed, the problem is still far from being solved. In this paper, an ensemble classifier for protein remote homology detection, called SVM-Ensemble, was proposed with a weighted voting strategy. SVM-Ensemble combined three basic classifiers based on different feature spaces, including Kmer, ACC, and SC-PseAAC. These features consider the characteristics of proteins from various perspectives, incorporating both the sequence composition and the sequence-order information along the protein sequences. Experimental results on a widely used benchmark dataset showed that the proposed SVM-Ensemble can obviously improve the predictive performance for the protein remote homology detection. Moreover, it achieved the best performance and outperformed other state-of-the-art methods.

  1. Homology modeling and validation of SAS2271 transcriptional regulator of AraC family in Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Money Gupta

    2013-02-01

    Full Text Available Objective: To predict three dimensional structure of AraC Family transcription regulator protein in staphylococcus aureus involved in causing virulence. Methods: Evolutionary dynamics of S. aureus reveled that several mutations preceding virulence lead to truncated proteins that plays an important role in virulence. The Structural templates are identified using homology search and then homology modelling is used to get the 3-D structure of the protein. Results: The 3-D structure of SAS2271 transcriptional factor of AraC family in MSSA476 strain of S. aureus was modelled and validated using the Ramachandran plot. Conclusions: The knowledge of 3-D structure of the protein will be helpful in identifying its biochemical function along with its regulatory mechanism in causing virulence.

  2. Flippers in Housing Market Search

    OpenAIRE

    Charles Ka Yui Leung; Chung-Yi Tse

    2012-01-01

    We add flippers-specialist investors who attempt to profit from buying low and selling high to a canonical housing market search model. These agents facilitate the turnover of mismatched houses on behalf of end-users and they may survive even if they face an arbitrarily large cost of financing vis-a-vis ordinary households. Multiple equilibrium may exist. In one equilibrium, most, if not all, transactions are intermediated by flippers, resulting in rapid turnover, a high vacancy rate, and hig...

  3. Distribution and evolution of het gene homologs in the basidiomycota.

    Science.gov (United States)

    Van der Nest, M A; Olson, A; Lind, M; Vélëz, H; Dalman, K; Brandström Durling, M; Karlsson, M; Stenlid, J

    2014-03-01

    In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Khovanov-Rozansky Graph Homology and Composition Product

    DEFF Research Database (Denmark)

    Wagner, Emmanuel

    2008-01-01

    In analogy with a recursive formula for the HOMFLY-PT polynomial of links given by Jaeger, we give a recursive formula for the graph polynomial introduced by Kauffman and Vogel. We show how this formula extends to the Khovanov–Rozansky graph homology.......In analogy with a recursive formula for the HOMFLY-PT polynomial of links given by Jaeger, we give a recursive formula for the graph polynomial introduced by Kauffman and Vogel. We show how this formula extends to the Khovanov–Rozansky graph homology....

  5. Ecdysone receptor homologs from mollusks, leeches and a polychaete worm.

    Science.gov (United States)

    Laguerre, Michel; Veenstra, Jan A

    2010-11-05

    The genomes of the mollusk Lottia gigantea, the leech Helobdella robusta and the polychaete worm Capitella teleta each have a gene encoding an ecdysone receptor homolog. Publicly available genomic and EST sequences also contain evidence for ecdysone receptors in the seahare Aplysia californica, the bobtail squid Euprymna scolopes and the medicinal leech Hirudo medicinalis. Three-dimensional models of the ligand binding domains of these predicted ecdysone receptor homologs suggest that each of them could potentially bind an ecdysone-related steroid. Thus, ecdysone receptors are not limited to arthropods and nematodes. Copyright © 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  6. Tumor malignancy is engaged to prokaryotic homolog toolbox.

    Science.gov (United States)

    Fernandes, Janaina; Guedes, Patrícia G; Lage, Celso Luiz S; Rodrigues, Juliany Cola F; Lage, Claudia de Alencar S

    2012-04-01

    Cancer cells display high proliferation rates and survival provided by high glycolysis, chemoresistance and radioresistance, metabolic features that appear to be activated with malignancy, and seemed to have arisen as early in evolution as in unicellular/prokaryotic organisms. Based on these assumptions, we hypothesize that aggressive phenotypes found in malignant cells may be related to acquired unicellular behavior, launched within a tumor when viral and prokaryotic homologs are overexpressed performing likely robust functions. The ensemble of these expressed viral and prokaryotic close homologs in the proteome of a tumor tissue gives them advantage over normal cells. To assess the hypothesis validity, sequences of human proteins involved in apoptosis, energetic metabolism, cell mobility and adhesion, chemo- and radio-resistance were aligned to homologs present in other life forms, excluding all eukaryotes, using PSI-BLAST, with further corroboration from data available in the literature. The analysis revealed that selected sequences of proteins involved in apoptosis and tumor suppression (as p53 and pRB) scored non-significant (E-value>0.001) with prokaryotic homologs; on the other hand, human proteins involved in cellular chemo- and radio-resistance scored highly significant with prokaryotic and viral homologs (as catalase, E-value=zero). We inferred that such upregulated and/or functionally activated proteins in aggressive malignant cells represent a toolbox of modern human homologs evolved from a similar key set that have granted survival of ancient prokaryotes against extremely harsh environments. According to what has been discussed along this analysis, high mutation rates usually hit hotspots in important conserved protein domains, allowing uncontrolled expansion of more resistant, death-evading malignant clones. That is the case of point mutations in key viral proteins affording viruses escape to chemotherapy, and human homologs of such retroviral

  7. Refining search terms for nanotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Porter, Alan L. [Georgia Institute of Technology (United States); Youtie, Jan [Georgia Institute of Technology, Enterprise Innovation Institute (United States)], E-mail: jan.youtie@innovate.gatech.edu; Shapira, Philip [Georgia Institute of Technology (United States); Schoeneck, David J. [Search Technology, Inc. (United States)

    2008-05-15

    The ability to delineate the boundaries of an emerging technology is central to obtaining an understanding of the technology's research paths and commercialization prospects. Nowhere is this more relevant than in the case of nanotechnology (hereafter identified as 'nano') given its current rapid growth and multidisciplinary nature. (Under the rubric of nanotechnology, we also include nanoscience and nanoengineering.) Past efforts have utilized several strategies, including simple term search for the prefix nano, complex lexical and citation-based approaches, and bootstrapping techniques. This research introduces a modularized Boolean approach to defining nanotechnology which has been applied to several research and patenting databases. We explain our approach to downloading and cleaning data, and report initial results. Comparisons of this approach with other nanotechnology search formulations are presented. Implications for search strategy development and profiling of the nanotechnology field are discussed.

  8. Refining search terms for nanotechnology

    Science.gov (United States)

    Porter, Alan L.; Youtie, Jan; Shapira, Philip; Schoeneck, David J.

    2008-05-01

    The ability to delineate the boundaries of an emerging technology is central to obtaining an understanding of the technology's research paths and commercialization prospects. Nowhere is this more relevant than in the case of nanotechnology (hereafter identified as "nano") given its current rapid growth and multidisciplinary nature. (Under the rubric of nanotechnology, we also include nanoscience and nanoengineering.) Past efforts have utilized several strategies, including simple term search for the prefix nano, complex lexical and citation-based approaches, and bootstrapping techniques. This research introduces a modularized Boolean approach to defining nanotechnology which has been applied to several research and patenting databases. We explain our approach to downloading and cleaning data, and report initial results. Comparisons of this approach with other nanotechnology search formulations are presented. Implications for search strategy development and profiling of the nanotechnology field are discussed.

  9. Susceptibility and pathogenesis of little brown bats (Myotis lucifugus) to heterologous and homologous rabies viruses.

    Science.gov (United States)

    Davis, April D; Jarvis, Jodie A; Pouliott, Craig E; Morgan, Shannon M D; Rudd, Robert J

    2013-08-01

    Rabies virus (RABV) maintenance in bats is not well understood. Big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifugus), and Mexican free-tailed bats (Tadarida brasiliensis) are the most common bats species in the United States. These colonial bat species also have the most frequent contact with humans and domestic animals. However, the silver-haired bat (Lasionycteris noctivagans) RABV is associated with the majority of human rabies virus infections in the United States and Canada. This is of interest because silver-haired bats are more solitary bats with infrequent human interaction. Our goal was to determine the likelihood of a colonial bat species becoming infected with and transmitting a heterologous RABV. To ascertain the potential of heterologous RABV infection in colonial bat species, little brown bats were inoculated with a homologous RABV or one of two heterologous RABVs. Additionally, to determine if the route of exposure influenced the disease process, bats were inoculated either intramuscularly (i.m.) or subcutaneously (s.c.) with a homologous or heterologous RABV. Our results demonstrate that intramuscular inoculation results in a more rapid progression of disease onset, whereas the incubation time in bats inoculated s.c. is significantly longer. Additionally, cross protection was not consistently achieved in bats previously inoculated with a heterologous RABV following a challenge with a homologous RABV 6 months later. Finally, bats that developed rabies following s.c. inoculation were significantly more likely to shed virus in their saliva and demonstrated increased viral dissemination. In summary, bats inoculated via the s.c. route are more likely to shed virus, thus increasing the likelihood of transmission.

  10. Susceptibility and Pathogenesis of Little Brown Bats (Myotis lucifugus) to Heterologous and Homologous Rabies Viruses

    Science.gov (United States)

    Jarvis, Jodie A.; Pouliott, Craig E.; Morgan, Shannon, M. D.; Rudd, Robert J.

    2013-01-01

    Rabies virus (RABV) maintenance in bats is not well understood. Big brown bats (Eptesicus fuscus), little brown bats (Myotis lucifugus), and Mexican free-tailed bats (Tadarida brasiliensis) are the most common bats species in the United States. These colonial bat species also have the most frequent contact with humans and domestic animals. However, the silver-haired bat (Lasionycteris noctivagans) RABV is associated with the majority of human rabies virus infections in the United States and Canada. This is of interest because silver-haired bats are more solitary bats with infrequent human interaction. Our goal was to determine the likelihood of a colonial bat species becoming infected with and transmitting a heterologous RABV. To ascertain the potential of heterologous RABV infection in colonial bat species, little brown bats were inoculated with a homologous RABV or one of two heterologous RABVs. Additionally, to determine if the route of exposure influenced the disease process, bats were inoculated either intramuscularly (i.m.) or subcutaneously (s.c.) with a homologous or heterologous RABV. Our results demonstrate that intramuscular inoculation results in a more rapid progression of disease onset, whereas the incubation time in bats inoculated s.c. is significantly longer. Additionally, cross protection was not consistently achieved in bats previously inoculated with a heterologous RABV following a challenge with a homologous RABV 6 months later. Finally, bats that developed rabies following s.c. inoculation were significantly more likely to shed virus in their saliva and demonstrated increased viral dissemination. In summary, bats inoculated via the s.c. route are more likely to shed virus, thus increasing the likelihood of transmission. PMID:23741002

  11. GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models

    Directory of Open Access Journals (Sweden)

    Kreuchwig Annika

    2011-05-01

    Full Text Available Abstract Background G protein-coupled receptors (GPCRs transduce a wide variety of extracellular signals to within the cell and therefore have a key role in regulating cell activity and physiological function. GPCR malfunction is responsible for a wide range of diseases including cancer, diabetes and hyperthyroidism and a large proportion of drugs on the market target these receptors. The three dimensional structure of GPCRs is important for elucidating the molecular mechanisms underlying these diseases and for performing structure-based drug design. Although structural data are restricted to only a handful of GPCRs, homology models can be used as a proxy for those receptors not having crystal structures. However, many researchers working on GPCRs are not experienced homology modellers and are therefore unable to benefit from the information that can be gleaned from such three-dimensional models. Here, we present a comprehensive database called the GPCR-SSFE, which provides initial homology models of the transmembrane helices for a large variety of family A GPCRs. Description Extending on our previous theoretical work, we have developed an automated pipeline for GPCR homology modelling and applied it to a large set of family A GPCR sequences. Our pipeline is a fragment-based approach that exploits available family A crystal structures. The GPCR-SSFE database stores the template predictions, sequence alignments, identified sequence and structure motifs and homology models for 5025 family A GPCRs. Users are able to browse the GPCR dataset according to their pharmacological classification or search for results using a UniProt entry name. It is also possible for a user to submit a GPCR sequence that is not contained in the database for analysis and homology model building. The models can be viewed using a Jmol applet and are also available for download along with the alignments. Conclusions The data provided by GPCR-SSFE are useful for investigating

  12. DEK is required for homologous recombination repair of DNA breaks

    DEFF Research Database (Denmark)

    Smith, Eric A; Gole, Boris; Willis, Nicholas A

    2017-01-01

    mice. Furthermore, DEK knockout cells were sensitive to apoptosis with NHEJ inhibition. Thus, we hypothesized DEK plays additional roles in homologous recombination (HR). Using episomal and integrated reporters, we demonstrate that HR repair of conventional DSBs is severely compromised in DEK...

  13. Phenylbutyrate inhibits homologous recombination induced by camptothecin and methyl methanesulfonate

    DEFF Research Database (Denmark)

    Kaiser, Gitte Schalck; Germann, Susanne Manuela; Westergaard, Tine

    2011-01-01

    . Treatment with PBA is accompanied by a dramatic reduction in histone H4 lysine 8 acetylation. Live cell imaging of homologous recombination proteins indicates that repair of CPT-induced DNA damage is redirected to a non-recombinogenic pathway in the presence of PBA without loss in cell viability...

  14. Synthesis and characterization of new homologous series of ...

    Indian Academy of Sciences (India)

    Two homologous series of unsymmetrical alkylated chalcones and 3,5-diaryl isoxazoles, consisting of 20 members, with various n-alkyl bromides (n=2−7, 10, 12, 14, 16) have been synthesized and studied for their liquid crystalline property. Simple strategy was employed to achieve the target materials. Flexibilityin the ...

  15. Hypoxia influences expression profile of Pleckstrin homology-like ...

    Indian Academy of Sciences (India)

    The deduced CbPHLDA2 protein of 139 amino acids shared high homology with PHLD2A of other fishes as well as that of vertebrates. Importantly, a single amino acid (asparagine/lysine) insertion was identified in the PH domain of CbPHLDA2 and other fishes, which was absent in other vertebrates studied. Furthermore ...

  16. Homeomorphisms and the homology of non-orientable surfaces

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Indian Acad. Sci. (Math. Sci.) Vol. 115, No. 3, August 2005, pp. 251–257. © Printed in India. Homeomorphisms and the homology of non-orientable surfaces ... that every element of K is induced by a homeomorphism of F. Further, we shall show that ... (up to sign) the elements representing the boundary components.

  17. Split marker transformation increases homologous integration frequency in Cryptococcus neoformans.

    Science.gov (United States)

    Fu, J; Hettler, E; Wickes, B L

    2006-03-01

    Gene disruption in Cryptococcus neoformans can be problematic due to high frequencies of ectopic integration and telomerization. To improve the frequency of homologous integration, a transformation strategy was employed called split marker, which utilizes a mixture of DNAs comprised of overlapping truncations of the selectable marker. Five genes were compared for homologous integration frequencies using various constructs. Homologous integration was highest when the split marker approach was used, with rates as high as 60% depending on target gene. A second factor that contributed to an increased homologous integration frequency was strain background, which was highest when a double auxotroph was used as a host. The split marker strategy was combined with an ura-blaster construct, which has been used in other fungi to recycle ura5 or ura3 mutations. When a hisG-URA5-hisG cassette was successfully integrated at the target locus, the URA5 gene could be easily evicted by plating onto 5-FOA agar. The cassette was then successfully used for a second cycle of transformation-eviction. The effectiveness of the split marker disruption strategy suggests that continued investigation and modification of traditional molecular techniques could increase the efficiency of C. neoformans molecular manipulation.

  18. Multiresolution persistent homology for excessively large biomolecular datasets

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin; Zhao, Zhixiong [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: wei@math.msu.edu [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (United States)

    2015-10-07

    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  19. Homology modelling and bivalent single-chain Fv construction of ...

    Indian Academy of Sciences (India)

    PRAKASH KUMAR

    structure of SLH10 was modelled by the Insight II molecule simulation software. The structure was refined using the molecular ... the Homology module of the Insight II software package. (Biosym/MSI, San Diego, Accelrys ..... Feng J, Xie Z, Guo N and Shen B 2003 Design and assembly of anti-CD16 ScFv antibody with two ...

  20. New mesogenic homologous series of α-methylcinnamates

    Indian Academy of Sciences (India)

    Compounds of a new smectogenic homologous series of -methylcinnamates were prepared by condensing different 4--alkoxybenzoyl chloride with methoxyethyl trans-4-hydroxy- -methylcinnamate. In this series, the first six members are non-mesogenic. -Heptyloxy derivative exhibits monotropic smectic A phase ...

  1. Cloning and expression analysis of a LFY homologous gene in ...

    African Journals Online (AJOL)

    madam

    2012-01-10

    Jan 10, 2012 ... LEAFY (LFY) homologous genes are necessary for the transition from vegetative to reproductive development in flowering plants. ... most important developmental switches in the life cycle of angiosperm that involves a ... far in some plant species including potato (Solanum tuberosum) (Guo and Yang, ...

  2. Practical Challenge of Shredded Documents: Clustering of Chinese Homologous Pieces

    Directory of Open Access Journals (Sweden)

    Nan Xing

    2017-09-01

    Full Text Available When recovering a shredded document that has numerous mixed pieces, the difficulty of the recovery process can be reduced by clustering, which is a method of grouping pieces that originally belonged to the same page. Restoring homologous shredded documents (pieces from different pages of the same file is a frequent problem, and because these pieces have nearly indistinguishable visual characteristics, grouping them is extremely difficult. Clustering research has important practical significance for document recovery because homologous pieces are ubiquitous. Because of the wide usage of Chinese and the huge demand for Chinese shredded document recovery, our research focuses on Chinese homologous pieces. In this paper, we propose a method of completely clustering Chinese homologous pieces in which the distribution features of the characters in the pieces and the document layout are used to correlate adjacent pieces and cluster them in different areas of a document. The experimental results show that the proposed method has a good clustering effect on real pieces. For the dataset containing 10 page documents (a total of 462 pieces, its average accuracy is 97.19%.

  3. Monitoring homologous recombination in rice (Oryza sativa L.)

    Energy Technology Data Exchange (ETDEWEB)

    Yang Zhuanying; Tang Li [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Li Meiru [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Chen Lei; Xu Jie [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China); Wu Goujiang [South China Botanic Garden, Chinese Academy of Sciences, Guangzhou 510650 (China); Li Hongqing, E-mail: hqli@scnu.edu.cn [Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631 (China)

    2010-09-10

    Here we describe a system to assay homologous recombination during the complete life cycle of rice (Oryza sativa L.). Rice plants were transformed with two copies of non-functional GUS reporter overlap fragments as recombination substrate. Recombination was observed in all plant organs examined, from the seed stage until the flowering stage of somatic plant development. Embryogenic cells exhibited the highest recombination ability with an average of 3 x 10{sup -5} recombination events per genome, which is about 10-fold of that observed in root cells, and two orders of that observed in leaf cells. Histological analysis revealed that recombination events occurred in diverse cell types, but preferentially in cells with small size. Examples of this included embryogenic cells in callus, phloem cells in the leaf vein, and cells located in the root apical meristem. Steady state RNA analysis revealed that the expression levels of rice Rad51 homologs are positively correlated with increased recombination rates in embryogenic calli, roots and anthers. Finally, radiation treatment of plantlets from distinct recombination lines increased the recombination frequency to different extents. These results showed that homologous recombination frequency can be effectively measured in rice using a transgene reporter assay. This system will facilitate the study of DNA damage signaling and homologous recombination in rice, a model monocot.

  4. Quantum algorithms for the Jones polynomial and Khovanov homology

    Science.gov (United States)

    Kauffman, Louis H.; Lomonaco, Samuel J., Jr.

    2012-06-01

    This paper generalizes the AJL algorithm for quantum computation of the Jones polynomial to continuous ranges of values on the unit circle for the Jones parameter and shows that the Kauffman-Lomonaco 3-strand algorithm for the Jones polynomial is a special case of this generalization. We then describe a quantum algorithm for the Jones polynomial that is related to Khovanov homology.

  5. The homological content of the Jones representations at $q = -1$

    DEFF Research Database (Denmark)

    Egsgaard, Jens Kristian; Fuglede Jørgensen, Søren

    We generalize a discovery of Kasahara and show that the Jones representations of braid groups, when evaluated at $q = -1$, are related to the action on homology of a branched double cover of the underlying punctured disk. As an application, we prove for a large family of pseudo-Anosov mapping cla...

  6. Hidden Markov Models for Protein Domain Homology Identification and Analysis.

    Science.gov (United States)

    Jablonowski, Karl

    2017-01-01

    Protein domain identification and analysis are cornerstones of modern proteomics. The tools available to protein domain researchers avail a variety of approaches to understanding large protein domain families. Hidden Markov Models (HMM) form the basis for identifying and categorizing evolutionarily linked protein domains. Here I describe the use of HMM models for predicting and identifying Src Homology 2 (SH2) domains within the proteome.

  7. Isolation and characterization of an AGAMOUS homolog from Fraxinus pennsylvanica

    Science.gov (United States)

    Ningxia Du; Paula M. Pijut

    2010-01-01

    An AGAMOUS homolog (FpAG) was isolated from green ash (Fraxinus pennsylvanica) using a reverse transcriptase polymerase chain reaction method. Southern blot analysis indicated that FpAG was present as a single-copy sequence in the genome of green ash. RNA accumulated in the reproductive tissues (female...

  8. PSI-BLAST-ISS: an intermediate sequence search tool for estimation of the position-specific alignment reliability

    Directory of Open Access Journals (Sweden)

    Venclovas Česlovas

    2005-07-01

    Full Text Available Abstract Background Protein sequence alignments have become indispensable for virtually any evolutionary, structural or functional study involving proteins. Modern sequence search and comparison methods combined with rapidly increasing sequence data often can reliably match even distantly related proteins that share little sequence similarity. However, even highly significant matches generally may have incorrectly aligned regions. Therefore when exact residue correspondence is used to transfer biological information from one aligned sequence to another, it is critical to know which alignment regions are reliable and which may contain alignment errors. Results PSI-BLAST-ISS is a standalone Unix-based tool designed to delineate reliable regions of sequence alignments as well as to suggest potential variants in unreliable regions. The region-specific reliability is assessed by producing multiple sequence alignments in different sequence contexts followed by the analysis of the consistency of alignment variants. The PSI-BLAST-ISS output enables the user to simultaneously analyze alignment reliability between query and multiple homologous sequences. In addition, PSI-BLAST-ISS can be used to detect distantly related homologous proteins. The software is freely available at: http://www.ibt.lt/bioinformatics/iss. Conclusion PSI-BLAST-ISS is an effective reliability assessment tool that can be useful in applications such as comparative modelling or analysis of individual sequence regions. It favorably compares with the existing similar software both in the performance and functional features.

  9. Illustrating and homology modeling the proteins of the Zika virus.

    Science.gov (United States)

    Ekins, Sean; Liebler, John; Neves, Bruno J; Lewis, Warren G; Coffee, Megan; Bienstock, Rachelle; Southan, Christopher; Andrade, Carolina H

    2016-01-01

    The Zika virus (ZIKV) is a flavivirus of the family Flaviviridae, which is similar to dengue virus, yellow fever and West Nile virus. Recent outbreaks in South America, Latin America, the Caribbean and in particular Brazil have led to concern for the spread of the disease and potential to cause Guillain-Barré syndrome and microcephaly. Although ZIKV has been known of for over 60 years there is very little in the way of knowledge of the virus with few publications and no crystal structures. No antivirals have been tested against it either in vitro or in vivo. ZIKV therefore epitomizes a neglected disease. Several suggested steps have been proposed which could be taken to initiate ZIKV antiviral drug discovery using both high throughput screens as well as structure-based design based on homology models for the key proteins. We now describe preliminary homology models created for NS5, FtsJ, NS4B, NS4A, HELICc, DEXDc, peptidase S7, NS2B, NS2A, NS1, E stem, glycoprotein M, propeptide, capsid and glycoprotein E using SWISS-MODEL. Eleven out of 15 models pass our model quality criteria for their further use. While a ZIKV glycoprotein E homology model was initially described in the immature conformation as a trimer, we now describe the mature dimer conformer which allowed the construction of an illustration of the complete virion. By comparing illustrations of ZIKV based on this new homology model and the dengue virus crystal structure we propose potential differences that could be exploited for antiviral and vaccine design. The prediction of sites for glycosylation on this protein may also be useful in this regard. While we await a cryo-EM structure of ZIKV and eventual crystal structures of the individual proteins, these homology models provide the community with a starting point for structure-based design of drugs and vaccines as well as a for computational virtual screening.

  10. Single-stranded heteroduplex intermediates in λ Red homologous recombination

    Directory of Open Access Journals (Sweden)

    Zhang Youming

    2010-07-01

    Full Text Available Abstract Background The Red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. However the mechanism of dsDNA recombination remains undefined. Results Here we show that the Red proteins can act via full length single stranded intermediates to establish single stranded heteroduplexes at the replication fork. We created asymmetrically digestible dsDNA substrates by exploiting the fact that Redα exonuclease activity requires a 5' phosphorylated end, or is blocked by phosphothioates. Using these substrates, we found that the most efficient configuration for dsDNA recombination occurred when the strand that can prime Okazaki-like synthesis contained both homology regions on the same ssDNA molecule. Furthermore, we show that Red recombination requires replication of the target molecule. Conclusions Hence we propose a new model for dsDNA recombination, termed 'beta' recombination, based on the formation of ssDNA heteroduplexes at the replication fork. Implications of the model were tested using (i an in situ assay for recombination, which showed that recombination generated mixed wild type and recombinant colonies; and (ii the predicted asymmetries of the homology arms, which showed that recombination is more sensitive to non-homologies attached to 5' than 3' ends. Whereas beta recombination can generate deletions in target BACs of at least 50 kb at about the same efficiency as small deletions, the converse event of insertion is very sensitive to increasing size. Insertions up to 3 kb are most efficiently achieved using beta recombination, however at greater sizes, an alternative Red-mediated mechanism(s appears to be equally efficient. These findings define a new intermediate in homologous recombination, which also has practical implications for recombineering with the Red proteins.

  11. Phylogenesys and homology modeling in Zika virus epidemic: food for thought.

    Science.gov (United States)

    Angeletti, Silvia; Lo Presti, Alessandra; Giovanetti, Marta; Grifoni, Alba; Amicosante, Massimo; Ciotti, Marco; Alcantara, Luiz-Carlos J; Cella, Eleonora; Ciccozzi, Massimo

    Zika virus (ZIKV) is an emerging Flavivirus that have recently caused an outbreak in Brazil and rapid spread in several countries. In this study, the consequences of ZIKV evolution on protein recognition by the host immune system have been analyzed. Evolutionary analysis was combined with homology modeling and T-B cells epitope predictions. Two separate clades, the African one with the Uganda sequence, as the most probable ancestor, and the second one containing all the most recent sequences from the equatorial belt were identified. Brazilian strains clustered all together and closely related to the French Polynesia isolates. A strong presence of a negatively selected site in the envelope gene (Env) protein was evidenced, suggesting a probable purging of deleterious polymorphisms in functionally important genes. Our results show relative conservancy of ZIKV sequences when envelope and other non-structural proteins (NS3 and NS5) are analyzed by homology modeling. However, some regions within the consensus sequence of NS5 protein and to a lesser extent in the envelope protein, show localized high mutation frequency corresponding to a considerable alteration in protein stability. In terms of viral immune escape, envelope protein is under a higher selective pressure than NS5 and NS3 proteins for HLA class I and II molecules. Moreover, envelope mutations that are not strictly related to T-cell immune responses are mostly located on the surface of the protein in putative B-cell epitopes, suggesting an important contribution of B cells in the immune response as well.

  12. Origins and evolution of the HET-s prion-forming protein: searching for other amyloid-forming solenoids.

    Directory of Open Access Journals (Sweden)

    Deena M A Gendoo

    Full Text Available The HET-s prion-forming domain from the filamentous fungus Podospora anserina is gaining considerable interest since it yielded the first well-defined atomic structure of a functional amyloid fibril. This structure has been identified as a left-handed beta solenoid with a triangular hydrophobic core. To delineate the origins of the HET-s prion-forming protein and to discover other amyloid-forming proteins, we searched for all homologs of the HET-s protein in a database of protein domains and fungal genomes, using a combined application of HMM, psi-blast and pGenThreader techniques, and performed a comparative evolutionary analysis of the N-terminal alpha-helical domain and the C-terminal prion-forming domain of HET-s. By assessing the tandem evolution of both domains, we observed that the prion-forming domain is restricted to Sordariomycetes, with a marginal additional sequence homolog in Arthroderma otae as a likely case of horizontal transfer. This suggests innovation and rapid evolution of the solenoid fold in the Sordariomycetes clade. In contrast, the N-terminal domain evolves at a slower rate (in Sordariomycetes and spans many diverse clades of fungi. We performed a full three-dimensional protein threading analysis on all identified HET-s homologs against the HET-s solenoid fold, and present detailed structural annotations for identified structural homologs to the prion-forming domain. An analysis of the physicochemical characteristics in our set of structural models indicates that the HET-s solenoid shape can be readily adopted in these homologs, but that they are all less optimized for fibril formation than the P. anserina HET-s sequence itself, due chiefly to the presence of fewer asparagine ladders and salt bridges. Our combined structural and evolutionary analysis suggests that the HET-s shape has "limited scope" for amyloidosis across the wider protein universe, compared to the 'generic' left-handed beta helix. We discuss the

  13. Charting novel allergens from date palm pollen (Phoenix sylvestris) using homology driven proteomics.

    Science.gov (United States)

    Saha, Bodhisattwa; Bhattacharya, Swati Gupta

    2017-08-08

    Pollen grains from Phoenix sylvestris (date palm), a commonly cultivated tree in India has been found to cause severe allergic diseases in an increasing percentage of hypersensitive individuals. To unearth its allergenic components, pollen protein were profiled by two-dimensional gel electrophoresis followed by immunoblotting with date palm pollen sensitive patient sera. Allergens were identified by MALDI-TOF/TOF employing a layered proteomic approach combining conventional database dependent search and manual de novo sequencing followed by homology-based search as Phoenix sylvestris is unsequenced. Derivatization of tryptic peptides by acetylation has been demonstrated to differentiate the 'b' from the 'y' ions facilitating efficient de novo sequencing. Ten allergenic proteins were identified, out of which six showed homology with known allergens while others were reported for the first time. Amongst these, isoflavone reductase, beta-conglycinin, S-adenosyl methionine synthase, 1, 4 glucan synthase and beta-galactosidase were commonly reported as allergens from coconut pollen and presumably responsible for cross-reactivity. One of the allergens had IgE binding epitope recognized by its glycan moiety. The allergenic potency of date palm pollen has been demonstrated using in vitro tests. The identified allergens can be used to develop vaccines for immunotherapy against date palm pollen allergy. Identification of allergenic proteins from sources harboring them is essential in developing therapeutic interventions. This is the first comprehensive study on the identification of allergens from Phoenix sylvestris (date palm) pollen, one of the major aeroallergens in India using a proteomic approach. Proteomic methods are being increasingly used to identify allergens. However, since many of these proteins arise from species which are un-sequenced, it becomes difficult to interpret those using conventional proteomics. Date palm being an unsequenced species, the Ig

  14. Topoisomerase II-mediated DNA damage is differently repaired during the cell cycle by non-homologous end joining and homologous recombination.

    Directory of Open Access Journals (Sweden)

    Marcelo de Campos-Nebel

    Full Text Available Topoisomerase II (Top2 is a nuclear enzyme involved in several metabolic processes of DNA. Chemotherapy agents that poison Top2 are known to induce persistent protein-mediated DNA double strand breaks (DSB. In this report, by using knock down experiments, we demonstrated that Top2alpha was largely responsible for the induction of gammaH2AX and cytotoxicity by the Top2 poisons idarubicin and etoposide in normal human cells. As DSB resulting from Top2 poisons-mediated damage may be repaired by non-homologous end joining (NHEJ or homologous recombination (HR, we aimed to analyze both DNA repair pathways. We found that DNA-PKcs was rapidly activated in human cells, as evidenced by autophosphorylation at serine 2056, following Top2-mediated DNA damage. The chemical inhibition of DNA-PKcs by wortmannin and vanillin resulted in an increased accumulation of DNA DSB, as evaluated by the comet assay. This was supported by a hypersensitive phenotype to Top2 poisons of Ku80- and DNA-PKcs- defective Chinese hamster cell lines. We also showed that Rad51 protein levels, Rad51 foci formation and sister chromatid exchanges were increased in human cells following Top2-mediated DNA damage. In support, BRCA2- and Rad51C- defective Chinese hamster cells displayed hypersensitivity to Top2 poisons. The analysis by immunofluorescence of the DNA DSB repair response in synchronized human cell cultures revealed activation of DNA-PKcs throughout the cell cycle and Rad51 foci formation in S and late S/G2 cells. Additionally, we found an increase of DNA-PKcs-mediated residual repair events, but not Rad51 residual foci, into micronucleated and apoptotic cells. Therefore, we conclude that in human cells both NHEJ and HR are required, with cell cycle stage specificity, for the repair of Top2-mediated reversible DNA damage. Moreover, NHEJ-mediated residual repair events are more frequently associated to irreversibly damaged cells.

  15. Google Ajax Search API

    CERN Document Server

    Fitzgerald, Michael

    2007-01-01

    Use the Google Ajax Search API to integrateweb search, image search, localsearch, and other types of search intoyour web site by embedding a simple, dynamicsearch box to display search resultsin your own web pages using a fewlines of JavaScript. For those who do not want to write code,the search wizards and solutions builtwith the Google Ajax Search API generatecode to accomplish common taskslike adding local search results to a GoogleMaps API mashup, adding videosearch thumbnails to your web site, oradding a news reel with the latest up todate stories to your blog. More advanced users can

  16. How doctors search

    DEFF Research Database (Denmark)

    Lykke, Marianne; Price, Susan; Delcambre, Lois

    2012-01-01

    Professional, workplace searching is different from general searching, because it is typically limited to specific facets and targeted to a single answer. We have developed the semantic component (SC) model, which is a search feature that allows searchers to structure and specify the search...... to context-specific aspects of the main topic of the documents. We have tested the model in an interactive searching study with family doctors with the purpose to explore doctors’ querying behaviour, how they applied the means for specifying a search, and how these features contributed to the search outcome....... In general, the doctors were capable of exploiting system features and search tactics during the searching. Most searchers produced well-structured queries that contained appropriate search facets. When searches failed it was not due to query structure or query length. Failures were mostly caused by the well...

  17. Searching and Indexing Genomic Databases via Kernelization

    Directory of Open Access Journals (Sweden)

    Travis eGagie

    2015-02-01

    Full Text Available The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors have recently suggested searching or indexing only one reference genome and the parts of the other genomes where they differ. In this paper we survey the twenty-year history of this idea and discuss its relation to kernelization in parameterized complexity.

  18. submitter Searches at LEP

    CERN Document Server

    Kawagoe, Kiyotomo

    2001-01-01

    Searches for new particles and new physics were extensively performed at LEP. Although no evidence for new particle/physics was discovered, the null results set very stringent limits to theories beyond the standard model. In this paper, searches at LEP and anomalies observed in the searches are presented. Future prospect of searches at the new energy frontier machines is also discussed.

  19. Web Search Engines

    OpenAIRE

    Rajashekar, TB

    1998-01-01

    The World Wide Web is emerging as an all-in-one information source. Tools for searching Web-based information include search engines, subject directories and meta search tools. We take a look at key features of these tools and suggest practical hints for effective Web searching.

  20. Sound Search Engine Concept

    DEFF Research Database (Denmark)

    2006-01-01

    Sound search is provided by the major search engines, however, indexing is text based, not sound based. We will establish a dedicated sound search services with based on sound feature indexing. The current demo shows the concept of the sound search engine. The first engine will be realased June...

  1. Electrostatic braiding and homologous pairing of DNA double helices.

    Science.gov (United States)

    Cortini, Ruggero; Kornyshev, Alexei A; Lee, Dominic J; Leikin, Sergey

    2011-08-17

    Homologous pairing and braiding (supercoiling) have crucial effects on genome organization, maintenance, and evolution. Generally, the pairing and braiding processes are discussed in different contexts, independently of each other. However, analysis of electrostatic interactions between DNA double helices suggests that in some situations these processes may be related. Here we present a theory of DNA braiding that accounts for the elastic energy of DNA double helices as well as for the chiral nature of the discrete helical patterns of DNA charges. This theory shows that DNA braiding may be affected, stabilized, or even driven by chiral electrostatic interactions. For example, electrostatically driven braiding may explain the surprising recent observation of stable pairing of homologous double-stranded DNA in solutions containing only monovalent salt. Electrostatic stabilization of left-handed braids may stand behind the chiral selectivity of type II topoisomerases and positive plasmid supercoiling in hyperthermophilic bacteria and archea. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  2. Homology and isomorphism: Bourdieu in conversation with New Institutionalism.

    Science.gov (United States)

    Wang, Yingyao

    2016-06-01

    Bourdieusian Field Theory (BFT) provided decisive inspiration for the early conceptual formulation of New Institutionalism (NI). This paper attempts to reinvigorate the stalled intellectual dialogue between NI and BFT by comparing NI's concept of isomorphism with BFT's notion of homology. I argue that Bourdieu's understanding of domination-oriented social action, transposable habitus, and a non-linear causality, embodied in his neglected concept of homology, provides an alternative theorization of field-level convergence to New Institutionalism's central idea of institutional isomorphism. To showcase how BFT can be useful for organizational research, I postulate a habitus-informed and field-conditioned theory of transference to enrich NI's spin-off thesis of 'diffusion'. I propose that while NI can benefit from BFT's potential of bringing social structure back into organizational research, BFT can enrich its social analysis by borrowing from NI's elaboration of the symbolic system of organizations. © London School of Economics and Political Science 2016.

  3. Targeted recombination between homologous chromosomes for precise breeding in tomato.

    Science.gov (United States)

    Filler Hayut, Shdema; Melamed Bessudo, Cathy; Levy, Avraham A

    2017-05-26

    Homologous recombination (HR) between parental chromosomes occurs stochastically. Here, we report on targeted recombination between homologous chromosomes upon somatic induction of DNA double-strand breaks (DSBs) via CRISPR-Cas9. We demonstrate this via a visual and molecular assay whereby DSB induction between two alleles carrying different mutations in the PHYTOENE SYNTHASE (PSY1) gene results in yellow fruits with wild type red sectors forming via HR-mediated DSB repair. We also show that in heterozygote plants containing one psy1 allele immune and one sensitive to CRISPR, repair of the broken allele using the unbroken allele sequence template is a common outcome. In another assay, we show evidence of a somatically induced DSB in a cross between a psy1 edible tomato mutant and wild type Solanum pimpinellifolium, targeting only the S. pimpinellifolium allele. This enables characterization of germinally transmitted targeted somatic HR events, demonstrating that somatically induced DSBs can be exploited for precise breeding of crops.

  4. Identification of rodent homologs of hepatitis C virus and pegiviruses

    DEFF Research Database (Denmark)

    Kapoor, Amit; Simmonds, Peter; Scheel, Troels K H

    2013-01-01

    Flaviviridae. The genetic diversity of the rodent hepaciviruses exceeded that observed for hepaciviruses infecting either humans or non-primates, leading to new insights into the origin, evolution, and host range of hepaciviruses. The presence of genes, encoded proteins, and translation elements homologous......UNLABELLED: Hepatitis C virus (HCV) and human pegivirus (HPgV or GB virus C) are globally distributed and infect 2 to 5% of the human population. The lack of tractable-animal models for these viruses, in particular for HCV, has hampered the study of infection, transmission, virulence, immunity...... to those found in human hepaciviruses and pegiviruses suggests the potential for the development of new animal systems with which to model HCV pathogenesis, vaccine design, and treatment. IMPORTANCE: The genetic and biological characterization of animal homologs of human viruses provides insights...

  5. Intersection spaces, spatial homology truncation, and string theory

    CERN Document Server

    Banagl, Markus

    2010-01-01

    Intersection cohomology assigns groups which satisfy a generalized form of Poincaré duality over the rationals to a stratified singular space. The present monograph introduces a method that assigns to certain classes of stratified spaces cell complexes, called intersection spaces, whose ordinary rational homology satisfies generalized Poincaré duality. The cornerstone of the method is a process of spatial homology truncation, whose functoriality properties are analyzed in detail. The material on truncation is autonomous and may be of independent interest to homotopy theorists. The cohomology of intersection spaces is not isomorphic to intersection cohomology and possesses algebraic features such as perversity-internal cup-products and cohomology operations that are not generally available for intersection cohomology. A mirror-symmetric interpretation, as well as applications to string theory concerning massless D-branes arising in type IIB theory during a Calabi-Yau conifold transition, are discussed.

  6. Homologous recombination in the archaea: the means justify the ends.

    Science.gov (United States)

    White, Malcolm F

    2011-01-01

    The process of information exchange between two homologous DNA duplexes is known as homologous recombination (HR) or double-strand break repair (DSBR), depending on the context. HR is the fundamental process underlying the genome shuffling that expands genetic diversity (for example during meiosis in eukaryotes). DSBR is an essential repair pathway in all three domains of life, and plays a major role in the rescue of stalled or collapsed replication forks, a phenomenon known as recombination-dependent replication (RDR). The process of HR in the archaea is gradually being elucidated, initially from structural and biochemical studies, but increasingly using new genetic systems. The present review focuses on our current understanding of the structures, functions and interactions of archaeal HR proteins, with an emphasis on recent advances. There are still many unknown aspects of archaeal HR, most notably the mechanism of branch migration of Holliday junctions, which is also an open question in eukarya.

  7. Morse homology for the Yang–Mills gradient flow

    National Research Council Canada - National Science Library

    Swoboda, Jan

    2012-01-01

    ...€¢â€¢â€¢ (••••) •••–••• www.elsevier.com/locate/matpur Morse homology for the Yang–Mills gradient flow Jan Swoboda ∗ Max-Planck-Institut...

  8. Quasi-homologous spherically symmetric branes and their symmetry breaking

    Energy Technology Data Exchange (ETDEWEB)

    Abdalla, M.C.B.; Carlesso, P.F. [UNESP - Universidade Estadual Paulista, Instituto de Fisica Teorica, Rua Dr. Bento Teobaldo Ferraz, 271, Bloco II, Barra-Funda, Caixa Postal 70532-2, Sao Paulo, SP (Brazil); Hoff da Silva, J.M. [UNESP - Universidade Estadual Paulista, Departamento de Fisica e Quimica, Guaratingueta, SP (Brazil)

    2013-06-15

    We revisit the dynamical system-based approach of spherically symmetric vacuum braneworlds, pointing out and studying the existence of a transcritical bifurcation as the dark pressure parameter changes its sign, we analyze some consequences of not discard the brane cosmological constant. For instance, it is noteworthy that the existence of an isothermal state equation between the dark fluid parameters cannot be obtained via the requirement of a quasi-homologous symmetry of the vacuum. (orig.)

  9. Protein Identification Pipeline for the Homology Driven Proteomics

    Science.gov (United States)

    Junqueira, Magno; Spirin, Victor; Balbuena, Tiago Santana; Thomas, Henrik; Adzhubei, Ivan; Sunyaev, Shamil; Shevchenko, Andrej

    2008-01-01

    Homology-driven proteomics is a major tool to characterize proteomes of organisms with unsequenced genomes. This paper addresses practical aspects of automated homology–driven protein identifications by LC-MS/MS on a hybrid LTQ Orbitrap mass spectrometer. All essential software elements supporting the presented pipeline are either hosted at the publicly accessible web server, or are available for free download. PMID:18639657

  10. Persistent homology for the quantitative prediction of fullerene stability.

    Science.gov (United States)

    Xia, Kelin; Feng, Xin; Tong, Yiying; Wei, Guo Wei

    2015-03-05

    Persistent homology is a relatively new tool often used for qualitative analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this article, we report novel quantitative predictions of the energy and stability of fullerene molecules, the very first attempt in using persistent homology in this context. The ground-state structures of a series of small fullerene molecules are first investigated with the standard Vietoris-Rips complex. We decipher all the barcodes, including both short-lived local bars and long-lived global bars arising from topological invariants, and associate them with fullerene structural details. Using accumulated bar lengths, we build quantitative models to correlate local and global Betti-2 bars, respectively with the heat of formation and total curvature energies of fullerenes. It is found that the heat of formation energy is related to the local hexagonal cavities of small fullerenes, while the total curvature energies of fullerene isomers are associated with their sphericities, which are measured by the lengths of their long-lived Betti-2 bars. Excellent correlation coefficients (>0.94) between persistent homology predictions and those of quantum or curvature analysis have been observed. A correlation matrix based filtration is introduced to further verify our findings. © 2014 Wiley Periodicals, Inc.

  11. Persistent Homology for The Quantitative Prediction of Fullerene Stability

    Science.gov (United States)

    Xia, Kelin; Feng, Xin; Tong, Yiying; Wei, Guo Wei

    2014-01-01

    Persistent homology is a relatively new tool often used for qualitative analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this paper, we report novel quantitative predictions of the energy and stability of fullerene molecules, the very first attempt in employing persistent homology in this context. The ground-state structures of a series of small fullerene molecules are first investigated with the standard Vietoris-Rips complex. We decipher all the barcodes, including both short-lived local bars and long-lived global bars arising from topological invariants, and associate them with fullerene structural details. By using accumulated bar lengths, we build quantitative models to correlate local and global Betti-2 bars respectively with the heat of formation and total curvature energies of fullerenes. It is found that the heat of formation energy is related to the local hexagonal cavities of small fullerenes, while the total curvature energies of fullerene isomers are associated with their sphericities, which are measured by the lengths of their long-lived Betti-2 bars. Excellent correlation coefficients (> 0.94) between persistent homology predictions and those of quantum or curvature analysis have been observed. A correlation matrix based filtration is introduced to further verify our findings. PMID:25523342

  12. Accelerated homologous recombination and subsequent genome modification in Drosophila.

    Science.gov (United States)

    Baena-Lopez, Luis Alberto; Alexandre, Cyrille; Mitchell, Alice; Pasakarnis, Laurynas; Vincent, Jean-Paul

    2013-12-01

    Gene targeting by 'ends-out' homologous recombination enables the deletion of genomic sequences and concurrent introduction of exogenous DNA with base-pair precision without sequence constraint. In Drosophila, this powerful technique has remained laborious and hence seldom implemented. We describe a targeting vector and protocols that achieve this at high frequency and with very few false positives in Drosophila, either with a two-generation crossing scheme or by direct injection in embryos. The frequency of injection-mediated gene targeting can be further increased with CRISPR-induced double-strand breaks within the region to be deleted, thus making homologous recombination almost as easy as conventional transgenesis. Our targeting vector replaces genomic sequences with a multifunctional fragment comprising an easy-to-select genetic marker, a fluorescent reporter, as well as an attP site, which acts as a landing platform for reintegration vectors. These vectors allow the insertion of a variety of transcription reporters or cDNAs to express tagged or mutant isoforms at endogenous levels. In addition, they pave the way for difficult experiments such as tissue-specific allele switching and functional analysis in post-mitotic or polyploid cells. Therefore, our method retains the advantages of homologous recombination while capitalising on the mutagenic power of CRISPR.

  13. Allergen homologs in the Euroglyphus maynei draft genome.

    Directory of Open Access Journals (Sweden)

    S Dean Rider

    Full Text Available Euroglyphus maynei is a house dust mite commonly found in homes worldwide and is the source of allergens that sensitize and induce allergic reactions in humans. It is the source of species-specific allergens as well as allergens that are cross-reactive with the allergens from house dust mites Dermatophagoides farinae and D. pteronyssinus, and the ectoparasitic scabies mite Sarcoptes scabiei. The genomics, proteomics and molecular biology of E. maynei and its allergens have not been as extensively investigated as those of D. farinae, D. pteronyssinus, and S. scabiei where natural and recombinant allergens from these species have been characterized. Until now, little was known about the genome of E. maynei and it allergens but this information will be important for producing recombinant allergens for diagnostic and therapeutic purposes and for understanding the allergic response mechanism by immune effector cells that mediate the allergic reaction. We sequenced and assembled the 59 Mb E. maynei genome to aid the identification of homologs for known allergenic proteins. The predicted proteome shared orthologs with D. farinae and S. scabiei, and included proteins with homology to more than 30 different groups of allergens. However, the majority of allergen candidates could not be assigned as clear orthologs to known mite allergens. The genomic sequence data, predicted proteome, and allergen homologs identified from E. maynei provide insight into the relationships among astigmatid mites and their allergens, which should allow for the development of improved diagnostics and immunotherapy.

  14. Homologous Recombination in Protozoan Parasites and Recombinase Inhibitors.

    Science.gov (United States)

    Kelso, Andrew A; Waldvogel, Sarah M; Luthman, Adam J; Sehorn, Michael G

    2017-01-01

    Homologous recombination (HR) is a DNA double-strand break (DSB) repair pathway that utilizes a homologous template to fully repair the damaged DNA. HR is critical to maintain genome stability and to ensure genetic diversity during meiosis. A specialized class of enzymes known as recombinases facilitate the exchange of genetic information between sister chromatids or homologous chromosomes with the help of numerous protein accessory factors. The majority of the HR machinery is highly conserved among eukaryotes. In many protozoan parasites, HR is an essential DSB repair pathway that allows these organisms to adapt to environmental conditions and evade host immune systems through genetic recombination. Therefore, small molecule inhibitors, capable of disrupting HR in protozoan parasites, represent potential therapeutic options. A number of small molecule inhibitors were identified that disrupt the activities of the human recombinase RAD51. Recent studies have examined the effect of two of these molecules on the Entamoeba recombinases. Here, we discuss the current understandings of HR in the protozoan parasites Trypanosoma, Leishmania, Plasmodium, and Entamoeba, and we review the small molecule inhibitors known to disrupt human RAD51 activity.

  15. Homologous Recombination in Protozoan Parasites and Recombinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Andrew A. Kelso

    2017-09-01

    Full Text Available Homologous recombination (HR is a DNA double-strand break (DSB repair pathway that utilizes a homologous template to fully repair the damaged DNA. HR is critical to maintain genome stability and to ensure genetic diversity during meiosis. A specialized class of enzymes known as recombinases facilitate the exchange of genetic information between sister chromatids or homologous chromosomes with the help of numerous protein accessory factors. The majority of the HR machinery is highly conserved among eukaryotes. In many protozoan parasites, HR is an essential DSB repair pathway that allows these organisms to adapt to environmental conditions and evade host immune systems through genetic recombination. Therefore, small molecule inhibitors, capable of disrupting HR in protozoan parasites, represent potential therapeutic options. A number of small molecule inhibitors were identified that disrupt the activities of the human recombinase RAD51. Recent studies have examined the effect of two of these molecules on the Entamoeba recombinases. Here, we discuss the current understandings of HR in the protozoan parasites Trypanosoma, Leishmania, Plasmodium, and Entamoeba, and we review the small molecule inhibitors known to disrupt human RAD51 activity.

  16. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily.

    Science.gov (United States)

    Lenoir, Marc; Kufareva, Irina; Abagyan, Ruben; Overduin, Michael

    2015-10-23

    The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH) domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH) and Tec homology (TH) domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA) program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  17. Membrane and Protein Interactions of the Pleckstrin Homology Domain Superfamily

    Directory of Open Access Journals (Sweden)

    Marc Lenoir

    2015-10-01

    Full Text Available The human genome encodes about 285 proteins that contain at least one annotated pleckstrin homology (PH domain. As the first phosphoinositide binding module domain to be discovered, the PH domain recruits diverse protein architectures to cellular membranes. PH domains constitute one of the largest protein superfamilies, and have diverged to regulate many different signaling proteins and modules such as Dbl homology (DH and Tec homology (TH domains. The ligands of approximately 70 PH domains have been validated by binding assays and complexed structures, allowing meaningful extrapolation across the entire superfamily. Here the Membrane Optimal Docking Area (MODA program is used at a genome-wide level to identify all membrane docking PH structures and map their lipid-binding determinants. In addition to the linear sequence motifs which are employed for phosphoinositide recognition, the three dimensional structural features that allow peripheral membrane domains to approach and insert into the bilayer are pinpointed and can be predicted ab initio. The analysis shows that conserved structural surfaces distinguish which PH domains associate with membrane from those that do not. Moreover, the results indicate that lipid-binding PH domains can be classified into different functional subgroups based on the type of membrane insertion elements they project towards the bilayer.

  18. Remote homology detection incorporating the context of physicochemical properties.

    Science.gov (United States)

    Bedoya, Oscar; Tischer, Irene

    2014-02-01

    A new method for remote protein homology detection, called support vector machine incorporating the context of physicochemical properties (SVM-CP), is presented. Recent discriminative methods are based on concatenating information extracted from each protein by considering several physicochemical properties. We show that there are physicochemical properties that reflect the functional or structural characteristics of each specific protein family, but there are also some physicochemical properties that affect the accuracy of the classification techniques. The research highlights the importance of the selection of physicochemical properties in remote homology detection. Most of the methods slide a window over every protein sequence to extract physicochemical information. This extraction is usually performed by giving the same importance to every value in the window, i.e., averaging the physicochemical values in the observation window. SVM-CP takes into account that every residue in a sliding window has a different weight, which reflects the importance or contribution to the representative value of the window. The SVM-CP method reaches a receiver operating characteristic (ROC) score of 0.93462, which is the highest value for a remote homology detection method based on the sequence composition information. © 2013 Published by Elsevier Ltd.

  19. A rapidly enlarging cutaneous hemangioma in pregnancy

    Directory of Open Access Journals (Sweden)

    Marwan Ma’ayeh

    2014-10-01

    Full Text Available This is a case of a rapidly enlarging cutaneous pedunculated tumor on a patient’s thumb during her pregnancy. This was excised and identified as a hemangioma. A literature search identified a possible hormonal factor in causing an accelerated growth of this tumor.

  20. A rapidly enlarging cutaneous hemangioma in pregnancy.

    LENUS (Irish Health Repository)

    Ma'ayeh, Marwan

    2014-06-18

    This is a case of a rapidly enlarging cutaneous pedunculated tumor on a patient\\'s thumb during her pregnancy. This was excised and identified as a hemangioma. A literature search identified a possible hormonal factor in causing an accelerated growth of this tumor.

  1. Anti-HmuY antibodies specifically recognize Porphyromonas gingivalis HmuY protein but not homologous proteins in other periodontopathogens.

    Directory of Open Access Journals (Sweden)

    Michał Śmiga

    Full Text Available Given the emerging evidence of an association between periodontal infections and systemic conditions, the search for specific methods to detect the presence of P. gingivalis, a principal etiologic agent in chronic periodontitis, is of high importance. The aim of this study was to characterize antibodies raised against purified P. gingivalis HmuY protein and selected epitopes of the HmuY molecule. Since other periodontopathogens produce homologs of HmuY, we also aimed to characterize responses of antibodies raised against the HmuY protein or its epitopes to the closest homologous proteins from Prevotella intermedia and Tannerella forsythia. Rabbits were immunized with purified HmuY protein or three synthetic, KLH-conjugated peptides, derived from the P. gingivalis HmuY protein. The reactivity of anti-HmuY antibodies with purified proteins or bacteria was determined using Western blotting and ELISA assay. First, we found homologs of P. gingivalis HmuY in P. intermedia (PinO and PinA proteins and T. forsythia (Tfo protein and identified corrected nucleotide and amino acid sequences of Tfo. All proteins were overexpressed in E. coli and purified using ion-exchange chromatography, hydrophobic chromatography and gel filtration. We demonstrated that antibodies raised against P. gingivalis HmuY are highly specific to purified HmuY protein and HmuY attached to P. gingivalis cells. No reactivity between P. intermedia and T. forsythia or between purified HmuY homologs from these bacteria and anti-HmuY antibodies was detected. The results obtained in this study demonstrate that P. gingivalis HmuY protein may serve as an antigen for specific determination of serum antibodies raised against this bacterium.

  2. Multiple search methods for similarity-based virtual screening: analysis of search overlap and precision

    Directory of Open Access Journals (Sweden)

    Holliday John D

    2011-08-01

    Full Text Available Abstract Background Data fusion methods are widely used in virtual screening, and make the implicit assumption that the more often a molecule is retrieved in multiple similarity searches, the more likely it is to be active. This paper tests the correctness of this assumption. Results Sets of 25 searches using either the same reference structure and 25 different similarity measures (similarity fusion or 25 different reference structures and the same similarity measure (group fusion show that large numbers of unique molecules are retrieved by just a single search, but that the numbers of unique molecules decrease very rapidly as more searches are considered. This rapid decrease is accompanied by a rapid increase in the fraction of those retrieved molecules that are active. There is an approximately log-log relationship between the numbers of different molecules retrieved and the number of searches carried out, and a rationale for this power-law behaviour is provided. Conclusions Using multiple searches provides a simple way of increasing the precision of a similarity search, and thus provides a justification for the use of data fusion methods in virtual screening.

  3. HAL-2 promotes homologous pairing during Caenorhabditis elegans meiosis by antagonizing inhibitory effects of synaptonemal complex precursors.

    Directory of Open Access Journals (Sweden)

    Weibin Zhang

    Full Text Available During meiosis, chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex (SC. Since the SC assembles cooperatively yet is indifferent to homology, pairing and SC assembly must be tightly coordinated. We identify HAL-2 as a key mediator in this coordination, showing that HAL-2 promotes pairing largely by preventing detrimental effects of SC precursors (SYP proteins. hal-2 mutants fail to establish pairing and lack multiple markers of chromosome movement mediated by pairing centers (PCs, chromosome sites that link chromosomes to cytoplasmic microtubules through nuclear envelope-spanning complexes. Moreover, SYP proteins load inappropriately along individual unpaired chromosomes in hal-2 mutants, and markers of PC-dependent movement and function are restored in hal-2; syp double mutants. These and other data indicate that SYP proteins can impede pairing and that HAL-2 promotes pairing predominantly but not exclusively by counteracting this inhibition, thereby enabling activation and regulation of PC function. HAL-2 concentrates in the germ cell nucleoplasm and colocalizes with SYP proteins in nuclear aggregates when SC assembly is prevented. We propose that HAL-2 functions to shepherd SYP proteins prior to licensing of SC assembly, preventing untimely interactions between SC precursors and chromosomes and allowing sufficient accumulation of precursors for rapid cooperative assembly upon homology verification.

  4. To Search or Not to Search!

    Science.gov (United States)

    Taylor, J. Rodney

    Constitutional guarantees, as provided by the Bill of Rights, are enjoyed by all citizens. This principle applies no less to students with respect to their college or university domicile. Case law on this subject suggests that three questions must be answered to determine the reasonableness of residence searching: (1) by whom the search is…

  5. Functional and evolutionary characterization of Ohr proteins in eukaryotes reveals many active homologs among pathogenic fungi

    Directory of Open Access Journals (Sweden)

    D.A. Meireles

    2017-08-01

    Full Text Available Ohr and OsmC proteins comprise two subfamilies within a large group of proteins that display Cys-based, thiol dependent peroxidase activity. These proteins were previously thought to be restricted to prokaryotes, but we show here, using iterated sequence searches, that Ohr/OsmC homologs are also present in 217 species of eukaryotes with a massive presence in Fungi (186 species. Many of these eukaryotic Ohr proteins possess an N-terminal extension that is predicted to target them to mitochondria. We obtained recombinant proteins for four eukaryotic members of the Ohr/OsmC family and three of them displayed lipoyl peroxidase activity. Further functional and biochemical characterization of the Ohr homologs from the ascomycete fungus Mycosphaerella fijiensis Mf_1 (MfOhr, the causative agent of Black Sigatoka disease in banana plants, was pursued. Similarly to what has been observed for the bacterial proteins, we found that: (i the peroxidase activity of MfOhr was supported by DTT or dihydrolipoamide (dithiols, but not by β-mercaptoethanol or GSH (monothiols, even in large excess; (ii MfOhr displayed preference for organic hydroperoxides (CuOOH and tBOOH over hydrogen peroxide; (iii MfOhr presented extraordinary reactivity towards linoleic acid hydroperoxides (k=3.18 (±2.13×108 M−1 s−1. Both Cys87 and Cys154 were essential to the peroxidase activity, since single mutants for each Cys residue presented no activity and no formation of intramolecular disulfide bond upon treatment with hydroperoxides. The pKa value of the Cysp residue was determined as 5.7±0.1 by a monobromobimane alkylation method. Therefore, eukaryotic Ohr peroxidases share several biochemical features with prokaryotic orthologues and are preferentially located in mitochondria.

  6. Genetic selection and DNA sequences of 4.5S RNA homologs

    DEFF Research Database (Denmark)

    Brown, S; Thon, G; Tolentino, E

    1989-01-01

    A general strategy for cloning the functional homologs of an Escherichia coli gene was used to clone homologs of 4.5S RNA from other bacteria. The genes encoding these homologs were selected by their ability to complement a deletion of the gene for 4.5S RNA. DNA sequences of the regions encoding...

  7. Intelligent Information Systems for Web Product Search

    NARCIS (Netherlands)

    D. Vandic (Damir)

    2017-01-01

    markdownabstractOver the last few years, we have experienced an increase in online shopping. Consequently, there is a need for efficient and effective product search engines. The rapid growth of e-commerce, however, has also introduced some challenges. Studies show that users can get overwhelmed by

  8. Cube search, revisited

    Science.gov (United States)

    Zhang, Xuetao; Huang, Jie; Yigit-Elliott, Serap; Rosenholtz, Ruth

    2015-01-01

    Observers can quickly search among shaded cubes for one lit from a unique direction. However, replace the cubes with similar 2-D patterns that do not appear to have a 3-D shape, and search difficulty increases. These results have challenged models of visual search and attention. We demonstrate that cube search displays differ from those with “equivalent” 2-D search items in terms of the informativeness of fairly low-level image statistics. This informativeness predicts peripheral discriminability of target-present from target-absent patches, which in turn predicts visual search performance, across a wide range of conditions. Comparing model performance on a number of classic search tasks, cube search does not appear unexpectedly easy. Easy cube search, per se, does not provide evidence for preattentive computation of 3-D scene properties. However, search asymmetries derived from rotating and/or flipping the cube search displays cannot be explained by the information in our current set of image statistics. This may merely suggest a need to modify the model's set of 2-D image statistics. Alternatively, it may be difficult cube search that provides evidence for preattentive computation of 3-D scene properties. By attributing 2-D luminance variations to a shaded 3-D shape, 3-D scene understanding may slow search for 2-D features of the target. PMID:25780063

  9. Large Neighborhood Search

    DEFF Research Database (Denmark)

    Pisinger, David; Røpke, Stefan

    2010-01-01

    Heuristics based on large neighborhood search have recently shown outstanding results in solving various transportation and scheduling problems. Large neighborhood search methods explore a complex neighborhood by use of heuristics. Using large neighborhoods makes it possible to find better candid...

  10. New particle searches

    CERN Document Server

    Ruhlmann-Kleider, V

    2000-01-01

    This review presents recent results on new particle searches achieved at Tevatron, Hera and LEP. After a brief outline of the searches on exotic particles, results on supersymmetric particles and Higgs bosons are detailed. Near future prospects are also given.

  11. The PIKE homolog Centaurin gamma regulates developmental timing in Drosophila.

    Directory of Open Access Journals (Sweden)

    Anna Lisa Gündner

    Full Text Available Phosphoinositide-3-kinase enhancer (PIKE proteins encoded by the PIKE/CENTG1 gene are members of the gamma subgroup of the Centaurin superfamily of small GTPases. They are characterized by their chimeric protein domain architecture consisting of a pleckstrin homology (PH domain, a GTPase-activating (GAP domain, Ankyrin repeats as well as an intrinsic GTPase domain. In mammals, three PIKE isoforms with variations in protein structure and subcellular localization are encoded by the PIKE locus. PIKE inactivation in mice results in a broad range of defects, including neuronal cell death during brain development and misregulation of mammary gland development. PIKE -/- mutant mice are smaller, contain less white adipose tissue, and show insulin resistance due to misregulation of AMP-activated protein kinase (AMPK and insulin receptor/Akt signaling. here, we have studied the role of PIKE proteins in metabolic regulation in the fly. We show that the Drosophila PIKE homolog, ceng1A, encodes functional GTPases whose internal GAP domains catalyze their GTPase activity. To elucidate the biological function of ceng1A in flies, we introduced a deletion in the ceng1A gene by homologous recombination that removes all predicted functional PIKE domains. We found that homozygous ceng1A mutant animals survive to adulthood. In contrast to PIKE -/- mouse mutants, genetic ablation of Drosophila ceng1A does not result in growth defects or weight reduction. Although metabolic pathways such as insulin signaling, sensitivity towards starvation and mobilization of lipids under high fed conditions are not perturbed in ceng1A mutants, homozygous ceng1A mutants show a prolonged development in second instar larval stage, leading to a late onset of pupariation. In line with these results we found that expression of ecdysone inducible genes is reduced in ceng1A mutants. Together, we propose a novel role for Drosophila Ceng1A in regulating ecdysone signaling-dependent second to

  12. A scoping review of rapid review methods.

    Science.gov (United States)

    Tricco, Andrea C; Antony, Jesmin; Zarin, Wasifa; Strifler, Lisa; Ghassemi, Marco; Ivory, John; Perrier, Laure; Hutton, Brian; Moher, David; Straus, Sharon E

    2015-09-16

    Rapid reviews are a form of knowledge synthesis in which components of the systematic review process are simplified or omitted to produce information in a timely manner. Although numerous centers are conducting rapid reviews internationally, few studies have examined the methodological characteristics of rapid reviews. We aimed to examine articles, books, and reports that evaluated, compared, used or described rapid reviews or methods through a scoping review. MEDLINE, EMBASE, the Cochrane Library, internet websites of rapid review producers, and reference lists were searched to identify articles for inclusion. Two reviewers independently screened literature search results and abstracted data from included studies. Descriptive analysis was conducted. We included 100 articles plus one companion report that were published between 1997 and 2013. The studies were categorized as 84 application papers, seven development papers, six impact papers, and four comparison papers (one was included in two categories). The rapid reviews were conducted between 1 and 12 months, predominantly in Europe (58 %) and North America (20 %). The included studies failed to report 6 % to 73 % of the specific systematic review steps examined. Fifty unique rapid review methods were identified; 16 methods occurred more than once. Streamlined methods that were used in the 82 rapid reviews included limiting the literature search to published literature (24 %) or one database (2 %), limiting inclusion criteria by date (68 %) or language (49 %), having one person screen and another verify or screen excluded studies (6 %), having one person abstract data and another verify (23 %), not conducting risk of bias/quality appraisal (7 %) or having only one reviewer conduct the quality appraisal (7 %), and presenting results as a narrative summary (78 %). Four case studies were identified that compared the results of rapid reviews to systematic reviews. Three studies found that the conclusions between

  13. Homology of the open moduli space of curves

    DEFF Research Database (Denmark)

    Madsen, Ib Henning

    2012-01-01

    This is a survey on the proof of a generalized version of the Mumford conjecture obtained in joint work with M. Weiss stating that a certain map between some classifying spaces which a priori have different natures induces an isomorphism at the level of integral homology. We also discuss our proof...... of the original Mumford conjecture stating that the stable rational cohomology of the moduli space of Riemann surfaces is a certain polynomial algebra generated by the Mumford–Morita–Miller cohomology classes of even degrees....

  14. Parallel Computation of Persistent Homology using the Blowup Complex

    Energy Technology Data Exchange (ETDEWEB)

    Lewis, Ryan [Stanford Univ., CA (United States); Morozov, Dmitriy [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2015-04-27

    We describe a parallel algorithm that computes persistent homology, an algebraic descriptor of a filtered topological space. Our algorithm is distinguished by operating on a spatial decomposition of the domain, as opposed to a decomposition with respect to the filtration. We rely on a classical construction, called the Mayer--Vietoris blowup complex, to glue global topological information about a space from its disjoint subsets. We introduce an efficient algorithm to perform this gluing operation, which may be of independent interest, and describe how to process the domain hierarchically. We report on a set of experiments that help assess the strengths and identify the limitations of our method.

  15. The colocalization transition of homologous chromosomes at meiosis

    Science.gov (United States)

    Nicodemi, Mario; Panning, Barbara; Prisco, Antonella

    2008-06-01

    Meiosis is the specialized cell division required in sexual reproduction. During its early stages, in the mother cell nucleus, homologous chromosomes recognize each other and colocalize in a crucial step that remains one of the most mysterious of meiosis. Starting from recent discoveries on the system molecular components and interactions, we discuss a statistical mechanics model of chromosome early pairing. Binding molecules mediate long-distance interaction of special DNA recognition sequences and, if their concentration exceeds a critical threshold, they induce a spontaneous colocalization transition of chromosomes, otherwise independently diffusing.

  16. A Hochschild homology Euler characteristic for circle actions

    OpenAIRE

    Geoghegan, Ross; Nicas, Andrew

    1998-01-01

    We define a "circle Euler characteristic" of a circle action on a compact manifold or finite complex X. It lies in the first Hochschild homology group of ZG where G is the fundamental group of X. It is analogous in many ways to the ordinary Euler characteristic. One application is an intuitively satisfying formula for the Euler class (integer coefficients) of the normal bundle to a smooth circle action without fixed points on a manifold. In the special case of a 3-dimensional Seifert fibered ...

  17. Integrated vs. Federated Search

    DEFF Research Database (Denmark)

    Løvschall, Kasper

    2009-01-01

    Oplæg om forskelle og ligheder mellem integrated og federated search i bibliotekskontekst. Holdt ved temadag om "Integrated Search - samsøgning i alle kilder" på Danmarks Biblioteksskole den 22. januar 2009.......Oplæg om forskelle og ligheder mellem integrated og federated search i bibliotekskontekst. Holdt ved temadag om "Integrated Search - samsøgning i alle kilder" på Danmarks Biblioteksskole den 22. januar 2009....

  18. Searching with Kids.

    Science.gov (United States)

    Valenza, Joyce Kasman

    2000-01-01

    Discusses student search tools for the World Wide Web and describes and compares seven that are appropriate for pre-kindergarten through secondary school. Highlights include access; age appropriateness; directories versus full search engines; filters; limits of some tools; and adult-oriented search tools that can be limited for students' access.…

  19. Adaptive Large Neighbourhood Search

    DEFF Research Database (Denmark)

    Røpke, Stefan

    Large neighborhood search is a metaheuristic that has gained popularity in recent years. The heuristic repeatedly moves from solution to solution by first partially destroying the solution and then repairing it. The best solution observed during this search is presented as the final solution....... This tutorial introduces the large neighborhood search metaheuristic and the variant adaptive large neighborhood search that dynamically tunes parameters of the heuristic while it is running. Both heuristics belong to a broader class of heuristics that are searching a solution space using very large...

  20. Keyword Search in Databases

    CERN Document Server

    Yu, Jeffrey Xu; Chang, Lijun

    2009-01-01

    It has become highly desirable to provide users with flexible ways to query/search information over databases as simple as keyword search like Google search. This book surveys the recent developments on keyword search over databases, and focuses on finding structural information among objects in a database using a set of keywords. Such structural information to be returned can be either trees or subgraphs representing how the objects, that contain the required keywords, are interconnected in a relational database or in an XML database. The structural keyword search is completely different from

  1. Bloom Syndrome Helicase Promotes Meiotic Crossover Patterning and Homolog Disjunction.

    Science.gov (United States)

    Hatkevich, Talia; Kohl, Kathryn P; McMahan, Susan; Hartmann, Michaelyn A; Williams, Andrew M; Sekelsky, Jeff

    2017-01-09

    In most sexually reproducing organisms, crossover formation between homologous chromosomes is necessary for proper chromosome disjunction during meiosis I. During meiotic recombination, a subset of programmed DNA double-strand breaks (DSBs) are repaired as crossovers, with the remainder becoming noncrossovers [1]. Whether a repair intermediate is designated to become a crossover is a highly regulated decision that integrates several crossover patterning processes, both along chromosome arms (interference and the centromere effect) and between chromosomes (crossover assurance) [2]. Because the mechanisms that generate crossover patterning have remained elusive for over a century, it has been difficult to assess the relationship between crossover patterning and meiotic chromosome behavior. We show here that meiotic crossover patterning is lost in Drosophila melanogaster mutants that lack the Bloom syndrome helicase. In the absence of interference and the centromere effect, crossovers are distributed more uniformly along chromosomes. Crossovers even occur on the small chromosome 4, which normally never has meiotic crossovers [3]. Regulated distribution of crossovers between chromosome pairs is also lost, resulting in an elevated frequency of homologs that do not receive a crossover, which in turn leads to elevated nondisjunction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Ontogeny and homology of the claustra in otophysan Ostariophysi (Teleostei).

    Science.gov (United States)

    Britz, Ralf; Hoffmann, Matthias

    2006-08-01

    We studied the ontogeny of the claustrum comparatively in representatives of all otophysan subgroups. The claustrum of cypriniforms has a cartilaginous precursor, the claustral cartilage, which subsequently ossifies perichondrally at its anterior face and develops an extensive lamina of membrane bone. The membrane bone component of the claustrum and its close association with the atrium sinus imparis, a perilymphatic space of the Weberian apparatus, are both synapomorphies of cypriniforms. The characiform claustrum is not preformed in cartilage and originates as a membrane bone ossification, a putative synapomorphy of that taxon. Among siluriforms, the claustrum is present only in more basal groups and originates as an elongate cartilage that ossifies in a characteristic ventrodorsal direction, possibly a synapomorphy of catfishes. Gymnotiforms lack the claustral cartilage and claustrum. We review all previous hypothesis of claustrum homology in light of the above findings and conclude that the most plausible hypothesis is the one originally proposed by Bloch ([1900] Jen Z Naturw 34:1-64) that claustra are homologs of the supradorsals of the first vertebra. Copyright 2006 Wiley-Liss, Inc.

  3. Change of gene structure and function by non-homologous end-joining, homologous recombination, and transposition of DNA.

    Directory of Open Access Journals (Sweden)

    Wolfgang Goettel

    2009-06-01

    Full Text Available An important objective in genome research is to relate genome structure to gene function. Sequence comparisons among orthologous and paralogous genes and their allelic variants can reveal sequences of functional significance. Here, we describe a 379-kb region on chromosome 1 of maize that enables us to reconstruct chromosome breakage, transposition, non-homologous end-joining, and homologous recombination events. Such a high-density composition of various mechanisms in a small chromosomal interval exemplifies the evolution of gene regulation and allelic diversity in general. It also illustrates the evolutionary pace of changes in plants, where many of the above mechanisms are of somatic origin. In contrast to animals, somatic alterations can easily be transmitted through meiosis because the germline in plants is contiguous to somatic tissue, permitting the recovery of such chromosomal rearrangements. The analyzed region contains the P1-wr allele, a variant of the genetically well-defined p1 gene, which encodes a Myb-like transcriptional activator in maize. The P1-wr allele consists of eleven nearly perfect P1-wr 12-kb repeats that are arranged in a tandem head-to-tail array. Although a technical challenge to sequence such a structure by shotgun sequencing, we overcame this problem by subcloning each repeat and ordering them based on nucleotide variations. These polymorphisms were also critical for recombination and expression analysis in presence and absence of the trans-acting epigenetic factor Ufo1. Interestingly, chimeras of the p1 and p2 genes, p2/p1 and p1/p2, are framing the P1-wr cluster. Reconstruction of sequence amplification steps at the p locus showed the evolution from a single Myb-homolog to the multi-gene P1-wr cluster. It also demonstrates how non-homologous end-joining can create novel gene fusions. Comparisons to orthologous regions in sorghum and rice also indicate a greater instability of the maize genome, probably due to

  4. Protein Alpha Shape (PAS) Dock: a new gaussian-based score function suitable for docking in homology modelled protein structures.

    Science.gov (United States)

    Tøndel, Kristin; Anderssen, Endre; Drabløs, Finn

    2006-03-01

    Protein Alpha Shape (PAS) Dock is a new empirical score function suitable for virtual library screening using homology modelled protein structures. Here, the score function is used in combination with the geometry search method Tabu search. A description of the protein binding site is generated using gaussian property fields like in Protein Alpha Shape Similarity Analysis (PASSA). Gaussian property fields are also used to describe the ligand properties. The overlap between the receptor and ligand hydrophilicity and lipophilicity fields is maximised, while minimising steric clashes. Gaussian functions introduce a smoothing of the property fields. This makes the score function robust against small structural variations, and therefore suitable for use with homology models. This also makes it less critical to include protein flexibility in the docking calculations. We use a fast and simplified version of the score function in the geometry search, while a more detailed version is used for the final prediction of the binding free energies. This use of a two-level scoring makes PAS-Dock computationally efficient, and well suited for virtual screening. The PAS-Dock score function is trained on 218 X-ray structures of protein- ligand complexes with experimental binding affinities. The performance of PAS-Dock is compared to two other docking methods, AutoDock and MOE-Dock, with respect to both accuracy and computational efficiency. According to this study, PAS-Dock is more computationally efficient than both AutoDock and MOE-Dock, and gives a better prediction of the free energies of binding. PAS-Dock is also more robust against structural variations than AutoDock.

  5. Quantum Search Algorithms

    Science.gov (United States)

    Korepin, Vladimir E.; Xu, Ying

    This article reviews recent progress in quantum database search algorithms. The subject is presented in a self-contained and pedagogical way. The problem of searching a large database (a Hilbert space) for a target item is performed by the famous Grover algorithm which locates the target item with high probability and a quadratic speed-up compared with the corresponding classical algorithm. If the database is partitioned into blocks and one is searching for the block containing the target item instead of the target item itself, then the problem is referred to as partial search. Partial search trades accuracy for speed and the most efficient version is the Grover-Radhakrishnan-Korepin (GRK) algorithm. The target block can be further partitioned into sub-blocks so that GRK's can be performed in a sequence called a hierarchy. We study the Grover search and GRK partial search in detail and prove that a GRK hierarchy is less efficient than a direct GRK partial search. Both the Grover search and the GRK partial search can be generalized to the case with several target items (or target blocks for a GRK). The GRK partial search algorithm can also be represented in terms of group theory.

  6. Homologous recombination and non-homologous end-joining repair pathways in bovine embryos with different developmental competence

    Energy Technology Data Exchange (ETDEWEB)

    Henrique Barreta, Marcos [Universidade Federal de Santa Catarina, Campus Universitario de Curitibanos, Curitibanos, SC (Brazil); Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Garziera Gasperin, Bernardo; Braga Rissi, Vitor; Cesaro, Matheus Pedrotti de [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Ferreira, Rogerio [Centro de Educacao Superior do Oeste-Universidade do Estado de Santa Catarina, Chapeco, SC (Brazil); Oliveira, Joao Francisco de; Goncalves, Paulo Bayard Dias [Laboratorio de Biotecnologia e Reproducao Animal-BioRep, Universidade Federal de Santa Maria, Santa Maria, RS (Brazil); Bordignon, Vilceu, E-mail: vilceu.bordignon@mcgill.ca [Department of Animal Science, McGill University, Ste-Anne-De-Bellevue, QC (Canada)

    2012-10-01

    This study investigated the expression of genes controlling homologous recombination (HR), and non-homologous end-joining (NHEJ) DNA-repair pathways in bovine embryos of different developmental potential. It also evaluated whether bovine embryos can respond to DNA double-strand breaks (DSBs) induced with ultraviolet irradiation by regulating expression of genes involved in HR and NHEJ repair pathways. Embryos with high, intermediate or low developmental competence were selected based on the cleavage time after in vitro insemination and were removed from in vitro culture before (36 h), during (72 h) and after (96 h) the expected period of embryonic genome activation. All studied genes were expressed before, during and after the genome activation period regardless the developmental competence of the embryos. Higher mRNA expression of 53BP1 and RAD52 was found before genome activation in embryos with low developmental competence. Expression of 53BP1, RAD51 and KU70 was downregulated at 72 h and upregulated at 168 h post-insemination in response to DSBs induced by ultraviolet irradiation. In conclusion, important genes controlling HR and NHEJ DNA-repair pathways are expressed in bovine embryos, however genes participating in these pathways are only regulated after the period of embryo genome activation in response to ultraviolet-induced DSBs.

  7. Book Review: Web Search-Public Searching of the Web

    OpenAIRE

    Yazdan Mansourian

    2004-01-01

    The book consists of four sections including (1) the context of web search, (2) how people search the web, (3) subjects of web search and (4) conclusion: trends and future directions. The first section includes three chapters addressing a brief but informative introduction about the main involved elements of web search process and web search research including search engines mechanism, human computer interaction in web searching and research design in web search studies.

  8. High-Risk Alphapapillomavirus Oncogenes Impair the Homologous Recombination Pathway.

    Science.gov (United States)

    Wallace, Nicholas A; Khanal, Sujita; Robinson, Kristin L; Wendel, Sebastian O; Messer, Joshua J; Galloway, Denise A

    2017-10-15

    Persistent high-risk genus human Alphapapillomavirus (HPV) infections cause nearly every cervical carcinoma and a subset of tumors in the oropharyngeal tract. During the decades required for HPV-associated tumorigenesis, the cellular genome becomes significantly destabilized. Our analysis of cervical tumors from four separate data sets found a significant upregulation of the homologous-recombination (HR) pathway genes. The increased abundance of HR proteins can be replicated in primary cells by expression of the two HPV oncogenes (E6 and E7) required for HPV-associated transformation. HPV E6 and E7 also enhanced the ability of HR proteins to form repair foci, and yet both E6 and E7 reduce the ability of the HR pathway to complete double-strand break (DSB) repair by about 50%. The HPV oncogenes hinder HR by allowing the process to begin at points in the cell cycle when the lack of a sister chromatid to serve as a homologous template prevents completion of the repair. Further, HPV E6 attenuates repair by causing RAD51 to be mislocalized away from both transient and persistent DSBs, whereas HPV E7 is only capable of impairing RAD51 localization to transient lesions. Finally, we show that the inability to robustly repair DSBs causes some of these lesions to be more persistent, a phenotype that correlates with increased integration of episomal DNA. Together, these data support our hypothesis that HPV oncogenes contribute to the genomic instability observed in HPV-associated malignancies by attenuating the repair of damaged DNA.IMPORTANCE This study expands the understanding of HPV biology, establishing a direct role for both HPV E6 and E7 in the destabilization of the host genome by blocking the homologous repair of DSBs. To our knowledge, this is the first time that both viral oncogenes were shown to disrupt this DSB repair pathway. We show that HPV E6 and E7 allow HR to initiate at an inappropriate part of the cell cycle. The mislocalization of RAD51 away from DSBs in

  9. Evolution, homology conservation, and identification of unique sequence signatures in GH19 family chitinases.

    Science.gov (United States)

    Udaya Prakash, N A; Jayanthi, M; Sabarinathan, R; Kangueane, P; Mathew, Lazar; Sekar, K

    2010-05-01

    The discovery of GH (Glycoside Hydrolase) 19 chitinases in Streptomyces sp. raises the possibility of the presence of these proteins in other bacterial species, since they were initially thought to be confined to higher plants. The present study mainly concentrates on the phylogenetic distribution and homology conservation in GH19 family chitinases. Extensive database searches are performed to identify the presence of GH19 family chitinases in the three major super kingdoms of life. Multiple sequence alignment of all the identified GH19 chitinase family members resulted in the identification of globally conserved residues. We further identified conserved sequence motifs across the major sub groups within the family. Estimation of evolutionary distance between the various bacterial and plant chitinases are carried out to better understand the pattern of evolution. Our study also supports the horizontal gene transfer theory, which states that GH19 chitinase genes are transferred from higher plants to bacteria. Further, the present study sheds light on the phylogenetic distribution and identifies unique sequence signatures that define GH19 chitinase family of proteins. The identified motifs could be used as markers to delineate uncharacterized GH19 family chitinases. The estimation of evolutionary distance between chitinase identified in plants and bacteria shows that the flowering plants are more related to chitinase in actinobacteria than that of identified in purple bacteria. We propose a model to elucidate the natural history of GH19 family chitinases.

  10. [Advanced online search techniques and dedicated search engines for physicians].

    Science.gov (United States)

    Nahum, Yoav

    2008-02-01

    In recent years search engines have become an essential tool in the work of physicians. This article will review advanced search techniques from the world of information specialists, as well as some advanced search engine operators that may help physicians improve their online search capabilities, and maximize the yield of their searches. This article also reviews popular dedicated scientific and biomedical literature search engines.

  11. University Students' Online Information Searching Strategies in Different Search Contexts

    Science.gov (United States)

    Tsai, Meng-Jung; Liang, Jyh-Chong; Hou, Huei-Tse; Tsai, Chin-Chung

    2012-01-01

    This study investigates the role of search context played in university students' online information searching strategies. A total of 304 university students in Taiwan were surveyed with questionnaires in which two search contexts were defined as searching for learning, and searching for daily life information. Students' online search strategies…

  12. Flexoelectric and elastic coefficients of odd and even homologous bimesogens

    Science.gov (United States)

    Atkinson, Katie L.; Morris, Stephen M.; Castles, Flynn; Qasim, Malik M.; Gardiner, Damian J.; Coles, Harry J.

    2012-01-01

    It is known that bimesogenic liquid crystals exhibit a marked “odd-even” effect in the flexoelastic ratio (the effective flexoelectric coefficient to the average elastic coefficient), with the ratio being higher for the “odd-spaced” bimesogens (those with an odd number of alkyl groups in the spacer chain) than their neighboring even-spaced counterparts. To determine the contribution of each property to the flexoelastic ratio, we present experimental results on the flexoelectric and elastic coefficients of two homologous nonsymmetric bimesogens which possess odd and even alkyl spacers. Our results show that, although there are differences in the flexoelectric coefficients, there are substantially larger differences in the effective elastic coefficient. Specifically, the odd bimesogen is found to have both a low splay elastic coefficient and a very low bend elastic coefficient which, when combined, results in a significantly lower effective elastic coefficient and consequently a higher flexoelastic ratio.

  13. Supersensitive gastrin assay using antibodies raised against a cholecystokinin homolog.

    Science.gov (United States)

    Rehfeld, Jens F; Ericsson, Peter

    2012-04-01

    Peptide hormones may occur in particularly low amounts in samples from small animals. Hence, in a rat microdialysis study conventional immunoassays were not sufficiently sensitive to measure gastrin in the dialysis samples. We therefore exploited the observation that antibodies raised against the homologous hormone cholecystokinin (CCK) occasionally bind gastrin peptides with significantly higher affinity than the proper ligand. The immunoassay thus established could detect 1.0 pmol/l in 15 μl microdialysate, which corresponds to 23 attomol gastrin. Such detection limit is five-fold lower than that obtained with the most avid conventional gastrin antibodies. The results may encourage similar approaches for other peptides using homologue-raised antibodies when supersensitivity is required.

  14. Supersensitive gastrin assay using antibodies raised against a cholecystokinin homolog

    DEFF Research Database (Denmark)

    Rehfeld, Jens F; Ericsson, Peter

    2012-01-01

    Peptide hormones may occur in particularly low amounts in samples from small animals. Hence, in a rat microdialysis study conventional immunoassays were not sufficiently sensitive to measure gastrin in the dialysis samples. We therefore exploited the observation that antibodies raised against...... the homologous hormone cholecystokinin (CCK) occasionally bind gastrin peptides with significantly higher affinity than the proper ligand. The immunoassay thus established could detect 1.0 pmol/l in 15 μl microdialysate, which corresponds to 23 attomol gastrin. Such detection limit is five-fold lower than...... that obtained with the most avid conventional gastrin antibodies. The results may encourage similar approaches for other peptides using homologue-raised antibodies when supersensitivity is required....

  15. Homology models of main proteinase from coronavirus associated with SARS

    Science.gov (United States)

    Liu, Hsuan-Liang; Lin, Jin-Chung; Ho, Yih; Chen, Chin-Wen

    2005-01-01

    In this study, two homology models of the main proteinase (M pro) from the novel coronavirus associated with severe acute respiratory syndrome (SARS-CoV) were constructed. These models reveal three distinct functional domains, in which an intervening loop connecting domains II and III as well as a catalytic cleft containing the substrate binding subsites S1 and S2 between domains I and II are observed. S2 exhibits structural variations more significantly than S1 during the 200 ps molecular dynamics simulations because it is located at the open mouth of the catalytic cleft and the amino acid residues lining up this subsite are least conserved. In addition, the higher structural variation of S2 makes it flexible enough to accommodate a bulky hydrophobic residue from the substrate.

  16. Representation theory a homological algebra point of view

    CERN Document Server

    Zimmermann, Alexander

    2014-01-01

      Introducing the representation theory of groups and finite dimensional algebras, this book first studies basic non-commutative ring theory, covering the necessary background of elementary homological algebra and representations of groups to block theory. It further discusses vertices, defect groups, Green and Brauer correspondences and Clifford theory. Whenever possible the statements are presented in a general setting for more general algebras, such as symmetric finite dimensional algebras over a field. Then, abelian and derived categories are introduced in detail and are used to explain stable module categories, as well as derived categories and their main invariants and links between them. Group theoretical applications of these theories are given – such as the structure of blocks of cyclic defect groups – whenever appropriate. Overall, many methods from the representation theory of algebras are introduced. Representation Theory assumes only the most basic knowledge of linear algebra, groups, rings ...

  17. Homologies and homeotic transformation of the theropod 'semilunate' carpal.

    Science.gov (United States)

    Xu, Xing; Han, Fenglu; Zhao, Qi

    2014-08-13

    The homology of the 'semilunate' carpal, an important structure linking non-avian and avian dinosaurs, has been controversial. Here we describe the morphology of some theropod wrists, demonstrating that the 'semilunate' carpal is not formed by the same carpal elements in all theropods possessing this feature and that the involvement of the lateralmost distal carpal in forming the 'semilunate' carpal of birds is an inheritance from their non-avian theropod ancestors. Optimization of relevant morphological features indicates that these features evolved in an incremental way and the 'semilunate' structure underwent a lateral shift in position during theropod evolution, possibly as a result of selection for foldable wings in birds and their close theropod relatives. We propose that homeotic transformation was involved in the evolution of the 'semilunate' carpal. In combination with developmental data on avian wing digits, this suggests that homeosis played a significant role in theropod hand evolution in general.

  18. Functional roles of enhancer of zeste homolog 2 in gliomas.

    Science.gov (United States)

    Yin, Yatao; Qiu, Shuwei; Peng, Ying

    2016-01-15

    Gliomas are the most common and lethal type of primary malignant brain tumor. Due to the infiltrative nature and high resistance to standard first line treatment with combinations of radiation and chemotherapy, the prognosis of patient is very poor. Recently, accumulated evidence suggests that enhancer of zeste homolog 2 (EZH2) serves as an oncogene and is involved in multiple glioma cell processes, including cell cycle, invasion, glioma stem cell maintenance, drug and radiotherapy resistance and so on. In this review, we will focus on updating current knowledge of EZH2 in gliomas. Moreover, the regulation of EZH2 by microRNAs and long non-coding RNAs and the therapeutic strategies targeting EZH2 for gliomas will also be discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Crystal Structure of a Fructokinase Homolog from Halothermothrix orenii

    Energy Technology Data Exchange (ETDEWEB)

    Khiang, C.; Seetharaman, J; Kasprzak, J; Cherlyn, N; Patel, B; Love, C; Bujnicki, J; Sivaraman, J

    2010-01-01

    Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of D-fructose to D-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrix orenii (Hore{_}18220 in sequence databases). The structure of the Hore{_}18220 protein reveals a catalytic domain with a Rossmann-like fold and a b-sheet 'lid' for dimerization. Based on comparison of Hore{_}18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore{_}18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.

  20. On the homology of the shoulder girdle in turtles.

    Science.gov (United States)

    Nagashima, Hiroshi; Sugahara, Fumiaki; Takechi, Masaki; Sato, Noboru; Kuratani, Shigeru

    2015-05-01

    The shoulder girdle in turtles is encapsulated in the shell and has a triradiate morphology. Due to its unique configuration among amniotes, many theories have been proposed about the skeletal identities of the projections for the past two centuries. Although the dorsal ramus represents the scapular blade, the ventral two rami remain uncertain. In particular, the ventrorostral process has been compared to a clavicle, an acromion, and a procoracoid based on its morphology, its connectivity to the rest of the skeleton and to muscles, as well as with its ossification center, cell lineage, and gene expression. In making these comparisons, the shoulder girdle skeleton of anurans has often been used as a reference. This review traces the history of the debate on the homology of the shoulder girdle in turtles. And based on the integrative aspects of developmental biology, comparative morphology, and paleontology, we suggest acromion and procoracoid identities for the two ventral processes. © 2014 Wiley Periodicals, Inc.

  1. DEK is required for homologous recombination repair of DNA breaks

    DEFF Research Database (Denmark)

    Smith, Eric A; Gole, Boris; Willis, Nicholas A

    2017-01-01

    DEK is a highly conserved chromatin-bound protein whose upregulation across cancer types correlates with genotoxic therapy resistance. Loss of DEK induces genome instability and sensitizes cells to DNA double strand breaks (DSBs), suggesting defects in DNA repair. While these DEK-deficiency pheno......DEK is a highly conserved chromatin-bound protein whose upregulation across cancer types correlates with genotoxic therapy resistance. Loss of DEK induces genome instability and sensitizes cells to DNA double strand breaks (DSBs), suggesting defects in DNA repair. While these DEK......-deficiency phenotypes were thought to arise from a moderate attenuation of non-homologous end joining (NHEJ) repair, the role of DEK in DNA repair remains incompletely understood. We present new evidence demonstrating the observed decrease in NHEJ is insufficient to impact immunoglobulin class switching in DEK knockout...

  2. Search on Rugged Landscapes

    DEFF Research Database (Denmark)

    Billinger, Stephan; Stieglitz, Nils; Schumacher, Terry

    2014-01-01

    This paper presents findings from a laboratory experiment on human decision-making in a complex combinatorial task. We find strong evidence for a behavioral model of adaptive search. Success narrows down search to the neighborhood of the status quo, while failure promotes gradually more explorative...... search. Task complexity does not have a direct effect on behavior, but systematically affects the feedback conditions that guide success-induced exploitation and failure-induced exploration. The analysis also shows that human participants were prone to over-exploration, since they broke off the search...... for local improvements too early. We derive stylized decision rules that generate the search behavior observed in the experiment and discuss the implications of our findings for individual decision-making and organizational search....

  3. Supporting complex search tasks

    DEFF Research Database (Denmark)

    Gäde, Maria; Hall, Mark; Huurdeman, Hugo

    2015-01-01

    There is broad consensus in the field of IR that search is complex in many use cases and applications, both on the Web and in domain specific collections, and both professionally and in our daily life. Yet our understanding of complex search tasks, in comparison to simple look up tasks......, is fragmented at best. The workshop addressed the many open research questions: What are the obvious use cases and applications of complex search? What are essential features of work tasks and search tasks to take into account? And how do these evolve over time? With a multitude of information, varying from...... introductory to specialized, and from authoritative to speculative or opinionated, when to show what sources of information? How does the information seeking process evolve and what are relevant differences between different stages? With complex task and search process management, blending searching, browsing...

  4. Homology and evolution of the chaetae in Echiura (Annelida).

    Science.gov (United States)

    Tilic, Ekin; Lehrke, Janina; Bartolomaeus, Thomas

    2015-01-01

    Echiura is traditionally regarded as a small phylum of unsegmented spiralian worms. Molecular analyses, however, provide unquestionable evidence that Echiura are derived annelids that lost segmentation. Like annelids, echiurans possess chaetae, a single ventral pair in all species and one or two additional caudal hemi-circles of chaetae in two subgroups, but their evolutionary origin and affiliation to annelid chaetae are unresolved. Since annelids possess segmental pairs of dorsal (notopodial) and ventral (neuropodial) chaetae that are arranged in a row, the ventral chaetae in Echiura either represent a single or a paired neuropodial group of chaetae, while the caudal circle may represent fused rows of chaetae. In annelids, chaetogenesis is generally restricted to the ventral part of the notopodial chaetal sac and to the dorsal part of the neuropodial chaetal sac. We used the exact position of the chaetal formation site in the echiuran species, Thalassema thalassemum (Pallas, 1766) and Echiurus echiurus (Pallas, 1767), to test different hypotheses of the evolution of echiurid chaetae. As in annelids, a single chaetoblast is responsible for chaetogenesis in both species. Each chaeta of the ventral pair arises from its own chaetal sac and possesses a lateral formation site, evidencing that the pair of ventral chaetae in Echiura is homologous to a pair of neuropodia that fused on the ventral side, while the notopodia were reduced. Both caudal hemi-circles of chaetae in Echiurus echiurus are composed of several individual chaetal sacs, each with its own formative site. This finding argues against a homology of these hemi-circles of chaetae and annelids' rows of chaetae and leads to the hypothesis that the caudal chaetal rings evolved once within the Echiura by multiplication of ventral chaetae.

  5. Reaktivitas Antibodi Poliklonal SSV terhadap Antigen Homolog dan Heterolog

    Directory of Open Access Journals (Sweden)

    Sri Sulandari

    1998-07-01

    Full Text Available Polyclonal antibodies for Soybean Stunt Virus (SSV were produced in white rabbit through the following procedures: approximately 100 mg of purified virions emulsified in Complete Freund’s Adjuvant (CFA were injected intramuscularly first. In the second and third injection 150 mg of purified virions in Incomplete Freund’s Adjuvant (IFA per injection were injected intramuscularly. Finally, about 300 mg of purified virions were injected intravenously as a booster. The injection were done at 2 weeks interval. Antiserum was collected 5 days after the final injection. Antisera was purified by precipitation in saturated ammonium sulfate. Purified antibody was tested for the titer and reactivity of antibodies against the homologous and heterologous antigen. The studies were conducted with non-precoated I-ELISA test. This research was able to obtain about 25 ml of crude antisera for SSV, the concentration of purified polyclonal antibodies was about 9 mg/ml. the titer of polyclonal antibodies was 10.000 in I-ELISA. Without absorbtion with sap of healthy plant, the antibodies could not be use to identify the infected and healthy plant samples. In the following test, the absorbed antibody was used. Using antibodies to SSV at a dilution of 1:1000 and 1:10.000 against sap extracts sample of healthy and infected plant at a dilution of 1:10 by non-precoated I-ELISA test, indicated that the antibody could be used to identify the healthy and infected samples. By the same test, the antibody could be reacted to both homologous antigen (SSV and heterologous antigen (CMV isolated from banana. Key words: SSV, polyclonal antibodies, ELISA

  6. Is homologous recombination really an error-free process?

    Directory of Open Access Journals (Sweden)

    Bernard S Lopez

    2014-06-01

    Full Text Available Homologous recombination (HR is an evolutionarily conserved process that plays a pivotal role in the equilibrium between genetic stability and diversity. HR is commonly considered to be error-free, but several studies have shown that HR can be error-prone. Here, we discuss the actual accuracy of HR.First, we present the product of genetic exchanges (gene conversion, GC, and crossing over, CO and the mechanisms of HR during double strand break repair and replication restart. We discuss the intrinsic capacities of HR to generate genome rearrangements by GC or CO, either during DSB repair or replication restart. During this process, abortive HR intermediates generate genetic instability and cell toxicity. In addition to genome rearrangements, HR also primes error-prone DNA synthesis and favors mutagenesis on single stranded DNA, a key DNA intermediate during the HR process. The fact that cells have developed several mechanisms protecting against HR excess emphasize its potential risks. Consistent with this duality, several pro-oncogenic situations have been consistently associated with either decreased or increased HR levels. Nevertheless, this versatility also has advantages that we outline here.We conclude that HR is a double-edged sword, which on one hand controls the equilibrium between genome stability and diversity but, on the other hand, can jeopardize the maintenance of genomic integrity. Therefore, whether non-homologous end joining (which, in contrast with HR, is not intrinsically mutagenic or HR is the more mutagenic process is a question that should be re-evaluated. Both processes can be Dr. Jekyll in maintaining genome stability/variability and Mr. Hyde in jeopardizing genome integrity.

  7. Analyses of homologous rotavirus infection in the mouse model.

    Science.gov (United States)

    Burns, J W; Krishnaney, A A; Vo, P T; Rouse, R V; Anderson, L J; Greenberg, H B

    1995-02-20

    The group A rotaviruses are significant human and veterinary pathogens in terms of morbidity, mortality, and economic loss. Despite its importance, an effective vaccine remains elusive due at least in part to our incomplete understanding of rotavirus immunity and protection. Both large and small animal model systems have been established to address these issues. One significant drawback of these models is the lack of well-characterized wild-type homologous viruses and their cell culture-adapted variants. We have characterized four strains of murine rotaviruses, EC, EHP, EL, and EW, in the infant and adult mouse model using wild-type isolates and cell culture-adapted variants of each strain. Wild-type murine rotaviruses appear to be equally infectious in infant and adult mice in terms of the intensity and duration of virus shedding following primary infection. Spread of infection to naive cagemates is seen in both age groups. Clearance of shedding following primary infection appears to correlate with the development of virus-specific intestinal IgA. Protective immunity is developed in both infant and adult mice following oral infection as demonstrated by a lack of shedding after subsequent wild-type virus challenge. Cell culture-adapted murine rotaviruses appear to be highly attenuated when administered to naive animals and do not spread efficiently to nonimmune cagemates. The availability of these wild-type and cell culture-adapted virus preparations should allow a more systematic evaluation of rotavirus infection and immunity. Furthermore, future vaccine strategies can be evaluated in the mouse model using several fully virulent homologous viruses for challenge.

  8. Gene expression and digit homology in the chicken embryo wing.

    Science.gov (United States)

    Welten, Monique C M; Verbeek, Fons J; Meijer, Annemarie H; Richardson, Michael K

    2005-01-01

    The bird wing is of special interest to students of homology and avian evolution. Fossil and developmental data give conflicting indications of digit homology if a pentadactyl "archetype" is assumed. Morphological signs of a vestigial digit I are seen in bird embryos, but no digit-like structure develops in wild-type embryos. To examine the developmental mechanisms of digit loss, we studied the expression of the high-mobility group box containing Sox9 gene, and bone morphogenetic protein receptor 1b (bmpR-1b)-markers for precondensation and prechondrogenic cells, respectively. We find an elongated domain of Sox9 expression, but no bmpR-1b expression, anterior to digit II. We interpret this as a digit I domain that reaches precondensation, but not condensation or precartilage stages. It develops late, when the tissue in which it is lodged is being remodeled. We consider these findings in the light of previous Hoxd-11 misexpression studies. Together, they suggest that there is a digit I vestige in the wing that can be rescued and undergo development if posterior patterning cues are enhanced. We observed Sox9 expression in the elusive "element X" that is sometimes stated to represent a sixth digit. Indeed, incongruity between digit domains and identities in theropods disappears if birds and other archosaurs are considered primitively polydactyl. Our study provides the first gene expression evidence for at least five digital domains in the chick wing. The failure of the first to develop may be plausibly linked to attenuation of posterior signals.

  9. Inhibition of homologous recombination with vorinostat synergistically enhances ganciclovir cytotoxicity.

    Science.gov (United States)

    Ladd, Brendon; Ackroyd, Jeffrey J; Hicks, J Kevin; Canman, Christine E; Flanagan, Sheryl A; Shewach, Donna S

    2013-12-01

    The nucleoside analog ganciclovir (GCV) elicits cytotoxicity in tumor cells via a novel mechanism in which drug incorporation into DNA produces minimal disruption of replication, but numerous DNA double strand breaks occur during the second S-phase after drug exposure. We propose that homologous recombination (HR), a major repair pathway for DNA double strand breaks, can prevent GCV-induced DNA damage, and that inhibition of HR will enhance cytotoxicity with GCV. Survival after GCV treatment in cells expressing a herpes simplex virus thymidine kinase was strongly dependent on HR (>14-fold decrease in IC50 in HR-deficient vs. HR-proficient CHO cells). In a homologous recombination reporter assay, the histone deacetylase inhibitor, suberoylanilide hydroxamic acid (SAHA; vorinostat), decreased HR repair events up to 85%. SAHA plus GCV produced synergistic cytotoxicity in U251tk human glioblastoma cells. Elucidation of the synergistic mechanism demonstrated that SAHA produced a concentration-dependent decrease in the HR proteins Rad51 and CtIP. GCV alone produced numerous Rad51 foci, demonstrating activation of HR. However, the addition of SAHA blocked GCV-induced Rad51 foci formation completely and increased γH2AX, a marker of DNA double strand breaks. SAHA plus GCV also produced synergistic cytotoxicity in HR-proficient CHO cells, but the combination was antagonistic or additive in HR-deficient CHO cells. Collectively, these data demonstrate that HR promotes survival with GCV and compromise of HR by SAHA results in synergistic cytotoxicity, revealing a new mechanism for enhancing anticancer activity with GCV. Copyright © 2013 Elsevier B.V. All rights reserved.

  10. Homologous Circular-ribbon Flares Driven by Twisted Flux Emergence

    Science.gov (United States)

    Xu, Z.; Yang, K.; Guo, Y.; Zhao, J.; Zhao, Z. J.; Kashapova, L.

    2017-12-01

    In this paper, we report two homologous circular-ribbon flares associated with two filament eruptions. They were well observed by the New Vacuum Solar Telescope and the Solar Dynamics Observatory on 2014 March 5. Prior to the flare, two small-scale filaments enclosed by a circular pre-flare brightening lie along the circular polarity inversion line around the parasitic polarity, which has shown a continuous rotation since its first appearance. Two filaments eventually erupt in sequence associated with two homologous circular-ribbon flares and display an apparent writhing signature. Supplemented by the nonlinear force-free field extrapolation and the magnetic field squashing factor investigation, the following are revealed. (1) This event involves the emergence of magnetic flux ropes into a pre-existing polarity area, which yields the formation of a 3D null-point topology in the corona. (2) Continuous input of the free energy in the form of a flux rope from beneath the photosphere may drive a breakout-type reconnection occurring high in the corona, supported by the pre-flare brightening. (3) This initiation reconnection could release the constraint on the flux rope and trigger the MHD instability to first make filament F1 lose equilibrium. The subsequent more violent magnetic reconnection with the overlying flux is driven during the filament rising. In return, the eruption of filament F2 is further facilitated by the reduction of the magnetic tension force above. These two processes form a positive feedback to each other to cause the energetic mass eruption and flare.

  11. Homology and Evolution of the Chaetae in Echiura (Annelida)

    Science.gov (United States)

    Tilic, Ekin; Lehrke, Janina; Bartolomaeus, Thomas

    2015-01-01

    Echiura is traditionally regarded as a small phylum of unsegmented spiralian worms. Molecular analyses, however, provide unquestionable evidence that Echiura are derived annelids that lost segmentation. Like annelids, echiurans possess chaetae, a single ventral pair in all species and one or two additional caudal hemi-circles of chaetae in two subgroups, but their evolutionary origin and affiliation to annelid chaetae are unresolved. Since annelids possess segmental pairs of dorsal (notopodial) and ventral (neuropodial) chaetae that are arranged in a row, the ventral chaetae in Echiura either represent a single or a paired neuropodial group of chaetae, while the caudal circle may represent fused rows of chaetae. In annelids, chaetogenesis is generally restricted to the ventral part of the notopodial chaetal sac and to the dorsal part of the neuropodial chaetal sac. We used the exact position of the chaetal formation site in the echiuran species, Thalassema thalassemum (Pallas, 1766) and Echiurus echiurus (Pallas, 1767), to test different hypotheses of the evolution of echiurid chaetae. As in annelids, a single chaetoblast is responsible for chaetogenesis in both species. Each chaeta of the ventral pair arises from its own chaetal sac and possesses a lateral formation site, evidencing that the pair of ventral chaetae in Echiura is homologous to a pair of neuropodia that fused on the ventral side, while the notopodia were reduced. Both caudal hemi-circles of chaetae in Echiurus echiurus are composed of several individual chaetal sacs, each with its own formative site. This finding argues against a homology of these hemi-circles of chaetae and annelids’ rows of chaetae and leads to the hypothesis that the caudal chaetal rings evolved once within the Echiura by multiplication of ventral chaetae. PMID:25734664

  12. ElasticSearch cookbook

    CERN Document Server

    Paro, Alberto

    2013-01-01

    Written in an engaging, easy-to-follow style, the recipes will help you to extend the capabilities of ElasticSearch to manage your data effectively.If you are a developer who implements ElasticSearch in your web applications, manage data, or have decided to start using ElasticSearch, this book is ideal for you. This book assumes that you've got working knowledge of JSON and Java

  13. Mastering ElasticSearch

    CERN Document Server

    Kuc, Rafal

    2013-01-01

    A practical tutorial that covers the difficult design, implementation, and management of search solutions.Mastering ElasticSearch is aimed at to intermediate users who want to extend their knowledge about ElasticSearch. The topics that are described in the book are detailed, but we assume that you already know the basics, like the query DSL or data indexing. Advanced users will also find this book useful, as the examples are getting deep into the internals where it is needed.

  14. Demystifying the Search Button

    Science.gov (United States)

    McKeever, Liam; Nguyen, Van; Peterson, Sarah J.; Gomez-Perez, Sandra

    2015-01-01

    A thorough review of the literature is the basis of all research and evidence-based practice. A gold-standard efficient and exhaustive search strategy is needed to ensure all relevant citations have been captured and that the search performed is reproducible. The PubMed database comprises both the MEDLINE and non-MEDLINE databases. MEDLINE-based search strategies are robust but capture only 89% of the total available citations in PubMed. The remaining 11% include the most recent and possibly relevant citations but are only searchable through less efficient techniques. An effective search strategy must employ both the MEDLINE and the non-MEDLINE portion of PubMed to ensure all studies have been identified. The robust MEDLINE search strategies are used for the MEDLINE portion of the search. Usage of the less robust strategies is then efficiently confined to search only the remaining 11% of PubMed citations that have not been indexed for MEDLINE. The current article offers step-by-step instructions for building such a search exploring methods for the discovery of medical subject heading (MeSH) terms to search MEDLINE, text-based methods for exploring the non-MEDLINE database, information on the limitations of convenience algorithms such as the “related citations feature,” the strengths and pitfalls associated with commonly used filters, the proper usage of Boolean operators to organize a master search strategy, and instructions for automating that search through “MyNCBI” to receive search query updates by email as new citations become available. PMID:26129895

  15. Rapid maxillary expansion treatment could produce long-term dental arch changes

    NARCIS (Netherlands)

    Ren, Yijin

    2005-01-01

    : Data Sources: Medline, Medline In-Process, LILACS (Latin American and Caribbean Health Sciences Literature), PUBMED, Embase, Web of Science and the Cochrane Library were searched. Search terms were rapid palatal expansion or rapid maxillary expansion (RME) and tooth or dental changes. Reference

  16. Exotic Higgs searches

    CERN Document Server

    Pelliccioni, Mario

    2016-01-01

    Exotic Higgs searches cover a wide range of signatures, thus leading to indications to new physics beyond Standard Model. We report a review on exotic Higgs searches for lepton flavour violating Higgs decays, for "mono-Higgs" searches, for Higgs decays to invisible and for high mass Higgs searches. Both ATLAS and CMS results will be shown, for Run-1 data statistics collected at the energy of $\\sqrt s$ = 7,8 TeV and for the first data collected during Run-2 phase at the energy of $\\sqrt s$ = 13 TeV.

  17. Google Power Search

    CERN Document Server

    Spencer, Stephan

    2011-01-01

    Behind Google's deceptively simple interface is immense power for both market and competitive research-if you know how to use it well. Sure, basic searches are easy, but complex searches require specialized skills. This concise book takes you through the full range of Google's powerful search-refinement features, so you can quickly find the specific information you need. Learn techniques ranging from simple Boolean logic to URL parameters and other advanced tools, and see how they're applied to real-world market research examples. Incorporate advanced search operators such as filetype:, intit

  18. Delaying information search

    Directory of Open Access Journals (Sweden)

    Yaniv Shani

    2012-11-01

    Full Text Available In three studies, we examined factors that may temporarily attenuate information search. People are generally curious and dislike uncertainty, which typically encourages them to look for relevant information. Despite these strong forces that promote information search, people sometimes deliberately delay obtaining valuable information. We find they may do so when they are concerned that the information might interfere with future pleasurable activities. Interestingly, the decision to search or to postpone searching for information is influenced not only by the value and importance of the information itself but also by well-being maintenance goals related to possible detrimental effects that negative knowledge may have on unrelated future plans.

  19. Searching the Online catalog and the World Wide Web

    Directory of Open Access Journals (Sweden)

    Shu-Hsien L. Chen

    2003-09-01

    Full Text Available The article discusses the searching behaviors of school children using the online catalog and the World Wide Web. The amount of information and search capability for the online catalog and the World Wide Web, though, differ to a great extent, students share several common problems in using them. They have problems in spelling and typing, phrasing of search terms, extracting key concept, formulating search strategy, and evaluating search results. Their specific problems of searching the World Wide Web include rapid navigation of the Internet, overuse of Back button and browsing strategy, and evaluating only the first screen. Teachers and media specialists need to address these problems in the instruction of information literacy skills so that students can fully utilize the power of online searching and become efficient information searchers.

  20. Possible quantum algorithm for the Lipshitz-Sarkar-Steenrod square for Khovanov homology

    Science.gov (United States)

    Ospina, Juan

    2013-05-01

    Recently the celebrated Khovanov Homology was introduced as a target for Topological Quantum Computation given that the Khovanov Homology provides a generalization of the Jones polynomal and then it is possible to think about of a generalization of the Aharonov.-Jones-Landau algorithm. Recently, Lipshitz and Sarkar introduced a space-level refinement of Khovanov homology. which is called Khovanov Homotopy. This refinement induces a Steenrod square operation Sq2 on Khovanov homology which they describe explicitly and then some computations of Sq2 were presented. Particularly, examples of links with identical integral Khovanov homology but with distinct Khovanov homotopy types were showed. In the presente work we will introduce possible quantum algorithms for the Lipshitz- Sarkar-Steenrod square for Khovanov Homolog and their possible simulations using computer algebra.

  1. What makes homologous chromosomes find each other in meiosis? A review and an hypothesis.

    Science.gov (United States)

    Sybenga, J

    1999-08-01

    The conditions re reviewed that must be met by any model of long distance attraction and transport of homologous chromosomes to the points of intimate DNA synapsis. A proposal for possible mechanisms is presented. It includes transcription and repair factors acting on coding sequences as a preparatory step toward pairing, and the attachment of specific pairing proteins to these sequences. Double-strand break formation is prepared but not immediately completed at the same sites. It is concluded that DNA-DNA interactions cannot bridge the distances between homologous chromosomes in the nucleus, and it is suggested that protein chains are formed between homologous segments. These attach to homologous chains emanating from homologous sequences in other chromosomes, and the chains move along each other until the homologous DNA sequences meet. Then, if required, a synaptonemal complex is formed, and exchange can take place.

  2. Rapid Prototyping Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The ARDEC Rapid Prototyping (RP) Laboratory was established in December 1992 to provide low cost RP capabilities to the ARDEC engineering community. The Stratasys,...

  3. Are Fireworms Venomous? Evidence for the Convergent Evolution of Toxin Homologs in Three Species of Fireworms (Annelida, Amphinomidae)

    Science.gov (United States)

    Simpson, Danny

    2018-01-01

    Abstract Amphinomids, more commonly known as fireworms, are a basal lineage of marine annelids characterized by the presence of defensive dorsal calcareous chaetae, which break off upon contact. It has long been hypothesized that amphinomids are venomous and use the chaetae to inject a toxic substance. However, studies investigating fireworm venom from a morphological or molecular perspective are scarce and no venom gland has been identified to date, nor any toxin characterized at the molecular level. To investigate this question, we analyzed the transcriptomes of three species of fireworms—Eurythoe complanata, Hermodice carunculata, and Paramphinome jeffreysii—following a venomics approach to identify putative venom compounds. Our venomics pipeline involved de novo transcriptome assembly, open reading frame, and signal sequence prediction, followed by three different homology search strategies: BLAST, HMMER sequence, and HMMER domain. Following this pipeline, we identified 34 clusters of orthologous genes, representing 13 known toxin classes that have been repeatedly recruited into animal venoms. Specifically, the three species share a similar toxin profile with C-type lectins, peptidases, metalloproteinases, spider toxins, and CAP proteins found among the most highly expressed toxin homologs. Despite their great diversity, the putative toxins identified are predominantly involved in three major biological processes: hemostasis, inflammatory response, and allergic reactions, all of which are commonly disrupted after fireworm stings. Although the putative fireworm toxins identified here need to be further validated, our results strongly suggest that fireworms are venomous animals that use a complex mixture of toxins for defense against predators. PMID:29293976

  4. The complex of looped diagrams and natural operations on Hochschild homology

    DEFF Research Database (Denmark)

    Klamt, Angela

    In this thesis natural operations on the (higher) Hochschild complex of a given family of algebras are investigated. We give a description of all formal operations (in the sense of Wahl) for the class of commutative algebras using Loday's lambda operation, Connes' boundary operator and shue produ...... of formal operations on Hochschild homology to higher Hochschild homology. We also generalize statements about the formal operations and give smaller models for the formal operations on higher Hochschild homology in certain cases....

  5. Genetic probing of homologous recombination and non-homologous end joining during meiotic prophase in irradiated mouse spermatocytes

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Emad A. [Department of Endocrinology and Metabolism, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Department of Zoology, Faculty of Science, Assiut University, 71516 Assiut (Egypt); Philippens, Marielle E.P.; Kal, Henk B. [Department of Radiotherapy, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht (Netherlands); Rooij, Dirk G. de, E-mail: d.g.derooij@uu.nl [Department of Endocrinology and Metabolism, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Center for Reproductive Medicine, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam (Netherlands); Boer, Peter de [Department of Obstetrics and Gynaecology, Radboud University Nijmegen Medical Centre, 6500 HB Nijmegen (Netherlands)

    2010-06-01

    This study was designed to obtain a better insight into the relative contribution of homologous recombination (HR) and non-homologous end joining (NHEJ) to the repair of radiation-induced DNA double-strand breaks (DSBs) at first meiotic prophase. Early and late pachytene and early diplotene spermatocytes that had completed crossing over were sampled. We studied the kinetics of {gamma}-H2AX chromatin foci removal after irradiation of mice deficient for HR and mice deficient for NHEJ. Analyzing {gamma}-H2AX signals in unirradiated RAD54/RAD54B deficient spermatocytes indicated incomplete meiotic recombination repair due to the pronounced increase of {gamma}-H2AX foci in late prophase primary spermatocytes. In these mice, 8 h after irradiation, early pachytene spermatocytes showed a reduction of the numbers of {gamma}-H2AX foci by 52% compared to 82% in the wild type, the difference being significant. However, after crossing over (in late pachytene and early diplotene), no effect of RAD54/RAD54B deficiency on the reduction of irradiation-induced foci was observed. In NHEJ deficient SCID mice, repair kinetics in early spermatocytes were similar to those in wild type mice. However, 1 h after irradiation in late pachytene and early diplotene spermatocytes 1.7 times more foci were found than in wild type mice. This difference might be related to the absence of a DNA-PKcs dependent fast repair component in SCID mice. As subsequent repair is normal, HR likely is taking over. Taken together, the results obtained in RAD54/RAD54B deficient mice and in SCID mice indicate that DSB repair in early pachytene spermatocytes is mainly carried out through HR. In late spermatocytes (late pachytenes and early diplotenes) NHEJ is active. However, probably there is an interplay between these repair pathways and when in late spermatocytes the NHEJ pathway is compromised HR may take over.

  6. Homologous cloning, characterization and expression of a new halophyte phytochelatin synthase gene in Suaeda salsa

    Science.gov (United States)

    Cong, Ming; Zhao, Jianmin; Lü, Jiasen; Ren, Zhiming; Wu, Huifeng

    2016-09-01

    The halophyte Suaeda salsa can grow in heavy metal-polluted areas along intertidal zones having high salinity. Since phytochelatins can eff ectively chelate heavy metals, it was hypothesized that S. salsa possessed a phytochelatin synthase (PCS) gene. In the present study, the cDNA of PCS was obtained from S. salsa (designated as SsPCS) using homologous cloning and the rapid amplification of cDNA ends (RACE). A sequence analysis revealed that SsPCS consisted of 1 916 bp nucleotides, encoding a polypeptide of 492 amino acids with one phytochelatin domain and one phytochelatin C domain. A similarity analysis suggested that SsPCS shared up to a 58.6% identity with other PCS proteins and clustered with PCS proteins from eudicots. There was a new kind of metal ion sensor motif in its C-terminal domain. The SsPCS transcript was more highly expressed in elongated and fibered roots and stems ( Pcloned from a halophyte, and it might contain a diff erent metal sensing capability than the first PCS from Thellungiella halophila. This study provided a new view of halophyte PCS genes in heavy metal tolerance.

  7. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination.

    Science.gov (United States)

    Soniat, Michael M; Myler, Logan R; Schaub, Jeffrey M; Kim, Yoori; Gallardo, Ignacio F; Finkelstein, Ilya J

    2017-01-01

    Homologous recombination (HR) is a universally conserved DNA double-strand break repair pathway. Single-molecule fluorescence imaging approaches have revealed new mechanistic insights into nearly all aspects of HR. These methods are especially suited for studying protein complexes because multicolor fluorescent imaging can parse out subassemblies and transient intermediates that associate with the DNA substrates on the millisecond to hour timescales. However, acquiring single-molecule datasets remains challenging because most of these approaches are designed to measure one molecular reaction at a time. The DNA curtains platform facilitates high-throughput single-molecule imaging by organizing arrays of DNA molecules on the surface of a microfluidic flowcell. Here, we describe a second-generation UV lithography-based protocol for fabricating flowcells for DNA curtains. This protocol greatly reduces the challenges associated with assembling DNA curtains and paves the way for the rapid acquisition of large datasets from individual single-molecule experiments. Drawing on our recent studies of human HR, we also provide an overview of how DNA curtains can be used for observing facilitated protein diffusion, processive enzyme translocation, and nucleoprotein filament dynamics on single-stranded DNA. Together, these protocols and case studies form a comprehensive introduction for other researchers that may want to adapt DNA curtains for high-throughput single-molecule studies of DNA replication, transcription, and repair. © 2017 Elsevier Inc. All rights reserved.

  8. RAD26, the functional S. cerevisiae homolog of the Cockayne syndrome B gene ERCC6.

    Science.gov (United States)

    van Gool, A J; Verhage, R; Swagemakers, S M; van de Putte, P; Brouwer, J; Troelstra, C; Bootsma, D; Hoeijmakers, J H

    1994-11-15

    Transcription-coupled repair (TCR) is a universal sub-pathway of the nucleotide excision repair (NER) system that is limited to the transcribed strand of active structural genes. It accomplishes the preferential elimination of transcription-blocking DNA lesions and permits rapid resumption of the vital process of transcription. A defect in TCR is responsible for the rare hereditary disorder Cockayne syndrome (CS). Recently we found that mutations in the ERCC6 repair gene, encoding a putative helicase, underly the repair defect of CS complementation group B. Here we report the cloning and characterization of the Saccharomyces cerevisiae homolog of CSB/ERCC6, which we designate RAD26. A rad26 disruption mutant appears viable and grows normally, indicating that the gene does not have an essential function. In analogy with CS, preferential repair of UV-induced cyclobutane pyrimidine dimers in the transcribed strand of the active RBP2 gene is severely impaired. Surprisingly, in contrast to the human CS mutant, yeast RAD26 disruption does not induce any UV-, cisPt- or X-ray sensitivity, explaining why it was not isolated as a mutant before. Recovery of growth after UV exposure was somewhat delayed in rad26. These findings suggest that TCR in lower eukaryotes is not very important for cell survival and that the global genome repair pathway of NER is the major determinant of cellular resistance to genotoxicity.

  9. In vivo genome editing via CRISPR/Cas9 mediated homology-independent targeted integration

    KAUST Repository

    Suzuki, Keiichiro

    2016-11-15

    Targeted genome editing via engineered nucleases is an exciting area of biomedical research and holds potential for clinical applications. Despite rapid advances in the field, in vivo targeted transgene integration is still infeasible because current tools are inefficient1, especially for non-dividing cells, which compose most adult tissues. This poses a barrier for uncovering fundamental biological principles and developing treatments for a broad range of genetic disorders2. Based on clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9)3, 4 technology, here we devise a homology-independent targeted integration (HITI) strategy, which allows for robust DNA knock-in in both dividing and non-dividing cells in vitro and, more importantly, in vivo (for example, in neurons of postnatal mammals). As a proof of concept of its therapeutic potential, we demonstrate the efficacy of HITI in improving visual function using a rat model of the retinal degeneration condition retinitis pigmentosa. The HITI method presented here establishes new avenues for basic research and targeted gene therapies.

  10. Conservation of the nucleotide excision repair pathway: characterization of hydra Xeroderma Pigmentosum group F homolog.

    Directory of Open Access Journals (Sweden)

    Apurva Barve

    Full Text Available Hydra, one of the earliest metazoans with tissue grade organization and nervous system, is an animal with a remarkable regeneration capacity and shows no signs of organismal aging. We have for the first time identified genes of the nucleotide excision repair (NER pathway from hydra. Here we report cloning and characterization of hydra homolog of xeroderma pigmentosum group F (XPF gene that encodes a structure-specific 5' endonuclease which is a crucial component of NER. In silico analysis shows that hydra XPF amino acid sequence is very similar to its counterparts from other animals, especially vertebrates, and shows all features essential for its function. By in situ hybridization, we show that hydra XPF is expressed prominently in the multipotent stem cell niche in the central region of the body column. Ectoderm of the diploblastic hydra was shown to express higher levels of XPF as compared to the endoderm by semi-quantitative RT-PCR. Semi-quantitative RT-PCR analysis also demonstrated that interstitial cells, a multipotent and rapidly cycling stem cell lineage of hydra, express higher levels of XPF mRNA than other cell types. Our data show that XPF and by extension, the NER pathway is highly conserved during evolution. The prominent expression of an NER gene in interstitial cells may have implications for the lack of senescence in hydra.

  11. Conservation of the nucleotide excision repair pathway: characterization of hydra Xeroderma Pigmentosum group F homolog.

    Science.gov (United States)

    Barve, Apurva; Ghaskadbi, Saroj; Ghaskadbi, Surendra

    2013-01-01

    Hydra, one of the earliest metazoans with tissue grade organization and nervous system, is an animal with a remarkable regeneration capacity and shows no signs of organismal aging. We have for the first time identified genes of the nucleotide excision repair (NER) pathway from hydra. Here we report cloning and characterization of hydra homolog of xeroderma pigmentosum group F (XPF) gene that encodes a structure-specific 5' endonuclease which is a crucial component of NER. In silico analysis shows that hydra XPF amino acid sequence is very similar to its counterparts from other animals, especially vertebrates, and shows all features essential for its function. By in situ hybridization, we show that hydra XPF is expressed prominently in the multipotent stem cell niche in the central region of the body column. Ectoderm of the diploblastic hydra was shown to express higher levels of XPF as compared to the endoderm by semi-quantitative RT-PCR. Semi-quantitative RT-PCR analysis also demonstrated that interstitial cells, a multipotent and rapidly cycling stem cell lineage of hydra, express higher levels of XPF mRNA than other cell types. Our data show that XPF and by extension, the NER pathway is highly conserved during evolution. The prominent expression of an NER gene in interstitial cells may have implications for the lack of senescence in hydra.

  12. A functional kinase homology domain is essential for the activity of photoreceptor guanylate cyclase 1.

    Science.gov (United States)

    Bereta, Grzegorz; Wang, Benlian; Kiser, Philip D; Baehr, Wolfgang; Jang, Geeng-Fu; Palczewski, Krzysztof

    2010-01-15

    Phototransduction is carried out by a signaling pathway that links photoactivation of visual pigments in retinal photoreceptor cells to a change in their membrane potential. Upon photoactivation, the second messenger of phototransduction, cyclic GMP, is rapidly degraded and must be replenished during the recovery phase of phototransduction by photoreceptor guanylate cyclases (GCs) GC1 (or GC-E) and GC2 (or GC-F) to maintain vision. Here, we present data that address the role of the GC kinase homology (KH) domain in cyclic GMP production by GC1, the major cyclase in photoreceptors. First, experiments were done to test which GC1 residues undergo phosphorylation and whether such phosphorylation affects cyclase activity. Using mass spectrometry, we showed that GC1 residues Ser-530, Ser-532, Ser-533, and Ser-538, located within the KH domain, undergo light- and signal transduction-independent phosphorylation in vivo. Mutations in the putative Mg(2+) binding site of the KH domain abolished phosphorylation, indicating that GC1 undergoes autophosphorylation. The dramatically reduced GC activity of these mutants suggests that a functional KH domain is essential for cyclic GMP production. However, evidence is presented that autophosphorylation does not regulate GC1 activity, in contrast to phosphorylation of other members of this cyclase family.

  13. A Functional Kinase Homology Domain Is Essential for the Activity of Photoreceptor Guanylate Cyclase 1*

    Science.gov (United States)

    Bereta, Grzegorz; Wang, Benlian; Kiser, Philip D.; Baehr, Wolfgang; Jang, Geeng-Fu; Palczewski, Krzysztof

    2010-01-01

    Phototransduction is carried out by a signaling pathway that links photoactivation of visual pigments in retinal photoreceptor cells to a change in their membrane potential. Upon photoactivation, the second messenger of phototransduction, cyclic GMP, is rapidly degraded and must be replenished during the recovery phase of phototransduction by photoreceptor guanylate cyclases (GCs) GC1 (or GC-E) and GC2 (or GC-F) to maintain vision. Here, we present data that address the role of the GC kinase homology (KH) domain in cyclic GMP production by GC1, the major cyclase in photoreceptors. First, experiments were done to test which GC1 residues undergo phosphorylation and whether such phosphorylation affects cyclase activity. Using mass spectrometry, we showed that GC1 residues Ser-530, Ser-532, Ser-533, and Ser-538, located within the KH domain, undergo light- and signal transduction-independent phosphorylation in vivo. Mutations in the putative Mg2+ binding site of the KH domain abolished phosphorylation, indicating that GC1 undergoes autophosphorylation. The dramatically reduced GC activity of these mutants suggests that a functional KH domain is essential for cyclic GMP production. However, evidence is presented that autophosphorylation does not regulate GC1 activity, in contrast to phosphorylation of other members of this cyclase family. PMID:19901021

  14. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB......) for structures of homologous proteins. The results are displayed both as an annotated sequence alignment, where the user-provided annotations as well as the sequence conservation between the query and the target sequence are displayed, and also as a publication-quality image of the 3D protein structure...... with the selected features and sequence conservation enhanced. The results are also returned in a readily parsable text format as well as a PyMol (http://pymol.sourceforge.net/) script file, which allows the user to easily modify the protein structure image to suit a specific purpose. FeatureMap3D can also be used...

  15. Forecasting the Energy Consumption of China’s Manufacturing Using a Homologous Grey Prediction Model

    Directory of Open Access Journals (Sweden)

    Bo Zeng

    2017-10-01

    Full Text Available With the rapid development of China’s manufacturing, energy consumption has increased rapidly, and this has become a major bottleneck affecting the sustainable development of China’s economy. This paper deduces and constructs a homologous grey prediction model with one variable and one first order equation (HGEM(1,1 for forecasting the total energy consumption of China’s manufacturing based on the Grey system theory. Both parameter estimation (PE and the deduction of the final restored expression (FRE of the HGEM(1,1 model are all from the time response expression of the whitenization differential equation, which solves the ‘non-homologous’ defects of PE and FRE with traditional grey prediction models. HGEM(1,1 has good performance and can unbiasedly simulate a homogeneous/non-homogeneous exponential function sequence and a linear function sequence. Then, the HGEM(1,1model is used to simulate and forecast the total energy consumption of China’s energy manufacturing, and the results show that the comprehensive performance of this model is much better than that of the classic Grey Model with one variable and single order equation, GM(1,1 for short and the frequently-used Discrete Grey Model with one variable and single order equation, DGM(1,1 for short. Finally, we forecast the total energy consumption of China’s manufacturing industry during the years 2018–2024. The results show that the total energy consumption in China’s manufacturing is slowing down but is still too large. For this, some measures, such as optimizing the manufacturing structure and speeding up the development and promotion of energy saving and emission reduction technologies, to ensure the effective supply of energy in China’s manufacturing industry are suggested.

  16. Spying on Search Strategies

    Science.gov (United States)

    Tenopir, Carol

    2004-01-01

    Only the most dedicated super-searchers are motivated to learn and control command systems, like DialogClassic, that rely on the user to input complex search strategies. Infrequent searchers and most end users choose interfaces that do some of the work for them and make the search process appear easy. However, the easier a good interface seems to…

  17. Agronomie Africaine: Advanced Search

    African Journals Online (AJOL)

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  18. Scientia Africana: Advanced Search

    African Journals Online (AJOL)

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  19. With News Search Engines

    Science.gov (United States)

    Gunn, Holly

    2005-01-01

    Although there are many news search engines on the Web, finding the news items one wants can be challenging. Choosing appropriate search terms is one of the biggest challenges. Unless one has seen the article that one is seeking, it is often difficult to select words that were used in the headline or text of the article. The limited archives of…

  20. Biokemistri: Advanced Search

    African Journals Online (AJOL)

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  1. Searches for Supersymmetry

    CERN Document Server

    Ventura, Andrea; The ATLAS collaboration

    2017-01-01

    New and recent results on Supersymmetry searches are shown for the ATLAS and the CMS experiments. Analyses with about 36 fb$^{-1}$ are considered for searches concerning light squarks and gluinos, direct pair production of 3$^{rd}$ generation squarks, electroweak production of charginos, neutralinos, sleptons, R-parity violating scenarios and long-lived particles.

  2. Search and Recommendation

    DEFF Research Database (Denmark)

    Bogers, Toine

    2014-01-01

    -scale application by companies like Amazon, Facebook, and Netflix. But are search and recommendation really two different fields of research that address different problems with different sets of algorithms in papers published at distinct conferences? In my talk, I want to argue that search and recommendation...

  3. Search and switching costs

    NARCIS (Netherlands)

    Siekman, Wilhelm Henricus

    2016-01-01

    This thesis analyses markets with search and with switching costs. It provides insights in several important issues in search markets, including how loss aversion may affect consumer behavior and firm conduct, and how prices, welfare, and profits may change when an intermediating platform orders

  4. Sciences & Nature: Advanced Search

    African Journals Online (AJOL)

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  5. Afrika Statistika: Advanced Search

    African Journals Online (AJOL)

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  6. Quaestiones Mathematicae: Advanced Search

    African Journals Online (AJOL)

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  7. Acta Theologica: Advanced Search

    African Journals Online (AJOL)

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  8. Nigerian Libraries: Advanced Search

    African Journals Online (AJOL)

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  9. Water SA: Advanced Search

    African Journals Online (AJOL)

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  10. Lexikos: Advanced Search

    African Journals Online (AJOL)

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  11. Philosophical Papers: Advanced Search

    African Journals Online (AJOL)

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  12. Kiswahili: Advanced Search

    African Journals Online (AJOL)

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  13. Afrimedic Journal: Advanced Search

    African Journals Online (AJOL)

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  14. Kenya Veterinarian: Advanced Search

    African Journals Online (AJOL)

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  15. Building Internet Search Engines

    Directory of Open Access Journals (Sweden)

    Mustafa Akgül

    1996-09-01

    Full Text Available Internet search engines are powerful tools to find electronics objects such as addresses of individuals and institutions, documents, statistics of all kinds, dictionaries, cata­logs, product information etc. This paper explains how to build and run some very common search engines on Unix platforms, so as to serve documents through the Web.

  16. ElasticSearch cookbook

    CERN Document Server

    Paro, Alberto

    2015-01-01

    If you are a developer who implements ElasticSearch in your web applications and want to sharpen your understanding of the core elements and applications, this is the book for you. It is assumed that you've got working knowledge of JSON and, if you want to extend ElasticSearch, of Java and related technologies.

  17. Searches for Supersymmetry

    CERN Document Server

    Ventura, Andrea; The ATLAS collaboration

    2017-01-01

    New and recents results on Supersymmetry searches are shown for the ATLAS and the CMS experiments. Analyses with about 36 fb^-1 are considered for searches concerning light squarks and gluinos, direct pair production of 3rd generation squarks, electroweak production of charginos, neutralinos, sleptons, R-parity violating scenarios and long-lived particles.

  18. African Environment: Advanced Search

    African Journals Online (AJOL)

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  19. Human memory search

    NARCIS (Netherlands)

    Davelaar, E.J.; Raaijmakers, J.G.W.; Hills, T.T.; Robbins, T.W.; Todd, P.M.

    2012-01-01

    The importance of understanding human memory search is hard to exaggerate: we build and live our lives based on what whe remember. This chapter explores the characteristics of memory search, with special emphasis on the use of retrieval cues. We introduce the dependent measures that are obtained

  20. Fixing Dataset Search

    Science.gov (United States)

    Lynnes, Chris

    2014-01-01

    Three current search engines are queried for ozone data at the GES DISC. The results range from sub-optimal to counter-intuitive. We propose a method to fix dataset search by implementing a robust relevancy ranking scheme. The relevancy ranking scheme is based on several heuristics culled from more than 20 years of helping users select datasets.

  1. Vulture News: Advanced Search

    African Journals Online (AJOL)

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  2. Ergonomics SA: Advanced Search

    African Journals Online (AJOL)

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  3. Zede Journal: Advanced Search

    African Journals Online (AJOL)

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  4. African Anthropologist: Advanced Search

    African Journals Online (AJOL)

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  5. Africa Development: Advanced Search

    African Journals Online (AJOL)

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  6. Innovation: Advanced Search

    African Journals Online (AJOL)

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  7. Acta Structilia: Advanced Search

    African Journals Online (AJOL)

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  8. Agrosearch: Advanced Search

    African Journals Online (AJOL)

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  9. African Zoology: Advanced Search

    African Journals Online (AJOL)

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  10. Rwanda Journal: Advanced Search

    African Journals Online (AJOL)

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  11. Distributed Deep Web Search

    NARCIS (Netherlands)

    Tjin-Kam-Jet, Kien

    2013-01-01

    The World Wide Web contains billions of documents (and counting); hence, it is likely that some document will contain the answer or content you are searching for. While major search engines like Bing and Google often manage to return relevant results to your query, there are plenty of situations in

  12. Search and Disrupt

    DEFF Research Database (Denmark)

    Ørding Olsen, Anders

    This paper analyzes how external search is affected by strategic interest alignment among knowledge sources. I focus on misalignment arising from the heterogeneous effects of disruptive technologies by analyzing the influence of incumbents on 2,855 non-incumbents? external knowledge search efforts....... The efforts most likely to solve innovation problems obtained funding from the European Commission?s 7th Framework Program (2007-2013). The results show that involving incumbents improves search in complementary technologies, while demoting it when strategic interests are misaligned in disruptive technologies....... However, incumbent sources engaged in capability reconfiguration to accommodate disruption improve search efforts in disruptive technologies. The paper concludes that the value of external sources is contingent on more than their knowledge. Specifically, interdependence of sources in search gives rise...

  13. The Cost of Cache-Oblivious Searching

    DEFF Research Database (Denmark)

    Bender, Michael A.; Brodal, Gert Stølting; Fagerberg, Rolf

    2003-01-01

    Tight bounds on the cost of cache-oblivious searching are proved. It is shown that no cache-oblivious search structure can guarantee that a search performs fewer than lg e log B N block transfers between any two levels of the memory hierarchy. This lower bound holds even if all of the block sizes......, multilevel memory hierarchies can be modelled. It is shown that as k grows, the search costs of the optimal k-level DAM search structure and of the optimal cache-oblivious search structure rapidly converge. This demonstrates that for a multilevel memory hierarchy, a simple cache-oblivious structure almost...... are limited to be powers of 2. A modied version of the van Emde Boas layout is proposed, whose expected block transfers between any two levels of the memory hierarchy arbitrarily close to [lg e +O(lg lg B = lg B)] log B N +O(1). This factor approaches lg e 1:443 as B increases. The expectation is taken over...

  14. The LUX Score: A Metric for Lipidome Homology.

    Directory of Open Access Journals (Sweden)

    Chakravarthy Marella

    Full Text Available A lipidome is the set of lipids in a given organism, cell or cell compartment and this set reflects the organism's synthetic pathways and interactions with its environment. Recently, lipidomes of biological model organisms and cell lines were published and the number of functional studies of lipids is increasing. In this study we propose a homology metric that can quantify systematic differences in the composition of a lipidome. Algorithms were developed to 1. consistently convert lipids structure into SMILES, 2. determine structural similarity between molecular species and 3. describe a lipidome in a chemical space model. We tested lipid structure conversion and structure similarity metrics, in detail, using sets of isomeric ceramide molecules and chemically related phosphatidylinositols. Template-based SMILES showed the best properties for representing lipid-specific structural diversity. We also show that sequence analysis algorithms are best suited to calculate distances between such template-based SMILES and we adjudged the Levenshtein distance as best choice for quantifying structural changes. When all lipid molecules of the LIPIDMAPS structure database were mapped in chemical space, they automatically formed clusters corresponding to conventional chemical families. Accordingly, we mapped a pair of lipidomes into the same chemical space and determined the degree of overlap by calculating the Hausdorff distance. We named this metric the 'Lipidome jUXtaposition (LUX score'. First, we tested this approach for estimating the lipidome similarity on four yeast strains with known genetic alteration in fatty acid synthesis. We show that the LUX score reflects the genetic relationship and growth temperature better than conventional methods although the score is based solely on lipid structures. Next, we applied this metric to high-throughput data of larval tissue lipidomes of Drosophila. This showed that the LUX score is sufficient to cluster

  15. Insights into hydrocarbon formation by nitrogenase cofactor homologs.

    Science.gov (United States)

    Lee, Chi Chung; Hu, Yilin; Ribbe, Markus W

    2015-04-14

    The L-cluster is an all-iron homolog of nitrogenase cofactors. Driven by europium(II) diethylenetriaminepentaacetate [Eu(II)-DTPA], the isolated L-cluster is capable of ATP-independent reduction of CO and CN(-) to C1 to C4 and C1 to C6 hydrocarbons, respectively. Compared to its cofactor homologs, the L-cluster generates considerably more CH4 from the reduction of CO and CN(-), which could be explained by the presence of a "free" Fe atom that is "unmasked" by homocitrate as an additional site for methanation. Moreover, the elevated CH4 formation is accompanied by a decrease in the amount of longer hydrocarbons and/or the lengths of the hydrocarbon products, illustrating a competition between CH4 formation/release and C-C coupling/chain extension. These observations suggest the possibility of designing simpler synthetic clusters for hydrocarbon formation while establishing the L-cluster as a platform for mechanistic investigations of CO and CN(-) reduction without complications originating from the heterometal and homocitrate components. Nitrogenase is a metalloenzyme that is highly complex in structure and uniquely versatile in function. It catalyzes two reactions that parallel two important industrial processes: the reduction of nitrogen to ammonia, which parallels the Haber-Bosch process in ammonia production, and the reduction of carbon monoxide to hydrocarbons, which parallels the Fischer-Tropsch process in fuel production. Thus, the significance of nitrogenase can be appreciated from the perspective of the useful products it generates: (i) ammonia, the "fixed" nitrogen that is essential for the existence of the entire human population; and (ii) hydrocarbons, the "recycled" carbon fuel that could be used to directly address the worldwide energy shortage. This article provides initial insights into the catalytic characteristics of various nitrogenase cofactors in hydrocarbon formation. The reported assay system provides a useful tool for mechanistic

  16. How Users Search the Library from a Single Search Box

    Science.gov (United States)

    Lown, Cory; Sierra, Tito; Boyer, Josh

    2013-01-01

    Academic libraries are turning increasingly to unified search solutions to simplify search and discovery of library resources. Unfortunately, very little research has been published on library user search behavior in single search box environments. This study examines how users search a large public university library using a prominent, single…

  17. TRF2-RAP1 is required to protect telomeres from engaging in homologous recombination-mediated deletions and fusions.

    Science.gov (United States)

    Rai, Rekha; Chen, Yong; Lei, Ming; Chang, Sandy

    2016-03-04

    Repressor/activator protein 1 (RAP1) is a highly conserved telomere-interacting protein. Yeast Rap1 protects telomeres from non-homologous end joining (NHEJ), plays important roles in telomere length control and is involved in transcriptional gene regulation. However, a role for mammalian RAP1 in telomere end protection remains controversial. Here we present evidence that mammalian RAP1 is essential to protect telomere from homology directed repair (HDR) of telomeres. RAP1 cooperates with the basic domain of TRF2 (TRF2(B)) to repress PARP1 and SLX4 localization to telomeres. Without RAP1 and TRF2(B), PARP1 and SLX4 HR factors promote rapid telomere resection, resulting in catastrophic telomere loss and the generation of telomere-free chromosome fusions in both mouse and human cells. The RAP1 Myb domain is required to repress both telomere loss and formation of telomere-free fusions. Our results highlight the importance of the RAP1-TRF2 heterodimer in protecting telomeres from inappropriate processing by the HDR pathway.

  18. Skewed Binary Search Trees

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Moruz, Gabriel

    2006-01-01

    It is well-known that to minimize the number of comparisons a binary search tree should be perfectly balanced. Previous work has shown that a dominating factor over the running time for a search is the number of cache faults performed, and that an appropriate memory layout of a binary search tree...... can reduce the number of cache faults by several hundred percent. Motivated by the fact that during a search branching to the left or right at a node does not necessarily have the same cost, e.g. because of branch prediction schemes, we in this paper study the class of skewed binary search trees....... For all nodes in a skewed binary search tree the ratio between the size of the left subtree and the size of the tree is a fixed constant (a ratio of 1/2 gives perfect balanced trees). In this paper we present an experimental study of various memory layouts of static skewed binary search trees, where each...

  19. Visual search: a retrospective.

    Science.gov (United States)

    Eckstein, Miguel P

    2011-12-30

    Visual search, a vital task for humans and animals, has also become a common and important tool for studying many topics central to active vision and cognition ranging from spatial vision, attention, and oculomotor control to memory, decision making, and rewards. While visual search often seems effortless to humans, trying to recreate human visual search abilities in machines has represented an incredible challenge for computer scientists and engineers. What are the brain computations that ensure successful search? This review article draws on efforts from various subfields and discusses the mechanisms and strategies the brain uses to optimize visual search: the psychophysical evidence, their neural correlates, and if unknown, possible loci of the neural computations. Mechanisms and strategies include use of knowledge about the target, distractor, background statistical properties, location probabilities, contextual cues, scene context, rewards, target prevalence, and also the role of saliency, center-surround organization of search templates, and eye movement plans. I provide overviews of classic and contemporary theories of covert attention and eye movements during search explaining their differences and similarities. To allow the reader to anchor some of the laboratory findings to real-world tasks, the article includes interviews with three expert searchers: a radiologist, a fisherman, and a satellite image analyst.

  20. The Search for Extraterrestrial Life

    Science.gov (United States)

    Peter, Ulmschneider

    Looking at the nature, origin, and evolution of life on Earth is one way of assessing whether extraterrestrial life exists on Earth-like planets elsewhere (see Chaps. 5 and 6). A more direct approach is to search for favorable conditions and traces of life on other celestial bodies, both in the solar system and beyond. Clearly, there is little chance of encountering nonhuman intelligent beings in the solar system. But there could well be primitive life on Mars, particularly as in the early history of the solar system the conditions on Mars were quite similar to those on Earth. In addition, surprisingly favorable conditions for life once existed on the moons of Jupiter. Yet even if extraterrestrial life is not encountered in forthcoming space missions, it would be of utmost importance to recover fossils of past organisms as such traces would greatly contribute to our basic understanding of the formation of life. In addition to the planned missions to Mars and Europa, there are extensive efforts to search for life outside the solar system. Rapid advances in the detection of extrasolar planets, outlined in Chap. 3, are expected to lead to the discovery of Earth-like planets in the near future. But how can we detect life on these distant bodies?

  1. Guidelines for Identifying Homologous Recombination Events in Influenza A Virus

    NARCIS (Netherlands)

    Boni, M.F.; de Jong, M.D.; van Doorn, H.R.; Holmes, E.C.

    2010-01-01

    The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of

  2. The insect antenna: segmentation, patterning and positional homology

    Directory of Open Access Journals (Sweden)

    A. Minelli

    2017-04-01

    Full Text Available The basic mechanism by which the antennal flagellum is subdivided into flagellomeres is probably the same in all insects, irrespective of whether the process occurs in the embryo, in the eye/antenna imaginal disc, or through a series of post-embryonic increments punctuated by moults. The ultimate origin of (all? flagellomeres is the first antennomere following the pedicel, from which split off in apical direction new primary flagellomeres, each of which is eventually the source of secondary flagellomeres, according to specific spatial and temporal patterns subject to heterochrony. Only a detailed knowledge of the underlying segmentation processes could provide the ultimate background for determining positional homology between flagellomeres of two antennae with different number of antennomeres. The antennae of the Heteroptera are likely re-segmented, as their second antennomere seems to include a flagellar component. The larval antennae of the holometabolans are temporal serial homologues of those of the adult, but their segmental composition is problematic. Significant progress will be done by understanding what differentiates antennomeres that divide, either embryonically or post-embryonically, from those that do not; and by discovering whether the spatial and temporal pattern of division along the flagellum depends on local cues, or on signals travelling along the whole proximo-distal axis of the appendage.

  3. A somatic origin of homologous Robertsonian translocations and isochromosomes

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, W.P.; Bernasconi, F.; Schinzel, A.A. (Univ. of Zurich (Switzerland)); Basaran, S.; Yueksel-Apak, M. (Univ. of Istanbul (Turkey)); Neri, G. (Universita Cattolica, Rome (Italy)); Serville, F. (Hopital d' Enfants Pellegrin, Bordeaux (France)); Balicek, P.; Haluza, R. (Univ. Hospital of Hradeck Kralove, Hradec Kralove (Czech Republic)); Farah, L.M.S. (Escuola Paulista de Medicina, Sao Paulo (Brazil)) (and others)

    1994-02-01

    One t(14q 14q), three t(15q 15q), two t(21q21q), and two t(22q22q) nonmosaic, apparently balanced, de novo Robertsonian translocation cases were investigated with polymorphic markers to establish the origin of the translocated chromosomes. Four cases had results indicative of an isochromosome: one t(14q14q) case with mild mental retardation and maternal uniparental disomy (UPD) for chromosome 14, one t(15q15q) case with the Prader-Willi syndrome and UPD(15), a phenotypically normal carrier of t(22q22q) with maternal UPD(22), and a phenotypically normal t(21q21q) case of paternal UPD(21). All UPD cases showed complete homozygosity throughout the involved chromosome, which is supportive of a postmeiotic origin. In the remaining four cases, maternal and paternal inheritance of the involved chromosome was found, which unambiguously implies a somatic origin. One t(15q15q) female had a child with a ring chromosome 15, which was also of probable postmeiotic origin as recombination between grandparental haplotypes had occurred prior to ring formation. UPD might be expected to result from de novo Robertsonian translocations of meiotic origin; however, all de novo homologous translocation cases, so far reported, with UPD of chromosomes 14, 15, 21, or 22 have been isochromosomes. These data provide the first direct evidence that nonmosaic Robertsonian translocations, as well as isochromosomes, are commonly the result of a mitotic exchange. 75 refs., 1 fig., 4 tabs.

  4. Transcription-coupled homologous recombination after oxidative damage.

    Science.gov (United States)

    Wei, Leizhen; Levine, Arthur Samuel; Lan, Li

    2016-08-01

    Oxidative DNA damage induces genomic instability and may lead to mutagenesis and carcinogenesis. As severe blockades to RNA polymerase II (RNA POLII) during transcription, oxidative DNA damage and the associated DNA strand breaks have a profoundly deleterious impact on cell survival. To protect the integrity of coding regions, high fidelity DNA repair at a transcriptionally active site in non-dividing somatic cells, (i.e., terminally differentiated and quiescent/G0 cells) is necessary to maintain the sequence integrity of transcribed regions. Recent studies indicate that an RNA-templated, transcription-associated recombination mechanism is important to protect coding regions from DNA damage-induced genomic instability. Here, we describe the discovery that G1/G0 cells exhibit Cockayne syndrome (CS) B (CSB)-dependent assembly of homologous recombination (HR) factors at double strand break (DSB) sites within actively transcribed regions. This discovery is a challenge to the current dogma that HR occurs only in S/G2 cells where undamaged sister chromatids are available as donor templates. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Identification, localization, and sequencing of fetal bovine VASA homolog.

    Science.gov (United States)

    Bartholomew, Rachel A; Parks, John E

    2007-10-01

    The vasa gene, first described in Drosophila, is purported to be important in germ cell development. Vasa is present across several invertebrate and vertebrate taxa, including frogs, fish, chickens, and humans. Vasa, a DEAD (asparagine-glutamine-alanine-asparagine) box protein shown to function as an RNA helicase in vitro, has not been investigated previously in fetal stage cattle. Total RNA was extracted from bovine fetal gonads obtained at 35-55 days, 55-80 days, and 80-120 days of gestation to amplify a 296 bp reverse transcription polymerase chain reaction (RT-PCR) product using primers for human vasa. The complete coding sequence of bovine vasa was cloned with 5' and 3' random amplification of cDNA ends polymerase chain reaction (RACE-PCR) and subsequently identified as bovine vasa homolog (BVH). Northern blot analysis revealed that among the tissues examined (gonad, liver, heart, brain, and femur), the vasa gene was expressed in the gonad. This localization, the conserved pattern of gene expression, and the gene sequence suggests that BVH plays a role in bovine germ cell development as proposed for other mammalian species.

  6. Coherent Structure Detection using Persistent Homology and other Topological Tools

    Science.gov (United States)

    Smith, Spencer; Roberts, Eric; Sindi, Suzanne; Mitchell, Kevin

    2017-11-01

    For non-autonomous, aperiodic fluid flows, coherent structures help organize the dynamics, much as invariant manifolds and periodic orbits do for autonomous or periodic systems. The prevalence of such flows in nature and industry has motivated many successful techniques for defining and detecting coherent structures. However, often these approaches require very fine trajectory data to reconstruct velocity fields and compute Cauchy-Green-tensor-related quantities. We use topological techniques to help detect coherent trajectory sets in relatively sparse 2D advection problems. More specifically, we have developed a homotopy-based algorithm, the ensemble-based topological entropy calculation (E-tec), which assigns to each edge in an initial triangulation of advected points a topologically forced lower bound on its future stretching rate. The triangulation and its weighted edges allow us to analyze flows using persistent homology. This topological data analysis tool detects clusters and loops in the triangulation that are robust in the presence of noise and in this case correspond to coherent trajectory sets.

  7. A persistent homology approach to collective behavior in insect swarms

    Science.gov (United States)

    Sinhuber, Michael; Ouellette, Nicholas T.

    Various animals from birds and fish to insects tend to form aggregates, displaying self-organized collective swarming behavior. Due to their frequent occurrence in nature and their implications for engineered, collective systems, these systems have been investigated and modeled thoroughly for decades. Common approaches range from modeling them with coupled differential equations on the individual level up to continuum approaches. We present an alternative, topology-based approach for describing swarming behavior at the macroscale rather than the microscale. We study laboratory swarms of Chironomus riparius, a flying, non-biting midge. To obtain the time-resolved three-dimensional trajectories of individual insects, we use a multi-camera stereoimaging and particle-tracking setup. To investigate the swarming behavior in a topological sense, we employ a persistent homology approach to identify persisting structures and features in the insect swarm that elude a direct, ensemble-averaging approach. We are able to identify features of sub-clusters in the swarm that show behavior distinct from that of the remaining swarm members. The coexistence of sub-swarms with different features resembles some non-biological systems such as active colloids or even thermodynamic systems.

  8. Soft Ngram Representation and Modeling for Protein Remote Homology Detection.

    Science.gov (United States)

    Lovato, Pietro; Cristani, Marco; Bicego, Manuele

    2017-01-01

    Remote homology detection represents a central problem in bioinformatics, where the challenge is to detect functionally related proteins when their sequence similarity is low. Recent solutions employ representations derived from the sequence profile, obtained by replacing each amino acid of the sequence by the corresponding most probable amino acid in the profile. However, the information contained in the profile could be exploited more deeply, provided that there is a representation able to capture and properly model such crucial evolutionary information. In this paper, we propose a novel profile-based representation for sequences, called soft Ngram. This representation, which extends the traditional Ngram scheme (obtained by grouping N consecutive amino acids), permits considering all of the evolutionary information in the profile: this is achieved by extracting Ngrams from the whole profile, equipping them with a weight directly computed from the corresponding evolutionary frequencies. We illustrate two different approaches to model the proposed representation and to derive a feature vector, which can be effectively used for classification using a support vector machine (SVM). A thorough evaluation on three benchmarks demonstrates that the new approach outperforms other Ngram-based methods, and shows very promising results also in comparison with a broader spectrum of techniques.

  9. Personalized online information search and visualization

    Directory of Open Access Journals (Sweden)

    Orthner Helmuth F

    2005-03-01

    Full Text Available Abstract Background The rapid growth of online publications such as the Medline and other sources raises the questions how to get the relevant information efficiently. It is important, for a bench scientist, e.g., to monitor related publications constantly. It is also important, for a clinician, e.g., to access the patient records anywhere and anytime. Although time-consuming, this kind of searching procedure is usually similar and simple. Likely, it involves a search engine and a visualization interface. Different words or combination reflects different research topics. The objective of this study is to automate this tedious procedure by recording those words/terms in a database and online sources, and use the information for an automated search and retrieval. The retrieved information will be available anytime and anywhere through a secure web server. Results We developed such a database that stored searching terms, journals and et al., and implement a piece of software for searching the medical subject heading-indexed sources such as the Medline and other online sources automatically. The returned information were stored locally, as is, on a server and visible through a Web-based interface. The search was performed daily or otherwise scheduled and the users logon to the website anytime without typing any words. The system has potentials to retrieve similarly from non-medical subject heading-indexed literature or a privileged information source such as a clinical information system. The issues such as security, presentation and visualization of the retrieved information were thus addressed. One of the presentation issues such as wireless access was also experimented. A user survey showed that the personalized online searches saved time and increased and relevancy. Handheld devices could also be used to access the stored information but less satisfactory. Conclusion The Web-searching software or similar system has potential to be an efficient

  10. Statistical search on the Semantic Web.

    Science.gov (United States)

    Kobayashi, Norio; Toyoda, Tetsuro

    2008-04-01

    Statistical analysis of links on the Semantic Web is important for various evaluation purposes such as quantifying an individual's scientific research output based on citation links. SPARQL has been proposed as a standardized query language for the Semantic Web and is intuitively understandable; however, it does not adequately support statistical evaluation of semantic links. We have extended SPARQL to a novel Resource Description Framework (RDF) query language termed General and Rapid Association Study Query Language (GRASQL) to generate inferences connecting semantic Boolean-based deduction and statistical evaluation of RDF resources. We have verified the descriptive capability of GRASQL by writing GRASQL queries for practical biomedical search patterns including in silico positional cloning studies and for ranking researchers in a specific domain of expertise by introducing k index, the number of papers containing specific keywords that are published in a fixed period by a researcher. We have also developed a search engine termed General and Rapid Association Study Engine (GRASE), which executes a restricted variety of GRASQL queries by requesting a dynamic and comprehensive evaluation of statistical significance of intersections between each group of documents assigned to URIs and those documents matching user-specified keywords and omics conditions. By performing practical in silico positional cloning searches with GRASE, we show the relevance of our approach on the Semantic Web for biomedical knowledge discovery problem solving. GRASE is used as the search engine for the Positional Medline (PosMed) service and Researcher Finder service at http://omicspace.riken.jp/.

  11. Modified harmony search

    Science.gov (United States)

    Mohamed, Najihah; Lutfi Amri Ramli, Ahmad; Majid, Ahmad Abd; Piah, Abd Rahni Mt

    2017-09-01

    A metaheuristic algorithm, called Harmony Search is quite highly applied in optimizing parameters in many areas. HS is a derivative-free real parameter optimization algorithm, and draws an inspiration from the musical improvisation process of searching for a perfect state of harmony. Propose in this paper Modified Harmony Search for solving optimization problems, which employs a concept from genetic algorithm method and particle swarm optimization for generating new solution vectors that enhances the performance of HS algorithm. The performances of MHS and HS are investigated on ten benchmark optimization problems in order to make a comparison to reflect the efficiency of the MHS in terms of final accuracy, convergence speed and robustness.

  12. ElasticSearch server

    CERN Document Server

    Rogozinski, Marek

    2014-01-01

    This book is a detailed, practical, hands-on guide packed with real-life scenarios and examples which will show you how to implement an ElasticSearch search engine on your own websites.If you are a web developer or a user who wants to learn more about ElasticSearch, then this is the book for you. You do not need to know anything about ElastiSeach, Java, or Apache Lucene in order to use this book, though basic knowledge about databases and queries is required.

  13. Entropy, Search, Complexity

    CERN Document Server

    Katona, Gyula O H; Tardos, Gábor

    2007-01-01

    The present volume is a collection of survey papers in the fields of entropy, search and complexity. They summarize the latest developments in their respective areas. More than half of the papers belong to search theory which lies on the borderline of mathematics and computer science, information theory and combinatorics, respectively. Search theory has variegated applications, among others in bioinformatics. Some of these papers also have links to linear statistics and communicational complexity. Further works survey the fundamentals of information theory and quantum source coding. The volume is recommended to experienced researchers as well as young scientists and students both in mathematics and computer science

  14. Rapid Airplane Parametric Input Design (RAPID)

    Science.gov (United States)

    Smith, Robert E.

    1995-01-01

    RAPID is a methodology and software system to define a class of airplane configurations and directly evaluate surface grids, volume grids, and grid sensitivity on and about the configurations. A distinguishing characteristic which separates RAPID from other airplane surface modellers is that the output grids and grid sensitivity are directly applicable in CFD analysis. A small set of design parameters and grid control parameters govern the process which is incorporated into interactive software for 'real time' visual analysis and into batch software for the application of optimization technology. The computed surface grids and volume grids are suitable for a wide range of Computational Fluid Dynamics (CFD) simulation. The general airplane configuration has wing, fuselage, horizontal tail, and vertical tail components. The double-delta wing and tail components are manifested by solving a fourth order partial differential equation (PDE) subject to Dirichlet and Neumann boundary conditions. The design parameters are incorporated into the boundary conditions and therefore govern the shapes of the surfaces. The PDE solution yields a smooth transition between boundaries. Surface grids suitable for CFD calculation are created by establishing an H-type topology about the configuration and incorporating grid spacing functions in the PDE equation for the lifting components and the fuselage definition equations. User specified grid parameters govern the location and degree of grid concentration. A two-block volume grid about a configuration is calculated using the Control Point Form (CPF) technique. The interactive software, which runs on Silicon Graphics IRIS workstations, allows design parameters to be continuously varied and the resulting surface grid to be observed in real time. The batch software computes both the surface and volume grids and also computes the sensitivity of the output grid with respect to the input design parameters by applying the precompiler tool

  15. Identification of tgh-2, a Filarial Nematode Homolog of Caenorhabditis elegans daf-7 and Human Transforming Growth Factor β, Expressed in Microfilarial and Adult Stages of Brugia malayi

    OpenAIRE

    Gomez-Escobar, Natalia; Gregory, William F.; Maizels, Rick M.

    2000-01-01

    A novel member of the transforming growth factor β (TGF-β) family has been identified in the filarial nematode parasite Brugia malayi by searching the recently developed Expressed Sequence Tag (EST) database produced by the Filarial Genome Project. Designated tgh-2, this new gene shows most similarity to a key product regulating dauer larva formation in Caenorhabditis elegans (DAF-7) and to the human down-modulatory cytokine TGF-β. Homology to DAF-7 extends throughout the length of the 349-am...

  16. An asymmetric PCR-based, reliable and rapid single-tube native DNA engineering strategy

    Directory of Open Access Journals (Sweden)

    Bi Yanzhen

    2012-07-01

    Full Text Available Abstract Background Widely used restriction-dependent cloning methods are labour-intensive and time-consuming, while several types of ligase-independent cloning approaches have inherent limitations. A rapid and reliable method of cloning native DNA sequences into desired plasmids are highly desired. Results This paper introduces ABI-REC, a novel strategy combining asymmetric bridge PCR with intramolecular homologous recombination in bacteria for native DNA cloning. ABI-REC was developed to precisely clone inserts into defined location in a directional manner within recipient plasmids. It featured an asymmetric 3-primer PCR performed in a single tube that could robustly amplify a chimeric insert-plasmid DNA sequence with homologous arms at both ends. Intramolecular homologous recombination occurred to the chimera when it was transformed into E.coli and produced the desired recombinant plasmids with high efficiency and fidelity. It is rapid, and does not involve any operational nucleotides. We proved the reliability of ABI-REC using a double-resistance reporter assay, and investigated the effects of homology and insert length upon its efficiency. We found that 15 bp homology was sufficient to initiate recombination, while 25 bp homology had the highest cloning efficiency. Inserts up to 4 kb in size could be cloned by this method. The utility and advantages of ABI-REC were demonstrated through a series of pig myostatin (MSTN promoter and terminator reporter plasmids, whose transcriptional activity was assessed in mammalian cells. We finally used ABI-REC to construct a pig MSTN promoter-terminator cassette reporter and showed that it could work coordinately to express EGFP. Conclusions ABI-REC has the following advantages: (i rapid and highly efficient; (ii native DNA cloning without introduction of extra bases; (iii restriction-free; (iv easy positioning of directional and site-specific recombination owing to formulated primer design. ABI

  17. An asymmetric PCR-based, reliable and rapid single-tube native DNA engineering strategy.

    Science.gov (United States)

    Bi, Yanzhen; Qiao, Xianfeng; Hua, Zaidong; Zhang, Liping; Liu, Ximei; Li, Li; Hua, Wenjun; Xiao, Hongwei; Zhou, Jingrong; Wei, Qingxin; Zheng, Xinmin

    2012-07-06

    Widely used restriction-dependent cloning methods are labour-intensive and time-consuming, while several types of ligase-independent cloning approaches have inherent limitations. A rapid and reliable method of cloning native DNA sequences into desired plasmids are highly desired. This paper introduces ABI-REC, a novel strategy combining asymmetric bridge PCR with intramolecular homologous recombination in bacteria for native DNA cloning. ABI-REC was developed to precisely clone inserts into defined location in a directional manner within recipient plasmids. It featured an asymmetric 3-primer PCR performed in a single tube that could robustly amplify a chimeric insert-plasmid DNA sequence with homologous arms at both ends. Intramolecular homologous recombination occurred to the chimera when it was transformed into E.coli and produced the desired recombinant plasmids with high efficiency and fidelity. It is rapid, and does not involve any operational nucleotides. We proved the reliability of ABI-REC using a double-resistance reporter assay, and investigated the effects of homology and insert length upon its efficiency. We found that 15 bp homology was sufficient to initiate recombination, while 25 bp homology had the highest cloning efficiency. Inserts up to 4 kb in size could be cloned by this method. The utility and advantages of ABI-REC were demonstrated through a series of pig myostatin (MSTN) promoter and terminator reporter plasmids, whose transcriptional activity was assessed in mammalian cells. We finally used ABI-REC to construct a pig MSTN promoter-terminator cassette reporter and showed that it could work coordinately to express EGFP. ABI-REC has the following advantages: (i) rapid and highly efficient; (ii) native DNA cloning without introduction of extra bases; (iii) restriction-free; (iv) easy positioning of directional and site-specific recombination owing to formulated primer design. ABI-REC is a novel approach to DNA engineering and gene functional

  18. CPHmodels-3.0--remote homology modeling using structure-guided sequence profiles

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2010-01-01

    CPHmodels-3.0 is a web server predicting protein 3D structure by use of single template homology modeling. The server employs a hybrid of the scoring functions of CPHmodels-2.0 and a novel remote homology-modeling algorithm. A query sequence is first attempted modeled using the fast CPHmodels-2...

  19. Translog, a web browser for studying the expression divergence of homologous genes.

    Science.gov (United States)

    Dong, Xianjun; Akalin, Altuna; Sharma, Yogita; Lenhard, Boris

    2010-01-18

    Increasing amount of data from comparative genomics, and newly developed technologies producing accurate gene expression data facilitate the study of the expression divergence of homologous genes. Previous studies have individually highlighted factors that contribute to the expression divergence of duplicate genes, e.g. promoter changes, exon structure heterogeneity, asymmetric histone modifications and genomic neighborhood conservation. However, there is a lack of a tool to integrate multiple factors and visualize their variety among homologous genes in a straightforward way. We introduce Translog (a web-based tool for Transcriptome comparison of homologous genes) that assists in the comparison of homologous genes by displaying the loci in three different views: promoter view for studying the sharing/turnover of transcription initiations, exon structure for displaying the exon-intron structure changes, and genomic neighborhood to show the macro-synteny conservation in a larger scale. CAGE data for transcription initiation are mapped for each transcript and can be used to study transcription turnover and expression changes. Alignment anchors between homologous loci can be used to define the precise homologous transcripts. We demonstrate how these views can be used to visualize the changes of homologous genes during evolution, particularly after the 2R and 3R whole genome duplication. We have developed a web-based tool for assisting in the transcriptome comparison of homologous genes, facilitating the study of expression divergence.

  20. Better Understanding of Homologous Recombination through a 12-Week Laboratory Course for Undergraduates Majoring in Biotechnology

    Science.gov (United States)

    Li, Ming; Shen, Xiaodong; Zhao, Yan; Hu, Xiaomei; Hu, Fuquan; Rao, Xiancai

    2017-01-01

    Homologous recombination, a central concept in biology, is defined as the exchange of DNA strands between two similar or identical nucleotide sequences. Unfortunately, undergraduate students majoring in biotechnology often experience difficulties in understanding the molecular basis of homologous recombination. In this study, we developed and…

  1. Homologous Recombination as a Replication Fork Escort: Fork-Protection and Recovery

    Directory of Open Access Journals (Sweden)

    Audrey Costes

    2012-12-01

    Full Text Available Homologous recombination is a universal mechanism that allows DNA repair and ensures the efficiency of DNA replication. The substrate initiating the process of homologous recombination is a single-stranded DNA that promotes a strand exchange reaction resulting in a genetic exchange that promotes genetic diversity and DNA repair. The molecular mechanisms by which homologous recombination repairs a double-strand break have been extensively studied and are now well characterized. However, the mechanisms by which homologous recombination contribute to DNA replication in eukaryotes remains poorly understood. Studies in bacteria have identified multiple roles for the machinery of homologous recombination at replication forks. Here, we review our understanding of the molecular pathways involving the homologous recombination machinery to support the robustness of DNA replication. In addition to its role in fork-recovery and in rebuilding a functional replication fork apparatus, homologous recombination may also act as a fork-protection mechanism. We discuss that some of the fork-escort functions of homologous recombination might be achieved by loading of the recombination machinery at inactivated forks without a need for a strand exchange step; as well as the consequence of such a model for the stability of eukaryotic genomes.

  2. Origin, fate and homology of the precarotid plate in Pterocles alchata caudacutus

    Directory of Open Access Journals (Sweden)

    M.M. Zaher

    2012-05-01

    Full Text Available A peculiar median transitory cartilaginous precarotid plate is developed forming a floor to the hypophyseal fenestra in the posterior orbital region of the intermediate developmental embryos of Pterocles alchata. Only its anterior portion is homologized with the precarotid commissure of some birds. Its homology to the taenia intertrabecularis of some other birds and reptiles, is refuted.

  3. Origin, fate and homology of the precarotid plate in Pterocles alchata caudacutus

    OpenAIRE

    Zaher, M.M.; A.M. Riad

    2012-01-01

    A peculiar median transitory cartilaginous precarotid plate is developed forming a floor to the hypophyseal fenestra in the posterior orbital region of the intermediate developmental embryos of Pterocles alchata. Only its anterior portion is homologized with the precarotid commissure of some birds. Its homology to the taenia intertrabecularis of some other birds and reptiles, is refuted.

  4. Density parameter estimation for finding clusters of homologous proteins-tracing actinobacterial pathogenicity lifestyles

    DEFF Research Database (Denmark)

    Röttger, Richard; Kalaghatgi, Prabhav; Sun, Peng

    2013-01-01

    Homology detection is a long-standing challenge in computational biology. To tackle this problem, typically all-versus-all BLAST results are coupled with data partitioning approaches resulting in clusters of putative homologous proteins. One of the main problems, however, has been widely neglected...

  5. Cloning and expression pattern of vat-1 homolog gene in zebrafish.

    Science.gov (United States)

    Loeb-Hennard, Christine; Cousin, Xavier; Prengel, Isabel; Kremmer, Elisabeth

    2004-11-01

    The VAT-1 protein is present in the electric organ of marine rays where it is suggested to play a central role in nerve signal transmission. VAT-1 homolog protein was also identified in mouse and human but its function remains to be determined. We have investigated VAT-1 homolog in zebrafish Danio rerio since it is an excellent model amenable to the combination of genetic, molecular and embryological studies. Amino acid sequence analysis shows that the zebrafish VAT-1 homolog shares approximately 51-61% identity with the electric ray, mouse, and human counterparts. By in situ hybridization, vat-1 homolog mRNA is first observed in the trigeminal nuclei at the 8-somite stage. At 20-somite stage, vat-1 homolog is detected in the brain, namely in primary clusters of neurons, in the epiphysis and in the hindbrain. vat-1 homolog is also present in the neural tube but this expression disappears after 72 h post-fertilization. At 24 h post-fertilization, vat-1 homolog starts to be expressed in the developing gut. At later stages, vat-1 homolog is present throughout the brain, appears in the maturing retina and the pharyngeal cavity.

  6. Stimulation of homology-directed gene targeting at an endogenous human locus by a nicking endonuclease

    NARCIS (Netherlands)

    G.P. van Nierop (Gijs); A.A.F. de Vries (Antoine); M. Holkers (Maarten); K.R. Vrijsen (Krijn); M.A.F.V. Gonçalves (Manuel)

    2009-01-01

    textabstractHomologous recombination (HR) is a highly accurate mechanism of DNA repair that can be exploited for homology-directed gene targeting. Since in most cell types HR occurs very infrequently (̃10.-6to 10.-8), its practical application has been largely restricted to specific experimental

  7. Custom Search Engines: Tools & Tips

    Science.gov (United States)

    Notess, Greg R.

    2008-01-01

    Few have the resources to build a Google or Yahoo! from scratch. Yet anyone can build a search engine based on a subset of the large search engines' databases. Use Google Custom Search Engine or Yahoo! Search Builder or any of the other similar programs to create a vertical search engine targeting sites of interest to users. The basic steps to…

  8. Search Engine Bias and the Demise of Search Engine Utopianism

    Science.gov (United States)

    Goldman, E.

    Due to search engines' automated operations, people often assume that search engines display search results neutrally and without bias. However, this perception is mistaken. Like any other media company, search engines affirmatively control their users' experiences, which has the consequence of skewing search results (a phenomenon called "search engine bias"). Some commentators believe that search engine bias is a defect requiring legislative correction. Instead, this chapter argues that search engine bias is the beneficial consequence of search engines optimizing content for their users. The chapter further argues that the most problematic aspect of search engine bias, the "winner-take-all" effect caused by top placement in search results, will be mooted by emerging personalized search technology.

  9. Rapid shallow breathing

    Science.gov (United States)

    ... the smallest air passages of the lungs in children ( bronchiolitis ) Pneumonia or other lung infection Transient tachypnea of the newborn Anxiety and panic Other serious lung disease Home Care Rapid, shallow breathing should not be treated at home. It is ...

  10. Rapid Strep Test

    Science.gov (United States)

    ... worse than normal. Your first thoughts turn to strep throat. A rapid strep test in your doctor’s office ... your suspicions.Viruses cause most sore throats. However, strep throat is an infection caused by the Group A ...

  11. The roles of non-retinotopic motions in visual search

    Directory of Open Access Journals (Sweden)

    Ryohei eNakayama

    2016-06-01

    Full Text Available In visual search, a moving target among stationary distracters is detected more rapidly and more efficiently than a static target among moving distracters. Here we examined how this search asymmetry depends on motion signals from three distinct coordinate system – retinal, relative, and spatiotopic (head/body-centered. Our search display consisted of a target element, distracters elements, and a fixation point tracked by observers. Each element was composed of a spatial carrier grating windowed by a Gaussian envelope, and the motions of carriers, windows, and fixation were manipulated independently and used in various combinations to decouple the respective effects of motion coordinates systems on visual search asymmetry. We found that retinal motion hardly contributes to reaction times and search slopes but that relative and spatiotopic motions contribute to them substantially. Results highlight the important roles of non-retinotopic motions for guiding observer attention in visual search.

  12. Chemical Search Web Utility

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Chemical Search Web Utility is an intuitive web application that allows the public to easily find the chemical that they are interested in using, and which...

  13. Searches at LEP

    CERN Document Server

    Junk, Tom

    2000-01-01

    Searches have been conducted for a broad range of new phenomena by the four experiments ALEPH, DELPHI, L3, and OPAL, at LEP2. Each experiment contributes approximately 150 pb-1 of e+e- annihilation data with a mean sqrt(s) of 205.9 GeV in 2000 to these searches (data prepared for the September 5 LEPC meeting). The statistical procedure for setting limits and evaluating the significance of excesses observed in the data is reviewed. Search results are presented for the Standard Model Higgs boson, the neutral Higgs bosons in the MSSM, charged Higgs bosons, invisibly decaying Higgs bosons produced by Higgs-strahlung, and fermiophobic Higgs bosons. Search results are briefly summarized for gauginos, stops, and staus. The photon recoil spectrum is checked for hints of new physics.

  14. Beyond the search process

    DEFF Research Database (Denmark)

    Hyldegård, Jette

    2009-01-01

    This paper reports on the findings from a longitudinal case study exploring Kuhlthau's information search process (ISP)-model in a group based academic setting. The research focus is on group members' activities and cognitive and emotional experiences during the task process of writing an assignm......This paper reports on the findings from a longitudinal case study exploring Kuhlthau's information search process (ISP)-model in a group based academic setting. The research focus is on group members' activities and cognitive and emotional experiences during the task process of writing...... seeking, the cognitive pattern associated with focus formulation and the tendency towards an increase in writing activities while searching activities decreased. Differences in behavior were also found, which were associated with contextual and social factors beyond the mere search process...

  15. RAPID3? Aptly named!

    Science.gov (United States)

    Berthelot, J-M

    2014-01-01

    The RAPID3 score is the sum of three 0-10 patient self-report scores: pain, functional impairment on MDHAQ, and patient global estimate. It requires 5 seconds for scoring and can be used in all rheumatologic conditions, although it has mostly been used in rheumatoid arthritis where cutoffs for low disease activity (12/30) have been set. A RAPID3 score of ≤ 3/30 with 1 or 0 swollen joints (RAPID3 ≤ 3 + ≤ SJ1) provides remission criteria comparable to Boolean, SDAI, CDAI, and DAS28 remission criteria, in far less time than a formal joint count. RAPID3 performs as well as the DAS28 in separating active drugs from placebos in clinical trials. RAPID3 also predicts subsequent structural disease progression. RAPID3 can be determined at short intervals at home, allowing the determination of the area under the curve of disease activity between two visits and flare detection. However, RAPID3 should not be seen as a substitute for DAS28 and face to face visits in routine care. Monitoring patient status with only self-report information without a rheumatologist's advice (including joints and physical examination, and consideration of imaging and laboratory tests) may indeed be as undesirable for most patients than joint examination without a patient questionnaire. Conversely, combining the RAPID3 and the DAS28 may consist in faster or more sensitive confirmation that a medication is effective. Similarly, better enquiring of most important concerns of patients (pain, functional status and overall opinion on their disorder) should reinforces patients' confidence in their rheumatologist and treatments.

  16. Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda.

    Science.gov (United States)

    Ragsdale, Erik J; Baldwin, James G

    2010-05-07

    Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate free-living outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype.

  17. PCR artifact in testing for homologous recombination in genomic editing in zebrafish.

    Directory of Open Access Journals (Sweden)

    Minho Won

    Full Text Available We report a PCR-induced artifact in testing for homologous recombination in zebrafish. We attempted to replace the lnx2a gene with a donor cassette, mediated by a TALEN induced double stranded cut. The donor construct was flanked with homology arms of about 1 kb at the 5' and 3' ends. Injected embryos (G0 were raised and outcrossed to wild type fish. A fraction of the progeny appeared to have undergone the desired homologous recombination, as tested by PCR using primer pairs extending from genomic DNA outside the homology region to a site within the donor cassette. However, Southern blots revealed that no recombination had taken place. We conclude that recombination happened during PCR in vitro between the donor integrated elsewhere in the genome and the lnx2a locus. We conclude that PCR alone may be insufficient to verify homologous recombination in genome editing experiments in zebrafish.

  18. Supersymmetry searches in ATLAS

    CERN Document Server

    Torro Pastor, Emma; The ATLAS collaboration

    2016-01-01

    Weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk summarises recent ATLAS results for searches for supersymmetric (SUSY) particles. Weak and strong production in both R-Parity conserving and R-Parity violating SUSY scenarios are considered. The searches involved final states including jets, missing transverse momentum, light leptons, taus or photons, as well as long-lived particle signatures.

  19. Accelerated Evidence Search Report

    Science.gov (United States)

    2014-07-01

    Accelerated Evidence Search Report IMPORTANT INFORMATIVE STATEMENTS Accelerated Multi-Camera Evidence Search and Retrieval CSSP Project #: CSSP -2013...CD-1063 was supported by the Canadian Safety and Security Program ( CSSP ) which is led by Defence Research and Development Canada’s Centre for...Border Technology Division The CSSP is a federally-funded program to strengthen Canada’s ability to anticipate, prevent/mitigate, prepare for, respond to

  20. Supporting Book Search

    DEFF Research Database (Denmark)

    Bogers, Toine; Petras, Vivien

    2017-01-01

    Book search is far from a solved problem. Complex information needs often go beyond bibliographic facts and cover a combination of different aspects, such as specific genres or plot elements, engagement or novelty. Conventional book metadata may not be sufficient to address these kinds of informa......Book search is far from a solved problem. Complex information needs often go beyond bibliographic facts and cover a combination of different aspects, such as specific genres or plot elements, engagement or novelty. Conventional book metadata may not be sufficient to address these kinds......-depth analysis of topical metadata, comparing controlled vocabularies with social tags. Tags perform better overall in this setting, but controlled vocabulary terms provide complementary information, which will improve a search. We analyze potential underlying factors that contribute to search performance......, such as the relevance aspect(s) mentioned in a request or the type of book. In addition, we investigate the possible causes of search failure. We conclude that neither tags nor controlled vocabularies are wholly suited to handling the complex information needs in book search, which means that different approaches...

  1. Fowlpox virus encodes nonessential homologs of cellular alpha-SNAP, PC-1, and an orphan human homolog of a secreted nematode protein.

    Science.gov (United States)

    Laidlaw, S M; Anwar, M A; Thomas, W; Green, P; Shaw, K; Skinner, M A

    1998-08-01

    The genome of fowlpox virus (FWPV), type species of the Avipoxviridae, is considerably rearranged compared with that of vaccinia virus (the prototypic poxvirus and type species of the Orthopoxviridae) and is 30% larger. It is likely that the genome of FWPV contains genes in addition to those found in vaccinia virus, probably involved with its replication and survival in the chicken. A 7,470-bp segment of the FWPV genome has five open reading frames (ORFs), two of which encode ankyrin repeat proteins, many examples of which have been found in poxviruses. The remaining ORFs encode homologs of cellular genes not reported in any other virus. ORF-2 encodes a homolog of the yeast Sec17p and mammalian SNAP proteins, crucial to vesicular transport in the exocytic pathway. ORF-3 encodes a homolog of an orphan human protein, R31240_2, encoded on 19p13.2. ORF-3 is also homologous to three proteins (YLS2, YMV6, and C07B5.5) from the free-living nematode Caenorhabditis elegans and to a 43-kDa antigen from the parasitic nematode Trichinella spiralis. ORF-5 encodes a homolog of the mammalian plasma cell antigen PC-1, a type II glycoprotein with exophosphodiesterase activity. The ORFs are present in the virulent precursor, HP1, of the sequenced attenuated virus (FP9) and are conserved in other strains of FWPV. They were shown, by deletion mutagenesis, to be nonessential to virus replication in tissue culture. RNA encoding the viral homolog of PC-1 is expressed strongly early and late in infection, but RNAs encoding the homologs of SNAP and R31240_2 are expressed weakly and late.

  2. A pluralistic account of homology: adapting the models to the data.

    Science.gov (United States)

    Haggerty, Leanne S; Jachiet, Pierre-Alain; Hanage, William P; Fitzpatrick, David A; Lopez, Philippe; O'Connell, Mary J; Pisani, Davide; Wilkinson, Mark; Bapteste, Eric; McInerney, James O

    2014-03-01

    Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as "public goods," subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define "family resemblances" to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet

  3. V-antigen homologs in pathogenic gram-negative bacteria.

    Science.gov (United States)

    Sawa, Teiji; Katoh, Hideya; Yasumoto, Hiroaki

    2014-05-01

    Gram-negative bacteria cause many types of infections in animals from fish and shrimps to humans. Bacteria use Type III secretion systems (TTSSs) to translocate their toxins directly into eukaryotic cells. The V-antigen is a multifunctional protein required for the TTSS in Yersinia and Pseudomonas aeruginosa. V-antigen vaccines and anti-V-antigen antisera confer protection against Yersinia or P. aeruginosa infections in animal models. The V-antigen forms a pentameric cap structure at the tip of the Type III secretory needle; this structure, which has evolved from the bacterial flagellar cap structure, is indispensable for toxin translocation. Various pathogenic gram-negative bacteria such as Photorhabdus luminescens, Vibrio spp., and Aeromonas spp. encode homologs of the V-antigen. Because the V-antigens of pathogenic gram-negative bacteria play a key role in toxin translocation, they are potential therapeutic targets for combatting bacterial virulence. In the USA and Europe, these vaccines and specific antibodies against V-antigens are in clinical trials investigating the treatment of Yersinia or P. aeruginosa infections. Pathogenic gram-negative bacteria are of great interest because of their ability to infect fish and shrimp farms, their potential for exploitation in biological terrorism attacks, and their ability to cause opportunistic infections in humans. Thus, elucidation of the roles of the V-antigen in the TTSS and mechanisms by which these functions can be blocked is critical to facilitating the development of improved anti-V-antigen strategies. © 2014 The Societies and Wiley Publishing Asia Pty Ltd.

  4. Genetic interactions among homologous recombination mutants in Candida albicans.

    Science.gov (United States)

    Bellido, Alberto; Andaluz, Encarnación; Gómez-Raja, Jonathan; Álvarez-Barrientos, Alberto; Larriba, Germán

    2015-01-01

    rad52-ΔΔ and, to a lesser extent, rad51-ΔΔ deletants of Candidaalbicans displayed slow growth and aberrant filamentous morphology whereas rad59-ΔΔ mutants, both by growth rate and morphology resembled wild type. In this study, we have constructed pair-wise double deletants to analyze genetic interactions among these homologous recombination (HR) proteins that affect growth and morphology traits. When grown in liquid YPD medium, double mutant rad51-ΔΔ rad59-ΔΔ exhibited growth rates, cell and colony morphologies, and plating efficiencies that were not significantly different from those observed for rad51-ΔΔ. The same was true for rad52-ΔΔ rad59-ΔΔ compared to rad52-ΔΔ. Slow growth and decreased plating efficiency were caused, at least in part, by a decreased viability, as deduced from FUN1 staining. Flow cytometry and microscopic studies of filamentous mutant populations revealed major changes in cell ploidy, size and morphology, whereas DAPI staining identified complex nuclear rearrangements in yeast and filamentous cells. These phenotypes were not observed in the rad59-ΔΔ mutant populations. Our results show that abolishing Rad51 functions induces the appearance of a subpopulation of aberrant yeast and filamentous forms with increased cell size and ploidy. The size of this complex subpopulation was exacerbated in rad52-ΔΔ mutants. The combination of filamentous cell morphology and viability phenotypes was reflected on the colony morphology of the respective mutants. We conclude that the rad52 mutation is epistatic to rad51 for all the morphological traits analyzed. We discuss these results in the light of the several functions of these recombination genes. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Homologous amino-terminal radioimmunoassay for rat parathyroid hormone.

    Science.gov (United States)

    Calvo, M S; Gundberg, C M; Heath, H; Fox, J

    1991-08-01

    Existing radioimmunoassays for parathyroid hormone (PTH) in rat plasma are based on cross-reactivity of rat PTH (rPTH) with heterologous antisera. We used the synthetic NH2-terminal fragment of rPTH [rPTH-(1-34)] to develop a homologous radioimmunoassay for circulating PTH. An antiserum to rPTH-(1-34) was raised in a goat (G-813), and the same peptide was used as radioligand (125I) and standard. Purification of the label by high-performance liquid chromatography (HPLC) increased specific binding greater than twofold and sensitivity by 50-100%. With a final antiserum dilution of 1:70,000, maximum specific binding of 30-33%, nonspecific binding of 1-5%, and 50-microliters sample additions, the assay detection limit was 1.8-2.5 pmol/l. A midregional fragment of human PTH did not displace 125I-labeled rPTH-(1-34). HPLC of extracts of rat parathyroid glands and hyperparathyroid plasma showed only a single peak of immunoreactivity that eluted 2 min after rPTH-(1-34). Dose dilution curves for rat parathyroid gland extracts, rPTH-(1-34) added to rat plasma, and endogenous rat plasma PTH all paralleled the standard curve. Immunoreactive PTH (irPTH) was detectable in greater than 90% of fasting normal rat plasma and changed appropriately in response to hyper- and hypocalcemia induced by low-calcium and vitamin D-deficient diets, injections of calcium and EDTA, and after thyroparathyroidectomy. The normal range for rat plasma irPTH was less than 2.0-12 pmol/l, in general agreement with bioassay results of others. Thus rPTH-(1-34) is an excellent immunogen for raising antisera to rPTH, and assays incorporating it may be of great value in studying rat parathyroid physiology.

  6. Search Tips: MedlinePlus

    Science.gov (United States)

    ... of this page: https://medlineplus.gov/searchtips.html Search Tips To use the sharing features on this page, please enable JavaScript. How do I search MedlinePlus? The search box appears at the top ...

  7. Axion Searches, Old and New

    CERN Multimedia

    CERN. Geneva

    2005-01-01

    Outline of the lecture: Constraints from laboratory searches and astrophysics, axion cosmology, the cavity detector of dark matter axions, solar axion searches, laser experiments, a telescope search, macroscopic forces mediated by axions.

  8. Face Search at Scale.

    Science.gov (United States)

    Wang, Dayong; Otto, Charles; Jain, Anil K

    2017-06-01

    Given the prevalence of social media websites, one challenge facing computer vision researchers is to devise methods to search for persons of interest among the billions of shared photos on these websites. Despite significant progress in face recognition, searching a large collection of unconstrained face images remains a difficult problem. To address this challenge, we propose a face search system which combines a fast search procedure, coupled with a state-of-the-art commercial off the shelf (COTS) matcher, in a cascaded framework. Given a probe face, we first filter the large gallery of photos to find the top- k most similar faces using features learned by a convolutional neural network. The k retrieved candidates are re-ranked by combining similarities based on deep features and those output by the COTS matcher. We evaluate the proposed face search system on a gallery containing 80 million web-downloaded face images. Experimental results demonstrate that while the deep features perform worse than the COTS matcher on a mugshot dataset (93.7 percent versus 98.6 percent TAR@FAR of 0.01 percent), fusing the deep features with the COTS matcher improves the overall performance ( 99.5 percent TAR@FAR of 0.01 percent). This shows that the learned deep features provide complementary information over representations used in state-of-the-art face matchers. On the unconstrained face image benchmarks, the performance of the learned deep features is competitive with reported accuracies. LFW database: 98.20 percent accuracy under the standard protocol and 88.03 percent TAR@FAR of 0.1 percent under the BLUFR protocol; IJB-A benchmark: 51.0 percent TAR@FAR of 0.1 percent (verification), rank 1 retrieval of 82.2 percent (closed-set search), 61.5 percent FNIR@FAR of 1 percent (open-set search). The proposed face search system offers an excellent trade-off between accuracy and scalability on galleries with millions of images. Additionally, in a face search experiment involving

  9. SEARCHES FOR SUPERSYMMETRY IN ATLAS

    CERN Document Server

    Xu, Da; The ATLAS collaboration

    2017-01-01

    A wide range of supersymmetric searches are presented. All searches are based on the proton- proton collision dataset collected by the ATLAS experiment during the 2015 and 2016 (before summer) run with a center-of-mass energy of 13 TeV, corresponding to an integrated lumi- nosity of 36.1 (36.7) fb-1. The searches are categorized into inclusive gluino and squark search, third generation search, electroweak search, prompt RPV search and long-lived par- ticle search. No evidence of new physics is observed. The results are intepreted in various models and expressed in terms of limits on the masses of new particles.

  10. Archaeal Tuc1/Ncs6 homolog required for wobble uridine tRNA thiolation is associated with ubiquitin-proteasome, translation, and RNA processing system homologs.

    Directory of Open Access Journals (Sweden)

    Nikita E Chavarria

    Full Text Available While cytoplasmic tRNA 2-thiolation protein 1 (Tuc1/Ncs6 and ubiquitin-related modifier-1 (Urm1 are important in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U at wobble uridines of tRNAs in eukaryotes, the biocatalytic roles and properties of Ncs6/Tuc1 and its homologs are poorly understood. Here we present the first report of an Ncs6 homolog of archaea (NcsA of Haloferax volcanii that is essential for maintaining cellular pools of thiolated tRNA(LysUUU and for growth at high temperature. When purified from Hfx. volcanii, NcsA was found to be modified at Lys204 by isopeptide linkage to polymeric chains of the ubiquitin-fold protein SAMP2. The ubiquitin-activating E1 enzyme homolog of archaea (UbaA was required for this covalent modification. Non-covalent protein partners that specifically associated with NcsA were also identified including UbaA, SAMP2, proteasome activating nucleotidase (PAN-A/1, translation elongation factor aEF-1α and a β-CASP ribonuclease homolog of the archaeal cleavage and polyadenylation specificity factor 1 family (aCPSF1. Together, our study reveals that NcsA is essential for growth at high temperature, required for formation of thiolated tRNA(LysUUU and intimately linked to homologs of ubiquitin-proteasome, translation and RNA processing systems.

  11. Enhanced photosynthesis and redox energy production contribute to salinity tolerance in Dunaliella as revealed by homology-based proteomics.

    Science.gov (United States)

    Liska, Adam J; Shevchenko, Andrej; Pick, Uri; Katz, Adriana

    2004-09-01

    Salinity is a major limiting factor for the proliferation of plants and inhibits central metabolic activities such as photosynthesis. The halotolerant green alga Dunaliella can adapt to hypersaline environments and is considered a model photosynthetic organism for salinity tolerance. To clarify the molecular basis for salinity tolerance, a proteomic approach has been applied for identification of salt-induced proteins in Dunaliella. Seventy-six salt-induced proteins were selected from two-dimensional gel separations of different subcellular fractions and analyzed by mass spectrometry (MS). Application of nanoelectrospray mass spectrometry, combined with sequence-similarity database-searching algorithms, MS BLAST and MultiTag, enabled identification of 80% of the salt-induced proteins. Salinity stress up-regulated key enzymes in the Calvin cycle, starch mobilization, and redox energy production; regulatory factors in protein biosynthesis and degradation; and a homolog of a bacterial Na(+)-redox transporters. The results indicate that Dunaliella responds to high salinity by enhancement of photosynthetic CO(2) assimilation and by diversion of carbon and energy resources for synthesis of glycerol, the osmotic element in Dunaliella. The ability of Dunaliella to enhance photosynthetic activity at high salinity is remarkable because, in most plants and cyanobacteria, salt stress inhibits photosynthesis. The results demonstrated the power of MS BLAST searches for the identification of proteins in organisms whose genomes are not known and paved the way for dissecting molecular mechanisms of salinity tolerance in algae and higher plants.

  12. Variability of patient spine education by Internet search engine.

    Science.gov (United States)

    Ghobrial, George M; Mehdi, Angud; Maltenfort, Mitchell; Sharan, Ashwini D; Harrop, James S

    2014-03-01

    Patients are increasingly reliant upon the Internet as a primary source of medical information. The educational experience varies by search engine, search term, and changes daily. There are no tools for critical evaluation of spinal surgery websites. To highlight the variability between common search engines for the same search terms. To detect bias, by prevalence of specific kinds of websites for certain spinal disorders. Demonstrate a simple scoring system of spinal disorder website for patient use, to maximize the quality of information exposed to the patient. Ten common search terms were used to query three of the most common search engines. The top fifty results of each query were tabulated. A negative binomial regression was performed to highlight the variation across each search engine. Google was more likely than Bing and Yahoo search engines to return hospital ads (P=0.002) and more likely to return scholarly sites of peer-reviewed lite (P=0.003). Educational web sites, surgical group sites, and online web communities had a significantly higher likelihood of returning on any search, regardless of search engine, or search string (P=0.007). Likewise, professional websites, including hospital run, industry sponsored, legal, and peer-reviewed web pages were less likely to be found on a search overall, regardless of engine and search string (P=0.078). The Internet is a rapidly growing body of medical information which can serve as a useful tool for patient education. High quality information is readily available, provided that the patient uses a consistent, focused metric for evaluating online spine surgery information, as there is a clear variability in the way search engines present information to the patient. Published by Elsevier B.V.

  13. [Sequence analysis of LEAFY homologous gene from Dendrobium moniliforme and application for identification of medicinal Dendrobium].

    Science.gov (United States)

    Xing, Wen-Rui; Hou, Bei-Wei; Guan, Jing-Jiao; Luo, Jing; Ding, Xiao-Yu

    2013-04-01

    The LEAFY (LFY) homologous gene of Dendrobium moniliforme (L.) Sw. was cloned by new primers which were designed based on the conservative region of known sequences of orchid LEAFY gene. Partial LFY homologous gene was cloned by common PCR, then we got the complete LFY homologous gene Den LFY by Tail-PCR. The complete sequence of DenLFY gene was 3 575 bp which contained three exons and two introns. Using BLAST method, comparison analysis among the exon of LFY homologous gene indicted that the DenLFY gene had high identity with orchids LFY homologous, including the related fragment of PhalLFY (84%) in Phalaenopsis hybrid cultivar, LFY homologous gene in Oncidium (90%) and in other orchid (over 80%). Using MP analysis, Dendrobium is found to be the sister to Oncidium and Phalaenopsis. Homologous analysis demonstrated that the C-terminal amino acids were highly conserved. When the exons and introns were separately considered, exons and the sequence of amino acid were good markers for the function research of DenLFY gene. The second intron can be used in authentication research of Dendrobium based on the length polymorphism between Dendrobium moniliforme and Dendrobium officinale.

  14. Better understanding of homologous recombination through a 12-week laboratory course for undergraduates majoring in biotechnology.

    Science.gov (United States)

    Li, Ming; Shen, Xiaodong; Zhao, Yan; Hu, Xiaomei; Hu, Fuquan; Rao, Xiancai

    2017-07-08

    Homologous recombination, a central concept in biology, is defined as the exchange of DNA strands between two similar or identical nucleotide sequences. Unfortunately, undergraduate students majoring in biotechnology often experience difficulties in understanding the molecular basis of homologous recombination. In this study, we developed and implemented a 12-week laboratory course for biotechnology undergraduates in which gene targeting in Streptococcus suis was used to facilitate their understanding of the basic concept and process of homologous recombination. Students worked in teams of two to select a gene of interest to create a knockout mutant using methods that relied on homologous recombination. By integrating abstract knowledge and practice in the process of scientific research, students gained hands-on experience in molecular biology techniques while learning about the principle and process of homologous recombination. The learning outcomes and survey-based assessment demonstrated that students substantially enhanced their understanding of how homologous recombination could be used to study gene function. Overall, the course was very effective for helping biotechnology undergraduates learn the theory and application of homologous recombination, while also yielding positive effects in developing confidence and scientific skills for future work in research. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):329-335, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

  15. SearchResultFinder: federated search made easy

    NARCIS (Netherlands)

    Trieschnigg, Rudolf Berend; Tjin-Kam-Jet, Kien; Hiemstra, Djoerd

    Building a federated search engine based on a large number existing web search engines is a challenge: implementing the programming interface (API) for each search engine is an exacting and time-consuming job. In this demonstration we present SearchResultFinder, a browser plugin which speeds up

  16. Market Dominance and Search Quality in the Search Engine Market

    NARCIS (Netherlands)

    Lianos, I.; Motchenkova, E.I.

    2013-01-01

    We analyze a search engine market from a law and economics perspective and incorporate the choice of quality-improving innovations by a search engine platform in a two-sided model of Internet search engine. In the proposed framework, we first discuss the legal issues the search engine market raises

  17. Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes.

    Directory of Open Access Journals (Sweden)

    Masako Ogura

    2007-08-01

    Full Text Available Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such "Sel1-like repeat" (SLR genes ("slr genes". Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, dN/dS = omega > 1 were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117 from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (omegaJ > 25, whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.

  18. Characterization of a serine proteinase homologous (SPH) in Chinese mitten crab Eriocheir sinensis.

    Science.gov (United States)

    Qin, Chuanjie; Chen, Liqiao; Qin, Jian G; Zhao, Daxian; Zhang, Hao; Wu, Ping; Li, Erchao

    2010-01-01

    The serine protease homologous (SPH) is an important cofactor of prophenoloxidase-activating enzyme (PPAE). The gene of SPH of Chinese mitten crab Eriocheir sinensis (EsSPH) in hemocytes was cloned and characterized using reverse transcript polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The SPH cDNA consisted of 1386 bp with an open reading frame (ORF) encoded a protein of 378 amino acids, 154 bp 5'-untranslated region, and 95 bp 3'-untranslated region. Sequence comparisons against the GenBank database showed that EsSPH deduced amino acids had an overall identity to the gene of serine protease family from 41% to 70% of 15 invertebrate species. The protein had the structural characteristics of SPH, including the conserved six cysteine residues in the N-terminal clip domain and the functional activity (His157, Asp209, Gly311) in the C-terminal serine proteinase-like domain. To analyze the role of EsSPH in an acute infection, the temporal expression of the EsSPH gene after the Aeromonas hydrophila challenge was measured by real-time RT-PCR. The EsSPH transcripts in hemocytes significantly increased at 6 h, 12 h and 48 h over time after the A. hydrophila injection. This expression pattern shows that EsSPH has the potential to defend against invading microorganisms. The mRNA transcripts of EsSPH were detected in all tissues with the highest in the hepatopancreas. Interestingly, the mRNA transcripts of EsSPH and proPO were found in ova and expressed in oosperms, suggesting that the maternal transfer of EsSPH and proPO may exit in crab, but this warrants confirmation in further research.

  19. Spinster homolog 2 (spns2 deficiency causes early onset progressive hearing loss.

    Directory of Open Access Journals (Sweden)

    Jing Chen

    2014-10-01

    Full Text Available Spinster homolog 2 (Spns2 acts as a Sphingosine-1-phosphate (S1P transporter in zebrafish and mice, regulating heart development and lymphocyte trafficking respectively. S1P is a biologically active lysophospholipid with multiple roles in signalling. The mechanism of action of Spns2 is still elusive in mammals. Here, we report that Spns2-deficient mice rapidly lost auditory sensitivity and endocochlear potential (EP from 2 to 3 weeks old. We found progressive degeneration of sensory hair cells in the organ of Corti, but the earliest defect was a decline in the EP, suggesting that dysfunction of the lateral wall was the primary lesion. In the lateral wall of adult mutants, we observed structural changes of marginal cell boundaries and of strial capillaries, and reduced expression of several key proteins involved in the generation of the EP (Kcnj10, Kcnq1, Gjb2 and Gjb6, but these changes were likely to be secondary. Permeability of the boundaries of the stria vascularis and of the strial capillaries appeared normal. We also found focal retinal degeneration and anomalies of retinal capillaries together with anterior eye defects in Spns2 mutant mice. Targeted inactivation of Spns2 in red blood cells, platelets, or lymphatic or vascular endothelial cells did not affect hearing, but targeted ablation of Spns2 in the cochlea using a Sox10-Cre allele produced a similar auditory phenotype to the original mutation, suggesting that local Spns2 expression is critical for hearing in mammals. These findings indicate that Spns2 is required for normal maintenance of the EP and hence for normal auditory function, and support a role for S1P signalling in hearing.

  20. Phosphoinositide binding by the pleckstrin homology domains of Ipl and Tih1.

    Science.gov (United States)

    Saxena, Anjana; Morozov, Pavel; Frank, Dale; Musalo, Raymond; Lemmon, Mark A; Skolnik, Edward Y; Tycko, Benjamin

    2002-12-20

    The Ipl protein consists of a single pleckstrin homology (PH) domain with short N- and C-terminal extensions. This protein is highly conserved among vertebrates, and it acts to limit placental growth in mice. However, its biochemical function is unknown. The closest paralogue of Ipl is Tih1, another small PH domain protein. By sequence comparisons, Ipl and Tih1 define an outlying branch of the PH domain superfamily. Here we describe phosphatidylinositol phosphate (PIP) binding by these proteins. Ipl and Tih1 bind to immobilized PIPs with moderate affinity, but this binding is weaker and more promiscuous than that of prototypical PH domains from the general receptor for phosphoinositides (GRP1), phospholipase C delta1, and dual adaptor for phosphoinositides and phosphotyrosine 1. In COS7 cells exposed to epidermal growth factor, green fluorescent protein (GFP)-Ipl and GFP-Tih1 accumulate at membrane ruffles without clearing from the cytoplasm, whereas control GFP-GRP1 translocates rapidly to the plasma membrane and clears from the cytoplasm. Ras*-Ipl and Ras*-Tih1 fusion proteins both rescue cdc25ts Saccharomyces cerevisiae, but Ras*-Ipl rescues more efficiently in the presence of phosphatidylinositol 3-kinase (PI3K), whereas PI3K-independent rescue is more efficient with Ras*-Tih1. Site-directed mutagenesis defines amino acids in the beta1-loop1-beta2 regions of Ipl and Tih1 as essential for growth rescue in this assay. Thus, Ipl and Tih1 are bona fide PH domain proteins, with broad specificity and moderate affinity for PIPs.

  1. Spinster homolog 2 (spns2) deficiency causes early onset progressive hearing loss.

    Science.gov (United States)

    Chen, Jing; Ingham, Neil; Kelly, John; Jadeja, Shalini; Goulding, David; Pass, Johanna; Mahajan, Vinit B; Tsang, Stephen H; Nijnik, Anastasia; Jackson, Ian J; White, Jacqueline K; Forge, Andrew; Jagger, Daniel; Steel, Karen P

    2014-10-01

    Spinster homolog 2 (Spns2) acts as a Sphingosine-1-phosphate (S1P) transporter in zebrafish and mice, regulating heart development and lymphocyte trafficking respectively. S1P is a biologically active lysophospholipid with multiple roles in signalling. The mechanism of action of Spns2 is still elusive in mammals. Here, we report that Spns2-deficient mice rapidly lost auditory sensitivity and endocochlear potential (EP) from 2 to 3 weeks old. We found progressive degeneration of sensory hair cells in the organ of Corti, but the earliest defect was a decline in the EP, suggesting that dysfunction of the lateral wall was the primary lesion. In the lateral wall of adult mutants, we observed structural changes of marginal cell boundaries and of strial capillaries, and reduced expression of several key proteins involved in the generation of the EP (Kcnj10, Kcnq1, Gjb2 and Gjb6), but these changes were likely to be secondary. Permeability of the boundaries of the stria vascularis and of the strial capillaries appeared normal. We also found focal retinal degeneration and anomalies of retinal capillaries together with anterior eye defects in Spns2 mutant mice. Targeted inactivation of Spns2 in red blood cells, platelets, or lymphatic or vascular endothelial cells did not affect hearing, but targeted ablation of Spns2 in the cochlea using a Sox10-Cre allele produced a similar auditory phenotype to the original mutation, suggesting that local Spns2 expression is critical for hearing in mammals. These findings indicate that Spns2 is required for normal maintenance of the EP and hence for normal auditory function, and support a role for S1P signalling in hearing.

  2. Rapid small lot manufacturing

    Energy Technology Data Exchange (ETDEWEB)

    Harrigan, R.W.

    1998-05-09

    The direct connection of information, captured in forms such as CAD databases, to the factory floor is enabling a revolution in manufacturing. Rapid response to very dynamic market conditions is becoming the norm rather than the exception. In order to provide economical rapid fabrication of small numbers of variable products, one must design with manufacturing constraints in mind. In addition, flexible manufacturing systems must be programmed automatically to reduce the time for product change over in the factory and eliminate human errors. Sensor based machine control is needed to adapt idealized, model based machine programs to uncontrolled variables such as the condition of raw materials and fabrication tolerances.

  3. Mastering Search Analytics Measuring SEO, SEM and Site Search

    CERN Document Server

    Chaters, Brent

    2011-01-01

    Many companies still approach Search Engine Optimization (SEO) and paid search as separate initiatives. This in-depth guide shows you how to use these programs as part of a comprehensive strategy-not just to improve your site's search rankings, but to attract the right people and increase your conversion rate. Learn how to measure, test, analyze, and interpret all of your search data with a wide array of analytic tools. Gain the knowledge you need to determine the strategy's return on investment. Ideal for search specialists, webmasters, and search marketing managers, Mastering Search Analyt

  4. Rapid Cycling and Its Treatment

    Science.gov (United States)

    ... Announcements Public Service Announcements Partnering with DBSA Rapid Cycling and its Treatment What is bipolar disorder? Bipolar ... to Depression and Manic Depression . What is rapid cycling? Rapid cycling is defined as four or more ...

  5. Cloning and characterization of WRKY gene homologs in Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How) and their expression in response to fusaric acid treatment.

    Science.gov (United States)

    Mao, Yizhou; Jiang, Biao; Peng, Qingwu; Liu, Wenrui; Lin, Yue; Xie, Dasen; He, Xiaoming; Li, Shaoshan

    2017-05-01

    The WRKY transcription factors play an important role in plant resistance for biotic and abiotic stresses. In the present study, we cloned 10 WRKY gene homologs (CqWRKY) in Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua) using the rapid-amplification of cDNA ends (RACE) or homology-based cloning methods. We characterized the structure of these CqWRKY genes. Phylogenetic analysis of these sequences with cucumber homologs suggested possible structural conservation of these genes among cucurbit crops. We examined the expression levels of these genes in response to fusaric acid (FA) treatment between resistant and susceptible Chieh-qua lines with quantitative real-time PCR. All genes could be upregulated upon FA treatment, but four CqWRKY genes exhibited differential expression between resistant and susceptible lines before and after FA application. CqWRKY31 seemed to be a positive regulator while CqWRKY1, CqWRKY23 and CqWRKY53 were negative regulators of fusaric resistance. This is the first report of characterization of WRKY family genes in Chieh-qua. The results may also be useful in breeding Chieh-qua for Fusarium wilt resistance.

  6. SUSY Searches at ATLAS

    CERN Document Server

    Mamuzic, Judita; The ATLAS collaboration

    2017-01-01

    Supersymmetry (SUSY) is considered one of the best motivated extensions of the Standard Model. It postulates a fundamental symmetry between fermions and bosons, and introduces a set of new supersymmetric particles at the electroweak scale. It addresses the hierarchy and naturalness problem, gives a solution to the gauge coupling unification, and offers a cold dark matter candidate. Different aspects of SUSY searches, using strong, electroweak, third generation production, and R-parity violation and long lived particles are being studied at the LHC. An overview of most recent SUSY searches results using the 13 TeV ATLAS RUN2 data will be presented.

  7. Searching with iterated maps

    Science.gov (United States)

    Elser, V.; Rankenburg, I.; Thibault, P.

    2007-01-01

    In many problems that require extensive searching, the solution can be described as satisfying two competing constraints, where satisfying each independently does not pose a challenge. As an alternative to tree-based and stochastic searching, for these problems we propose using an iterated map built from the projections to the two constraint sets. Algorithms of this kind have been the method of choice in a large variety of signal-processing applications; we show here that the scope of these algorithms is surprisingly broad, with applications as diverse as protein folding and Sudoku. PMID:17202267

  8. Upgrading Enterprise Search

    Energy Technology Data Exchange (ETDEWEB)

    McDunn, R

    2005-04-28

    This presentation will describe the process we went through this past year to upgrade our enterprise search tool from a very old version of Inktomi to the latest version of Verity Ultraseek. We started with requirements gathering and then compared requirements against several available products to determine which product to choose. After purchasing the product, we worked through several defined phases of implementation and customization, with initial rollout late January 2004. Finally, we will show you where we are today and describe future search plans.

  9. Search for $2\

    CERN Document Server

    :,; Auty, D J; Barbeau, P S; Beck, D; Belov, V; Breidenbach, M; Brunner, T; Burenkov, A; Cao, G F; Chambers, C; Chaves, J; Cleveland, B; Coon, M; Craycraft, A; Daniels, T; Danilov, M; Daugherty, S J; Davis, J; Delaquis, S; Der Mesrobian-Kabakian, A; DeVoe, R; Didberidze, T; Dilling, J; Dolgolenko, A; Dolinski, M J; Dunford, M; Fairbank, W; Farine, J; Feldmeier, W; Feyzbakhsh, S; Fierlinger, P; Fudenberg, D; Gornea, R; Graham, K; Gratta, G; Hall, C; Hughes, M; Jewell, M J; Johnson, A; Johnson, T N; Johnston, S; Karelin, A; Kaufman, L J; Killick, R; King, J; Koffas, T; Kravitz, S; Krücken, R; Kuchenkov, A; Kumar, K S; Leonard, D S; Licciardi, C; Lin, Y H; Ling, J; MacLellan, R; Marino, M G; Mong, B; Moore, D; Njoya, O; Nelson, R; Odian, A; Ostrovskiy, I; Piepke, A; Pocar, A; Prescott, C Y; Retière, F; Rowson, P C; Russell, J J; Schubert, A; Sinclair, D; Smith, E; Stekhanov, V; Tarka, M; Tolba, T; Tsang, R; Twelker, K; Vogel, P; Vuilleumier, J -L; Waite, A; Walton, J; Walton, T; Weber, M; Wen, L J; Wichoski, U; Winick, T A; Wood, J; Xu, Q Y; Yang, L; Yen, Y -R; Zeldovich, O Ya

    2015-01-01

    EXO-200 is a single phase liquid xenon detector designed to search for neutrinoless double-beta decay of $^{136}$Xe to the ground state of $^{136}$Ba. We report here on a search for the two-neutrino double-beta decay of $^{136}$Xe to the first $0^+$ excited state, $0^+_1$, of $^{136}$Ba based on a 100 kg$\\cdot$yr exposure of $^{136}$Xe. Using a specialized analysis employing a machine learning algorithm, we obtain a 90% CL half-life sensitivity of $1.7 \\times 10^{24}$ yr. We find no statistically significant evidence for the $2\

  10. Search for glueballs

    Energy Technology Data Exchange (ETDEWEB)

    Toki, W. [Colorado State Univ., Ft. Collins, CO (United States). Dept. of Physics

    1997-06-01

    In these Summer School lectures, the author reviews the results of recent glueball searches. He begins with a brief review of glueball phenomenology and meson spectroscopy, including a discussion of resonance behavior. The results on the f{sub o}(1500) and f{sub J}(1700) resonances from proton-antiproton experiments and radiative J/{Psi} decays are discussed. Finally, {pi}{pi} and {eta}{pi} studies from D{sub s} decays and exotic meson searches are reviewed. 46 refs., 40 figs.

  11. Searching for excellence

    Science.gov (United States)

    Yager, Robert E.

    Visits to six school districts which were identified by the National Science Teachers Association's Search for Excellence program were made during 1983 by teams of 17 researchers. The reports were analyzed in search for common characteristics that can explain the requirements necessary for excellent science programs. The results indicate that creative ideas, administrative and community involvement, local ownership and pride, and well-developed in-service programs and implementation strategies are vital. Exceptional teachers with boundless energies also seem to exist where exemplary science programs are found.

  12. PaperBLAST: Text Mining Papers for Information about Homologs.

    Science.gov (United States)

    Price, Morgan N; Arkin, Adam P

    2017-01-01

    Large-scale genome sequencing has identified millions of protein-coding genes whose function is unknown. Many of these proteins are similar to characterized proteins from other organisms, but much of this information is missing from annotation databases and is hidden in the scientific literature. To make this information accessible, PaperBLAST uses EuropePMC to search the full text of scientific articles for references to genes. PaperBLAST also takes advantage of curated resources (Swiss-Prot, GeneRIF, and EcoCyc) that link protein sequences to scientific articles. PaperBLAST's database includes over 700,000 scientific articles that mention over 400,000 different proteins. Given a protein of interest, PaperBLAST quickly finds similar proteins that are discussed in the literature and presents snippets of text from relevant articles or from the curators. PaperBLAST is available at http://papers.genomics.lbl.gov/. IMPORTANCE With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins' functions.

  13. Homologous Recombination via Synthesis-Dependent Strand Annealing in Yeast Requires the Irc20 and Srs2 DNA Helicases

    OpenAIRE

    Miura, Tohru; Yamana, Yoshimasa; Usui, Takehiko; Ogawa, Hiroaki I.; Yamamoto, Masa-Toshi; Kusano, Kohji

    2012-01-01

    Synthesis-dependent strand-annealing (SDSA)-mediated homologous recombination replaces the sequence around a DNA double-strand break (DSB) with a copy of a homologous DNA template, while maintaining the original configuration of the flanking regions. In somatic cells at the 4n stage, Holliday-junction-mediated homologous recombination and nonhomologous end joining (NHEJ) cause crossovers (CO) between homologous chromosomes and deletions, respectively, resulting in loss of heterozygosity (LOH)...

  14. Rapid manufacturing for microfluidics

    CSIR Research Space (South Africa)

    Land, K

    2012-10-01

    Full Text Available . Microfluidics is at the forefront of developing solutions for drug discovery, diagnostics (from glucose tests to malaria and TB testing) and environmental diagnostics (E-coli monitoring of drinking water). In order to quickly implement new designs, a rapid...

  15. Rapid Prototyping in PVS

    Science.gov (United States)

    Munoz, Cesar A.; Butler, Ricky (Technical Monitor)

    2003-01-01

    PVSio is a conservative extension to the PVS prelude library that provides basic input/output capabilities to the PVS ground evaluator. It supports rapid prototyping in PVS by enhancing the specification language with built-in constructs for string manipulation, floating point arithmetic, and input/output operations.

  16. Rapid Prototyping Reconsidered

    Science.gov (United States)

    Desrosier, James

    2011-01-01

    Continuing educators need additional strategies for developing new programming that can both reduce the time to market and lower the cost of development. Rapid prototyping, a time-compression technique adapted from the high technology industry, represents one such strategy that merits renewed evaluation. Although in higher education rapid…

  17. SUSY Searches at the Tevatron

    Energy Technology Data Exchange (ETDEWEB)

    Zivkovic, L.

    2011-07-01

    In this article results from supersymmetry searches at D0 and CDF are reported. Searches for third generation squarks, searches for gauginos, and searches for models with R-parity violation are described. As no signs of supersymmetry for these models are observed, the most stringent limits to date are presented.

  18. Complete local search with memory

    NARCIS (Netherlands)

    Ghosh, D.; Sierksma, G.

    2000-01-01

    Neighborhood search heuristics like local search and its variants are some of the most popular approaches to solve discrete optimization problems of moderate to large size. Apart from tabu search, most of these heuristics are memoryless. In this paper we introduce a new neighborhood search heuristic

  19. Complete local search with memory

    NARCIS (Netherlands)

    Ghosh, D.; Sierksma, G.

    2002-01-01

    Neighborhood search heuristics like local search and its variants are some of the most popular approaches to solve discrete optimization problems of moderate to large size. Apart from tabu search, most of these heuristics are memoryless. In this paper we introduce a new neighborhood search heuristic

  20. The Evolution of Web Searching.

    Science.gov (United States)

    Green, David

    2000-01-01

    Explores the interrelation between Web publishing and information retrieval technologies and lists new approaches to Web indexing and searching. Highlights include Web directories; search engines; portalisation; Internet service providers; browser providers; meta search engines; popularity based analysis; natural language searching; links-based…

  1. Prices and heterogeneous search costs

    NARCIS (Netherlands)

    Moraga Gonzalez, J.L.; Sandor, Z.; Wildenbeest, M.R.

    2017-01-01

    We study price formation in a model of consumer search for differentiated products in which consumers have heterogeneous search costs. We provide conditions under which a pure-strategy symmetric Nash equilibrium exists and is unique. Search costs affect two margins—the intensive search margin (or

  2. Self-learning search engines

    NARCIS (Netherlands)

    Schuth, A.

    How does a search engine such as Google know which search results to display? There are many competing algorithms that generate search results, but which one works best? We developed a new probabilistic method for quickly comparing large numbers of search algorithms by examining the results users

  3. Standardization of Keyword Search Mode

    Science.gov (United States)

    Su, Di

    2010-01-01

    In spite of its popularity, keyword search mode has not been standardized. Though information professionals are quick to adapt to various presentations of keyword search mode, novice end-users may find keyword search confusing. This article compares keyword search mode in some major reference databases and calls for standardization. (Contains 3…

  4. Detecting remote sequence homology in disordered proteins: discovery of conserved motifs in the N-termini of Mononegavirales phosphoproteins.

    Directory of Open Access Journals (Sweden)

    David Karlin

    Full Text Available Paramyxovirinae are a large group of viruses that includes measles virus and parainfluenza viruses. The viral Phosphoprotein (P plays a central role in viral replication. It is composed of a highly variable, disordered N-terminus and a conserved C-terminus. A second viral protein alternatively expressed, the V protein, also contains the N-terminus of P, fused to a zinc finger. We suspected that, despite their high variability, the N-termini of P/V might all be homologous; however, using standard approaches, we could previously identify sequence conservation only in some Paramyxovirinae. We now compared the N-termini using sensitive sequence similarity search programs, able to detect residual similarities unnoticeable by conventional approaches. We discovered that all Paramyxovirinae share a short sequence motif in their first 40 amino acids, which we called soyuz1. Despite its short length (11-16aa, several arguments allow us to conclude that soyuz1 probably evolved by homologous descent, unlike linear motifs. Conservation across such evolutionary distances suggests that soyuz1 plays a crucial role and experimental data suggest that it binds the viral nucleoprotein to prevent its illegitimate self-assembly. In some Paramyxovirinae, the N-terminus of P/V contains a second motif, soyuz2, which might play a role in blocking interferon signaling. Finally, we discovered that the P of related Mononegavirales contain similarly overlooked motifs in their N-termini, and that their C-termini share a previously unnoticed structural similarity suggesting a common origin. Our results suggest several testable hypotheses regarding the replication of Mononegavirales and suggest that disordered regions with little overall sequence similarity, common in viral and eukaryotic proteins, might contain currently overlooked motifs (intermediate in length between linear motifs and disordered domains that could be detected simply by comparing orthologous proteins.

  5. Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum

    Directory of Open Access Journals (Sweden)

    Santana Clara

    2009-10-01

    Full Text Available Abstract Background Schistosomes are trematode parasites of the phylum Platyhelminthes. They are considered the most important of the human helminth parasites in terms of morbidity and mortality. Draft genome sequences are now available for Schistosoma mansoni and Schistosoma japonicum. Non-coding RNA (ncRNA plays a crucial role in gene expression regulation, cellular function and defense, homeostasis, and pathogenesis. The genome-wide annotation of ncRNAs is a non-trivial task unless well-annotated genomes of closely related species are already available. Results A homology search for structured ncRNA in the genome of S. mansoni resulted in 23 types of ncRNAs with conserved primary and secondary structure. Among these, we identified rRNA, snRNA, SL RNA, SRP, tRNAs and RNase P, and also possibly MRP and 7SK RNAs. In addition, we confirmed five miRNAs that have recently been reported in S. japonicum and found two additional homologs of known miRNAs. The tRNA complement of S. mansoni is comparable to that of the free-living planarian Schmidtea mediterranea, although for some amino acids differences of more than a factor of two are observed: Leu, Ser, and His are overrepresented, while Cys, Meth, and Ile are underrepresented in S. mansoni. On the other hand, the number of tRNAs in the genome of S. japonicum is reduced by more than a factor of four. Both schistosomes have a complete set of minor spliceosomal snRNAs. Several ncRNAs that are expected to exist in the S. mansoni genome were not found, among them the telomerase RNA, vault RNAs, and Y RNAs. Conclusion The ncRNA sequences and structures presented here represent the most complete dataset of ncRNA from any lophotrochozoan reported so far. This data set provides an important reference for further analysis of the genomes of schistosomes and indeed eukaryotic genomes at large.

  6. Structure and Protein-Protein Interaction Studies on Chlamydia trachomatis Protein CT670 (YscO Homolog)

    Energy Technology Data Exchange (ETDEWEB)

    Lorenzini, Emily; Singer, Alexander; Singh, Bhag; Lam, Robert; Skarina, Tatiana; Chirgadze, Nickolay Y.; Savchenko, Alexei; Gupta, Radhey S. (Toronto); (McMaster U.); (OCI)

    2010-07-28

    Comparative genomic studies have identified many proteins that are found only in various Chlamydiae species and exhibit no significant sequence similarity to any protein in organisms that do not belong to this group. The CT670 protein of Chlamydia trachomatis is one of the proteins whose genes are in one of the type III secretion gene clusters but whose cellular functions are not known. CT670 shares several characteristics with the YscO protein of Yersinia pestis, including the neighboring genes, size, charge, and secondary structure, but the structures and/or functions of these proteins remain to be determined. Although a BLAST search with CT670 did not identify YscO as a related protein, our analysis indicated that these two proteins exhibit significant sequence similarity. In this paper, we report that the CT670 crystal, solved at a resolution of 2 {angstrom}, consists of a single coiled coil containing just two long helices. Gel filtration and analytical ultracentrifugation studies showed that in solution CT670 exists in both monomeric and dimeric forms and that the monomer predominates at lower protein concentrations. We examined the interaction of CT670 with many type III secretion system-related proteins (viz., CT091, CT665, CT666, CT667, CT668, CT669, CT671, CT672, and CT673) by performing bacterial two-hybrid assays. In these experiments, CT670 was found to interact only with the CT671 protein (YscP homolog), whose gene is immediately downstream of ct670. A specific interaction between CT670 and CT671 was also observed when affinity chromatography pull-down experiments were performed. These results suggest that CT670 and CT671 are putative homologs of the YcoO and YscP proteins, respectively, and that they likely form a chaperone-effector pair.

  7. GPR99, a new G protein-coupled receptor with homology to a new subgroup of nucleotide receptors

    Directory of Open Access Journals (Sweden)

    Chica Schaller H

    2002-07-01

    Full Text Available Abstract Background Based on sequence similarity, the superfamily of G protein-coupled receptors (GPRs can be subdivided into several subfamilies, the members of which often share similar ligands. The sequence data provided by the human genome project allows us to identify new GPRs by in silico homology screening, and to predict their ligands. Results By searching the human genomic database with known nucleotide receptors we discovered the gene for GPR99, a new orphan GPR. The mRNA of GPR99 was found in kidney and placenta. Phylogenetic analysis groups GPR99 into the P2Y subfamily of GPRs. Based on the phylogenetic tree we propose a new classification of P2Y nucleotide receptors into two subgroups predicting a nucleotide ligand for GPR99. By assaying known nucleotide ligands on heterologously expressed GPR99, we could not identify specifically activating substances, indicating that either they are not agonists of GPR99 or that GPR99 was not expressed at the cell surface. Analysis of the chromosomal localization of all genes of the P2Y subfamily revealed that all members of subgroup "a" are encoded by less than 370 kb on chromosome 3q24, and that the genes of subgroup "b" are clustered on one hand to chromosome 11q13.5 and on the other on chromosome 3q24-25.1 close to the subgroup "a" position. Therefore, the P2Y subfamily is a striking example for local gene amplification. Conclusions We identified a new orphan receptor, GPR99, with homology to the family of G protein-coupled nucleotide receptors. Phylogenetic analysis separates this family into different subgroups predicting a nucleotide ligand for GPR99.

  8. Searching for Movies

    DEFF Research Database (Denmark)

    Bogers, Toine

    2015-01-01

    Despite a surge in popularity of work on casual leisure search, some leisure domains are still relatively underrepresented. Movies are good example of such a domain, which is peculiar given the popularity of movie-centered websites and discovery services such as IMDB, RottenTomatoes, and Netflix...

  9. SUSY Search at LHC

    CERN Document Server

    Xu, Da; The ATLAS collaboration

    2018-01-01

    Despite the absence of experimental evidence, weak scale supersymmetry remains one of the best motivated and studied Standard Model extensions. This talk gives an overview of the most recent SUSY searches in ATLAS and CMS experiments using 13 TeV ATLAS Run2 data.

  10. Pentaquark searches with ALICE

    CERN Document Server

    Bobulska, Dana

    2016-01-01

    In this report we present the results of the data analysis for searching for possible invariant mass signals from pentaquarks in the ALICE data. Analysis was based on filtered data from real p-Pb events at psNN=5.02 TeV collected in 2013. The motivation for this project was the recent discovery of pentaquark states by the LHCb collaboration (c ¯ cuud resonance P+ c ) [1]. The search for similar not yet observed pentaquarks is an interesting research topic [2]. In this analysis we searched for a s ¯ suud pentaquark resonance P+ s and its possible decay channel to f meson and proton. The ALICE detector is well suited for the search of certain candidates thanks to its low material budget and strong PID capabilities. Additionally we might expect the production of such particles in ALICE as in heavy-ion and proton-ion collisions the thermal models describes well the particle yields and ratios [3]. Therefore it is reasonable to expect other species of hadrons, including also possible pentaquarks, to be produced w...

  11. Next Generation Search Interfaces

    Science.gov (United States)

    Roby, W.; Wu, X.; Ly, L.; Goldina, T.

    2015-09-01

    Astronomers are constantly looking for easier ways to access multiple data sets. While much effort is spent on VO, little thought is given to the types of User Interfaces we need to effectively search this sort of data. For instance, an astronomer might need to search Spitzer, WISE, and 2MASS catalogs and images then see the results presented together in one UI. Moving seamlessly between data sets is key to presenting integrated results. Results need to be viewed using first class, web based, integrated FITS viewers, XY Plots, and advanced table display tools. These components should be able to handle very large datasets. To make a powerful Web based UI that can manage and present multiple searches to the user requires taking advantage of many HTML5 features. AJAX is used to start searches and present results. Push notifications (Server Sent Events) monitor background jobs. Canvas is required for advanced result displays. Lesser known CSS3 technologies makes it all flow seamlessly together. At IPAC, we have been developing our Firefly toolkit for several years. We are now using it to solve this multiple data set, multiple queries, and integrated presentation problem to create a powerful research experience. Firefly was created in IRSA, the NASA/IPAC Infrared Science Archive (http://irsa.ipac.caltech.edu). Firefly is the core for applications serving many project archives, including Spitzer, Planck, WISE, PTF, LSST and others. It is also used in IRSA's new Finder Chart and catalog and image displays.

  12. Internet video search

    NARCIS (Netherlands)

    Snoek, C.G.M.; Smeulders, A.W.M.

    2011-01-01

    In this tutorial, we focus on the challenges in internet video search, present methods how to achieve state-of-the-art performance while maintaining efficient execution, and indicate how to obtain improvements in the near future. Moreover, we give an overview of the latest developments and future

  13. The Great Superintendent Search.

    Science.gov (United States)

    Mayo, C. Russell

    2003-01-01

    Discusses three sequential questions boards should reach consensus on before beginning a superintendent search. Questions involve district's position related to education issues deemed important to the community, a new superintendent's personality traits and leadership skills required to address these issues, and whether the board should seek to…

  14. Google Search Mastery Basics

    Science.gov (United States)

    Hill, Paul; MacArthur, Stacey; Read, Nick

    2014-01-01

    Effective Internet search skills are essential with the continually increasing amount of information available on the Web. Extension personnel are required to find information to answer client questions and to conduct research on programs. Unfortunately, many lack the skills necessary to effectively navigate the Internet and locate needed…

  15. Search for intervalmodels

    DEFF Research Database (Denmark)

    Høskuldsson, Agnar

    1996-01-01

    Methods are presented that carry out sorting of data according to some criteria, and investigate the possibilities of finding intervals that give separate models relative to the given data. The methods presented are more reliable than related clustering methods, because the search is carried out...

  16. Searching low and high

    DEFF Research Database (Denmark)

    Laursen, Keld; Salter, Ammon

    2003-01-01

    AbstractThis paper examines the factors that influence whether firms draw from universities in theirinnovative activities. The link between the universities and industrial innovation, and the role ofdifferent search strategies in influencing the propensity of firms to use universities is explored...

  17. Searching circular DNA strands

    Energy Technology Data Exchange (ETDEWEB)

    Eliazar, Iddo [Department of Technology Management, Holon Institute of Technology, Holon 58102 (Israel); Koren, Tal [School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel); Klafter, Joseph [School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978 (Israel)

    2007-02-14

    We introduce and explore a model of an ensemble of enzymes searching, in parallel, a circular DNA strand for a target site. The enzymes performing the search combine local scanning-conducted by a 1D motion along the strand-and random relocations on the strand-conducted via a confined motion in the medium containing the strand. Both the local scan mechanism and the relocation mechanism are considered general. The search durations are analysed, and their limiting probability distributions-for long DNA strands-are obtained in closed form. The results obtained (i) encompass the cases of single, parallel and massively parallel searches, taking place in the presence of either finite-mean or heavy-tailed relocation times, (ii) are applicable to a wide spectrum of local scan mechanisms including linear, Brownian, selfsimilar, and sub-diffusive motions (iii) provide a quantitative theoretical justification for the necessity of the relocation mechanism, and (iv) facilitate the derivation of optimal relocation strategies.

  18. Biased predecessor search

    DEFF Research Database (Denmark)

    Bose, Prosenjit; Fagerberg, Rolf; Howat, John

    2014-01-01

    We consider the problem of performing predecessor searches in a bounded universe while achieving query times that depend on the distribution of queries. We obtain several data structures with various properties: in particular, we give data structures that achieve expected query times logarithmic...... structures with general weights on universe elements, as well as the case when the distribution is not known in advance....

  19. Artificial restriction DNA cutters to promote homologous recombination in human cells.

    Science.gov (United States)

    Katada, Hitoshi; Komiyama, Makoto

    2011-02-01

    Homologous recombination is almost the only way to modify the genome in a predetermined fashion, despite its quite low frequency in mammalian cells. It has been already reported that the frequency of this biological process can be notably increased by inducing a double strand break (DSB) at target site. This article presents completely chemistry-based artificial restriction DNA cutter (ARCUT) for the promotion of homologous recombination in human cells. This cutter is composed of Ce(IV)/EDTA complex (molecular scissors) and two strands of peptide nucleic acid (PNA), and contains no proteins. Its scission site in the genome is determined simply by Watson-Crick rule so that ARCUT for desired homologous recombination is easily and straightforwardly designed and synthesized. The site-specificity of the scission is high enough to cut human genome at one target site. The DSB induced by this cutter is satisfactorily recognized by the repair system in human cells and promotes the targeted homologous recombination.

  20. An Approach for Zika Virus Inhibition Using Homology Structure of the Envelope Protein

    Czech Academy of Sciences Publication Activity Database

    Fernando, S.; Fernando, T.; Štefánik, M.; Eyer, Luděk; Růžek, Daniel

    2016-01-01

    Roč. 58, č. 12 (2016), s. 801-806 ISSN 1073-6085 Institutional support: RVO:60077344 Keywords : Zika virus * homology model * druggability * drug discovery Subject RIV: EE - Microbiology, Virology Impact factor: 1.634, year: 2016

  1. Single-cell template strand sequencing by Strand-seq enables the characterization of individual homologs

    NARCIS (Netherlands)

    Sanders, Ashley D; Falconer, Ester; Hills, Mark; Spierings, Diana C J; Lansdorp, Peter M.

    The ability to distinguish between genome sequences of homologous chromosomes in single cells is important for studies of copy-neutral genomic rearrangements (such as inversions and translocations), building chromosome-length haplotypes, refining genome assemblies, mapping sister chromatid exchange

  2. Homology building as a means to define antigenic epitopes on dihydrofolate reductase (DHFR) from Plasmodium falciparum

    DEFF Research Database (Denmark)

    Alifrangis, Michael; Christensen, Inge T; Jørgensen, Flemming S

    2004-01-01

    in the gene coding for Pf-DHFR. Furthermore, we wanted to study the potential use of homology models in general and of Pf-DHFR in particular in predicting antigenic malarial surface epitopes. METHODS: A homology model of Pf-DHFR domain was employed to define an epitope for the development of site......-specific antibodies against Pf-DHFR. The homology model suggested an exposed loop encompassing amino acid residues 64-100. A synthetic peptide of 37-mers whose sequence corresponded to the sequence of amino acid residues 64-100 of Pf-DHFR was synthesized and used to immunize mice for antibodies. Additionally...... of homology models in general and of Pf-DHFR in particular in predicting antigenic malarial surface epitopes....

  3. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

    National Research Council Canada - National Science Library

    Arnold, Konstantin; Bordoli, Lorenza; Kopp, Jürgen; Schwede, Torsten

    2006-01-01

    ...s. Integrating all required tools, programs and databases into a single web-based workspace facilitates access to homology modelling from a computer with web connection without the need of downloading...

  4. The ITS2 Database II: homology modelling RNA structure for molecular systematics

    National Research Council Canada - National Science Library

    Selig, Christian; Wolf, Matthias; Müller, Tobias; Dandekar, Thomas; Schultz, Jörg

    .... To overcome this hindrance for a wider application of the ITS2, we have developed a homology modelling approach to predict the structure of RNA and present the results of modelling the ITS2 in the ITS2 Database...

  5. An HMM posterior decoder for sequence feature prediction that includes homology information

    DEFF Research Database (Denmark)

    Käll, Lukas; Krogh, Anders Stærmose; Sonnhammer, Erik L. L.

    2005-01-01

    Motivation: When predicting sequence features like transmembrane topology, signal peptides, coil-coil structures, protein secondary structure or genes, extra support can be gained from homologs. Results: We present here a general hidden Markov model (HMM) decoding algorithm that combines...... probabilities for sequence features of homologs by considering the average of the posterior label probability of each position in a global sequence alignment. The algorithm is an extension of the previously described ‘optimal accuracy' decoder, allowing homology information to be used. It was benchmarked using...... an HMM for transmembrane topology and signal peptide prediction, Phobius. We found that the performance was substantially increased when incorporating information from homologs. Availability: A prediction server for transmembrane topology and signal peptides that uses the algorithm is available at http...

  6. Interactive and fuzzy search: a dynamic way to explore MEDLINE.

    Science.gov (United States)

    Wang, Jiannan; Cetindil, Inci; Ji, Shengyue; Li, Chen; Xie, Xiaohui; Li, Guoliang; Feng, Jianhua

    2010-09-15

    The MEDLINE database, consisting of over 19 million publication records, is the primary source of information for biomedicine and health questions. Although the database itself has been growing rapidly, the search paradigm of MEDLINE has remained largely unchanged. Here, we propose a new system for exploring the entire MEDLINE collection, represented by two unique features: (i) interactive: providing instant feedback to users' query letter by letter, and (ii) fuzzy: allowing approximate search. We develop novel index structures and search algorithms to make such a search model possible. We also develop incremental-update techniques to keep the data up to date. Interactive and fuzzy searching algorithms for exploring MEDLINE are implemented in a system called iPubMed, freely accessible over the web at http://ipubmed.ics.uci.edu/ and http://tastier.cs.tsinghua.edu.cn/ipubmed.

  7. Research on Personalized Information Filtering of Search Engine

    Science.gov (United States)

    Zhang, Shu; Chen, Xinrong; Luo, Changshou

    Since network has been created and developing rapidly in recent years, the age of information exploding is coming. The Search Engine becomes more and more important for people, but the traditional search engine retrieves and provides information just according to the keywords that users input. How to recommend the right information to users has become the hot point. The technology of personalized information filtering brings people hope .The paper I present analyzed the achievements of those filtering technologies ,and adopted user-system complex-operating modeling to build User-activitycollecting module, User-interest-updating module and User-searching module, in order to meet theme-oriented searching's needs. Experiments showed that the user-interest model can provide personalized service and enhance search engine's precision.

  8. To Internationalize Rapidly from Inception: Crowdsource

    Directory of Open Access Journals (Sweden)

    Nirosh Kannangara

    2012-10-01

    Full Text Available Technology entrepreneurs continuously search for tools to accelerate the internationalization of their startups. For the purpose of internationalizing rapidly from inception, we propose that technology startups use crowdsourcing to internalize the tacit knowledge embodied in members of a crowd distributed across various geographies. For example, a technology startup can outsource to a large crowd the definition of a customer problem that occurs across various geographies, the development of the best solution to the problem, and the identification of attractive business expansion opportunities. In this article, we analyze how three small firms use crowdsourcing, discuss the benefits of crowdsourcing, and offer six recommendations to technology entrepreneurs interested in using crowdsourcing to rapidly internationalize their startups from inception.

  9. Searching PubMed during a pandemic.

    Directory of Open Access Journals (Sweden)

    Ole Norgaard

    Full Text Available BACKGROUND: The 2009 influenza A(H1N1 pandemic has generated thousands of articles and news items. However, finding relevant scientific articles in such rapidly developing health crises is a major challenge which, in turn, can affect decision-makers' ability to utilise up-to-date findings and ultimately shape public health interventions. This study set out to show the impact that the inconsistent naming of the pandemic can have on retrieving relevant scientific articles in PubMed/MEDLINE. METHODOLOGY: We first formulated a PubMed search algorithm covering different names of the influenza pandemic and simulated the results that it would have retrieved from weekly searches for relevant new records during the first 10 weeks of the pandemic. To assess the impact of failing to include every term in this search, we then conducted the same searches but omitted in turn "h1n1," "swine," "influenza" and "flu" from the search string, and compared the results to those for the full string. PRINCIPAL FINDINGS: On average, our core search string identified 44.3 potentially relevant new records at the end of each week. Of these, we determined that an average of 27.8 records were relevant. When we excluded one term from the string, the percentage of records missed out of the total number of relevant records averaged 18.7% for omitting "h1n1," 13.6% for "swine," 17.5% for "influenza," and 20.6% for "flu." CONCLUSIONS: Due to inconsistent naming, while searching for scientific material about rapidly evolving situations such as the influenza A(H1N1 pandemic, there is a risk that one will miss relevant articles. To address this problem, the international scientific community should agree on nomenclature and the specific name to be used earlier, and the National Library of Medicine in the US could index potentially relevant materials faster and allow publishers to add alert tags to such materials.

  10. What's trending now? An analysis of trends in internet searches for labor epidurals.

    Science.gov (United States)

    Sutton, C D; Carvalho, B

    2017-05-01

    The study aim was to investigate internet use for obtaining information about epidurals for labor and delivery. Google Trends for US data was queried from 2004 to 2015 to find the most common searches and determine temporal trends. The Google Trends query used the term [epidural] and evaluated changes in search trends over time. Search comparisons were made for each year from 2004 to 2015, and three equal time epochs during the study period (2004-07, 2008-11, 2012-15) were compared. We also compared searches for epidurals with commonly searched birth-related terms. Internet searches are increasing; there were 726000 searches for [epidural] in 2015. Search terms with the most significant growth in the past 4years (2012-15) were "birth with epidural," "pain after epidural," "labor without epidural," "epidural birth video," and "epidural vs natural". Searches for epidural side effects, risks, and pain on insertion were among the most common and were increasing most rapidly. Searches related to epidurals were more common than searches related to "natural births", "home births", and "labor pain", but were less common than searches for "midwives" or "doulas". The findings provide an insight into internet use by those seeking information about labor analgesic options. Identifying the most common and rapidly increasing online search queries may guide physician-parturient interactions and online content creation, to address labor analgesic topics that most interest users. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Eye movement feedback fails to improve visual search performance.

    Science.gov (United States)

    Peltier, Chad; Becker, Mark W

    2017-01-01

    Many real-world searches (e.g., radiology and baggage screening) have rare targets. When targets are rare, observers perform rapid, incomplete searches, leading to higher miss rates. To improve search for rare (10% prevalence) targets, we provided eye movement feedback (EMF) to observers during their searches. Although the nature of the EMF varied across experiments, each method informed observers about the regions of the display that had not yet been inspected. We hypothesized that feedback would help guide attention to unsearched areas and increase the proportion of the display searched before making a target-absent response, thereby increasing accuracy. An eye tracker was used to mark fixated areas by either removing a semiopaque gray overlay (Experiments 1 and 4) as portions of the display were fixated or by adding the overlay once the eye left a segment of the image (Experiments 2 and 4). Experiment 3 provided automated EMF, such that a new region was uncovered every 540 milliseconds. Across experiments, we varied whether people searched for "Waldo" in images from "Where's Waldo?" search books or searched for a T among offset Ls. We found weak evidence that EMF improves accuracy in Experiment 1. However, in the remaining experiments, EMF had no effect (Experiment 4), or even reduced accuracy (Experiments 2 and 3). We conclude that the one positive result we found is likely a Type I error and that the EMF method that we used is unlikely to improve visual search performance.

  12. Foraging patterns in online searches

    Science.gov (United States)

    Wang, Xiangwen; Pleimling, Michel

    2017-03-01

    Nowadays online searches are undeniably the most common form of information gathering, as witnessed by billions of clicks generated each day on search engines. In this work we describe online searches as foraging processes that take place on the semi-infinite line. Using a variety of quantities like probability distributions and complementary cumulative distribution functions of step length and waiting time as well as mean square displacements and entropies, we analyze three different click-through logs that contain the detailed information of millions of queries submitted to search engines. Notable differences between the different logs reveal an increased efficiency of the search engines. In the language of foraging, the newer logs indicate that online searches overwhelmingly yield local searches (i.e., on one page of links provided by the search engines), whereas for the older logs the foraging processes are a combination of local searches and relocation phases that are power law distributed. Our investigation of click logs of search engines therefore highlights the presence of intermittent search processes (where phases of local explorations are separated by power law distributed relocation jumps) in online searches. It follows that good search engines enable the users to find the information they are looking for through a local exploration of a single page with search results, whereas for poor search engine users are often forced to do a broader exploration of different pages.

  13. Evolutionary origin, diversification and specialization of eukaryotic MutS homolog mismatch repair proteins

    OpenAIRE

    Culligan, Kevin M.; Meyer-Gauen, Gilbert; Lyons-Weiler, James; Hays, John B.

    2000-01-01

    Most eubacteria, and all eukaryotes examined thus far, encode homologs of the DNA mismatch repair protein MutS. Although eubacteria encode only one or two MutS-like proteins, eukaryotes encode at least six distinct MutS homolog (MSH) proteins, corresponding to conserved (orthologous) gene families. This suggests evolution of individual gene family lines of descent by several duplication/specialization events. Using quantitative phylogenetic analyses (RASA, or relative apparent synapomorphy an...

  14. Gene Disruption by Homologous Recombination in the Xylella fastidiosa Citrus Variegated Chlorosis Strain

    Science.gov (United States)

    Gaurivaud, Patrice; Souza, Leonardo C. A.; Virgílio, Andrea C. D.; Mariano, Anelise G.; Palma, Renê R.; Monteiro, Patrícia B.

    2002-01-01

    Mutagenesis by homologous recombination was evaluated in Xylella fastidiosa by using the bga gene, coding for β-galactosidase, as a model. Integration of replicative plasmids by homologous recombination between the cloned truncated copy of bga and the endogenous gene was produced by one or two crossover events leading to β-galactosidase mutants. A promoterless chloramphenicol acetyltransferase gene was used to monitor the expression of the target gene and to select a cvaB mutant. PMID:12200328

  15. Somatic association of telocentric chromosomes carrying homologous centromeres in common wheat.

    Science.gov (United States)

    Mello-Sampayo, T

    1973-01-01

    Measurements of distances between telocentric chromosomes, either homologous or representing the opposite arms of a metacentric chromosome (complementary telocentrics), were made at metaphase in root tip cells of common wheat carrying two homologous pairs of complementary telocentrics of chromosome 1 B or 6 B (double ditelosomic 1 B or 6 B). The aim was to elucidate the relative locations of the telocentric chromosomes within the cell. The data obtained strongly suggest that all four telocentrics of chromosome 1 B or 6 B are spacially and simultaneously co-associated. In plants carrying two complementary (6 B (S) and 6 B (L)) and a non-related (5 B (L)) telocentric, only the complementary chromosomes were found to be somatically associated. It is thought, therefore, that the somatic association of chromosomes may involve more than two chromosomes in the same association and, since complementary telocentrics are as much associated as homologous, that the homology between centromeres (probably the only homologous region that exists between complementary telocentrics) is a very important condition for somatic association of chromosomes. The spacial arrangement of chromosomes was studied at anaphase and prophase and the polar orientation of chromosomes at prophase was found to resemble anaphase orientation. This was taken as good evidence for the maintenance of the chromosome arrangement - the Rabl orientation - and of the peripheral location of the centromere and its association with the nuclear membrane. Within this general arrangement homologous telocentric chromosomes were frequently seen to have their centromeres associated or directed towards each other. The role of the centromere in somatic association as a spindle fibre attachment and chromosome binder is discussed. It is suggested that for non-homologous chromosomes to become associated in root tips, the only requirement needed should be the homology of centromeres such as exists between complementary

  16. Parasegmental appendage allocation in annelids and arthropods and the homology of parapodia and arthropodia

    OpenAIRE

    Prpic Nikola-Michael

    2008-01-01

    Abstract The new animal phylogeny disrupts the traditional taxon Articulata (uniting arthropods and annelids) and thus calls into question the homology of the body segments and appendages in the two groups. Recent work in the annelid Platynereis dumerilii has shown that although the set of genes involved in body segmentation is similar in the two groups, the body units of annelids correspond to arthropod parasegments not segments. This challenges traditional ideas about the homology of "segme...

  17. Myxococcus xanthus Chemotaxis Homologs DifD and DifG Negatively Regulate Fibril Polysaccharide Production

    OpenAIRE

    Black, Wesley P.; Yang, Zhaomin

    2004-01-01

    The extracellular matrix fibrils of Myxococcus xanthus are essential for the social lifestyle of this unusual bacterium. These fibrils form networks linking or encasing cells and are tightly correlated with cellular cohesion, development, and social (S) gliding motility. Previous studies identified a set of bacterial chemotaxis homologs encoded by the dif locus. It was determined that difA, difC, and difE, encoding respective homologs of a methyl-accepting chemotaxis protein, CheW, and CheA, ...

  18. Recovery of arrested replication forks by homologous recombination is error-prone.

    Directory of Open Access Journals (Sweden)

    Ismail Iraqui

    Full Text Available Homologous recombination is a universal mechanism that allows repair of DNA and provides support for DNA replication. Homologous recombination is therefore a major pathway that suppresses non-homology-mediated genome instability. Here, we report that recovery of impeded replication forks by homologous recombination is error-prone. Using a fork-arrest-based assay in fission yeast, we demonstrate that a single collapsed fork can cause mutations and large-scale genomic changes, including deletions and translocations. Fork-arrest-induced gross chromosomal rearrangements are mediated by inappropriate ectopic recombination events at the site of collapsed forks. Inverted repeats near the site of fork collapse stimulate large-scale genomic changes up to 1,500 times over spontaneous events. We also show that the high accuracy of DNA replication during S-phase is impaired by impediments to fork progression, since fork-arrest-induced mutation is due to erroneous DNA synthesis during recovery of replication forks. The mutations caused are small insertions/duplications between short tandem repeats (micro-homology indicative of replication slippage. Our data establish that collapsed forks, but not stalled forks, recovered by homologous recombination are prone to replication slippage. The inaccuracy of DNA synthesis does not rely on PCNA ubiquitination or trans-lesion-synthesis DNA polymerases, and it is not counteracted by mismatch repair. We propose that deletions/insertions, mediated by micro-homology, leading to copy number variations during replication stress may arise by progression of error-prone replication forks restarted by homologous recombination.

  19. Rapid Identification of Emerging Human-Pathogenic Sporothrix Species with Rolling Circle Amplification

    Science.gov (United States)

    Rodrigues, Anderson M.; Najafzadeh, Mohammad J.; de Hoog, G. Sybren; de Camargo, Zoilo P.

    2015-01-01

    Sporothrix infections are emerging as an important human and animal threat among otherwise healthy patients, especially in Brazil and China. Correct identification of sporotrichosis agents is beneficial for epidemiological surveillance, enabling implementation of adequate public-health policies and guiding antifungal therapy. In areas of limited resources where sporotrichosis is endemic, high-throughput detection methods that are specific and sensitive are preferred over phenotypic methods that usually result in misidentification of closely related Sporothrix species. We sought to establish rolling circle amplification (RCA) as a low-cost screening tool for species-specific identification of human-pathogenic Sporothrix. We developed six species-specific padlock probes targeting polymorphisms in the gene encoding calmodulin. BLAST-searches revealed candidate probes that were conserved intraspecifically; no significant homology with sequences from humans, mice, plants or microorganisms outside members of Sporothrix were found. The accuracy of our RCA-based assay was demonstrated through the specificity of probe-template binding to 25 S. brasiliensis, 58 S. schenckii, 5 S. globosa, 1 S. luriei, 4 S. mexicana, and 3 S. pallida samples. No cross reactivity between closely related species was evident in vitro, and padlock probes yielded 100% specificity and sensitivity down to 3 × 106 copies of the target sequence. RCA-based speciation matched identifications via phylogenetic analysis of the gene encoding calmodulin and the rDNA operon (kappa 1.0; 95% confidence interval 1.0-1.0), supporting its use as a reliable alternative to DNA sequencing. This method is a powerful tool for rapid identification and specific detection of medically relevant Sporothrix, and due to its robustness has potential for ecological studies. PMID:26696992

  20. Rapid manufacturing facilitated customisation

    OpenAIRE

    Tuck, Christopher John; Hague, Richard; Ruffo, Massimiliano; Ransley, Michelle; Adams, Paul Russell

    2008-01-01

    Abstract This paper describes the production of body-fitting customised seat profiles utilising the following digital methods: three dimensional laser scanning, reverse engineering and Rapid Manufacturing (RM). The seat profiles have been manufactured in order to influence the comfort characteristics of an existing ejector seat manufactured by Martin Baker Aircraft Ltd. The seat, known as Navy Aircrew Common Ejection Seat (NACES), was originally designed with a generic profile. ...