Codon-triplet context unveils unique features of the Candida albicans protein coding genome

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Oliveira José L

2007-11-01

Full Text Available Abstract Background The evolutionary forces that determine the arrangement of synonymous codons within open reading frames and fine tune mRNA translation efficiency are not yet understood. In order to tackle this question we have carried out a large scale study of codon-triplet contexts in 11 fungal species to unravel associations or relationships between codons present at the ribosome A-, P- and E-sites during each decoding cycle. Results Our analysis unveiled high bias within the context of codon-triplets, in particular strong preference for triplets of identical codons. We have also identified a surprisingly large number of codon-triplet combinations that vanished from fungal ORFeomes. Candida albicans exacerbated these features, showed an unbalanced tRNA population for decoding its pool of codons and used near-cognate decoding for a large set of codons, suggesting that unique evolutionary forces shaped the evolution of its ORFeome. Conclusion We have developed bioinformatics tools for large-scale analysis of codon-triplet contexts. These algorithms identified codon-triplets context biases, allowed for large scale comparative codon-triplet analysis, and identified rules governing codon-triplet context. They could also detect alterations to the standard genetic code.

Relative codon adaptation: a generic codon bias index for prediction of gene expression.

Science.gov (United States)

Fox, Jesse M; Erill, Ivan

2010-06-01

The development of codon bias indices (CBIs) remains an active field of research due to their myriad applications in computational biology. Recently, the relative codon usage bias (RCBS) was introduced as a novel CBI able to estimate codon bias without using a reference set. The results of this new index when applied to Escherichia coli and Saccharomyces cerevisiae led the authors of the original publications to conclude that natural selection favours higher expression and enhanced codon usage optimization in short genes. Here, we show that this conclusion was flawed and based on the systematic oversight of an intrinsic bias for short sequences in the RCBS index and of biases in the small data sets used for validation in E. coli. Furthermore, we reveal that how the RCBS can be corrected to produce useful results and how its underlying principle, which we here term relative codon adaptation (RCA), can be made into a powerful reference-set-based index that directly takes into account the genomic base composition. Finally, we show that RCA outperforms the codon adaptation index (CAI) as a predictor of gene expression when operating on the CAI reference set and that this improvement is significantly larger when analysing genomes with high mutational bias.

Harmonic Analysis of Offshore Wind Farms with Full Converter Wind Turbines

DEFF Research Database (Denmark)

Kocewiak, Lukasz Hubert; Hjerrild, Jesper; Bak, Claus Leth

2009-01-01

to a shore with a long HV cable. The way of propagation and effects of harmonics are presented for different study cases. Modeling strategies of harmonic sources for harmonic analysis are described and compared. Different results dependent on applied harmonic models are shown and discussed in this paper...

Hand gesture recognition by analysis of codons

Science.gov (United States)

Ramachandra, Poornima; Shrikhande, Neelima

2007-09-01

The problem of recognizing gestures from images using computers can be approached by closely understanding how the human brain tackles it. A full fledged gesture recognition system will substitute mouse and keyboards completely. Humans can recognize most gestures by looking at the characteristic external shape or the silhouette of the fingers. Many previous techniques to recognize gestures dealt with motion and geometric features of hands. In this thesis gestures are recognized by the Codon-list pattern extracted from the object contour. All edges of an image are described in terms of sequence of Codons. The Codons are defined in terms of the relationship between maxima, minima and zeros of curvature encountered as one traverses the boundary of the object. We have concentrated on a catalog of 24 gesture images from the American Sign Language alphabet (Letter J and Z are ignored as they are represented using motion) [2]. The query image given as an input to the system is analyzed and tested against the Codon-lists, which are shape descriptors for external parts of a hand gesture. We have used the Weighted Frequency Indexing Transform (WFIT) approach which is used in DNA sequence matching for matching the Codon-lists. The matching algorithm consists of two steps: 1) the query sequences are converted to short sequences and are assigned weights and, 2) all the sequences of query gestures are pruned into match and mismatch subsequences by the frequency indexing tree based on the weights of the subsequences. The Codon sequences with the most weight are used to determine the most precise match. Once a match is found, the identified gesture and corresponding interpretation are shown as output.

Codon usage vis-a-vis start and stop codon context analysis of three ...

Indian Academy of Sciences (India)

Prosenjit Paul

2018-02-20

Feb 20, 2018 ... Keywords. codon; dinucleotide; selection; mutation; genome. Introduction ..... influence of other factors, for example natural selection, is 91.7%, 99.5% ..... measure of directional synonymous codon usage bias, and its potential ...

Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias.

Science.gov (United States)

Barik, Sailen

2017-12-01

A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes.

Positive selection for unpreferred codon usage in eukaryotic genomes

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Galagan James E

2007-07-01

Full Text Available Abstract Background Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral mutation and genetic drift. We looked for evidence of directional selection resulting in increased unpreferred codon usage (and presumably reduced translational efficiency in three divergent clusters of eukaryotic genomes using a simple optimal-codon-based metric (Kp/Ku. Results Here we show that for some genes natural selection is indeed responsible for causing accelerated unpreferred codon substitution, and document the scope of this selection. In Cryptococcus and to a lesser extent Drosophila, we find many genes showing a statistically significant signal of selection for unpreferred codon usage in one or more lineages. We did not find evidence for this type of selection in Saccharomyces. The signal of positive selection observed from unpreferred synonymous codon substitutions is coincident in Cryptococcus and Drosophila with the distribution of upstream open reading frames (uORFs, another genic feature known to reduce translational efficiency. Functional enrichment analysis of genes exhibiting low Kp/Ku ratios reveals that genes in regulatory roles are particularly subject to this type of selection. Conclusion Through genome-wide scans, we find recent selection for unpreferred codon usage at approximately 1% of genetic loci in a Cryptococcus and several genes in Drosophila. Unpreferred codons can impede translation efficiency, and we find that genes with translation-impeding uORFs are enriched for this selection signal. We find that regulatory genes are particularly likely to be subject to selection for unpreferred codon usage. Given that expression noise can propagate through regulatory cascades, and that low translational efficiency can reduce expression noise, this finding supports the hypothesis that translational

Codon cassette mutagenesis: a general method to insert or replace individual codons by using universal mutagenic cassettes.

OpenAIRE

Kegler-Ebo, D M; Docktor, C M; DiMaio, D

1994-01-01

We describe codon cassette mutagenesis, a simple method of mutagenesis that uses universal mutagenic cassettes to deposit single codons at specific sites in double-stranded DNA. A target molecule is first constructed that contains a blunt, double-strand break at the site targeted for mutagenesis. A double-stranded mutagenic codon cassette is then inserted at the target site. Each mutagenic codon cassette contains a three base pair direct terminal repeat and two head-to-head recognition sequen...

Full absorption of 3rd harmonic ECH in TCV target plasmas produced by 2nd harmonic ECH and ECCD

International Nuclear Information System (INIS)

Alberti, S.; Goodman, T.; Henderson, M.A.

2001-01-01

An experimental study of the extraordinary mode (X-mode) absorption at the third cyclotron harmonic frequency (118GHz) has been performed on the TCV Tokamak in plasmas preheated by X-mode at the second harmonic (82.7GHz). Various preheating configurations have been experimentally investigated, ranging from counter-ECCD, ECH to CO-ECCD at various power levels. Full absorption of the 470kW of injected X3 power was measured with as little as 350kW of X2-CO-ECCD preheating. The measured absorption exceeds that predicted by the linear ray tracing code TORAY by more than a factor of 2 for the CO-ECCD case. Experimental evidence indicates that a large fraction of the X3 power is absorbed by electrons in an energetic tail created by the X2-ECCD preheating. (author)

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.

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Trotta, Edoardo

2016-05-17

The three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies. In this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences. In human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.

Codon usage vis-a-vis start and stop codon context analysis of three ...

Indian Academy of Sciences (India)

To understand the variation in genomic composition and its effect on codon usage, we performed the comparative analysis of codon usage and nucleotide usage in the genes of three dicots, Glycine max, Arabidopsis thaliana and Medicago truncatula. The dicot genes were found to be A/T rich and have predominantly ...

P-value based visualization of codon usage data

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Fricke Wolfgang

2006-06-01

Full Text Available Abstract Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose a multidimensional scaling approach using a novel similarity measure for codon usage tables. Our probabilistic similarity measure is based on P-values derived from the well-known chi-square test for comparison of two distributions. Experimental results on four microbial genomes indicate that the new method is well-suited for the analysis of horizontal gene transfer and translational selection. As compared with the widely-used correspondence analysis, our method did not suffer from outlier sensitivity and showed a better clustering of putative alien genes in most cases.

Codon Distribution in Error-Detecting Circular Codes

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Elena Fimmel

2016-03-01

Full Text Available In 1957, Francis Crick et al. suggested an ingenious explanation for the process of frame maintenance. The idea was based on the notion of comma-free codes. Although Crick’s hypothesis proved to be wrong, in 1996, Arquès and Michel discovered the existence of a weaker version of such codes in eukaryote and prokaryote genomes, namely the so-called circular codes. Since then, circular code theory has invariably evoked great interest and made significant progress. In this article, the codon distributions in maximal comma-free, maximal self-complementary C3 and maximal self-complementary circular codes are discussed, i.e., we investigate in how many of such codes a given codon participates. As the main (and surprising result, it is shown that the codons can be separated into very few classes (three, or five, or six with respect to their frequency. Moreover, the distribution classes can be hierarchically ordered as refinements from maximal comma-free codes via maximal self-complementary C3 codes to maximal self-complementary circular codes.

Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses.

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Naveen Kumar

Full Text Available Equine influenza viruses (EIVs of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts.

A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli

DEFF Research Database (Denmark)

Gonzalez de Valdivia, Ernesto I; Isaksson, Leif A

2004-01-01

and GGG, but not GGN or GNG (where N is non-G), are unique since they are associated with a very low gene expression also if located at positions +2, +3 and +5. All codons, including NGG, give a normal gene expression if placed at positions +7. The negative effect by the NGG codons is true for both...

Phylogenetic inference with weighted codon evolutionary distances.

Science.gov (United States)

Criscuolo, Alexis; Michel, Christian J

2009-04-01

We develop a new approach to estimate a matrix of pairwise evolutionary distances from a codon-based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance matrices are weighted according to an estimate of the global evolutionary rate of each codon position and averaged into a unique distance matrix. Using a large set of both real and simulated codon-based alignments of nucleotide sequences, we show that this approach leads to distance matrices that have a significantly better treelikeness compared to those obtained by standard nucleotide evolutionary distances. We also propose an alternative weighting to eliminate the part of the noise often associated with some codon positions, particularly the third position, which is known to induce a fast evolutionary rate. Simulation results show that fast distance-based tree reconstruction algorithms on distance matrices based on this codon position weighting can lead to phylogenetic trees that are at least as accurate as, if not better, than those inferred by maximum likelihood. Finally, a well-known multigene dataset composed of eight yeast species and 106 codon-based alignments is reanalyzed and shows that our codon evolutionary distances allow building a phylogenetic tree which is similar to those obtained by non-distance-based methods (e.g., maximum parsimony and maximum likelihood) and also significantly improved compared to standard nucleotide evolutionary distance estimates.

Synonymous codon ordering: a subtle but prevalent strategy of bacteria to improve translational efficiency.

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Zhu-Qing Shao

Full Text Available BACKGROUND: In yeast coding sequences, once a particular codon has been used, subsequent occurrence of the same amino acid tends to use codons sharing the same tRNA. Such a phenomenon of co-tRNA codons pairing bias (CTCPB is also found in some other eukaryotes but it is not known whether it occurs in prokaryotes. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we focused on a total of 773 bacterial genomes to investigate their synonymous codon pairing preferences. After calculating the actual frequencies of synonymous codon pairs and comparing them with their expected values, we detected an obvious pairing bias towards identical codon pairs. This seems consistent with the previously reported CTCPB phenomenon, since identical codons are certainly read by the same tRNA. However, among co-tRNA but non-identical codon pairs, only 22 were often found overrepresented, suggesting that many co-tRNA codons actually do not preferentially pair together in prokaryotes. Therefore, the previously reported co-tRNA codons pairing rule needs to be more rigorously defined. The affinity differences between a tRNA anticodon and its readable codons should be taken into account. Moreover, both within-gene-shuffling tests and phylogenetic analyses support the idea that translational selection played an important role in shaping the observed synonymous codon pairing pattern in prokaryotes. CONCLUSIONS: Overall, a high level of synonymous codon pairing bias was detected in 73% investigated bacterial species, suggesting the synonymous codon ordering strategy has been prevalently adopted by prokaryotes to improve their translational efficiencies. The findings in this study also provide important clues to better understand the complex dynamics of translational process.

Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

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Jibin Liu

2016-08-01

Full Text Available Riemerella anatipestifer (RA belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC3 (p > 0.05. Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA.

The distribution of synonymous codon choice in the translation initiation region of dengue virus.

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Jian-hua Zhou

Full Text Available Dengue is the most common arthropod-borne viral (Arboviral illness in humans. The genetic features concerning the codon usage of dengue virus (DENV were analyzed by the relative synonymous codon usage, the effective number of codons and the codon adaptation index. The evolutionary distance between DENV and the natural hosts (Homo sapiens, Pan troglodytes, Aedes albopictus and Aedes aegypti was estimated by a novel formula. Finally, the synonymous codon usage preference for the translation initiation region of this virus was also analyzed. The result indicates that the general trend of the 59 synonymous codon usage of the four genotypes of DENV are similar to each other, and this pattern has no link with the geographic distribution of the virus. The effect of codon usage pattern of Aedes albopictus and Aedes aegypti on the formation of codon usage of DENV is stronger than that of the two primates. Turning to the codon usage preference of the translation initiation region of this virus, some codons pairing to low tRNA copy numbers in the two primates have a stronger tendency to exist in the translation initiation region than those in the open reading frame of DENV. Although DENV, like other RNA viruses, has a high mutation to adapt its hosts, the regulatory features about the synonymous codon usage have been 'branded' on the translation initiation region of this virus in order to hijack the translational mechanisms of the hosts.

Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins.

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Nicholas J Hudson

Full Text Available Codon bias in the genome of an organism influences its phenome by changing the speed and efficiency of mRNA translation and hence protein abundance. We hypothesized that differences in codon bias, either between-species differences in orthologous genes, or within-species differences between genes, may play an evolutionary role. To explore this hypothesis, we compared the genome-wide codon bias in six species that occupy vital positions in the Eukaryotic Tree of Life. We acquired the entire protein coding sequences for these organisms, computed the codon bias for all genes in each organism and explored the output for relationships between codon bias and protein function, both within- and between-lineages. We discovered five notable coordinated patterns, with extreme codon bias most pronounced in traits considered highly characteristic of a given lineage. Firstly, the Homo sapiens genome had stronger codon bias for DNA-binding transcription factors than the Saccharomyces cerevisiae genome, whereas the opposite was true for ribosomal proteins--perhaps underscoring transcriptional regulation in the origin of complexity. Secondly, both mammalian species examined possessed extreme codon bias in genes relating to hair--a tissue unique to mammals. Thirdly, Arabidopsis thaliana showed extreme codon bias in genes implicated in cell wall formation and chloroplast function--which are unique to plants. Fourthly, Gallus gallus possessed strong codon bias in a subset of genes encoding mitochondrial proteins--perhaps reflecting the enhanced bioenergetic efficiency in birds that co-evolved with flight. And lastly, the G. gallus genome had extreme codon bias for the Ciliary Neurotrophic Factor--which may help to explain their spontaneous recovery from deafness. We propose that extreme codon bias in groups of genes that encode functionally related proteins has a pathway-level energetic explanation.

A single sequence context cannot satisfy all non-AUG initiator codons in yeast†

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Wang Tzu-Ling

2010-07-01

Full Text Available Abstract Background Previous studies in Saccharomyces cerevisiae showed that ALA1 (encoding alanyl-tRNA synthetase and GRS1 (encoding glycyl-tRNA synthetase respectively use ACG and TTG as their alternative translation initiator codons. To explore if any other non-ATG triplets can act as initiator codons in yeast, ALA1 was used as a reporter for screening. Results We show herein that except for AAG and AGG, all triplets that differ from ATG by a single nucleotide were able to serve as initiator codons in ALA1. Among these initiator codons, TTG, CTG, ACG, and ATT had ~50% initiating activities relative to that of ATG, while GTG, ATA, and ATC had ~20% initiating activities relative to that of ATG. Unexpectedly, these non-AUG initiator codons exhibited different preferences toward various sequence contexts. In particular, GTG was one of the most efficient non-ATG initiator codons, while ATA was essentially inactive in the context of GRS1. Conclusion This finding indicates that a sequence context that is favorable for a given non-ATG initiator codon might not be as favorable for another.

Genome-wide analysis of codon usage bias in Ebolavirus.

Science.gov (United States)

Cristina, Juan; Moreno, Pilar; Moratorio, Gonzalo; Musto, Héctor

2015-01-22

Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species. The interplay of codon usage among viruses and their hosts is expected to affect overall viral survival, fitness, evasion from host's immune system and evolution. In the present study, we performed comprehensive analyses of codon usage and composition of ZEBOV. Effective number of codons (ENC) indicates that the overall codon usage among ZEBOV strains is slightly biased. Different codon preferences in ZEBOV genes in relation to codon usage of human genes were found. Highly preferred codons are all A-ending triplets, which strongly suggests that mutational bias is a main force shaping codon usage in ZEBOV. Dinucleotide composition also plays a role in the overall pattern of ZEBOV codon usage. ZEBOV does not seem to use the most abundant tRNAs present in the human cells for most of their preferred codons. Copyright © 2014 Elsevier B.V. All rights reserved.

Codon cassette mutagenesis: a general method to insert or replace individual codons by using universal mutagenic cassettes.

Science.gov (United States)

Kegler-Ebo, D M; Docktor, C M; DiMaio, D

1994-05-11

We describe codon cassette mutagenesis, a simple method of mutagenesis that uses universal mutagenic cassettes to deposit single codons at specific sites in double-stranded DNA. A target molecule is first constructed that contains a blunt, double-strand break at the site targeted for mutagenesis. A double-stranded mutagenic codon cassette is then inserted at the target site. Each mutagenic codon cassette contains a three base pair direct terminal repeat and two head-to-head recognition sequences for the restriction endonuclease Sapl, an enzyme that cleaves outside of its recognition sequence. The intermediate molecule containing the mutagenic cassette is then digested with Sapl, thereby removing most of the mutagenic cassette, leaving only a three base cohesive overhang that is ligated to generate the final insertion or substitution mutation. A general method for constructing blunt-end target molecules suitable for this approach is also described. Because the mutagenic cassette is excised during this procedure and alters the target only by introducing the desired mutation, the same cassette can be used to introduce a particular codon at all target sites. Each cassette can deposit two different codons, depending on the orientation in which it is inserted into the target molecule. Therefore, a series of eleven cassettes is sufficient to insert all possible amino acids at any constructed target site. Thus codon cassettes are 'off-the-shelf' reagents, and this methodology should be a particularly useful and inexpensive approach for subjecting multiple different positions in a protein sequence to saturation mutagenesis.

Analysis of synonymous codon usage patterns in the genus Rhizobium.

Science.gov (United States)

Wang, Xinxin; Wu, Liang; Zhou, Ping; Zhu, Shengfeng; An, Wei; Chen, Yu; Zhao, Lin

2013-11-01

The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.

Codon usage is associated with the evolutionary age of genes in metazoan genomes

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Linial Nathan

2009-12-01

Full Text Available Abstract Background Codon usage may vary significantly between different organisms and between genes within the same organism. Several evolutionary processes have been postulated to be the predominant determinants of codon usage: selection, mutation, and genetic drift. However, the relative contribution of each of these factors in different species remains debatable. The availability of complete genomes for tens of multicellular organisms provides an opportunity to inspect the relationship between codon usage and the evolutionary age of genes. Results We assign an evolutionary age to a gene based on the relative positions of its identified homologues in a standard phylogenetic tree. This yields a classification of all genes in a genome to several evolutionary age classes. The present study starts from the observation that each age class of genes has a unique codon usage and proceeds to provide a quantitative analysis of the codon usage in these classes. This observation is made for the genomes of Homo sapiens, Mus musculus, and Drosophila melanogaster. It is even more remarkable that the differences between codon usages in different age groups exhibit similar and consistent behavior in various organisms. While we find that GC content and gene length are also associated with the evolutionary age of genes, they can provide only a partial explanation for the observed codon usage. Conclusion While factors such as GC content, mutational bias, and selection shape the codon usage in a genome, the evolutionary history of an organism over hundreds of millions of years is an overlooked property that is strongly linked to GC content, protein length, and, even more significantly, to the codon usage of metazoan genomes.

Harmonic statistics

International Nuclear Information System (INIS)

Eliazar, Iddo

2017-01-01

The exponential, the normal, and the Poisson statistical laws are of major importance due to their universality. Harmonic statistics are as universal as the three aforementioned laws, but yet they fall short in their ‘public relations’ for the following reason: the full scope of harmonic statistics cannot be described in terms of a statistical law. In this paper we describe harmonic statistics, in their full scope, via an object termed harmonic Poisson process: a Poisson process, over the positive half-line, with a harmonic intensity. The paper reviews the harmonic Poisson process, investigates its properties, and presents the connections of this object to an assortment of topics: uniform statistics, scale invariance, random multiplicative perturbations, Pareto and inverse-Pareto statistics, exponential growth and exponential decay, power-law renormalization, convergence and domains of attraction, the Langevin equation, diffusions, Benford’s law, and 1/f noise. - Highlights: • Harmonic statistics are described and reviewed in detail. • Connections to various statistical laws are established. • Connections to perturbation, renormalization and dynamics are established.

Harmonic statistics

Energy Technology Data Exchange (ETDEWEB)

Eliazar, Iddo, E-mail: eliazar@post.tau.ac.il

2017-05-15

The exponential, the normal, and the Poisson statistical laws are of major importance due to their universality. Harmonic statistics are as universal as the three aforementioned laws, but yet they fall short in their ‘public relations’ for the following reason: the full scope of harmonic statistics cannot be described in terms of a statistical law. In this paper we describe harmonic statistics, in their full scope, via an object termed harmonic Poisson process: a Poisson process, over the positive half-line, with a harmonic intensity. The paper reviews the harmonic Poisson process, investigates its properties, and presents the connections of this object to an assortment of topics: uniform statistics, scale invariance, random multiplicative perturbations, Pareto and inverse-Pareto statistics, exponential growth and exponential decay, power-law renormalization, convergence and domains of attraction, the Langevin equation, diffusions, Benford’s law, and 1/f noise. - Highlights: • Harmonic statistics are described and reviewed in detail. • Connections to various statistical laws are established. • Connections to perturbation, renormalization and dynamics are established.

Gaining insights into the codon usage patterns of TP53 gene across eight mammalian species.

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Tarikul Huda Mazumder

Full Text Available TP53 gene is known as the "guardian of the genome" as it plays a vital role in regulating cell cycle, cell proliferation, DNA damage repair, initiation of programmed cell death and suppressing tumor growth. Non uniform usage of synonymous codons for a specific amino acid during translation of protein known as codon usage bias (CUB is a unique property of the genome and shows species specific deviation. Analysis of codon usage bias with compositional dynamics of coding sequences has contributed to the better understanding of the molecular mechanism and the evolution of a particular gene. In this study, the complete nucleotide coding sequences of TP53 gene from eight different mammalian species were used for CUB analysis. Our results showed that the codon usage patterns in TP53 gene across different mammalian species has been influenced by GC bias particularly GC3 and a moderate bias exists in the codon usage of TP53 gene. Moreover, we observed that nature has highly favored the most over represented codon CTG for leucine amino acid but selected against the ATA codon for isoleucine in TP53 gene across all mammalian species during the course of evolution.

Emergent Rules for Codon Choice Elucidated by Editing Rare Arginine Codons in Escherichia coli

Science.gov (United States)

2016-09-20

the successful 110 CGU con- versions with the 13 optimized codon substitutions to produce strain C123, in which all 123 AGR codons have been removed...culture medium consisted of LBL autoclaved with 1.5% (wt/vol) Bacto Agar (Fisher), containing the same concentrations of antibiotics as necessary. ColE1...controlling the ef- ficiency of protein translation. Cell 141(2):344–354. 15. Li GW (2015) How do bacteria tune translation efficiency? Curr Opin Microbiol

Codon 201Gly Polymorphic Type of the DCC Gene is Related to Disseminated Neuroblastoma

Directory of Open Access Journals (Sweden)

Xiao-Tang Kong

2001-01-01

Full Text Available The deleted in colorectal carcinoma (DCC gene is a potential tumor- suppressor gene on chromosome 18821.3. The relatively high frequency of loss of heterozygosity (LOH and loss of expression of this gene in neuroblastoma, especially in the advanced stages, imply the possibility of involvement of the DCC gene in progression of neuroblastoma. However, only few typical mutations have been identified in this gene, indicating that other possible mechanisms for the inactivation of this gene may exist. A polymorphic change (Arg to Gly at DCC codon 201 is related to advanced colorectal carcinoma and increases in the tumors with absent DCC protein expression. In order to understand whether this change is associated with the development or progression of neuroblastoma, we investigated codon 201 polymorphism of the DCC gene in 102 primary neuroblastomas by polymerase chain reaction single-strand conformation polymorphism. We found no missense or nonsense mutations, but a polymorphic change from CGA (Arg to GGA (Gly at codon 201 resulting in three types of polymorphism: codon 201Gly type, codon 201Arg/Gly type, and codon 201Arg type. The codon 201Gly type occurred more frequently in disseminated (stages IV and IVs neuroblastomas (72% than in localized (stages I, II, and III tumors (48% (P=.035, and normal controls (38% (P=.024. In addition, the codon 201Gly type was significantly more common in tumors found clinically (65% than in those found by mass screening (35% (P=.002. The results suggested that the codon 201Gly type of the DCC gene might be associated with a higher risk of disseminating neuroblastoma.

A common periodic table of codons and amino acids.

Science.gov (United States)

Biro, J C; Benyó, B; Sansom, C; Szlávecz, A; Fördös, G; Micsik, T; Benyó, Z

2003-06-27

A periodic table of codons has been designed where the codons are in regular locations. The table has four fields (16 places in each) one with each of the four nucleotides (A, U, G, C) in the central codon position. Thus, AAA (lysine), UUU (phenylalanine), GGG (glycine), and CCC (proline) were placed into the corners of the fields as the main codons (and amino acids) of the fields. They were connected to each other by six axes. The resulting nucleic acid periodic table showed perfect axial symmetry for codons. The corresponding amino acid table also displaced periodicity regarding the biochemical properties (charge and hydropathy) of the 20 amino acids and the position of the stop signals. The table emphasizes the importance of the central nucleotide in the codons and predicts that purines control the charge while pyrimidines determine the polarity of the amino acids. This prediction was experimentally tested.

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

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Edgar E. Lara-Ramírez

2014-01-01

Full Text Available The increasing number of dengue virus (DENV genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4 has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3 as well as the effective number of codons (ENC, ENCp versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA and clustering analysis on relative synonymous codon usage (RSCU within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution.

Large scale comparative codon-pair context analysis unveils general rules that fine-tune evolution of mRNA primary structure.

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Gabriela Moura

Full Text Available BACKGROUND: Codon usage and codon-pair context are important gene primary structure features that influence mRNA decoding fidelity. In order to identify general rules that shape codon-pair context and minimize mRNA decoding error, we have carried out a large scale comparative codon-pair context analysis of 119 fully sequenced genomes. METHODOLOGIES/PRINCIPAL FINDINGS: We have developed mathematical and software tools for large scale comparative codon-pair context analysis. These methodologies unveiled general and species specific codon-pair context rules that govern evolution of mRNAs in the 3 domains of life. We show that evolution of bacterial and archeal mRNA primary structure is mainly dependent on constraints imposed by the translational machinery, while in eukaryotes DNA methylation and tri-nucleotide repeats impose strong biases on codon-pair context. CONCLUSIONS: The data highlight fundamental differences between prokaryotic and eukaryotic mRNA decoding rules, which are partially independent of codon usage.

eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments

OpenAIRE

Moore, Gregory L.; Maranas, Costas D.

2002-01-01

We present a systematic computational framework, eCodonOpt, for designing parental DNA sequences for directed evolution experiments through codon usage optimization. Given a set of homologous parental proteins to be recombined at the DNA level, the optimal DNA sequences encoding these proteins are sought for a given diversity objective. We find that the free energy of annealing between the recombining DNA sequences is a much better descriptor of the extent of crossover formation than sequence...

Codon adaptation and synonymous substitution rate in diatom plastid genes.

Science.gov (United States)

Morton, Brian R; Sorhannus, Ulf; Fox, Martin

2002-07-01

Diatom plastid genes are examined with respect to codon adaptation and rates of silent substitution (Ks). It is shown that diatom genes follow the same pattern of codon usage as other plastid genes studied previously. Highly expressed diatom genes display codon adaptation, or a bias toward specific major codons, and these major codons are the same as those in red algae, green algae, and land plants. It is also found that there is a strong correlation between Ks and variation in codon adaptation across diatom genes, providing the first evidence for such a relationship in the algae. It is argued that this finding supports the notion that the correlation arises from selective constraints, not from variation in mutation rate among genes. Finally, the diatom genes are examined with respect to variation in Ks among different synonymous groups. Diatom genes with strong codon adaptation do not show the same variation in synonymous substitution rate among codon groups as the flowering plant psbA gene which, previous studies have shown, has strong codon adaptation but unusually high rates of silent change in certain synonymous groups. The lack of a similar finding in diatoms supports the suggestion that the feature is unique to the flowering plant psbA due to recent relaxations in selective pressure in that lineage.

Codon Deviation Coefficient: A novel measure for estimating codon usage bias and its statistical significance

KAUST Repository

Zhang, Zhang

2012-03-22

Background: Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution. However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis.Results: Here we propose a novel measure--Codon Deviation Coefficient (CDC)--that provides an informative measurement of CUB and its statistical significance without requiring any prior knowledge. Unlike previous measures, CDC estimates CUB by accounting for background nucleotide compositions tailored to codon positions and adopts the bootstrapping to assess the statistical significance of CUB for any given sequence. We evaluate CDC by examining its effectiveness on simulated sequences and empirical data and show that CDC outperforms extant measures by achieving a more informative estimation of CUB and its statistical significance.Conclusions: As validated by both simulated and empirical data, CDC provides a highly informative quantification of CUB and its statistical significance, useful for determining comparative magnitudes and patterns of biased codon usage for genes or genomes with diverse sequence compositions. 2012 Zhang et al; licensee BioMed Central Ltd.

HARMONIC DRIVE SELECTION

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Piotr FOLĘGA

2014-03-01

Full Text Available The variety of types and sizes currently in production harmonic drive is a problem in their rational choice. Properly selected harmonic drive must meet certain requirements during operation, and achieve the anticipated service life. The paper discusses the problems associated with the selection of the harmonic drive. It also presents the algorithm correct choice of harmonic drive. The main objective of this study was to develop a computer program that allows the correct choice of harmonic drive by developed algorithm.

Codon 129 polymorphism of prion protein gene in is not a risk factor for Alzheimer's disease

Directory of Open Access Journals (Sweden)

Jerusa Smid

2013-07-01

Full Text Available Interaction of prion protein and amyloid-b oligomers has been demonstrated recently. Homozygosity at prion protein gene (PRNP codon 129 is associated with higher risk for Creutzfeldt-Jakob disease. This polymorphism has been addressed as a possible risk factor in Alzheimer disease (AD. Objective To describe the association between codon 129 polymorphisms and AD. Methods We investigated the association of codon 129 polymorphism of PRNP in 99 AD patients and 111 controls, and the association between this polymorphism and cognitive performance. Other polymorphisms of PRNP and additive effect of apolipoprotein E gene (ApoE were evaluated. Results Codon 129 genotype distribution in AD 45.5% methionine (MM, 42.2% methionine valine (MV, 12.1% valine (VV; and 39.6% MM, 50.5% MV, 9.9% VV among controls (p>0.05. There were no differences of cognitive performance concerning codon 129. Stratification according to ApoE genotype did not reveal difference between groups. Conclusion Codon 129 polymorphism is not a risk factor for AD in Brazilian patients.

Codon usage bias analysis for the coding sequences of Camellia ...

African Journals Online (AJOL)

sunny t

2016-02-24

Feb 24, 2016 ... suggested that codon usage bias is driven by selection, particularly for .... For example, as mentioned above, highly expressed genes tend to use fewer ... directional codon bias measure effective number of codons (ENc) was ...

Selection on start codons in prokaryotes and potential compensatory nucleotide substitutions.

Science.gov (United States)

Belinky, Frida; Rogozin, Igor B; Koonin, Eugene V

2017-09-29

Reconstruction of the evolution of start codons in 36 groups of closely related bacterial and archaeal genomes reveals purifying selection affecting AUG codons. The AUG starts are replaced by GUG and especially UUG significantly less frequently than expected under the neutral expectation derived from the frequencies of the respective nucleotide triplet substitutions in non-coding regions and in 4-fold degenerate sites. Thus, AUG is the optimal start codon that is actively maintained by purifying selection. However, purifying selection on start codons is significantly weaker than the selection on the same codons in coding sequences, although the switches between the codons result in conservative amino acid substitutions. The only exception is the AUG to UUG switch that is strongly selected against among start codons. Selection on start codons is most pronounced in evolutionarily conserved, highly expressed genes. Mutation of the start codon to a sub-optimal form (GUG or UUG) tends to be compensated by mutations in the Shine-Dalgarno sequence towards a stronger translation initiation signal. Together, all these findings indicate that in prokaryotes, translation start signals are subject to weak but significant selection for maximization of initiation rate and, consequently, protein production.

Improved linearity using harmonic error rejection in a full-field range imaging system

Science.gov (United States)

Payne, Andrew D.; Dorrington, Adrian A.; Cree, Michael J.; Carnegie, Dale A.

2008-02-01

Full field range imaging cameras are used to simultaneously measure the distance for every pixel in a given scene using an intensity modulated illumination source and a gain modulated receiver array. The light is reflected from an object in the scene, and the modulation envelope experiences a phase shift proportional to the target distance. Ideally the waveforms are sinusoidal, allowing the phase, and hence object range, to be determined from four measurements using an arctangent function. In practice these waveforms are often not perfectly sinusoidal, and in some cases square waveforms are instead used to simplify the electronic drive requirements. The waveforms therefore commonly contain odd harmonics which contribute a nonlinear error to the phase determination, and therefore an error in the range measurement. We have developed a unique sampling method to cancel the effect of these harmonics, with the results showing an order of magnitude improvement in the measurement linearity without the need for calibration or lookup tables, while the acquisition time remains unchanged. The technique can be applied to existing range imaging systems without having to change or modify the complex illumination or sensor systems, instead only requiring a change to the signal generation and timing electronics.

Codon usage and amino acid usage influence genes expression level.

Science.gov (United States)

Paul, Prosenjit; Malakar, Arup Kumar; Chakraborty, Supriyo

2018-02-01

Highly expressed genes in any species differ in the usage frequency of synonymous codons. The relative recurrence of an event of the favored codon pair (amino acid pairs) varies between gene and genomes due to varying gene expression and different base composition. Here we propose a new measure for predicting the gene expression level, i.e., codon plus amino bias index (CABI). Our approach is based on the relative bias of the favored codon pair inclination among the genes, illustrated by analyzing the CABI score of the Medicago truncatula genes. CABI showed strong correlation with all other widely used measures (CAI, RCBS, SCUO) for gene expression analysis. Surprisingly, CABI outperforms all other measures by showing better correlation with the wet-lab data. This emphasizes the importance of the neighboring codons of the favored codon in a synonymous group while estimating the expression level of a gene.

The relationship between codon usage bias and cold resistant genes

International Nuclear Information System (INIS)

Barozai, M.Y.; Din, M.

2014-01-01

This research is based on synonymous codon usage which has been well-known as a feature that affects typical expression level of protein in an organism. Different organisms prefer different codons for same amino acid and this is called Codon Usage Bias (CUB). The codon usage directly affects the level or even direction of changes in protein expression in responses to environmental stimuli. Cold stress is a major abiotic factor that limits the agricultural productivity of plants. In the recent study CUB has been studied in Arabidopsis thaliana cold resistant and housekeeping genes and their homologs in rice (Oryza sativa) to understand the cold stress and housekeeping genes relation with CUB. Six cold resistant and three housekeeping genes in Arabidopsis thaliana and their homologs in rice, were subjected to CUB analysis. The three cold resistant genes (DREB1B, RCI and MYB15) showed more than 50% (52%, 61% and 66% respectively) similar codon usage bias for Arabidopsis thaliana and rice. On the other hand three cold resistant genes (MPK3, ICE1 and ZAT12) showed less than 50% (38%, 38% and 47% respectively) similar codon usage bias for Arabidopsis thaliana and rice. The three housekeeping genes (Actin, Tubulin and Ubiquitin) showed 76% similar codon usage bias for Arabidopsis thaliana and rice. This study will help to manage the plant gene expression through codon optimization under the cold stress. (author)

Codon-optimized antibiotic resistance gene improves efficiency of ...

Indian Academy of Sciences (India)

2013-10-01

Oct 1, 2013 ... transient transformation and cell growth in selective culture were significantly increased by use of fgmR ... Our result shows that similarity in codon usage pattern is an important factor ... Codon adaptation index (CAI) (Sharp.

Control of ribosome traffic by position-dependent choice of synonymous codons

DEFF Research Database (Denmark)

Mitarai, Namiko; Pedersen, Steen

2013-01-01

Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino...... acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby...... ribosomes by affecting the appearance of 'traffic jams' where multiple ribosomes collide and form queues. To test this 'context effect' further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated...

Codes in the codons: construction of a codon/amino acid periodic table and a study of the nature of specific nucleic acid-protein interactions.

Science.gov (United States)

Benyo, B; Biro, J C; Benyo, Z

2004-01-01

The theory of "codon-amino acid coevolution" was first proposed by Woese in 1967. It suggests that there is a stereochemical matching - that is, affinity - between amino acids and certain of the base triplet sequences that code for those amino acids. We have constructed a common periodic table of codons and amino acids, where the nucleic acid table showed perfect axial symmetry for codons and the corresponding amino acid table also displayed periodicity regarding the biochemical properties (charge and hydrophobicity) of the 20 amino acids and the position of the stop signals. The table indicates that the middle (2/sup nd/) amino acid in the codon has a prominent role in determining some of the structural features of the amino acids. The possibility that physical contact between codons and amino acids might exist was tested on restriction enzymes. Many recognition site-like sequences were found in the coding sequences of these enzymes and as many as 73 examples of codon-amino acid co-location were observed in the 7 known 3D structures (December 2003) of endonuclease-nucleic acid complexes. These results indicate that the smallest possible units of specific nucleic acid-protein interaction are indeed the stereochemically compatible codons and amino acids.

The Effect of Codon Mismatch on the Protein Translation System.

Science.gov (United States)

Zhang, Dinglin; Chen, Danfeng; Cao, Liaoran; Li, Guohui; Cheng, Hong

2016-01-01

Incorrect protein translation, caused by codon mismatch, is an important problem of living cells. In this work, a computational model was introduced to quantify the effects of codon mismatch and the model was used to study the protein translation of Saccharomyces cerevisiae. According to simulation results, the probability of codon mismatch will increase when the supply of amino acids is unbalanced, and the longer is the codon sequence, the larger is the probability for incorrect translation to occur, making the synthesis of long peptide chain difficult. By comparing to simulation results without codon mismatch effects taken into account, the fraction of mRNAs with bound ribosome decrease faster along the mRNAs, making the 5' ramp phenomenon more obvious. It was also found in our work that the premature mechanism resulted from codon mismatch can reduce the proportion of incorrect translation when the amino acid supply is extremely unbalanced, which is one possible source of high fidelity protein synthesis after peptidyl transfer.

Differential trends in the codon usage patterns in HIV-1 genes.

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Aridaman Pandit

Full Text Available Host-pathogen interactions underlie one of the most complex evolutionary phenomena resulting in continual adaptive genetic changes, where pathogens exploit the host's molecular resources for growth and survival, while hosts try to eliminate the pathogen. Deciphering the molecular basis of host-pathogen interactions is useful in understanding the factors governing pathogen evolution and disease propagation. In host-pathogen context, a balance between mutation, selection, and genetic drift is known to maintain codon bias in both organisms. Studies revealing determinants of the bias and its dynamics are central to the understanding of host-pathogen evolution. We considered the Human Immunodeficiency Virus (HIV type 1 and its human host to search for evolutionary signatures in the viral genome. Positive selection is known to dominate intra-host evolution of HIV-1, whereas high genetic variability underlies the belief that neutral processes drive inter-host differences. In this study, we analyze the codon usage patterns of HIV-1 genomes across all subtypes and clades sequenced over a period of 23 years. We show presence of unique temporal correlations in the codon bias of three HIV-1 genes illustrating differential adaptation of the HIV-1 genes towards the host preferred codons. Our results point towards gene-specific translational selection to be an important force driving the evolution of HIV-1 at the population level.

Automated design of degenerate codon libraries.

Science.gov (United States)

Mena, Marco A; Daugherty, Patrick S

2005-12-01

Degenerate codon libraries are frequently used in protein engineering and evolution studies but are often limited to targeting a small number of positions to adequately limit the search space. To mitigate this, codon degeneracy can be limited using heuristics or previous knowledge of the targeted positions. To automate design of libraries given a set of amino acid sequences, an algorithm (LibDesign) was developed that generates a set of possible degenerate codon libraries, their resulting size, and their score relative to a user-defined scoring function. A gene library of a specified size can then be constructed that is representative of the given amino acid distribution or that includes specific sequences or combinations thereof. LibDesign provides a new tool for automated design of high-quality protein libraries that more effectively harness existing sequence-structure information derived from multiple sequence alignment or computational protein design data.

Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome.

Science.gov (United States)

Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

2016-02-24

Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts.

Genome-wide analysis of codon usage bias in four sequenced cotton species.

Science.gov (United States)

Wang, Liyuan; Xing, Huixian; Yuan, Yanchao; Wang, Xianlin; Saeed, Muhammad; Tao, Jincai; Feng, Wei; Zhang, Guihua; Song, Xianliang; Sun, Xuezhen

2018-01-01

Codon usage bias (CUB) is an important evolutionary feature in a genome which provides important information for studying organism evolution, gene function and exogenous gene expression. The CUB and its shaping factors in the nuclear genomes of four sequenced cotton species, G. arboreum (A2), G. raimondii (D5), G. hirsutum (AD1) and G. barbadense (AD2) were analyzed in the present study. The effective number of codons (ENC) analysis showed the CUB was weak in these four species and the four subgenomes of the two tetraploids. Codon composition analysis revealed these four species preferred to use pyrimidine-rich codons more frequently than purine-rich codons. Correlation analysis indicated that the base content at the third position of codons affect the degree of codon preference. PR2-bias plot and ENC-plot analyses revealed that the CUB patterns in these genomes and subgenomes were influenced by combined effects of translational selection, directional mutation and other factors. The translational selection (P2) analysis results, together with the non-significant correlation between GC12 and GC3, further revealed that translational selection played the dominant role over mutation pressure in the codon usage bias. Through relative synonymous codon usage (RSCU) analysis, we detected 25 high frequency codons preferred to end with T or A, and 31 low frequency codons inclined to end with C or G in these four species and four subgenomes. Finally, 19 to 26 optimal codons with 19 common ones were determined for each species and subgenomes, which preferred to end with A or T. We concluded that the codon usage bias was weak and the translation selection was the main shaping factor in nuclear genes of these four cotton genomes and four subgenomes.

Universality and Shannon entropy of codon usage

CERN Document Server

Frappat, L; Sciarrino, A; Sorba, Paul

2003-01-01

The distribution functions of the codon usage probabilities, computed over all the available GenBank data, for 40 eukaryotic biological species and 5 chloroplasts, do not follow a Zipf law, but are best fitted by the sum of a constant, an exponential and a linear function in the rank of usage. For mitochondriae the analysis is not conclusive. A quantum-mechanics-inspired model is proposed to describe the observed behaviour. These functions are characterized by parameters that strongly depend on the total GC content of the coding regions of biological species. It is predicted that the codon usage is the same in all exonic genes with the same GC content. The Shannon entropy for codons, also strongly depending on the exonic GC content, is computed.

Correlation matrix for quartet codon usage

CERN Document Server

Frappat, L; Sorba, Paul

2005-01-01

It has been argued that the sum of usage probabilities for codons, belonging to quartets, that have as third nucleotide C or A, is independent of the biological species for vertebrates. The comparison between the theoretical correlation matrix derived from these sum rules and the experimentally computed matrix for 26 species shows a satisfactory agreement. The Shannon entropy, weakly depending on the biological species, gives further support. Suppression of codons containing the dinucleotides CG or AU is put in evidence.

Codon usage bias in phylum Actinobacteria: relevance to environmental adaptation and host pathogenicity.

Science.gov (United States)

Lal, Devi; Verma, Mansi; Behura, Susanta K; Lal, Rup

2016-10-01

Actinobacteria are Gram-positive bacteria commonly found in soil, freshwater and marine ecosystems. In this investigation, bias in codon usages of ninety actinobacterial genomes was analyzed by estimating different indices of codon bias such as Nc (effective number of codons), SCUO (synonymous codon usage order), RSCU (relative synonymous codon usage), as well as sequence patterns of codon contexts. The results revealed several characteristic features of codon usage in Actinobacteria, as follows: 1) C- or G-ending codons are used frequently in comparison with A- and U ending codons; 2) there is a direct relationship of GC content with use of specific amino acids such as alanine, proline and glycine; 3) there is an inverse relationship between GC content and Nc estimates, 4) there is low SCUO value (Actinobacteria, extreme GC content and codon bias are driven by mutation rather than natural selection; (2) traits like aerobicity are associated with effective natural selection and therefore low GC content and low codon bias, demonstrating the role of both mutational bias and translational selection in shaping the habitat and phenotype of actinobacterial species. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Control of ribosome traffic by position-dependent choice of synonymous codons

International Nuclear Information System (INIS)

Mitarai, Namiko; Pedersen, Steen

2013-01-01

Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby ribosomes by affecting the appearance of ‘traffic jams’ where multiple ribosomes collide and form queues. To test this ‘context effect’ further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated from experiments. We compare the ribosome traffic on wild-type (WT) sequences and sequences where the synonymous codons were swapped randomly. By simulating translation of 87 genes, we demonstrate that the WT sequences, especially those with a high bias in codon usage, tend to have the ability to reduce ribosome collisions, hence optimizing the cellular investment in the translation apparatus. The magnitude of such reduction of the translation time might have a significant impact on the cellular growth rate and thereby have importance for the survival of the species. (paper)

Gene expression, nucleotide composition and codon usage bias of genes associated with human Y chromosome.

Science.gov (United States)

Choudhury, Monisha Nath; Uddin, Arif; Chakraborty, Supriyo

2017-06-01

Analysis of codon usage pattern is important to understand the genetic and evolutionary characteristics of genomes. We have used bioinformatic approaches to analyze the codon usage bias (CUB) of the genes located in human Y chromosome. Codon bias index (CBI) indicated that the overall extent of codon usage bias was low. The relative synonymous codon usage (RSCU) analysis suggested that approximately half of the codons out of 59 synonymous codons were most frequently used, and possessed a T or G at the third codon position. The codon usage pattern was different in different genes as revealed from correspondence analysis (COA). A significant correlation between effective number of codons (ENC) and various GC contents suggests that both mutation pressure and natural selection affect the codon usage pattern of genes located in human Y chromosome. In addition, Y-linked genes have significant difference in GC contents at the second and third codon positions, expression level, and codon usage pattern of some codons like the SPANX genes in X chromosome.

A detailed analysis of codon usage patterns and influencing factors in Zika virus.

Science.gov (United States)

Singh, Niraj K; Tyagi, Anuj

2017-07-01

Recent outbreaks of Zika virus (ZIKV) in Africa, Latin America, Europe, and Southeast Asia have resulted in serious health concerns. To understand more about evolution and transmission of ZIKV, detailed codon usage analysis was performed for all available strains. A high effective number of codons (ENC) value indicated the presence of low codon usage bias in ZIKV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations between nucleotide compositions at third codon positions and ENCs. Correlation analysis between Gravy values, Aroma values and nucleotide compositions at third codon positions also indicated some influence of natural selection. However, the low codon adaptation index (CAI) value of ZIKV with reference to human and mosquito indicated poor adaptation of ZIKV codon usage towards its hosts, signifying that natural selection has a weaker influence than mutational pressure. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern to some extent.

AUG is the only initiation codon in eukaryotes

Energy Technology Data Exchange (ETDEWEB)

Sherman, F; McKnight, G; Stewart, J W

1980-01-01

An analysis of mutants of the yeast Saccharomyces cerevisiae indicates that AUG is the sole codon capable of initiating translation of iso-1-cytochrome c. This result with yeast and the sequence results of numerous eukaryotic genes indicate that AUG is the only initiation codon in eukaryotes; in contrast, results with Escherichia colia and bacteriophages indicate that both AUG and GUG are initiation codons in prokaryotes. The difference can be explained by the lack of the t/sup 6/ A hypermodified nucleoside (N-(9-(..beta..-D-ribofuranosyl)purin-6-ylcarbamoyl)threonine) in prokaryotic initiator tRNA and its presence in eukaryotic initiator tRNA.

Analysis of transcriptome data reveals multifactor constraint on codon usage in Taenia multiceps.

Science.gov (United States)

Huang, Xing; Xu, Jing; Chen, Lin; Wang, Yu; Gu, Xiaobin; Peng, Xuerong; Yang, Guangyou

2017-04-20

Codon usage bias (CUB) is an important evolutionary feature in genomes that has been widely observed in many organisms. However, the synonymous codon usage pattern in the genome of T. multiceps remains to be clarified. In this study, we analyzed the codon usage of T. multiceps based on the transcriptome data to reveal the constraint factors and to gain an improved understanding of the mechanisms that shape synonymous CUB. Analysis of a total of 8,620 annotated mRNA sequences from T. multiceps indicated only a weak codon bias, with mean GC and GC3 content values of 49.29% and 51.43%, respectively. Our analysis indicated that nucleotide composition, mutational pressure, natural selection, gene expression level, amino acids with grand average of hydropathicity (GRAVY) and aromaticity (Aromo) and the effective selection of amino-acids all contributed to the codon usage in T. multiceps. Among these factors, natural selection was implicated as the major factor affecting the codon usage variation in T. multiceps. The codon usage of ribosome genes was affected mainly by mutations, while the essential genes were affected mainly by selection. In addition, 21codons were identified as "optimal codons". Overall, the optimal codons were GC-rich (GC:AU, 41:22), and ended with G or C (except CGU). Furthermore, different degrees of variation in codon usage were found between T. multiceps and Escherichia coli, yeast, Homo sapiens. However, little difference was found between T. multiceps and Taenia pisiformis. In this study, the codon usage pattern of T. multiceps was analyzed systematically and factors affected CUB were also identified. This is the first study of codon biology in T. multiceps. Understanding the codon usage pattern in T. multiceps can be helpful for the discovery of new genes, molecular genetic engineering and evolutionary studies.

ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes.

Science.gov (United States)

Engqvist, Martin K M; Nielsen, Jens

2015-08-21

The Ambiguous Nucleotide Tool (ANT) is a desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms. The Python source code for ANT is freely distributed so that it may be used without restriction, modified, and incorporated in other software or custom data pipelines.

Codon 219 polymorphism of PRNP in healthy caucasians and Creutzfeldt-Jakob disease patients

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Petraroli, R.; Pocchiari, M. [Instituto Superiore di Sanita, Rome (Italy)

1996-04-01

A number of point and insert mutations of the PrP gene (PRNP) have been linked to familial Creutzfeldt-Jakob disease (CJD) and Gerstmann-Straussler-Scheinker disease (GSS). Moreover, the methionine/valine homozygosity at the polymorphic codon 129 of PRNP may cause a predisposition to sporadic and iatrogenic CJD or may control the age at onset of familial cases carrying either the 144-bp insertion or codon 178, codon 198, and codon 210 pathogenic mutations in PRNP. In addition, the association of methionine or valine at codon 129 and the point mutation at codon 178 on the same allele seem to play an important role in determining either fatal familial insomnia or CJD. However, it is noteworthy that a relationship between codon 129 polymorphism and accelerated pathogenesis (early age at onset or shorter duration of the disease) has not been seen in familial CJD patients with codon 200 mutation or in GSS patients with codon 102 mutation, arguing that other, as yet unidentified, gene products or environmental factors, or both, may influence the clinical expression of these diseases. 17 refs.

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis.

Science.gov (United States)

Bae, Young-An

2017-04-01

Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC 12 and GC 3 was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC 3 vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

Stringent Nucleotide Recognition by the Ribosome at the Middle Codon Position.

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Liu, Wei; Shin, Dongwon; Ng, Martin; Sanbonmatsu, Karissa Y; Tor, Yitzhak; Cooperman, Barry S

2017-08-29

Accurate translation of the genetic code depends on mRNA:tRNA codon:anticodon base pairing. Here we exploit an emissive, isosteric adenosine surrogate that allows direct measurement of the kinetics of codon:anticodon University of California base formation during protein synthesis. Our results suggest that codon:anticodon base pairing is subject to tighter constraints at the middle position than at the 5'- and 3'-positions, and further suggest a sequential mechanism of formation of the three base pairs in the codon:anticodon helix.

Codon Usage Bias and Determining Forces in Taenia solium Genome.

Science.gov (United States)

Yang, Xing; Ma, Xusheng; Luo, Xuenong; Ling, Houjun; Zhang, Xichen; Cai, Xuepeng

2015-12-01

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Drug resistance is conferred on the model yeast Saccharomyces cerevisiae by expression of full-length melanoma-associated human ATP-binding cassette transporter ABCB5.

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Keniya, Mikhail V; Holmes, Ann R; Niimi, Masakazu; Lamping, Erwin; Gillet, Jean-Pierre; Gottesman, Michael M; Cannon, Richard D

2014-10-06

ABCB5, an ATP-binding cassette (ABC) transporter, is highly expressed in melanoma cells, and may contribute to the extreme resistance of melanomas to chemotherapy by efflux of anti-cancer drugs. Our goal was to determine whether we could functionally express human ABCB5 in the model yeast Saccharomyces cerevisiae, in order to demonstrate an efflux function for ABCB5 in the absence of background pump activity from other human transporters. Heterologous expression would also facilitate drug discovery for this important target. DNAs encoding ABCB5 sequences were cloned into the chromosomal PDR5 locus of a S. cerevisiae strain in which seven endogenous ABC transporters have been deleted. Protein expression in the yeast cells was monitored by immunodetection using both a specific anti-ABCB5 antibody and a cross-reactive anti-ABCB1 antibody. ABCB5 function in recombinant yeast cells was measured by determining whether the cells possessed increased resistance to known pump substrates, compared to the host yeast strain, in assays of yeast growth. Three ABCB5 constructs were made in yeast. One was derived from the ABCB5-β mRNA, which is highly expressed in human tissues but is a truncation of a canonical full-size ABC transporter. Two constructs contained full-length ABCB5 sequences: either a native sequence from cDNA or a synthetic sequence codon-harmonized for S. cerevisiae. Expression of all three constructs in yeast was confirmed by immunodetection. Expression of the codon-harmonized full-length ABCB5 DNA conferred increased resistance, relative to the host yeast strain, to the putative substrates rhodamine 123, daunorubicin, tetramethylrhodamine, FK506, or clorgyline. We conclude that full-length ABCB5 can be functionally expressed in S. cerevisiae and confers drug resistance.

Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses

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Bhatia, Sandeep; Sood, Richa; Selvaraj, Pavulraj

2016-01-01

Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts. PMID:27119730

High-harmonic spectroscopy of oriented OCS molecules: emission of even and odd harmonics.

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Kraus, P M; Rupenyan, A; Wörner, H J

2012-12-07

We study the emission of even and odd high-harmonic orders from oriented OCS molecules. We use an intense, nonresonant femtosecond laser pulse superimposed with its phase-controlled second harmonic field to impulsively align and orient a dense sample of molecules from which we subsequently generate high-order harmonics. The even harmonics appear around the full revivals of the rotational dynamics. We demonstrate perfect coherent control over their intensity through the subcycle delay of the two-color fields. The odd harmonics are insensitive to the degree of orientation, but modulate with the degree of axis alignment, in agreement with calculated photorecombination dipole moments. We further compare the shape of the even and odd harmonic spectra with our calculations and determine the degree of orientation.

Comparative analysis of codon usage patterns and identification of predicted highly expressed genes in five Salmonella genomes

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Mondal U

2008-01-01

Full Text Available Purpose: To anlyse codon usage patterns of five complete genomes of Salmonella , predict highly expressed genes, examine horizontally transferred pathogenicity-related genes to detect their presence in the strains, and scrutinize the nature of highly expressed genes to infer upon their lifestyle. Methods: Protein coding genes, ribosomal protein genes, and pathogenicity-related genes were analysed with Codon W and CAI (codon adaptation index Calculator. Results: Translational efficiency plays a role in codon usage variation in Salmonella genes. Low bias was noticed in most of the genes. GC3 (guanine cytosine at third position composition does not influence codon usage variation in the genes of these Salmonella strains. Among the cluster of orthologous groups (COGs, translation, ribosomal structure biogenesis [J], and energy production and conversion [C] contained the highest number of potentially highly expressed (PHX genes. Correspondence analysis reveals the conserved nature of the genes. Highly expressed genes were detected. Conclusions: Selection for translational efficiency is the major source of variation of codon usage in the genes of Salmonella . Evolution of pathogenicity-related genes as a unit suggests their ability to infect and exist as a pathogen. Presence of a lot of PHX genes in the information and storage-processing category of COGs indicated their lifestyle and revealed that they were not subjected to genome reduction.

Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions.

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David J Hauber

Full Text Available Codon-tRNA coevolution to maximize protein production has been, until recently, the dominant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two predictions of this hypothesis are 1 selection is weak; and 2 similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent sites in the highly expressed Escherichia coli ribosomal protein gene rplQ from the wild type to a less-preferred alternative. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked leucine codons and an AAA to AAG mutation being introduced at two closely linked lysine codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a valine codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the araA gene as a selectively neutral phenotypic marker to distinguish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of |s| > 0.02, which is contradictory to the prediction that selection will be weak. The two leucine mutations had significantly different fitness effects, as did the two lysine mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness values, suggesting that negative synergistic epistasis acts on the combination allele.

Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli.

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Ho, Joanne M; Reynolds, Noah M; Rivera, Keith; Connolly, Morgan; Guo, Li-Tao; Ling, Jiqiang; Pappin, Darryl J; Church, George M; Söll, Dieter

2016-02-19

Expansion of the genetic code through engineering the translation machinery has greatly increased the chemical repertoire of the proteome. This has been accomplished mainly by read-through of UAG or UGA stop codons by the noncanonical aminoacyl-tRNA of choice. While stop codon read-through involves competition with the translation release factors, sense codon reassignment entails competition with a large pool of endogenous tRNAs. We used an engineered pyrrolysyl-tRNA synthetase to incorporate 3-iodo-l-phenylalanine (3-I-Phe) at a number of different serine and leucine codons in wild-type Escherichia coli. Quantitative LC-MS/MS measurements of amino acid incorporation yields carried out in a selected reaction monitoring experiment revealed that the 3-I-Phe abundance at the Ser208AGU codon in superfolder GFP was 65 ± 17%. This method also allowed quantification of other amino acids (serine, 33 ± 17%; phenylalanine, 1 ± 1%; threonine, 1 ± 1%) that compete with 3-I-Phe at both the aminoacylation and decoding steps of translation for incorporation at the same codon position. Reassignments of different serine (AGU, AGC, UCG) and leucine (CUG) codons with the matching tRNA(Pyl) anticodon variants were met with varying success, and our findings provide a guideline for the choice of sense codons to be reassigned. Our results indicate that the 3-iodo-l-phenylalanyl-tRNA synthetase (IFRS)/tRNA(Pyl) pair can efficiently outcompete the cellular machinery to reassign select sense codons in wild-type E. coli.

Nucleotide composition bias and codon usage trends of gene ...

Indian Academy of Sciences (India)

2015-06-10

Jun 10, 2015 ... In a wide variety of organisms, synonymous codons are selected with different ... In addition, a series of GC skew and AT skew data was calculated for codon positions 1, ..... bias from different perspectives. Interestingly .... This study was supported by programme for Changjiang Scholars and Innovative ...

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius

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Christopher D Johnston

2014-09-01

Full Text Available It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of two MAP genes (MAP2121c and MAP3733c can enhance the heterologous expression of two antigens (MMP and MptD respectively, analogous to the form to which they are produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, codon optimised MptD displayed the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adhered with the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne’s disease.

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI

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Garcia-Vallvé Santiago

2008-01-01

Full Text Available Abstract Background The Codon Adaptation Index (CAI is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a large impact on differential preference for synonymous codons. It is thence essential to define the limits for the expected value of CAI on the basis of sequence composition in order to properly interpret the CAI and provide statistical support to CAI analyses. Though several freely available programs calculate the CAI for a given DNA sequence, none of them corrects for compositional biases or provides confidence intervals for CAI values. Results The E-CAI server, available at http://genomes.urv.es/CAIcal/E-CAI, is a web-application that calculates an expected value of CAI for a set of query sequences by generating random sequences with G+C and amino acid content similar to those of the input. An executable file, a tutorial, a Frequently Asked Questions (FAQ section and several examples are also available. To exemplify the use of the E-CAI server, we have analysed the codon adaptation of human mitochondrial genes that codify a subunit of the mitochondrial respiratory chain (excluding those genes that lack a prokaryotic orthologue and are encoded in the nuclear genome. It is assumed that these genes were transferred from the proto-mitochondrial to the nuclear genome and that its codon usage was then ameliorated. Conclusion The E-CAI server provides a direct threshold value for discerning whether the differences in CAI are statistically significant or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences.

Stop Codon Reassignment in the Wild

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Ivanova, Natalia [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Schwientek, Patrick [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Tripp, H. James [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Rinke, Christian [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Pati, Amrita [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Huntemann, Marcel [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Visel, Axel [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Woyke, Tanja [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Kyrpides, Nikos [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Rubin, Edward [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2014-03-21

Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hosts must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages (6). These initial findings suggest that large scale systematic studies of uncultivated microorganisms and viruses may reveal the extent and modes of divergence from the canonical genetic code operating in nature. To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber, TGA opal, and TAA ochre codons in assembled metagenomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of phage sequences

Harmonic supergraphs

International Nuclear Information System (INIS)

Galperin, A.; Ivanov, E.; Ogievetsky, V.; Sokatchev, E.

1985-01-01

This paper completes a descrption of the quantization procedure in the harmonic superspace approach. The Feynman rules for N=2 matter and Yang-Mills theories are derived and the various examples of harmonic supergraph calculations are given. Calculations appear to be not more difficult than those in the N=1 case. The integration over harmonic variables does not lead to any troubles, a non-locality in these disappears on-shell. The important property is that the quantum corrections are always writen as integrals over the full harmonic superspace even though the initial action is an integral over the analytic subspace. As a by-product our results imply a very simple proof of finiteness of a wide class of the N=4, d=2 non-linear Σ-models. The most general self-couplings of hypermultiplets including those with broken SU(2) are considered.The duality relations among the N=2 linear multiplet and both kinds of hypermultiplet are established

Complete motif analysis of sequence requirements for translation initiation at non-AUG start codons.

Science.gov (United States)

Diaz de Arce, Alexander J; Noderer, William L; Wang, Clifford L

2018-01-25

The initiation of mRNA translation from start codons other than AUG was previously believed to be rare and of relatively low impact. More recently, evidence has suggested that as much as half of all translation initiation utilizes non-AUG start codons, codons that deviate from AUG by a single base. Furthermore, non-AUG start codons have been shown to be involved in regulation of expression and disease etiology. Yet the ability to gauge expression based on the sequence of a translation initiation site (start codon and its flanking bases) has been limited. Here we have performed a comprehensive analysis of translation initiation sites that utilize non-AUG start codons. By combining genetic-reporter, cell-sorting, and high-throughput sequencing technologies, we have analyzed the expression associated with all possible variants of the -4 to +4 positions of non-AUG translation initiation site motifs. This complete motif analysis revealed that 1) with the right sequence context, certain non-AUG start codons can generate expression comparable to that of AUG start codons, 2) sequence context affects each non-AUG start codon differently, and 3) initiation at non-AUG start codons is highly sensitive to changes in the flanking sequences. Complete motif analysis has the potential to be a key tool for experimental and diagnostic genomics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Combination of the Endogenous lhcsr1 Promoter and Codon Usage Optimization Boosts Protein Expression in the Moss Physcomitrella patens

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Manuel Hiss

2017-10-01

Full Text Available The moss Physcomitrella patens is used both as an evo-devo model and biotechnological production system for metabolites and pharmaceuticals. Strong in vivo expression of genes of interest is important for production of recombinant proteins, e.g., selectable markers, fluorescent proteins, or enzymes. In this regard, the choice of the promoter sequence as well as codon usage optimization are two important inside factors to consider in order to obtain optimum protein accumulation level. To reliably quantify fluorescence, we transfected protoplasts with promoter:GFP fusion constructs and measured fluorescence intensity of living protoplasts in a plate reader system. We used the red fluorescent protein mCherry under 2x 35S promoter control as second reporter to normalize for different transfection efficiencies. We derived a novel endogenous promoter and compared deletion variants with exogenous promoters. We used different codon-adapted green fluorescent protein (GFP genes to evaluate the influence of promoter choice and codon optimization on protein accumulation in P. patens, and show that the promoter of the gene of P. patens chlorophyll a/b binding protein lhcsr1 drives expression of GFP in protoplasts significantly (more than twofold better than the commonly used 2x 35S promoter or the rice actin1 promoter. We identified a shortened 677 bp version of the lhcsr1 promoter that retains full activity in protoplasts. The codon optimized GFP yields significantly (more than twofold stronger fluorescence signals and thus demonstrates that adjusting codon usage in P. patens can increase expression strength. In combination, new promotor and codon optimized GFP conveyed sixfold increased fluorescence signal.

Analysis of codon usage patterns in Morus notabilis based on genome and transcriptome data.

Science.gov (United States)

Wen, Yan; Zou, Ziliang; Li, Hongshun; Xiang, Zhonghuai; He, Ningjia

2017-06-01

Codons play important roles in regulating gene expression levels and mRNA half-lives. However, codon usage and related studies in multicellular organisms still lag far behind those in unicellular organisms. In this study, we describe for the first time genome-wide patterns of codon bias in Morus notabilis (mulberry tree), and analyze genome-wide codon usage in 12 other species within the order Rosales. The codon usage of M. notabilis was affected by nucleotide composition, mutation pressure, nature selection, and gene expression level. Translational selection optimal codons were identified and highly expressed genes of M. notabilis tended to use the optimal codons. Genes with higher expression levels have shorter coding region and lower amino acid complexity. Housekeeping genes showed stronger translational selection, which, notably, was not caused by the large differences between the expression level of housekeeping genes and other genes.

Codon Distribution in Error-Detecting Circular Codes.

Science.gov (United States)

Fimmel, Elena; Strüngmann, Lutz

2016-03-15

In 1957, Francis Crick et al. suggested an ingenious explanation for the process of frame maintenance. The idea was based on the notion of comma-free codes. Although Crick's hypothesis proved to be wrong, in 1996, Arquès and Michel discovered the existence of a weaker version of such codes in eukaryote and prokaryote genomes, namely the so-called circular codes. Since then, circular code theory has invariably evoked great interest and made significant progress. In this article, the codon distributions in maximal comma-free, maximal self-complementary C³ and maximal self-complementary circular codes are discussed, i.e., we investigate in how many of such codes a given codon participates. As the main (and surprising) result, it is shown that the codons can be separated into very few classes (three, or five, or six) with respect to their frequency. Moreover, the distribution classes can be hierarchically ordered as refinements from maximal comma-free codes via maximal self-complementary C(3) codes to maximal self-complementary circular codes.

Codon size reduction as the origin of the triplet genetic code.

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Pavel V Baranov

Full Text Available The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon

Analysis of the synonymous codon usage bias in recently emerged enterovirus D68 strains.

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Karniychuk, Uladzimir U

2016-09-02

Understanding the codon usage pattern of a pathogen and relationship between pathogen and host's codon usage patterns has fundamental and applied interests. Enterovirus D68 (EV-D68) is an emerging pathogen with a potentially high public health significance. In the present study, the synonymous codon usage bias of 27 recently emerged, and historical EV-D68 strains was analyzed. In contrast to previously studied enteroviruses (enterovirus 71 and poliovirus), EV-D68 and human host have a high discrepancy between favored codons. Analysis of viral synonymous codon usage bias metrics, viral nucleotide/dinucleotide compositional parameters, and viral protein properties showed that mutational pressure is more involved in shaping the synonymous codon usage bias of EV-D68 than translation selection. Computation of codon adaptation indices allowed to estimate expression potential of the EV-D68 genome in several commonly used laboratory animals. This approach requires experimental validation and may provide an auxiliary tool for the rational selection of laboratory animals to model emerging viral diseases. Enterovirus D68 genome compositional and codon usage data can be useful for further pathogenesis, animal model, and vaccine design studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Translational selection on codon usage in the genus Aspergillus.

Science.gov (United States)

Iriarte, Andrés; Sanguinetti, Manuel; Fernández-Calero, Tamara; Naya, Hugo; Ramón, Ana; Musto, Héctor

2012-09-10

Aspergillus is a genus of mold fungi that includes more than 200 described species. Many members of the group are relevant pathogens and other species are economically important. Only one species has been analyzed for codon usage, and this was performed with a small number of genes. In this paper, we report the codon usage patterns of eight completely sequenced genomes which belong to this genus. The results suggest that selection for translational efficiency and accuracy are the major factors shaping codon usage in all of the species studied so far, and therefore they were active in the last common ancestor of the group. Composition and molecular distances analyses show that highly expressed genes evolve slower at synonymous sites. We identified a conserved core of translationally optimal codons and study the tRNA gene pool in each genome. We found that the great majority of preferred triplets match the respective cognate tRNA with more copies in the respective genome. We discuss the possible scenarios that can explain the observed differences among the species analyzed. Finally we highlight the biotechnological application of this research regarding heterologous protein expression. Copyright © 2012 Elsevier B.V. All rights reserved.

Rare codons effect on expression of recombinant gene cassette in Escherichia coli BL21(DE3

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Aghil Esmaeili-Bandboni

2017-11-01

Full Text Available Objective: To demonstrate the sensitivity of expression of fusion genes to existence of a large number of rare codons in recombinant gene sequenced. Methods: Primers for amplification of cholera toxin B, Shiga toxin B and gfp genes were designed by Primer3 software and synthesized. All of these 3 genes were cloned. Then the genes were fused together by restriction sites and enzymatic method. Two linkers were used as a flexible bridge in connection of these genes. Results: Cloning and fusion of cholera toxin B, Shiga toxin B and gfp genes were done correctly. After that, expression of the recombinant gene construction was surveyed. Conclusions: According to what was seen, because of the accumulation of 12 rare codons of Shiga toxin B and 19 rare codons of cholera toxin B in this gene cassette, the expression of the recombinant gene cassette, in Escherichia coli BL21, failed.

Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites

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Sun, Yu; Tamarit, Daniel

2017-01-01

Abstract The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bacterial genomes with extreme nucleotide composition biases provide informative model systems. Switches in the background substitution biases from GC to AT have occurred in Gardnerella vaginalis (GC = 32%), and from AT to GC in Lactobacillus delbrueckii (GC = 62%) and Lactobacillus fermentum (GC = 63%). We show that despite the large effects on codon usage patterns by these switches, all three species evolve under selection on synonymous sites. In G. vaginalis, the dramatic codon frequency changes coincide with shifts of optimal codons. In contrast, the optimal codons have not shifted in the two Lactobacillus genomes despite an increased fraction of GC-ending codons. We suggest that all three species are in different phases of an on-going shift of optimal codons, and attribute the difference to a stronger background substitution bias and/or longer time since the switch in G. vaginalis. We show that comparative and correlative methods for optimal codon identification yield conflicting results for genomes in flux and discuss possible reasons for the mispredictions. We conclude that switches in the direction of the background substitution biases can drive major shifts in codon preference patterns even under sustained selection on synonymous codon sites. PMID:27540085

ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.

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Sablok, Gaurav; Chen, Ting-Wen; Lee, Chi-Ching; Yang, Chi; Gan, Ruei-Chi; Wegrzyn, Jill L; Porta, Nicola L; Nayak, Kinshuk C; Huang, Po-Jung; Varotto, Claudio; Tang, Petrus

2017-06-01

Organelle genomes are widely thought to have arisen from reduction events involving cyanobacterial and archaeal genomes, in the case of chloroplasts, or α-proteobacterial genomes, in the case of mitochondria. Heterogeneity in base composition and codon preference has long been the subject of investigation of topics ranging from phylogenetic distortion to the design of overexpression cassettes for transgenic expression. From the overexpression point of view, it is critical to systematically analyze the codon usage patterns of the organelle genomes. In light of the importance of codon usage patterns in the development of hyper-expression organelle transgenics, we present ChloroMitoCU, the first-ever curated, web-based reference catalog of the codon usage patterns in organelle genomes. ChloroMitoCU contains the pre-compiled codon usage patterns of 328 chloroplast genomes (29,960 CDS) and 3,502 mitochondrial genomes (49,066 CDS), enabling genome-wide exploration and comparative analysis of codon usage patterns across species. ChloroMitoCU allows the phylogenetic comparison of codon usage patterns across organelle genomes, the prediction of codon usage patterns based on user-submitted transcripts or assembled organelle genes, and comparative analysis with the pre-compiled patterns across species of interest. ChloroMitoCU can increase our understanding of the biased patterns of codon usage in organelle genomes across multiple clades. ChloroMitoCU can be accessed at: http://chloromitocu.cgu.edu.tw/. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Analysis of Low Frequency Protein Truncating Stop-Codon Variants and Fasting Concentration of Growth Hormone.

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Erik Hallengren

Full Text Available The genetic background of Growth Hormone (GH secretion is not well understood. Mutations giving rise to a stop codon have a high likelihood of affecting protein function.To analyze likely functional stop codon mutations that are associated with fasting plasma concentration of Growth Hormone.We analyzed stop codon mutations in 5451 individuals in the Malmö Diet and Cancer study by genotyping the Illumina Exome Chip. To enrich for stop codon mutations with likely functional effects on protein function, we focused on those disrupting >80% of the predicted amino acid sequence, which were carried by ≥ 10 individuals. Such mutations were related to GH concentration, measured with a high sensitivity assay (hs-GH and, if nominally significant, to GH related phenotypes, using linear regression analysis.Two stop codon mutations were associated with the fasting concentration of hs-GH. rs121909305 (NP_005370.1:p.R93* [Minor Allele Frequency (MAF = 0.8%] in the Myosin 1A gene (MYO1A was associated with a 0.36 (95%CI, 0.04 to 0.54; p=0.02 increment of the standardized value of the natural logarithm of hs-GH per 1 minor allele and rs35699176 (NP_067040.1:p.Q100* in the Zink Finger protein 77 gene (ZNF77 (MAF = 4.8% was associated with a 0.12 (95%CI, 0.02 to 0.22; p = 0.02 increase of hs-GH. The mutated high hs-GH associated allele of MYO1A was related to lower BMI (β-coefficient, -0.22; p = 0.05, waist (β-coefficient, -0.22; p = 0.04, body fat percentage (β-coefficient, -0.23; p = 0.03 and with higher HDL (β-coefficient, 0.23; p = 0.04. The ZNF77 stop codon was associated with height (β-coefficient, 0.11; p = 0.02 but not with cardiometabolic risk factors.We here suggest that a stop codon of MYO1A, disrupting 91% of the predicted amino acid sequence, is associated with higher hs-GH and GH-related traits suggesting that MYO1A is involved in GH metabolism and possibly body fat distribution. However, our results are preliminary and need replication in

Chloroplast DNA codon use: evidence for selection at the psb A locus based on tRNA availability.

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Morton, B R

1993-09-01

Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the psb A gene of all three genomes and other psb A sequences examined. In this gene, the codon use favors NNC over NNT for twofold degenerate amino acids. In each case the only tRNA coded by the genome is complementary to the NNC codon. This codon use is similar to the codon use by chloroplast genes examined from Chlamydomonas reinhardtii. Since psb A is the major translation product of the chloroplast, this suggests that selection is acting on the codon use of this gene to adapt codons to tRNA availability, as previously suggested for unicellular organisms.

A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering.

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Belsare, Ketaki D; Andorfer, Mary C; Cardenas, Frida S; Chael, Julia R; Park, Hyun June; Lewis, Jared C

2017-03-17

Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450 BM3 , pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated. Each of these libraries provided improved enzymes for their respective transformations, which highlights the generality, simplicity, and tunability of CCM for targeted protein engineering.

Why has nature invented three stop codons of DNA and only one start codon?

Czech Academy of Sciences Publication Activity Database

Křížek, Michal; Křížek, P.

2012-01-01

Roč. 304, Jul 7 (2012), s. 183-187 ISSN 0022-5193 R&D Projects: GA AV ČR(CZ) IAA100190803 Institutional support: RVO:67985840 Keywords : DNA * RNA * stop codon * synchronization shift * drosophila genome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.351, year: 2012 http://www.sciencedirect.com/science/article/pii/S0022519312001580

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells.

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Zhao, Fangzhou; Yu, Chien-Hung; Liu, Yi

2017-08-21

Codon usage biases are found in all eukaryotic and prokaryotic genomes and have been proposed to regulate different aspects of translation process. Codon optimality has been shown to regulate translation elongation speed in fungal systems, but its effect on translation elongation speed in animal systems is not clear. In this study, we used a Drosophila cell-free translation system to directly compare the velocity of mRNA translation elongation. Our results demonstrate that optimal synonymous codons speed up translation elongation while non-optimal codons slow down translation. In addition, codon usage regulates ribosome movement and stalling on mRNA during translation. Finally, we show that codon usage affects protein structure and function in vitro and in Drosophila cells. Together, these results suggest that the effect of codon usage on translation elongation speed is a conserved mechanism from fungi to animals that can affect protein folding in eukaryotic organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes.

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Behura, Susanta K; Severson, David W

2013-02-01

Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance. © 2012 The Authors. Biological Reviews © 2012 Cambridge Philosophical Society.

Gene Composer: database software for protein construct design, codon engineering, and gene synthesis

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Mixon Mark

2009-04-01

Full Text Available Abstract Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene

Analysis of amino acid and codon usage in Paramecium bursaria.

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Dohra, Hideo; Fujishima, Masahiro; Suzuki, Haruo

2015-10-07

The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Three-Phase Harmonic Analysis Method for Unbalanced Distribution Systems

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Jen-Hao Teng

2014-01-01

Full Text Available Due to the unbalanced features of distribution systems, a three-phase harmonic analysis method is essential to accurately analyze the harmonic impact on distribution systems. Moreover, harmonic analysis is the basic tool for harmonic filter design and harmonic resonance mitigation; therefore, the computational performance should also be efficient. An accurate and efficient three-phase harmonic analysis method for unbalanced distribution systems is proposed in this paper. The variations of bus voltages, bus current injections and branch currents affected by harmonic current injections can be analyzed by two relationship matrices developed from the topological characteristics of distribution systems. Some useful formulas are then derived to solve the three-phase harmonic propagation problem. After the harmonic propagation for each harmonic order is calculated, the total harmonic distortion (THD for bus voltages can be calculated accordingly. The proposed method has better computational performance, since the time-consuming full admittance matrix inverse employed by the commonly-used harmonic analysis methods is not necessary in the solution procedure. In addition, the proposed method can provide novel viewpoints in calculating the branch currents and bus voltages under harmonic pollution which are vital for harmonic filter design. Test results demonstrate the effectiveness and efficiency of the proposed method.

Comparative evolutionary genomics of Corynebacterium with special reference to codon and amino acid usage diversities.

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Pal, Shilpee; Sarkar, Indrani; Roy, Ayan; Mohapatra, Pradeep K Das; Mondal, Keshab C; Sen, Arnab

2018-02-01

The present study has been aimed to the comparative analysis of high GC composition containing Corynebacterium genomes and their evolutionary study by exploring codon and amino acid usage patterns. Phylogenetic study by MLSA approach, indel analysis and BLAST matrix differentiated Corynebacterium species in pathogenic and non-pathogenic clusters. Correspondence analysis on synonymous codon usage reveals that, gene length, optimal codon frequencies and tRNA abundance affect the gene expression of Corynebacterium. Most of the optimal codons as well as translationally optimal codons are C ending i.e. RNY (R-purine, N-any nucleotide base, and Y-pyrimidine) and reveal translational selection pressure on codon bias of Corynebacterium. Amino acid usage is affected by hydrophobicity, aromaticity, protein energy cost, etc. Highly expressed genes followed the cost minimization hypothesis and are less diverged at their synonymous positions of codons. Functional analysis of core genes shows significant difference in pathogenic and non-pathogenic Corynebacterium. The study reveals close relationship between non-pathogenic and opportunistic pathogenic Corynebaterium as well as between molecular evolution and survival niches of the organism.

Polymorphism at codon 36 of the p53 gene.

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Felix, C A; Brown, D L; Mitsudomi, T; Ikagaki, N; Wong, A; Wasserman, R; Womer, R B; Biegel, J A

1994-01-01

A polymorphism at codon 36 in exon 4 of the p53 gene was identified by single strand conformation polymorphism (SSCP) analysis and direct sequencing of genomic DNA PCR products. The polymorphic allele, present in the heterozygous state in genomic DNAs of four of 100 individuals (4%), changes the codon 36 CCG to CCA, eliminates a FinI restriction site and creates a BccI site. Including this polymorphism there are four known polymorphisms in the p53 coding sequence.

Development of a codon optimization strategy using the efor RED reporter gene as a test case

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Yip, Chee-Hoo; Yarkoni, Orr; Ajioka, James; Wan, Kiew-Lian; Nathan, Sheila

2018-04-01

Synthetic biology is a platform that enables high-level synthesis of useful products such as pharmaceutically related drugs, bioplastics and green fuels from synthetic DNA constructs. Large-scale expression of these products can be achieved in an industrial compliant host such as Escherichia coli. To maximise the production of recombinant proteins in a heterologous host, the genes of interest are usually codon optimized based on the codon usage of the host. However, the bioinformatics freeware available for standard codon optimization might not be ideal in determining the best sequence for the synthesis of synthetic DNA. Synthesis of incorrect sequences can prove to be a costly error and to avoid this, a codon optimization strategy was developed based on the E. coli codon usage using the efor RED reporter gene as a test case. This strategy replaces codons encoding for serine, leucine, proline and threonine with the most frequently used codons in E. coli. Furthermore, codons encoding for valine and glycine are substituted with the second highly used codons in E. coli. Both the optimized and original efor RED genes were ligated to the pJS209 plasmid backbone using Gibson Assembly and the recombinant DNAs were transformed into E. coli E. cloni 10G strain. The fluorescence intensity per cell density of the optimized sequence was improved by 20% compared to the original sequence. Hence, the developed codon optimization strategy is proposed when designing an optimal sequence for heterologous protein production in E. coli.

Full-Band Quasi-Harmonic Analysis and Synthesis of Musical Instrument Sounds with Adaptive Sinusoids

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Marcelo Caetano

2016-05-01

Full Text Available Sinusoids are widely used to represent the oscillatory modes of musical instrument sounds in both analysis and synthesis. However, musical instrument sounds feature transients and instrumental noise that are poorly modeled with quasi-stationary sinusoids, requiring spectral decomposition and further dedicated modeling. In this work, we propose a full-band representation that fits sinusoids across the entire spectrum. We use the extended adaptive Quasi-Harmonic Model (eaQHM to iteratively estimate amplitude- and frequency-modulated (AM–FM sinusoids able to capture challenging features such as sharp attacks, transients, and instrumental noise. We use the signal-to-reconstruction-error ratio (SRER as the objective measure for the analysis and synthesis of 89 musical instrument sounds from different instrumental families. We compare against quasi-stationary sinusoids and exponentially damped sinusoids. First, we show that the SRER increases with adaptation in eaQHM. Then, we show that full-band modeling with eaQHM captures partials at the higher frequency end of the spectrum that are neglected by spectral decomposition. Finally, we demonstrate that a frame size equal to three periods of the fundamental frequency results in the highest SRER with AM–FM sinusoids from eaQHM. A listening test confirmed that the musical instrument sounds resynthesized from full-band analysis with eaQHM are virtually perceptually indistinguishable from the original recordings.

Comprehensive analysis of the codon usage patterns in the envelope glycoprotein E2 gene of the classical swine fever virus.

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Ye Chen

Full Text Available The classical swine fever virus (CSFV, circulating worldwide, is a highly contagious virus. Since the emergence of CSFV, it has caused great economic loss in swine industry. The envelope glycoprotein E2 gene of the CSFV is an immunoprotective antigen that induces the immune system to produce neutralizing antibodies. Therefore, it is essential to study the codon usage of the E2 gene of the CSFV. In this study, 140 coding sequences of the E2 gene were analyzed. The value of effective number of codons (ENC showed low codon usage bias in the E2 gene. Our study showed that codon usage could be described mainly by mutation pressure ENC plot analysis combined with principal component analysis (PCA and translational selection-correlation analysis between the general average hydropathicity (Gravy and aromaticity (Aroma, and nucleotides at the third position of codons (A3s, T3s, G3s, C3s and GC3s. Furthermore, the neutrality analysis, which explained the relationship between GC12s and GC3s, revealed that natural selection had a key role compared with mutational bias during the evolution of the E2 gene. These results lay a foundation for further research on the molecular evolution of CSFV.

Harmonics Monitoring Survey on LED Lamps

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Abdelrahman Ahmed Akila

2017-03-01

Full Text Available Light Emitting Diode (LED lamps are being increasingly used in many applications. These LED lamps operate using a driver, which is a switching device. Hence, LED lamps will be a source of harmonics in the power system. These harmonics if not well treated, may cause severe performance and operational problems. In this paper, harmonics (amplitude and phase angles generated by both LED lamps and conventional fluorescent lamps will be studied practically. Then they will be analyzed and evaluated. Compared to each other harmonics generated by both LED and conventional florescent lamps, self mitigation may occur based on the phase angle of these harmonics. All data will be measured using power analyzer and will be done on a sample of actual lamps.

Elevation of the Yields of Very Long Chain Polyunsaturated Fatty Acids via Minimal Codon Optimization of Two Key Biosynthetic Enzymes.

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Fei Xia

Full Text Available Eicosapentaenoic acid (EPA, 20:5Δ5,8,11,14,17 and Docosahexaenoic acid (DHA, 22:6Δ4,7,10,13,16,19 are nutritionally beneficial to human health. Transgenic production of EPA and DHA in oilseed crops by transferring genes originating from lower eukaryotes, such as microalgae and fungi, has been attempted in recent years. However, the low yield of EPA and DHA produced in these transgenic crops is a major hurdle for the commercialization of these transgenics. Many factors can negatively affect transgene expression, leading to a low level of converted fatty acid products. Among these the codon bias between the transgene donor and the host crop is one of the major contributing factors. Therefore, we carried out codon optimization of a fatty acid delta-6 desaturase gene PinD6 from the fungus Phytophthora infestans, and a delta-9 elongase gene, IgASE1 from the microalga Isochrysis galbana for expression in Saccharomyces cerevisiae and Arabidopsis respectively. These are the two key genes encoding enzymes for driving the first catalytic steps in the Δ6 desaturation/Δ6 elongation and the Δ9 elongation/Δ8 desaturation pathways for EPA/DHA biosynthesis. Hence expression levels of these two genes are important in determining the final yield of EPA/DHA. Via PCR-based mutagenesis we optimized the least preferred codons within the first 16 codons at their N-termini, as well as the most biased CGC codons (coding for arginine within the entire sequences of both genes. An expression study showed that transgenic Arabidopsis plants harbouring the codon-optimized IgASE1 contained 64% more elongated fatty acid products than plants expressing the native IgASE1 sequence, whilst Saccharomyces cerevisiae expressing the codon optimized PinD6 yielded 20 times more desaturated products than yeast expressing wild-type (WT PinD6. Thus the codon optimization strategy we developed here offers a simple, effective and low-cost alternative to whole gene synthesis for high

Disruption of the Opal Stop Codon Attenuates Chikungunya Virus-Induced Arthritis and Pathology.

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Jones, Jennifer E; Long, Kristin M; Whitmore, Alan C; Sanders, Wes; Thurlow, Lance R; Brown, Julia A; Morrison, Clayton R; Vincent, Heather; Peck, Kayla M; Browning, Christian; Moorman, Nathaniel; Lim, Jean K; Heise, Mark T

2017-11-14

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus responsible for several significant outbreaks of debilitating acute and chronic arthritis and arthralgia over the past decade. These include a recent outbreak in the Caribbean islands and the Americas that caused more than 1 million cases of viral arthralgia. Despite the major impact of CHIKV on global health, viral determinants that promote CHIKV-induced disease are incompletely understood. Most CHIKV strains contain a conserved opal stop codon at the end of the viral nsP3 gene. However, CHIKV strains that encode an arginine codon in place of the opal stop codon have been described, and deep-sequencing analysis of a CHIKV isolate from the Caribbean identified both arginine and opal variants within this strain. Therefore, we hypothesized that the introduction of the arginine mutation in place of the opal termination codon may influence CHIKV virulence. We tested this by introducing the arginine mutation into a well-characterized infectious clone of a CHIKV strain from Sri Lanka and designated this virus Opal524R. This mutation did not impair viral replication kinetics in vitro or in vivo Despite this, the Opal524R virus induced significantly less swelling, inflammation, and damage within the feet and ankles of infected mice. Further, we observed delayed induction of proinflammatory cytokines and chemokines, as well as reduced CD4 + T cell and NK cell recruitment compared to those in the parental strain. Therefore, the opal termination codon plays an important role in CHIKV pathogenesis, independently of effects on viral replication. IMPORTANCE Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes significant outbreaks of viral arthralgia. Studies with CHIKV and other alphaviruses demonstrated that the opal termination codon within nsP3 is highly conserved. However, some strains of CHIKV and other alphaviruses contain mutations in the opal termination codon. These mutations alter the virulence

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

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Lara-Ramírez, Edgar E.; Salazar, Ma Isabel; López-López, María de Jesús; Salas-Benito, Juan Santiago; Sánchez-Varela, Alejandro

2014-01-01

The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution. PMID:25136631

Association between the p53 codon 72 polymorphism and primary open-angle glaucoma risk: Meta-analysis based on 11 case–control studies

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Mohsen Gohari

2016-01-01

Full Text Available The TP53 is important in functions of cell cycle control, apoptosis, and maintenance of DNA integrity. Studies on the association between p53 codon 72 polymorphism and primary open-angle glaucoma (POAG risk have yielded conflicting results. Published literature from PubMed and Web of Science databases was retrieved. All studies evaluating the association between p53 codon 72 polymorphisms and POAG were included. Pooled odds ratio (OR and 95% confidence interval (CI were calculated. Eleven separate studies including 2541 cases and 1844 controls were pooled in the meta-analysis. We did not detect a significant association between POAG risk and p53 codon 72 polymorphism overall population except allele genetic model (C vs. G: OR = 0.961, 95% CI = 0.961–0.820, P = 0.622. In the stratified analysis for Asians and Caucasians, there was an association between p53 codon 72 polymorphism and POAG. In the dominant model in the overall population and by ethnicity subgroups, the highest elevated POAG risk was presented. In summary, these results indicate that p53 codon 72 polymorphism is likely an important genetic factor contributing to susceptibility of POAG. However, more case–controls studies based on larger sample size and stratified by ethnicity are suggested to further clarify the relationship between p53 codon 72 polymorphism and POAG.

Second harmonic inversion for ultrasound contrast harmonic imaging

Energy Technology Data Exchange (ETDEWEB)

Pasovic, Mirza; Danilouchkine, Mike; Faez, Telli; Van Neer, Paul L M J; Van der Steen, Antonius F W; De Jong, Nico [THORAXCENTER, Department of Biomedical Engineering Ee2302, Erasmus MC, Rotterdam (Netherlands); Cachard, Christian; Basset, Olivier, E-mail: mirza.pasovic@creatis.insa-lyon.fr [CREATIS-LRMN, Universite de Lyon, INSA-Lyon, Universite Lyon 1, Inserm U630, CNRS UMR 5220 (France)

2011-06-07

Ultrasound contrast agents (UCAs) are small micro-bubbles that behave nonlinearly when exposed to an ultrasound wave. This nonlinear behavior can be observed through the generated higher harmonics in a back-scattered echo. In past years several techniques have been proposed to detect or image harmonics produced by UCAs. In these proposed works, the harmonics generated in the medium during the propagation of the ultrasound wave played an important role, since these harmonics compete with the harmonics generated by the micro-bubbles. We present a method for the reduction of the second harmonic generated during nonlinear-propagation-dubbed second harmonic inversion (SHI). A general expression for the suppression signals is also derived. The SHI technique uses two pulses, p' and p'', of the same frequency f{sub 0} and the same amplitude P{sub 0} to cancel out the second harmonic generated by nonlinearities of the medium. Simulations show that the second harmonic is reduced by 40 dB on a large axial range. Experimental SHI B-mode images, from a tissue-mimicking phantom and UCAs, show an improvement in the agent-to-tissue ratio (ATR) of 20 dB compared to standard second harmonic imaging and 13 dB of improvement in harmonic power Doppler.

Second harmonic inversion for ultrasound contrast harmonic imaging

International Nuclear Information System (INIS)

Pasovic, Mirza; Danilouchkine, Mike; Faez, Telli; Van Neer, Paul L M J; Van der Steen, Antonius F W; De Jong, Nico; Cachard, Christian; Basset, Olivier

2011-01-01

Ultrasound contrast agents (UCAs) are small micro-bubbles that behave nonlinearly when exposed to an ultrasound wave. This nonlinear behavior can be observed through the generated higher harmonics in a back-scattered echo. In past years several techniques have been proposed to detect or image harmonics produced by UCAs. In these proposed works, the harmonics generated in the medium during the propagation of the ultrasound wave played an important role, since these harmonics compete with the harmonics generated by the micro-bubbles. We present a method for the reduction of the second harmonic generated during nonlinear-propagation-dubbed second harmonic inversion (SHI). A general expression for the suppression signals is also derived. The SHI technique uses two pulses, p' and p'', of the same frequency f 0 and the same amplitude P 0 to cancel out the second harmonic generated by nonlinearities of the medium. Simulations show that the second harmonic is reduced by 40 dB on a large axial range. Experimental SHI B-mode images, from a tissue-mimicking phantom and UCAs, show an improvement in the agent-to-tissue ratio (ATR) of 20 dB compared to standard second harmonic imaging and 13 dB of improvement in harmonic power Doppler.

Genomic analysis of codon usage shows influence of mutation pressure, natural selection, and host features on Marburg virus evolution.

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Nasrullah, Izza; Butt, Azeem M; Tahir, Shifa; Idrees, Muhammad; Tong, Yigang

2015-08-26

The Marburg virus (MARV) has a negative-sense single-stranded RNA genome, belongs to the family Filoviridae, and is responsible for several outbreaks of highly fatal hemorrhagic fever. Codon usage patterns of viruses reflect a series of evolutionary changes that enable viruses to shape their survival rates and fitness toward the external environment and, most importantly, their hosts. To understand the evolution of MARV at the codon level, we report a comprehensive analysis of synonymous codon usage patterns in MARV genomes. Multiple codon analysis approaches and statistical methods were performed to determine overall codon usage patterns, biases in codon usage, and influence of various factors, including mutation pressure, natural selection, and its two hosts, Homo sapiens and Rousettus aegyptiacus. Nucleotide composition and relative synonymous codon usage (RSCU) analysis revealed that MARV shows mutation bias and prefers U- and A-ended codons to code amino acids. Effective number of codons analysis indicated that overall codon usage among MARV genomes is slightly biased. The Parity Rule 2 plot analysis showed that GC and AU nucleotides were not used proportionally which accounts for the presence of natural selection. Codon usage patterns of MARV were also found to be influenced by its hosts. This indicates that MARV have evolved codon usage patterns that are specific to both of its hosts. Moreover, selection pressure from R. aegyptiacus on the MARV RSCU patterns was found to be dominant compared with that from H. sapiens. Overall, mutation pressure was found to be the most important and dominant force that shapes codon usage patterns in MARV. To our knowledge, this is the first detailed codon usage analysis of MARV and extends our understanding of the mechanisms that contribute to codon usage and evolution of MARV.

De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.

Science.gov (United States)

Cho, Namjin; Hwang, Byungjin; Yoon, Jung-ki; Park, Sangun; Lee, Joongoo; Seo, Han Na; Lee, Jeewon; Huh, Sunghoon; Chung, Jinsoo; Bang, Duhee

2015-09-21

Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

Codon usage and expression level of human mitochondrial 13 protein coding genes across six continents.

Science.gov (United States)

Chakraborty, Supriyo; Uddin, Arif; Mazumder, Tarikul Huda; Choudhury, Monisha Nath; Malakar, Arup Kumar; Paul, Prosenjit; Halder, Binata; Deka, Himangshu; Mazumder, Gulshana Akthar; Barbhuiya, Riazul Ahmed; Barbhuiya, Masuk Ahmed; Devi, Warepam Jesmi

2017-12-02

The study of codon usage coupled with phylogenetic analysis is an important tool to understand the genetic and evolutionary relationship of a gene. The 13 protein coding genes of human mitochondria are involved in electron transport chain for the generation of energy currency (ATP). However, no work has yet been reported on the codon usage of the mitochondrial protein coding genes across six continents. To understand the patterns of codon usage in mitochondrial genes across six different continents, we used bioinformatic analyses to analyze the protein coding genes. The codon usage bias was low as revealed from high ENC value. Correlation between codon usage and GC3 suggested that all the codons ending with G/C were positively correlated with GC3 but vice versa for A/T ending codons with the exception of ND4L and ND5 genes. Neutrality plot revealed that for the genes ATP6, COI, COIII, CYB, ND4 and ND4L, natural selection might have played a major role while mutation pressure might have played a dominant role in the codon usage bias of ATP8, COII, ND1, ND2, ND3, ND5 and ND6 genes. Phylogenetic analysis indicated that evolutionary relationships in each of 13 protein coding genes of human mitochondria were different across six continents and further suggested that geographical distance was an important factor for the origin and evolution of 13 protein coding genes of human mitochondria. Copyright © 2017 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.

Science.gov (United States)

Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

2016-07-01

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. © 2016 Mühlhausen et al.; Published by Cold Spring Harbor Laboratory Press.

Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid.

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Lluís Aragonès

2010-03-01

Full Text Available Hepatitis A virus (HAV, the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

Double Harmonic Transmission (D.H.T.

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Sava Ianici

2006-10-01

Full Text Available The paper presents the construction and functioning of a new type of harmonic drive named double harmonic transmission (D.H.T.. In the second part of this paper is presented the dynamic analysis of the double harmonic transmission, which is based on the results of the experimental researches on the D.H.T. This study of the stress status and the forces distribution is necessary for to determine the durability on the portant elements of the D.H.T.

Reassigning stop codons via translation termination: How a few eukaryotes broke the dogma.

Science.gov (United States)

Alkalaeva, Elena; Mikhailova, Tatiana

2017-03-01

The genetic code determines how amino acids are encoded within mRNA. It is universal among the vast majority of organisms, although several exceptions are known. Variant genetic codes are found in ciliates, mitochondria, and numerous other organisms. All revealed genetic codes (standard and variant) have at least one codon encoding a translation stop signal. However, recently two new genetic codes with a reassignment of all three stop codons were revealed in studies examining the protozoa transcriptomes. Here, we discuss this finding and the recent studies of variant genetic codes in eukaryotes. We consider the possible molecular mechanisms allowing the use of certain codons as sense and stop signals simultaneously. The results obtained by studying these amazing organisms represent a new and exciting insight into the mechanism of stop codon decoding in eukaryotes. Also see the video abstract here. © 2017 WILEY Periodicals, Inc.

Benzimidazole -Resistance in Haemonchus Contortus: New PCR-RFLP Method for the Detection of Point Mutation at Codon 167 of Isotype 1 Β-Tubulin Gene

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A Eslami

2012-12-01

Full Text Available Background: Due to the lack of a suitable and economic test for the analysis of the polymorphism at codon 167, we developed a new PCR-RFLP technique, based on a modified forward primer (UT-HC167 MF-primer, to identify simultaneously the SNPs at codons 167 and 200 of isotype 1 β-tubu­lin gene of Haemonchus contortus.Methods: There already are several safe and easy methods for identification of point mutations at codons 198 and 200. Due to the lack of a reliable and easy method for the detection of the single nucleo­tide polymorphism (SNP at codon 167, we developed an innovative PCR-RFLP technique based on a modified forward primer (UT-HC167 MF-primer, in which the nucleotide T at the posi­tion 443 was substituted through a nucleotide A creating a restriction site for restriction endonuc­lease SnaB I in the nucleotide sequences including codon 167. A total of 138 adult male H. contortus were collected from three different geo-climatic areas of Iran. The isolated genomic DNA of each single worm was amplified by PCR using primers flanking codon 167. The PCR product (527 bp was then amplified by semi-nested PCR using the UT-HC167 MF-primer and the reverse primer achiev­ing a PCR product of 451 bp in length. This PCR product was subsequently digested with the restriction endonucleases SnaB I and TaaI for analysis of the mutations at codons 167 and 200, respec­tively.Results: All worms had two alleles encoding for phenylalanine (BZss homozygote for both codons.Conclusion: Using the UT-HC167 MF-primer and a suitable reverse primer designed upstream from codon 200, it is possible to amplify a PCR product which can be used for analysis of the SNPs at all three mentioned codons using RFLP.

Stabilization of the genome of the mismatch repair deficient Mycobacterium tuberculosis by context-dependent codon choice

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Ackermann Martin

2008-05-01

Full Text Available Abstract Background The rate at which a stretch of DNA mutates is determined by the cellular systems for DNA replication and repair, and by the nucleotide sequence of the stretch itself. One sequence feature with a particularly strong influence on the mutation rate are nucleotide repeats. Some microbial pathogens use nucleotide repeats in their genome to stochastically vary phenotypic traits and thereby evade host defense. However, such unstable sequences also come at a cost, as mutations are often deleterious. Here, we analyzed how these opposing forces shaped genome stability in the human pathogen Mycobacterium tuberculosis. M. tuberculosis lacks a mismatch repair system, and this renders nucleotide repeats particularly unstable. Results We found that proteins of M. tuberculosis are encoded by using codons in a context-dependent manner that prevents the emergence of nucleotide repeats. This context-dependent codon choice leads to a strong decrease in the estimated frame-shift mutation rate and thus to an increase in genome stability. Conclusion These results indicate that a context-specific codon choice can partially compensate for the lack of a mismatch repair system, and helps to maintain genome integrity in this pathogen.

Probable relationship between partitions of the set of codons and the origin of the genetic code.

Science.gov (United States)

Salinas, Dino G; Gallardo, Mauricio O; Osorio, Manuel I

2014-03-01

Here we study the distribution of randomly generated partitions of the set of amino acid-coding codons. Some results are an application from a previous work, about the Stirling numbers of the second kind and triplet codes, both to the cases of triplet codes having four stop codons, as in mammalian mitochondrial genetic code, and hypothetical doublet codes. Extending previous results, in this work it is found that the most probable number of blocks of synonymous codons, in a genetic code, is similar to the number of amino acids when there are four stop codons, as well as it could be for a primigenious doublet code. Also it is studied the integer partitions associated to patterns of synonymous codons and it is shown, for the canonical code, that the standard deviation inside an integer partition is one of the most probable. We think that, in some early epoch, the genetic code might have had a maximum of the disorder or entropy, independent of the assignment between codons and amino acids, reaching a state similar to "code freeze" proposed by Francis Crick. In later stages, maybe deterministic rules have reassigned codons to amino acids, forming the natural codes, such as the canonical code, but keeping the numerical features describing the set partitions and the integer partitions, like a "fossil numbers"; both kinds of partitions about the set of amino acid-coding codons. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Animal products and K-ras codon 12 and 13 mutations in colon carcinomas

NARCIS (Netherlands)

Kampman, E.; Voskuil, D.W.; Kraats, A.A. van; Balder, H.F.; Muijen, G.N.P. van; Goldbohm, R.A.; Veer, P. van 't

2000-01-01

K-ras gene mutations (codons 12 and 13) were determined by PCR-based mutant allele-specific amplification (MASA) in tumour tissue of 185 colon cancer patients: 36% harboured mutations, of which 82% were located in codon 12. High intakes of animal protein, calcium and poultry were differently

HARMONICS SURFACES OF GRAPHIC TYPE IN R3

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Carlos Carrión Riveros

2016-06-01

Full Text Available In this research we study harmonic surfaces immersed in R3. We dened Harmonic surfaces of graphic type and showed that a harmonious surface graphic type is minimal if and only if it is part of a plane or a helix. Also, we give a characterization of harmonic surfaces graphic type parameterized by asymptotic lines and some examples.

Codon usage bias and phylogenetic analysis of mitochondrial ND1 gene in pisces, aves, and mammals.

Science.gov (United States)

Uddin, Arif; Choudhury, Monisha Nath; Chakraborty, Supriyo

2018-01-01

The mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 1 (MT-ND1) gene is a subunit of the respiratory chain complex I and involved in the first step of the electron transport chain of oxidative phosphorylation (OXPHOS). To understand the pattern of compositional properties, codon usage and expression level of mitochondrial ND1 genes in pisces, aves, and mammals, we used bioinformatic approaches as no work was reported earlier. In this study, a perl script was used for calculating nucleotide contents and different codon usage bias parameters. The codon usage bias of MT-ND1 was low but the expression level was high as revealed from high ENC and CAI value. Correspondence analysis (COA) suggests that the pattern of codon usage for MT-ND1 gene is not same across species and that compositional constraint played an important role in codon usage pattern of this gene among pisces, aves, and mammals. From the regression equation of GC12 on GC3, it can be inferred that the natural selection might have played a dominant role while mutation pressure played a minor role in influencing the codon usage patterns. Further, ND1 gene has a discrepancy with cytochrome B (CYB) gene in preference of codons as evident from COA. The codon usage bias was low. It is influenced by nucleotide composition, natural selection, mutation pressure, length (number) of amino acids, and relative dinucleotide composition. This study helps in understanding the molecular biology, genetics, evolution of MT-ND1 gene, and also for designing a synthetic gene.

Improved secretory production of calf prochymosin by codon ...

African Journals Online (AJOL)

Administrator

2011-09-12

Sep 12, 2011 ... results show that codon optimization and disruption of the PMR1 gene synergistically stimulate the secretion of ... With developments in recombinant DNA technology, .... regulated, it is of importance to optimize the variables.

SCREENING FOR GENETIC CHANGES AND CODON 129 POLYMORPHISM IN PRNP GENE IN HEALTHY SLOVENIAN POPULATION AND SPORADIC CASES OF CREUTZFELDT-JAKOB DISEASE

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Sava Smerkolj

2004-11-01

Full Text Available Background. Prion protein has an important role in development of prion diseases, fatal neurodegenerative disorders. As the codon 129 genotype of the prion protein gene (PRNP is a known susceptibility factor for the diseases, we wanted to determine its distribution in healthy Slovenian population and also in cases of sporadic Creutzfeldt-Jakob disease (sCJD. Furthermore, we wanted to screen the whole gene in order to establish the presence of genetic changes.Methods. We screened 350 DNA samples of healthy blood donors and 12 DNA samples of patients deceased of sCJD. After the amplification and conformation analysis had been done, the gene was sequenced using an automatic sequencer.Results. Methionine homozygotes comprised 46.8% of healthy population, valine homozygotes 12.1% and heterozygotes 41.1%; out of 12 sCJD patients 10 were methionine homozygotes (83.3%, 1 was valine homozygote (8.3% and 1 was heterozygote (8.3%.Found SNPs were combination of codon 76 change (228C > T and codon 84 change (252T > C in a single sample of healthy population, combination of codon 68 change (204T > C and codon 76 change (228C > T in two samples of healthy population and codon 117 change (351A > G in a healthy population sample and in a valine homozygote patient.Conclusions. In comparison to the pooled Caucasian population is genotype M/M frequency slightly increased on account of decreased genotype M/V frequency in healthy Slovenian population, suggesting a little higher risk for acquiring a new variant of CJD (vCJD, because up to date all confirmed vCJD cases except one heterozygote were methionine homozygotes. Codon 129 genotype distribution in sCJD can be described as disease-specific. The absence of pathogenic mutations in sCJD patients confirms the non-familial, sporadic disease form.

The highly conserved codon following the slippery sequence supports -1 frameshift efficiency at the HIV-1 frameshift site.

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Suneeth F Mathew

Full Text Available HIV-1 utilises -1 programmed ribosomal frameshifting to translate structural and enzymatic domains in a defined proportion required for replication. A slippery sequence, U UUU UUA, and a stem-loop are well-defined RNA features modulating -1 frameshifting in HIV-1. The GGG glycine codon immediately following the slippery sequence (the 'intercodon' contributes structurally to the start of the stem-loop but has no defined role in current models of the frameshift mechanism, as slippage is inferred to occur before the intercodon has reached the ribosomal decoding site. This GGG codon is highly conserved in natural isolates of HIV. When the natural intercodon was replaced with a stop codon two different decoding molecules-eRF1 protein or a cognate suppressor tRNA-were able to access and decode the intercodon prior to -1 frameshifting. This implies significant slippage occurs when the intercodon is in the (perhaps distorted ribosomal A site. We accommodate the influence of the intercodon in a model of frame maintenance versus frameshifting in HIV-1.

HARMONIZATION OF TAX POLICIES: REVIEWING MACEDONIA AND CROATIA

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Sasho Kozuharov

2015-12-01

Full Text Available The tax harmonization is a complex issue in the process of European integration. The tax harmonization is a process of convergence of the tax system based on mutual set of rules and, in general, it means existence of identical or similar tax rates for the tax payers in European Union, i.e. Euro zone. In case there are identical tax rates, then we are talking about a, so called, total explicit tax harmonization, whereas, if there are similar tax rates, we are talking about partial explicit tax harmonization, which refers to determination of the highest and the lowest tax rates. Thus, countries can determine the tax rates of certain taxes. The total harmonization, besides tax rates harmonization, means structural harmonization or harmonization of the tax structure. The harmonization of direct taxes mainly relies on the following main objectives: avoiding tax evasion and elimination of double taxation. The harmonization of regulations and directives in the field of indirect taxes is necessary in terms of establishing a single market, or removal of barriers to the free movement of goods, people, services and capital.

Reduce manual curation by combining gene predictions from multiple annotation engines, a case study of start codon prediction.

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Thomas H A Ederveen

Full Text Available Nowadays, prokaryotic genomes are sequenced faster than the capacity to manually curate gene annotations. Automated genome annotation engines provide users a straight-forward and complete solution for predicting ORF coordinates and function. For many labs, the use of AGEs is therefore essential to decrease the time necessary for annotating a given prokaryotic genome. However, it is not uncommon for AGEs to provide different and sometimes conflicting predictions. Combining multiple AGEs might allow for more accurate predictions. Here we analyzed the ab initio open reading frame (ORF calling performance of different AGEs based on curated genome annotations of eight strains from different bacterial species with GC% ranging from 35-52%. We present a case study which demonstrates a novel way of comparative genome annotation, using combinations of AGEs in a pre-defined order (or path to predict ORF start codons. The order of AGE combinations is from high to low specificity, where the specificity is based on the eight genome annotations. For each AGE combination we are able to derive a so-called projected confidence value, which is the average specificity of ORF start codon prediction based on the eight genomes. The projected confidence enables estimating likeliness of a correct prediction for a particular ORF start codon by a particular AGE combination, pinpointing ORFs notoriously difficult to predict start codons. We correctly predict start codons for 90.5±4.8% of the genes in a genome (based on the eight genomes with an accuracy of 81.1±7.6%. Our consensus-path methodology allows a marked improvement over majority voting (9.7±4.4% and with an optimal path ORF start prediction sensitivity is gained while maintaining a high specificity.

Triplet-Based Codon Organization Optimizes the Impact of Synonymous Mutation on Nucleic Acid Molecular Dynamics.

Science.gov (United States)

Babbitt, Gregory A; Coppola, Erin E; Mortensen, Jamie S; Ekeren, Patrick X; Viola, Cosmo; Goldblatt, Dallan; Hudson, André O

2018-02-01

Since the elucidation of the genetic code almost 50 years ago, many nonrandom aspects of its codon organization remain only partly resolved. Here, we investigate the recent hypothesis of 'dual-use' codons which proposes that in addition to allowing adjustment of codon optimization to tRNA abundance, the degeneracy in the triplet-based genetic code also multiplexes information regarding DNA's helical shape and protein-binding dynamics while avoiding interference with other protein-level characteristics determined by amino acid properties. How such structural optimization of the code within eukaryotic chromatin could have arisen from an RNA world is a mystery, but would imply some preadaptation in an RNA context. We analyzed synonymous (protein-silent) and nonsynonymous (protein-altering) mutational impacts on molecular dynamics in 13823 identically degenerate alternative codon reorganizations, defined by codon transitions in 7680 GPU-accelerated molecular dynamic simulations of implicitly and explicitly solvated double-stranded aRNA and bDNA structures. When compared to all possible alternative codon assignments, the standard genetic code minimized the impact of synonymous mutations on the random atomic fluctuations and correlations of carbon backbone vector trajectories while facilitating the specific movements that contribute to DNA polymer flexibility. This trend was notably stronger in the context of RNA supporting the idea that dual-use codon optimization and informational multiplexing in DNA resulted from the preadaptation of the RNA duplex to resist changes to thermostability. The nonrandom and divergent molecular dynamics of synonymous mutations also imply that the triplet-based code may have resulted from adaptive functional expansion enabling a primordial doublet code to multiplex gene regulatory information via the shape and charge of the minor groove.

Correcting the bias of empirical frequency parameter estimators in codon models.

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Sergei Kosakovsky Pond

2010-07-01

Full Text Available Markov models of codon substitution are powerful inferential tools for studying biological processes such as natural selection and preferences in amino acid substitution. The equilibrium character distributions of these models are almost always estimated using nucleotide frequencies observed in a sequence alignment, primarily as a matter of historical convention. In this note, we demonstrate that a popular class of such estimators are biased, and that this bias has an adverse effect on goodness of fit and estimates of substitution rates. We propose a "corrected" empirical estimator that begins with observed nucleotide counts, but accounts for the nucleotide composition of stop codons. We show via simulation that the corrected estimates outperform the de facto standard estimates not just by providing better estimates of the frequencies themselves, but also by leading to improved estimation of other parameters in the evolutionary models. On a curated collection of sequence alignments, our estimators show a significant improvement in goodness of fit compared to the approach. Maximum likelihood estimation of the frequency parameters appears to be warranted in many cases, albeit at a greater computational cost. Our results demonstrate that there is little justification, either statistical or computational, for continued use of the -style estimators.

Prevalence of codon 72 P53 polymorphism in Brazilian women with cervix cancer

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Sylvia Michelina Fernandes Brenna

2004-01-01

Full Text Available The p53 codon 72 polymorphism seems to be associated with HPV-carcinogenesis, although controversial data have been reported. A series of Brazilian women with cervix carcinomas were analyzed. Ninety-nine (67% of 148 women were found to be homozygous (arg/arg for the arginine polymorphism, and 49 (33% were heterozygous (arg/pro. This polymorphism may be an important determinant of the risk for cervix cancer, but does not seem to be sufficient for carcinogenesis.

TP53 codon 72 polymorphism in pigmentary phenotypes

Indian Academy of Sciences (India)

2012-01-20

Jan 20, 2012 ... pigmentation by acting as a transcription factor for other genes that are ... skin phototype I-II, burns after exposure to UVR and the development of .... morphisms of TP53 codon 72 with breast carcinoma risk: evidence from ...

Establishment and comparison of three different codon optimization ...

African Journals Online (AJOL)

Yomi

2012-02-16

C. elegan). It can raise the n-3/n-6 .... value) could help to judge the numbers of codon types. High level ..... function and health in mammal, especially in .... Generation of cloned transgenic pigs rich in omega-3 fatty acids. Nat.

Effect of the scrape-off layer in AORSA full wave simulations of fast wave minority, mid/high harmonic, and helicon heating regimes

Energy Technology Data Exchange (ETDEWEB)

Bertelli, N., E-mail: nbertell@pppl.gov; Gerhardt, S.; Hosea, J. C.; LeBlanc, B.; Perkins, R. J.; Phillips, C. K.; Taylor, G.; Valeo, E. J.; Wilson, J. R. [Princeton Plasma Physics Laboratory, Princeton, NJ 08543 (United States); Jaeger, E. F. [XCEL Engineering Inc., Oak Ridge, TN 37830 (United States); Lau, C.; Blazevski, D.; Green, D. L.; Berry, L.; Ryan, P. M. [Oak Ridge National Laboratory, Oak Ridge, TN 37831-6169 (United States); Bonoli, P. T.; Wright, J. C. [MIT Plasma Science and Fusion Center, Cambridge, MA 02139 (United States); Pinsker, R. I.; Prater, R. [General Atomics, PO Box 85608, San Diego, CA 92186-5608 (United States); Qin, C. M. [Institute of Plasma Physics, Chinese Academy of Sciences, Hefei 230031 (China); and others

2015-12-10

Several experiments on different machines and in different fast wave (FW) heating regimes, such as hydrogen minority heating and high harmonic fast waves, have found strong interactions between radio-frequency (RF) waves and the scrape-off layer (SOL) region. This paper examines the propagation and the power loss in the SOL by using the full wave code AORSA, in which the edge plasma beyond the last closed flux surface (LCFS) is included in the solution domain and a collisional damping parameter is used as a proxy to represent the real, and most likely nonlinear, damping processes. 3D AORSA results for the National Spherical Torus eXperiment (NSTX), where a full antenna spectrum is reconstructed, are shown, confirming the same behavior found for a single toroidal mode results in Bertelli et al, Nucl. Fusion, 54 083004, 2014, namely, a strong transition to higher SOL power losses (driven by the RF field) when the FW cut-off is moved away from in front of the antenna by increasing the edge density. Additionally, full wave simulations have been extended to “conventional” tokamaks with higher aspect ratios, such as the DIII-D, Alcator C-Mod, and EAST devices. DIII-D results show similar behavior found in NSTX and NSTX-U, consistent with previous DIII-D experimental observations. In contrast, a different behavior has been found for Alcator C-Mod and EAST, which operate in the minority heating regime unlike NSTX/NSTX-U and DIII-D, which operate in the mid/high harmonic regime. A substantial discussion of some of the main aspects, such as (i) the pitch angle of the magnetic field; (ii) minority heating vs. mid/high harmonic regimes is presented showing the different behavior of the RF field in the SOL region for NSTX-U scenarios with different plasma current. Finally, the preliminary results of the impact of the SOL region on the evaluation of the helicon current drive efficiency in DIII-D is presented for the first time and briefly compared with the different regimes

Optical klystron and harmonic generation free electron laser

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Qika Jia

2005-06-01

Full Text Available The optical field evolution of an optical klystron free electron laser is analytically described for both low gain and high gain cases. The harmonic optical klystron (HOK in which the second undulator is resonant on the higher harmonic of the first undulator is analyzed as a harmonic amplifier. The optical field evolution equation of the HOK is derived analytically for both the CHG mode (coherent harmonic generation, the quadratic gain regime and the HGHG mode (high gain harmonic generation, the exponential gain regime, the effects of energy spread, energy modulation, and dispersion in the whole process are taken into account. The linear theory is given and discussed for the HGHG mode. The analytical formula is given for the CHG mode.

Comparative analysis of codon usage bias in Crenarchaea and ...

Indian Academy of Sciences (India)

ending codons even within the WWY (nucleotide ambiguity code) families in Crenarchaea ...... this work. Acknowledgements. Authors thank Mr Ajit Kumar Sahoo and Ms ... November J. A. 2002 Accounting for background nucleotide com-.

The mitochondrial genome sequence of the ciliate Paramecium caudatum reveals a shift in nucleotide composition and codon usage within the genus Paramecium

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Berendonk Thomas U

2011-05-01

Full Text Available Abstract Background Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents are very different between Paramecium tetraurelia and all studied Tetrahymena species. This raises the question of whether the high mitochondrial G+C content observed in P. tetraurelia is a characteristic property of Paramecium mtDNA, or whether it is an exception of the ciliate mitochondrial genomes known so far. To test this question, we determined the mitochondrial genome sequence of Paramecium caudatum and compared the gene content and sequence properties to the closely related P. tetraurelia. Results The guanine + cytosine content of the P. caudatum mitochondrial genome was significantly lower than that of P. tetraurelia (22.4% vs. 41.2%. This difference in the mitochondrial nucleotide composition was accompanied by significantly different codon usage patterns in both species, i.e. within P. caudatum clearly A/T ending codons dominated, whereas for P. tetraurelia the synonymous codons were more balanced with a higher number of G/C ending codons. Further analyses indicated that the nucleotide composition of most members of the genus Paramecium resembles that of P. caudatum and that the shift observed in P. tetraurelia is restricted to the P. aurelia species complex. Conclusions Surprisingly, the codon usage bias in the P. caudatum mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related T. pyriformis and other single-celled eukaryotes such as Chlamydomonas, than to the closely related P. tetraurelia. These differences in base composition and codon usage bias were, however, not reflected in the amino

A Method for Harmonic Sources Detection based on Harmonic Distortion Power Rate

Science.gov (United States)

Lin, Ruixing; Xu, Lin; Zheng, Xian

2018-03-01

Harmonic sources detection at the point of common coupling is an essential step for harmonic contribution determination and harmonic mitigation. The harmonic distortion power rate index is proposed for harmonic source location based on IEEE Std 1459-2010 in the paper. The method only based on harmonic distortion power is not suitable when the background harmonic is large. To solve this problem, a threshold is determined by the prior information, when the harmonic distortion power is larger than the threshold, the customer side is considered as the main harmonic source, otherwise, the utility side is. A simple model of public power system was built in MATLAB/Simulink and field test results of typical harmonic loads verified the effectiveness of proposed method.

Reduction of Harmonics by 18-Pulse Rectifier

Directory of Open Access Journals (Sweden)

Stanislav Kocman

2008-01-01

Full Text Available Operation of such electrical devices as data processing and electronics devices, adjustable speed drives or uninterruptible power supply can cause problems by generating harmonic currents into the network, from which they are supplied. Effects of these harmonic currents are various, they can get worse the quality of supply voltage in the network or to have negative influences on devices connected to this network. There are various technical solutions for reduction of harmonics. One of them is using of multi-pulse rectifiers, whereas the 18-pulse rectifier in the structure of adjustable speed drive is briefly presented in this paper including some results of its behaviour. The examined experimental measurements confirmed its very good efficiency in the harmonic mitigation.

Harmonization versus Mutual Recognition

DEFF Research Database (Denmark)

Jørgensen, Jan Guldager; Schröder, Philipp

The present paper examines trade liberalization driven by the coordination of product standards. For oligopolistic firms situated in separate markets that are initially sheltered by national standards, mutual recognition of standards implies entry and reduced profits at home paired with the oppor......The present paper examines trade liberalization driven by the coordination of product standards. For oligopolistic firms situated in separate markets that are initially sheltered by national standards, mutual recognition of standards implies entry and reduced profits at home paired...... countries and three firms, where firms first lobby for the policy coordination regime (harmonization versus mutual recognition), and subsequently, in case of harmonization, the global standard is auctioned among the firms. We discuss welfare effects and conclude with policy implications. In particular......, harmonized standards may fail to harvest the full pro-competitive effects from trade liberalization compared to mutual recognition; moreover, the issue is most pronounced in markets featuring price competition....

Establishment and comparison of three different codon optimization ...

African Journals Online (AJOL)

C. elegan). It can raise the n-3/n-6 polyunsaturated fatty acids (PUFAs) ratio in mammalian cells. To reveal the impact of different codon optimizations of fat1 gene in influencing the catalysis efficiency of n-6 PUFAs into n-3 PUFAs in mammalian ...

Mapping the Plasticity of the E. coli Genetic Code with Orthogonal Pair Directed Sense Codon Reassignment.

Science.gov (United States)

Schmitt, Margaret A; Biddle, Wil; Fisk, John Domenic

2018-04-18

The relative quantitative importance of the factors that determine the fidelity of translation is largely unknown, which makes predicting the extent to which the degeneracy of the genetic code can be broken challenging. Our strategy of using orthogonal tRNA/aminoacyl tRNA synthetase pairs to precisely direct the incorporation of a single amino acid in response to individual sense and nonsense codons provides a suite of related data with which to examine the plasticity of the code. Each directed sense codon reassignment measurement is an in vivo competition experiment between the introduced orthogonal translation machinery and the natural machinery in E. coli. This report discusses 20 new, related genetic codes, in which a targeted E. coli wobble codon is reassigned to tyrosine utilizing the orthogonal tyrosine tRNA/aminoacyl tRNA synthetase pair from Methanocaldococcus jannaschii. One at a time, reassignment of each targeted sense codon to tyrosine is quantified in cells by measuring the fluorescence of GFP variants in which the essential tyrosine residue is encoded by a non-tyrosine codon. Significantly, every wobble codon analyzed may be partially reassigned with efficiencies ranging from 0.8% to 41%. The accumulation of the suite of data enables a qualitative dissection of the relative importance of the factors affecting the fidelity of translation. While some correlation was observed between sense codon reassignment and either competing endogenous tRNA abundance or changes in aminoacylation efficiency of the altered orthogonal system, no single factor appears to predominately drive translational fidelity. Evaluation of relative cellular fitness in each of the 20 quantitatively-characterized proteome-wide tyrosine substitution systems suggests that at a systems level, E. coli is robust to missense mutations.

Transient erythromycin resistance phenotype associated with peptidyl-tRNA drop-off on early UGG and GGG codons

DEFF Research Database (Denmark)

Macvanin, Mirjana; Gonzalez de Valdivia, Ernesto I; Ardell, David H

2007-01-01

-peptide-encoding sequence, we asked whether the codons UGG and GGG, which are known to promote peptidyl-tRNA drop-off at early positions in mRNA, would result in a phenotype of erythromycin resistance if located after this sequence. We find that UGG or GGG, at either position +4 or +5, without a following stop codon......, is associated with an erythromycin resistance phenotype upon gene induction. Our results suggest that, while a stop codon at +4 gives a tripeptide product (MIL) and erythromycin sensitivity, UGG or GGG codons at the same position give a tetrapeptide product (MILW or MILG) and phenotype of erythromycin...... resistance. Thus, the drop-off event on GGG or UGG codons occurs after incorporation of the corresponding amino acid into the growing peptide chain. Drop-off gives rise to a peptidyl-tRNA where the peptide moiety functionally mimics a minigene peptide product of the type previously associated...

Evaluating codon bias perspective in barbiturase gene using ...

African Journals Online (AJOL)

Abdullah

2014-01-08

Jan 8, 2014 ... along with codon usage was done to reveal dynamics of gene evolution and expression ... analysis is a potent approach for detecting mutations, selection methods and finding rationale of biased and unbiased gene changes and hence, evolutionary ... in the perception of the molecular basics plus potential.

One dimension harmonic oscillator

International Nuclear Information System (INIS)

Cohen-Tannoudji, Claude; Diu, Bernard; Laloe, Franck.

1977-01-01

The importance of harmonic oscillator in classical and quantum physics, eigenvalues and eigenstates of hamiltonian operator are discussed. In complement are presented: study of some physical examples of harmonic oscillators; study of stationnary states in the /x> representation; Hermite polynomials; resolution of eigenvalue equation of harmonic oscillator by polynomial method; isotope harmonic oscillator with three dimensions; charged harmonic oscillator in uniform electric field; quasi classical coherent states of harmonic oscillator; eigenmodes of vibration of two coupled harmonic oscillators; vibration modus of a continuous physical system (application to radiation: photons); vibration modus of indefinite linear chain of coupled harmonic oscillators (phonons); one-dimensional harmonic oscillator in thermodynamic equilibrium at temperature T [fr

The effect of tRNA levels on decoding times of mRNA codons.

Science.gov (United States)

Dana, Alexandra; Tuller, Tamir

2014-08-01

The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (-0.38 to -0.66, all P values decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels

DEFF Research Database (Denmark)

Frenkel-Morgenstern, Milana; Danon, Tamar; Christian, Thomas

2012-01-01

The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons. Moreover, genes encoding proteins that cycle a...

Codon usage determines translation rate in Escherichia coli

DEFF Research Database (Denmark)

Sørensen, Michael Askvad; Kurland, C G; Pedersen, Steen

1989-01-01

We wish to determine whether differences in translation rate are correlated with differences in codon usage or with differences in mRNA secondary structure. We therefore inserted a small DNA fragment in the lacZ gene either directly or flanked by a few frame-shifting bases, leaving the reading fr...

Functional role of bacteriophage transfer RNAs: codon usage analysis of genomic sequences stored in the GENBANK/EMBL/DDBJ databases

Directory of Open Access Journals (Sweden)

T Kunisawa

2006-01-01

Full Text Available Complete genomic sequence data are stored in the public GenBank/EMBL/DDBJ databases so that any investigator can make use of the data. This report describes a comparative analysis of codon usage that is impossible without such a public and open data system. A limited number of bacteriophages harbor their own transfer RNAs. Based on a comparison between T4 phage-encoded tRNA species and the relative cellular amounts of host Escherichia coli tRNAs, it is hypothesized that T4 tRNAs could serve to supplement host isoacceptor tRNA species that are present in minor amounts and thus enhance the translational efficiency of phage proteins. When compared to their respective host bacteria, the codon usage data of bacteriophages D3, φC31, HP1, D29 and 933W all show an increased frequency of synonymous codons or amino acids that correspond to phage tRNA species, suggesting their supplemental role in the efficient production of phage proteins. The data-analysis presents an example in which the availability of an open and fully accessible database system would allow one to obtain comprehensive insights into a fundamental problem in molecular biology.

Operator Arithmetic-Harmonic Mean Inequality on Krein Spaces

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M. Dehghani

2014-03-01

Full Text Available We prove an operator arithmetic-harmonic mean type inequality in Krein space setting, by using some block matrix techniques of indefinite type. We also give an example which shows that the operator arithmetic-geometric-harmonic mean inequality for two invertible selfadjoint operators on Krein spaces is not valid, in general.

Idiosyncratic recognition of UUG/UUA codons by modified nucleoside 5-taurinomethyluridine, τm5U present at 'wobble' position in anticodon loop of tRNALeu: A molecular modeling approach.

Directory of Open Access Journals (Sweden)

Asmita S Kamble

Full Text Available Lack of naturally occurring modified nucleoside 5-taurinomethyluridine (τm5U at the 'wobble' 34th position in tRNALeu causes mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS. The τm5U34 specifically recognizes UUG and UUA codons. Structural consequences of τm5U34 to read cognate codons have not been studied so far in detail at the atomic level. Hence, 50ns multiple molecular dynamics (MD simulations of various anticodon stem loop (ASL models of tRNALeu in presence and absence of τm5U34 along with UUG and UUA codons were performed to explore the dynamic behaviour of τm5U34 during codon recognition process. The MD simulation results revealed that τm5U34 recognizes G/A ending codons by 'wobble' as well as a novel 'single' hydrogen bonding interactions. RMSD and RMSF values indicate the comparative stability of the ASL models containing τm5U34 modification over the other models, lacking τm5U34. Another MD simulation study of 55S mammalian mitochondrial rRNA with tRNALeu showed crucial interactions between the A-site residues, A918, A919, G256 and codon-anticodon bases. Thus, these results could improve our understanding about the decoding efficiency of human mt tRNALeu with τm5U34 to recognize UUG and UUA codons.

Optical Third-Harmonic Generation in Graphene

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Sung-Young Hong

2013-06-01

Full Text Available We report strong third-harmonic generation in monolayer graphene grown by chemical vapor deposition and transferred to an amorphous silica (glass substrate; the photon energy is in three-photon resonance with the exciton-shifted van Hove singularity at the M point of graphene. The polarization selection rules are derived and experimentally verified. In addition, our polarization- and azimuthal-rotation-dependent third-harmonic-generation measurements reveal in-plane isotropy as well as anisotropy between the in-plane and out-of-plane nonlinear optical responses of graphene. Since the third-harmonic signal exceeds that from bulk glass by more than 2 orders of magnitude, the signal contrast permits background-free scanning of graphene and provides insight into the structural properties of graphene.

Static harmonization of dynamically harmonized Fourier transform ion cyclotron resonance cell.

Science.gov (United States)

Zhdanova, Ekaterina; Kostyukevich, Yury; Nikolaev, Eugene

2017-08-01

Static harmonization in the Fourier transform ion cyclotron resonance cell improves the resolving power of the cell and prevents dephasing of the ion cloud in the case of any trajectory of the charged particle, not necessarily axisymmetric cyclotron (as opposed to dynamic harmonization). We reveal that the Fourier transform ion cyclotron resonance cell with dynamic harmonization (paracell) is proved to be statically harmonized. The volume of the statically harmonized potential distribution increases with an increase in the number of trap segments.

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

Science.gov (United States)

Wohlin, Åsa

2015-03-21

The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. Copyright © 2015 The Author. Published by Elsevier Ltd.. All rights reserved.

Abortive translation caused by peptidyl-tRNA drop-off at NGG codons in the early coding region of mRNA

DEFF Research Database (Denmark)

Gonzalez de Valdivia, Ernesto I; Isaksson, Leif A

2005-01-01

In Escherichia coli the codons CGG, AGG, UGG or GGG (NGG codons) but not GGN or GNG (where N is non-G) are associated with low expression of a reporter gene, if located at positions +2 to +5. Induction of a lacZ reporter gene with any one of the NGG codons at position +2 to +5 does not influence......-type or the mutant strain. The inhibitory effect on the pth mutant strain by NGG codons at location +5 was suppressed by overexpression of the Pth enzyme from a plasmid. However, the overexpression of cognate tRNAs for AGG or GGG did not rescue from the growth inhibition associated with these codons early...

Synonymous codon bias and functional constraint on GC3-related DNA backbone dynamics in the prokaryotic nucleoid.

Science.gov (United States)

Babbitt, Gregory A; Alawad, Mohammed A; Schulze, Katharina V; Hudson, André O

2014-01-01

While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (≈GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an 'accessory' during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Twistor Interpretation of Harmonic Spheres and Yang–Mills Fields

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Armen Sergeev

2015-03-01

Full Text Available We consider the twistor descriptions of harmonic maps of the Riemann sphere into Kähler manifolds and Yang–Mills fields on four-dimensional Euclidean space. The motivation to study twistor interpretations of these objects comes from the harmonic spheres conjecture stating the existence of the bijective correspondence between based harmonic spheres in the loop space \\(\\Omega G\\ of a compact Lie group \\(G\\ and the moduli space of Yang–Mills \\(G\\-fields on \\(\\mathbb R^4\\.

Evaluation of Harmonics Impact on Digital Relays

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Kinan Wannous

2018-04-01

Full Text Available This paper presents the concept of the impact of harmonic distortion on a digital protection relay. The aim is to verify and determine the reasons of a mal-trip or failure to trip the protection relays; the suggested solution of the harmonic distortion is explained by a mathematical model in the Matlab Simulink programming environment. The digital relays have been tested under harmonic distortions in order to verify the function of the relays algorithm under abnormal conditions. The comparison between the protection relay algorithm under abnormal conditions and a mathematical model in the Matlab Simulink programming environment based on injected harmonics of high values is provided. The test is separated into different levels; the first level is based on the harmonic effect of an individual harmonic and mixed harmonics. The test includes the effect of the harmonics in the location of the fault point into distance protection zones. This paper is a new proposal in the signal processing of power quality disturbances using Matlab Simulink and the power quality impact on the measurements of the power system quantities; the test simulates the function of protection in power systems in terms of calculating the current and voltage values of short circuits and their faults. The paper includes several tests: frequency variations and decomposition of voltage waveforms with Fourier transforms (model and commercial relay, the effect of the power factor on the location of fault points, the relation between the tripping time and the total harmonic distortion (THD levels in a commercial relay, and a comparison of the THD capture between the commercial relay and the model.

Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates

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Bergthorsson Ulfar

2011-09-01

Full Text Available Abstract Background Duplicated genes frequently experience asymmetric rates of sequence evolution. Relaxed selective constraints and positive selection have both been invoked to explain the observation that one paralog within a gene-duplicate pair exhibits an accelerated rate of sequence evolution. In the majority of studies where asymmetric divergence has been established, there is no indication as to which gene copy, ancestral or derived, is evolving more rapidly. In this study we investigated the effect of local synteny (gene-neighborhood conservation and codon usage on the sequence evolution of gene duplicates in the S. cerevisiae genome. We further distinguish the gene duplicates into those that originated from a whole-genome duplication (WGD event (ohnologs versus small-scale duplications (SSD to determine if there exist any differences in their patterns of sequence evolution. Results For SSD pairs, the derived copy evolves faster than the ancestral copy. However, there is no relationship between rate asymmetry and synteny conservation (ancestral-like versus derived-like in ohnologs. mRNA abundance and optimal codon usage as measured by the CAI is lower in the derived SSD copies relative to ancestral paralogs. Moreover, in the case of ohnologs, the faster-evolving copy has lower CAI and lowered expression. Conclusions Together, these results suggest that relaxation of selection for codon usage and gene expression contribute to rate asymmetry in the evolution of duplicated genes and that in SSD pairs, the relaxation of selection stems from the loss of ancestral regulatory information in the derived copy.

Enhanced resonant second harmonic generation in plasma based on density transition

Directory of Open Access Journals (Sweden)

Kant Niti

2015-06-01

Full Text Available Resonant second harmonic generation of a relativistic self-focusing laser in plasma with density ramp profile has been investigated. A high intense Gaussian laser beam generates resonant second harmonic beam in plasma with density ramp profile. The second harmonic undergoes periodic focusing in the plasma channel created by the fundamental wave. The normalized second harmonic amplitude varies periodically with distance and attains maximum value in the focal region. Enhancement in the second harmonic amplitude on account of relativistic self-focusing of laser based on plasma density transition is seen. Plasma density ramp plays an important role to make self-focusing stronger which leads to enhance the second harmonic generation in plasma.

Identification of the translational start site of codon-optimized mCherry in Mycobacterium tuberculosis

OpenAIRE

Carroll, Paul; Muwanguzi-Karugaba, Julian; Melief, Eduard; Files, Megan; Parish, Tanya

2014-01-01

Background Fluorescent proteins are used widely as reporter genes in many organisms. We previously codon-optimized mCherry for Mycobacterium tuberculosis and generated expression constructs with high level expression in mycobacteria with multiple uses in vitro and in vivo. However, little is known about the expression of fluorescent proteins in mycobacteria and the translational start codon for mCherry has not been experimentally determined. Results We determined the translational start site ...

Demonstration of efficient full-aperture type I/type II third harmonic conversion on Nova

International Nuclear Information System (INIS)

Wegner, P.J.; Henesian, M.A.; Marchi, F.T.; Speck, D.R.

1988-01-01

The ten arms of the Nova laser system readily deliver 22.5 kJ of third harmonic radiation in 1-ns pulses to targets for fusion experiments. Frequency conversion experiments conducted on a single arm have produced >7.5 kJ of 3ω radiation in longer (2.5-ns) pulses at the output of a Nova crystal array with 15 kJ of 1ω drive. Equivalent on-target energies (40-60 kJ) in 2-3-ns pulses is available at target chamber center when the laser disks in the output section of the Nova amplifier are replaced with new high-damage threshold glass. The remaining issue facing frequency conversion on Nova is to demonstrate similar 3-ω energy (>40 kJ) on-target at shorter (1-ns) pulse lengths with controlled pulse shape at 1→ drive energies up to 9 kJ. Frequency conversion to 40 kJ of 3→ with precisely shaped pulses is required for future experiments. The authors assembled a full-aperture (74-cm) array of these crystals to test on an arm outfitted with the new laser glass. Measurements of conversion efficiency, pulse time history, and optical quality of the converted beam are reported

Mutations at the cysteine codons of the recA gene of Escherichia coli

International Nuclear Information System (INIS)

Weisemann, J.M.; Weinstock, G.M.

1988-01-01

Each of the three cysteine residues in the Escherichia coli RecA protein was replaced with a number of other amino acids. To do this, each cysteine codon was first converted to a chain-terminating amber codon by oligonucleotide-directed mutagenesis. These amber mutants were then either assayed for function in different suppressor strains or reverted by a second round of mutagenesis with oligonucleotides that had random sequences at the amber codon. Thirty-three different amino acid substitutions were obtained. Mutants were tested for three functions of RecA: survival following UV irradiation, homologous recombination, and induction of the SOS response. It was found that although none of the cysteines is essential for activity, mutations at each of these positions can affect one or more of the activities of RecA, depending on the particular amino acid substitution. In addition, the cysteine at position 116 appears to be involved in the RecA-promoted cleavage of the LexA protein

HARMONIZED EUROPE OR EUROPEAN HARMONY?

Directory of Open Access Journals (Sweden)

Cosmin Marinescu

2007-07-01

Full Text Available Recent evolutions in Europe raise questions on the viability of the present economic and social model that defines the European construction project. In this paper, the author will try to explain the viability of institutional European model that sticks between free market mechanisms and protectionism. The main challenge for the EU is about the possibility to bring together the institutional convergence and the welfare for all Europeans. This is the result of the view, still dominant, of European politics elite, according to which institutional harmonization is the solution of a more dynamic and prosper Europe. But, economic realities convince us that, more and more, a harmonized, standardized Europe is not necessarily identical with a Europe of harmony and social cooperation. If „development through integration” seems to be harmonization through „institutional transplant”, how could then be the European model one sufficiently wide open to market, which creates the prosperity so long waited for by new member countries?

Comparative studies on codon usage pattern of chloroplasts and ...

Indian Academy of Sciences (India)

Unknown

different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots ... As an important organelle of plants, the chloroplast has its own genomic environment and ... leading to the suggestion that the translation mechanism and patterns of codon usage in ...

Decoding options and accuracy of translation of developmentally regulated UUA codon in Streptomyces: bioinformatic analysis.

Science.gov (United States)

Rokytskyy, Ihor; Koshla, Oksana; Fedorenko, Victor; Ostash, Bohdan

2016-01-01

The gene bldA for leucyl [Formula: see text] is known for almost 30 years as a key regulator of morphogenesis and secondary metabolism in genus Streptomyces. Codon UUA is the rarest one in Streptomyces genomes and is present exclusively in genes with auxiliary functions. Delayed accumulation of translation-competent [Formula: see text] is believed to confine the expression of UUA-containing transcripts to stationary phase. Implicit to the regulatory function of UUA codon is the assumption about high accuracy of its translation, e.g. the latter should not occur in the absence of cognate [Formula: see text]. However, a growing body of facts points to the possibility of mistranslation of UUA-containing transcripts in the bldA-deficient mutants. It is not known what type of near-cognate tRNA(s) may decode UUA in the absence of cognate tRNA in Streptomyces, and whether UUA possesses certain inherent properties (such as increased/decreased accuracy of decoding) that would favor its use for regulatory purposes. Here we took bioinformatic approach to address these questions. We catalogued the entire complement of tRNA genes from several relevant Streptomyces and identified genes for posttranscriptional modifications of tRNA that might be involved in UUA decoding by cognate and near-cognate tRNAs. Based on tRNA gene content in Streptomyces genomes, we propose possible scenarios of UUA codon mistranslation. UUA is not associated with an increased rate of missense errors as compared to other leucyl codons, contrasting general belief that low-abundant codons are more error-prone than the high-abundant ones.

Stop codons in the hepatitis B surface proteins are enriched during antiviral therapy and are associated with host cell apoptosis

International Nuclear Information System (INIS)

Colledge, Danielle; Soppe, Sally; Yuen, Lilly; Selleck, Lucy; Walsh, Renae; Locarnini, Stephen; Warner, Nadia

2017-01-01

Premature stop codons in the hepatitis B virus (HBV) surface protein can be associated with nucleos(t)ide analogue resistance due to overlap of the HBV surface and polymerase genes. The aim of this study was to determine the effect of the replication of three common surface stop codon variants on the hepatocyte. Cell lines were transfected with infectious HBV clones encoding surface stop codons rtM204I/sW196*, rtA181T/sW172*, rtV191I/sW182*, and a panel of substitutions in the surface proteins. HBsAg was measured by Western blotting. Proliferation and apoptosis were measured using flow cytometry. All three surface stop codon variants were defective in HBsAg secretion. Cells transfected with these variants were less proliferative and had higher levels of apoptosis than those transfected with variants that did not encode surface stop codons. The most cytopathic variant was rtM204I/sW196*. Replication of HBV encoding surface stop codons was toxic to the cell and promoted apoptosis, exacerbating disease progression. - Highlights: •Under normal circumstances, HBV replication is not cytopathic. •Premature stop codons in the HBV surface protein can be selected and enriched during nucleos(t)ide analogue therapy. •Replication of these variants can be cytopathic to the cell and promote apoptosis. •Inadequate antiviral therapy may actually promote disease progression.

Stop codons in the hepatitis B surface proteins are enriched during antiviral therapy and are associated with host cell apoptosis

Energy Technology Data Exchange (ETDEWEB)

Colledge, Danielle; Soppe, Sally; Yuen, Lilly; Selleck, Lucy; Walsh, Renae; Locarnini, Stephen, E-mail: stephen.locarnini@mh.org.au; Warner, Nadia

2017-01-15

Premature stop codons in the hepatitis B virus (HBV) surface protein can be associated with nucleos(t)ide analogue resistance due to overlap of the HBV surface and polymerase genes. The aim of this study was to determine the effect of the replication of three common surface stop codon variants on the hepatocyte. Cell lines were transfected with infectious HBV clones encoding surface stop codons rtM204I/sW196*, rtA181T/sW172*, rtV191I/sW182*, and a panel of substitutions in the surface proteins. HBsAg was measured by Western blotting. Proliferation and apoptosis were measured using flow cytometry. All three surface stop codon variants were defective in HBsAg secretion. Cells transfected with these variants were less proliferative and had higher levels of apoptosis than those transfected with variants that did not encode surface stop codons. The most cytopathic variant was rtM204I/sW196*. Replication of HBV encoding surface stop codons was toxic to the cell and promoted apoptosis, exacerbating disease progression. - Highlights: •Under normal circumstances, HBV replication is not cytopathic. •Premature stop codons in the HBV surface protein can be selected and enriched during nucleos(t)ide analogue therapy. •Replication of these variants can be cytopathic to the cell and promote apoptosis. •Inadequate antiviral therapy may actually promote disease progression.

Gene composer: database software for protein construct design, codon engineering, and gene synthesis.

Science.gov (United States)

Lorimer, Don; Raymond, Amy; Walchli, John; Mixon, Mark; Barrow, Adrienne; Wallace, Ellen; Grice, Rena; Burgin, Alex; Stewart, Lance

2009-04-21

To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease

PCR-RFLP to Detect Codon 248 Mutation in Exon 7 of "p53" Tumor Suppressor Gene

Science.gov (United States)

Ouyang, Liming; Ge, Chongtao; Wu, Haizhen; Li, Suxia; Zhang, Huizhan

2009-01-01

Individual genome DNA was extracted fast from oral swab and followed up with PCR specific for codon 248 of "p53" tumor suppressor gene. "Msp"I restriction mapping showed the G-C mutation in codon 248, which closely relates to cancer susceptibility. Students learn the concepts, detection techniques, and research significance of point mutations or…

ARTIFICIAL INTELLIGENT SYSTEM FOR MEASUREMENT OF HARMONIC POWERS

Directory of Open Access Journals (Sweden)

Jovitha Jerome

2017-11-01

Full Text Available The importance of the electric power quality (PQ demands new methodologies and measurement tools in the power industry for the analysis and measurement of the basic electric magnitudes necessary. This paper presents a new measurement procedure based on neural networks for the estimation of harmonic amplitudes of current/voltage and respective harmonic powers. The measurement scheme is built with two neural network modules. The first module is an adaptive linear neuron (ADALINE that is the kernel part of estimation of complex harmonic coefficients of the current/voltage. The second module is feedforward neural network that obtains the harmonic active/reactive powers. In order to perform digital simulation the Feedforward and Adaline neural network tools were developed in LabVIEW. This measurement algorithm was tested for the practical cases and found to be robust, computationally fast and efficient.

Voltage Harmonics Mitigation through Hybrid Active Power Filter

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Anwer Ali Sahito

2016-01-01

Full Text Available Fast dynamic response, high efficiency, low cost and small size of power electronic converters have exponentially increased their use in modern power system which resulted in harmonically distorted voltage and currents. Voltage harmonics mainly caused by current harmonics are more dangerous as performance and expected operating life of other power system equipment are affected by harmonically distorted supply voltage. Electronic filter circuits are used to improve system power quality by mitigating adverse effects of harmonics. Hybrid filters having advantages of both passive and active filters are preferred to resolve the problem of harmonics efficiently and avoiding any chance of resonance. In this paper, a three phase three wire network is considered to supply an adjustable speed drive represented by a resistive load connected across a three phase bridge rectifier. Simulation of the considered system shows THD (Total Harmonic Distortion of 18.91 and 7.61% in supply current and voltage respectively. A HAPF (Hybrid Active Power Filter is proposed to reduce these THD values below 5% as recommended by IEEE Standard-519. P-Q theorem is used to calculate required parameters for proposed filter, which is implemented through hysteresis control. Simulation results confirm the effectiveness of the designed filter as THD for both current and voltage have reduced below allowable limit of 5%.

CodonTest: modeling amino acid substitution preferences in coding sequences.

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Wayne Delport

2010-08-01

Full Text Available Codon models of evolution have facilitated the interpretation of selective forces operating on genomes. These models, however, assume a single rate of non-synonymous substitution irrespective of the nature of amino acids being exchanged. Recent developments have shown that models which allow for amino acid pairs to have independent rates of substitution offer improved fit over single rate models. However, these approaches have been limited by the necessity for large alignments in their estimation. An alternative approach is to assume that substitution rates between amino acid pairs can be subdivided into rate classes, dependent on the information content of the alignment. However, given the combinatorially large number of such models, an efficient model search strategy is needed. Here we develop a Genetic Algorithm (GA method for the estimation of such models. A GA is used to assign amino acid substitution pairs to a series of rate classes, where is estimated from the alignment. Other parameters of the phylogenetic Markov model, including substitution rates, character frequencies and branch lengths are estimated using standard maximum likelihood optimization procedures. We apply the GA to empirical alignments and show improved model fit over existing models of codon evolution. Our results suggest that current models are poor approximations of protein evolution and thus gene and organism specific multi-rate models that incorporate amino acid substitution biases are preferred. We further anticipate that the clustering of amino acid substitution rates into classes will be biologically informative, such that genes with similar functions exhibit similar clustering, and hence this clustering will be useful for the evolutionary fingerprinting of genes.

Harmonics and energy management

International Nuclear Information System (INIS)

Andresen, M.

1993-01-01

To summarize what this paper has presented: Voltage and current non-sinusoidal wave shapes exist in our power system. These harmonics result from the prolific use of non-linear loads. The use of these types of loads is increasing dramatically, partly due to the push to implement energy management techniques involving harmonic generating equipment. Harmonic analysis can identify specific harmonics, their frequency, magnitude, and phase shift referenced to the fundamental. Harmonic distortion forces the use of true RMS multimeters for measurement accuracy. High levels of neutral current and N-G voltages are now possible. Transformers may overheat and fail even though they are below rated capacity. Low power factors due to harmonics cannot be corrected by the installation of capacitors, and knowledge of the fundamental VARs or the displacement power factor is needed to use capacitors alone for power factor correction. The harmonic related problems presented are by no means an exhaustive list. Many other concerns arise when harmonics are involved in the power system. The critical issue behind these problems is that many of the devices being recommended from an energy management point of view are contributing to the harmonic levels, and thus to the potential for harmonic problems. We can no longer live in the sinusoidal mentality if we are to be effective in saving energy and reducing costs

Insight into pattern of codon biasness and nucleotide base usage in serotonin receptor gene family from different mammalian species.

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Dass, J Febin Prabhu; Sudandiradoss, C

2012-07-15

5-HT (5-Hydroxy-tryptamine) or serotonin receptors are found both in central and peripheral nervous system as well as in non-neuronal tissues. In the animal and human nervous system, serotonin produces various functional effects through a variety of membrane bound receptors. In this study, we focus on 5-HT receptor family from different mammals and examined the factors that account for codon and nucleotide usage variation. A total of 110 homologous coding sequences from 11 different mammalian species were analyzed using relative synonymous codon usage (RSCU), correspondence analysis (COA) and hierarchical cluster analysis together with nucleotide base usage frequency of chemically similar amino acid codons. The mean effective number of codon (ENc) value of 37.06 for 5-HT(6) shows very high codon bias within the family and may be due to high selective translational efficiency. The COA and Spearman's rank correlation reveals that the nucleotide compositional mutation bias as the major factors influencing the codon usage in serotonin receptor genes. The hierarchical cluster analysis suggests that gene function is another dominant factor that affects the codon usage bias, while species is a minor factor. Nucleotide base usage was reported using Goldman, Engelman, Stietz (GES) scale reveals the presence of high uracil (>45%) content at functionally important hydrophobic regions. Our in silico approach will certainly help for further investigations on critical inference on evolution, structure, function and gene expression aspects of 5-HT receptors family which are potential antipsychotic drug targets. Copyright © 2012 Elsevier B.V. All rights reserved.

Codon optimisation to improve expression of a Mycobacterium avium ssp. paratuberculosis-specific membrane-associated antigen by Lactobacillus salivarius.

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Johnston, Christopher; Douarre, Pierre E; Soulimane, Tewfik; Pletzer, Daniel; Weingart, Helge; MacSharry, John; Coffey, Aidan; Sleator, Roy D; O'Mahony, Jim

2013-06-01

Subunit and DNA-based vaccines against Mycobacterium avium ssp. paratuberculosis (MAP) attempt to overcome inherent issues associated with whole-cell formulations. However, these vaccines can be hampered by poor expression of recombinant antigens from a number of disparate hosts. The high G+C content of MAP invariably leads to a codon bias throughout gene expression. To investigate if the codon bias affects recombinant MAP antigen expression, the open reading frame of a MAP-specific antigen MptD (MAP3733c) was codon optimised for expression against a Lactobacillus salivarius host. Of the total 209 codons which constitute MAP3733c, 172 were modified resulting in a reduced G+C content from 61% for the native gene to 32.7% for the modified form. Both genes were placed under the transcriptional control of the PnisA promoter; allowing controlled heterologous expression in L. salivarius. Expression was monitored using fluorescence microscopy and microplate fluorometry via GFP tags translationally fused to the C-termini of the two MptD genes. A > 37-fold increase in expression was observed for the codon-optimised MAP3733synth variant over the native gene. Due to the low cost and improved expression achieved, codon optimisation significantly improves the potential of L. salivarius as an oral vaccine stratagem against Johne's disease. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects.

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Selva Kumar, C; Nair, Rahul R; Sivaramakrishnan, K G; Ganesh, D; Janarthanan, S; Arunachalam, M; Sivaruban, T

2012-12-01

Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages.

Effect of DNA sequence of Fab fragment on yield characteristics and cell growth of E. coli.

Science.gov (United States)

Kulmala, Antti; Huovinen, Tuomas; Lamminmäki, Urpo

2017-06-19

Codon usage is one of the factors influencing recombinant protein expression. We were interested in the codon usage of an antibody Fab fragment gene exhibiting extreme toxicity in the E. coli host. The toxic synthetic human Fab gene contained domains optimized by the "one amino acid-one codon" method. We redesigned five segments of the Fab gene with a "codon harmonization" method described by Angov et al. and studied the effects of these changes on cell viability, Fab yield and display on filamentous phage using different vectors and bacterial strains. The harmonization considerably reduced toxicity, increased Fab expression from negligible levels to 10 mg/l, and restored the display on phage. Testing the impact of the individual redesigned segments revealed that the most significant effects were conferred by changes in the constant domain of the light chain. For some of the Fab gene variants, we also observed striking differences in protein yields when cloned from a chloramphenicol resistant vector into an identical vector, except with ampicillin resistance. In conclusion, our results show that the expression of a heterodimeric secretory protein can be improved by harmonizing selected DNA segments by synonymous codons and reveal additional complexity involved in heterologous protein expression.

Harmonics rejection in pixelated interferograms using spatio-temporal demodulation.

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Padilla, J M; Servin, M; Estrada, J C

2011-09-26

Pixelated phase-mask interferograms have become an industry standard in spatial phase-shifting interferometry. These pixelated interferograms allow full wavefront encoding using a single interferogram. This allows the study of fast dynamic events in hostile mechanical environments. Recently an error-free demodulation method for ideal pixelated interferograms was proposed. However, non-ideal conditions in interferometry may arise due to non-linear response of the CCD camera, multiple light paths in the interferometer, etc. These conditions generate non-sinusoidal fringes containing harmonics which degrade the phase estimation. Here we show that two-dimensional Fourier demodulation of pixelated interferograms rejects most harmonics except the complex ones at {-3(rd), +5(th), -7(th), +9(th), -11(th),…}. We propose temporal phase-shifting to remove these remaining harmonics. In particular, a 2-step phase-shifting algorithm is used to eliminate the -3(rd) and +5(th) complex harmonics, while a 3-step one is used to remove the -3(rd), +5harmonics. © 2011 Optical Society of America

Variational Integrals of a Class of Nonhomogeneous -Harmonic Equations

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Guanfeng Li

2014-01-01

Full Text Available We introduce a class of variational integrals whose Euler equations are nonhomogeneous -harmonic equations. We investigate the relationship between the minimization problem and the Euler equation and give a simple proof of the existence of some nonhomogeneous -harmonic equations by applying direct methods of the calculus of variations. Besides, we establish some interesting results on variational integrals.

Atto second high harmonic sources

International Nuclear Information System (INIS)

Nam, Chang Hee

2008-01-01

High harmonic generation is a powerful method to produce attosecond pulses. The high harmonics, emitted from atoms driven by intense femtosecond laser pulses, can from an attosecond pulse train with equally spaced harmonic spectrum or an isolated single attosecond pulse with broad continuum spectrum. Using high power femtosecond laser technology developed at CXRC, we have investigated the spectral and temporal characteristics of high harmonics obtained from gaseous atoms. The spectral structure of harmonics could be manipulated by controlling laser chirp, and continuous tuning of harmonic wavelengths was achieved. For rigorous temporal characterization of attosecond harmonic pulses a cross correlation technique was applied to the photoionization process by harmonic and IR femtosecond pulses and achieved the complete temporal reconstruction of attosecond pulse trains, revealing the detailed temporal structure of the attosecond chirp by material dispersion. The duration of attosecond high harmonic pulses is usually much longer than that of transform limited pulses due to the inherent chirp originating from the harmonic generation process. The attosecond chirp compensation in the harmonic generation medium itself was demonstrated, thereby realizing the generation of near transform limited attosecond pulses. The interference of attosecond electron wave packets, generated from an atom by attosecond harmonic pulses, will be also presented

The Harmonization of Accounting

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Hajnal Noémi

2017-11-01

Full Text Available The development and configuration of the regulatory framework of the accounting systems in Romania and Hungary took place in different ways. Among the reasons for the diversities in these countries’ accounting systems, the following can be certainly mentioned: different purposes of taxation, legal structure, the accountancy’s connection with the corporate law and family law, diversification on corporate financing policy, and cultural heterogeneity. Both countries quickly caught up with the international accounting harmonization standards. The adaptation of the international accounting standards has many advantages and disadvantages; these have been discussed in several previous researches. This paper aims at comparing the Romanian and Hungarian states’ accounting regulations from the early 1990s, which were implemented in order to harmonize the states’ accountancy regulations with the international standards, and their impact on the economy, based on secondary analysis.

Effects of low harmonics on tone identification in natural and vocoded speech.

Science.gov (United States)

Liu, Chang; Azimi, Behnam; Tahmina, Qudsia; Hu, Yi

2012-11-01

This study investigated the contribution of low-frequency harmonics to identifying Mandarin tones in natural and vocoded speech in quiet and noisy conditions. Results showed that low-frequency harmonics of natural speech led to highly accurate tone identification; however, for vocoded speech, low-frequency harmonics yielded lower tone identification than stimuli with full harmonics, except for tone 4. Analysis of the correlation between tone accuracy and the amplitude-F0 correlation index suggested that "more" speech contents (i.e., more harmonics) did not necessarily yield better tone recognition for vocoded speech, especially when the amplitude contour of the signals did not co-vary with the F0 contour.

Genomic composition factors affect codon usage in porcine genome

African Journals Online (AJOL)

j.khobondo

2015-01-28

Jan 28, 2015 ... The mutational bias hypothesis predicted that genes in the GC-rich regions of the genome ... observed codon divided by its expected frequency at equilibrium. An RSCU value close to 1 indicates lack of bias, ..... study our results points to preferred usage of both C or G and A or T at the synonyms sites as ...

Quantization of a 3D Nonstationary Harmonic plus an Inverse Harmonic Potential System

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Salim Medjber

2016-01-01

Full Text Available The Schrödinger solutions for a three-dimensional central potential system whose Hamiltonian is composed of a time-dependent harmonic plus an inverse harmonic potential are investigated. Because of the time-dependence of parameters, we cannot solve the Schrödinger solutions relying only on the conventional method of separation of variables. To overcome this difficulty, special mathematical methods, which are the invariant operator method, the unitary transformation method, and the Nikiforov-Uvarov method, are used when we derive solutions of the Schrödinger equation for the system. In particular, the Nikiforov-Uvarov method with an appropriate coordinate transformation enabled us to reduce the eigenvalue equation of the invariant operator, which is a second-order differential equation, to a hypergeometric-type equation that is convenient to treat. Through this procedure, we derived exact Schrödinger solutions (wave functions of the system. It is confirmed that the wave functions are represented in terms of time-dependent radial functions, spherical harmonics, and general time-varying global phases. Such wave functions are useful for studying various quantum properties of the system. As an example, the uncertainty relations for position and momentum are derived by taking advantage of the wave functions.

Codon Optimization Significantly Improves the Expression Level of α-Amylase Gene from Bacillus licheniformis in Pichia pastoris

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Jian-Rong Wang

2015-01-01

Full Text Available α-Amylase as an important industrial enzyme has been widely used in starch processing, detergent, and paper industries. To improve expression efficiency of recombinant α-amylase from Bacillus licheniformis (B. licheniformis, the α-amylase gene from B. licheniformis was optimized according to the codon usage of Pichia pastoris (P. pastoris and expressed in P. pastoris. Totally, the codons encoding 305 amino acids were optimized in which a total of 328 nucleotides were changed and the G+C content was increased from 47.6 to 49.2%. The recombinants were cultured in 96-deep-well microplates and screened by a new plate assay method. Compared with the wild-type gene, the optimized gene is expressed at a significantly higher level in P. pastoris after methanol induction for 168 h in 5- and 50-L bioreactor with the maximum activity of 8100 and 11000 U/mL, which was 2.31- and 2.62-fold higher than that by wild-type gene. The improved expression level makes the enzyme a good candidate for α-amylase production in industrial use.

High-order harmonic generation in solid slabs beyond the single-active-electron approximation

Science.gov (United States)

Hansen, Kenneth K.; Deffge, Tobias; Bauer, Dieter

2017-11-01

High-harmonic generation by a laser-driven solid slab is simulated using time-dependent density functional theory. Multiple harmonic plateaus up to very high harmonic orders are observed already at surprisingly low field strengths. The full all-electron harmonic spectra are, in general, very different from those of any individual Kohn-Sham orbital. Freezing the Kohn-Sham potential instead is found to be a good approximation for the laser intensities and harmonic orders considered. The origins of the plateau cutoffs are explained in terms of band gaps that can be reached by Kohn-Sham electrons and holes moving through the band structure.

Genetic and codon usage bias analyses of polymerase genes of equine influenza virus and its relation to evolution.

Science.gov (United States)

Bera, Bidhan Ch; Virmani, Nitin; Kumar, Naveen; Anand, Taruna; Pavulraj, S; Rash, Adam; Elton, Debra; Rash, Nicola; Bhatia, Sandeep; Sood, Richa; Singh, Raj Kumar; Tripathi, Bhupendra Nath

2017-08-23

Equine influenza is a major health problem of equines worldwide. The polymerase genes of influenza virus have key roles in virus replication, transcription, transmission between hosts and pathogenesis. Hence, the comprehensive genetic and codon usage bias of polymerase genes of equine influenza virus (EIV) were analyzed to elucidate the genetic and evolutionary relationships in a novel perspective. The group - specific consensus amino acid substitutions were identified in all polymerase genes of EIVs that led to divergence of EIVs into various clades. The consistent amino acid changes were also detected in the Florida clade 2 EIVs circulating in Europe and Asia since 2007. To study the codon usage patterns, a total of 281,324 codons of polymerase genes of EIV H3N8 isolates from 1963 to 2015 were systemically analyzed. The polymerase genes of EIVs exhibit a weak codon usage bias. The ENc-GC3s and Neutrality plots indicated that natural selection is the major influencing factor of codon usage bias, and that the impact of mutation pressure is comparatively minor. The methods for estimating host imposed translation pressure suggested that the polymerase acidic (PA) gene seems to be under less translational pressure compared to polymerase basic 1 (PB1) and polymerase basic 2 (PB2) genes. The multivariate statistical analysis of polymerase genes divided EIVs into four evolutionary diverged clusters - Pre-divergent, Eurasian, Florida sub-lineage 1 and 2. Various lineage specific amino acid substitutions observed in all polymerase genes of EIVs and especially, clade 2 EIVs underwent major variations which led to the emergence of a phylogenetically distinct group of EIVs originating from Richmond/1/07. The codon usage bias was low in all the polymerase genes of EIVs that was influenced by the multiple factors such as the nucleotide compositions, mutation pressure, aromaticity and hydropathicity. However, natural selection was the major influencing factor in defining the

Codon bias and gene ontology in holometabolous and hemimetabolous insects.

Science.gov (United States)

Carlini, David B; Makowski, Matthew

2015-12-01

The relationship between preferred codon use (PCU), developmental mode, and gene ontology (GO) was investigated in a sample of nine insect species with sequenced genomes. These species were selected to represent two distinct modes of insect development, holometabolism and hemimetabolism, with an aim toward determining whether the differences in developmental timing concomitant with developmental mode would be mirrored by differences in PCU in their developmental genes. We hypothesized that the developmental genes of holometabolous insects should be under greater selective pressure for efficient translation, manifest as increased PCU, than those of hemimetabolous insects because holometabolism requires abundant protein expression over shorter time intervals than hemimetabolism, where proteins are required more uniformly in time. Preferred codon sets were defined for each species, from which the frequency of PCU for each gene was obtained. Although there were substantial differences in the genomic base composition of holometabolous and hemimetabolous insects, both groups exhibited a general preference for GC-ending codons, with the former group having higher PCU averaged across all genes. For each species, the biological process GO term for each gene was assigned that of its Drosophila homolog(s), and PCU was calculated for each GO term category. The top two GO term categories for PCU enrichment in the holometabolous insects were anatomical structure development and cell differentiation. The increased PCU in the developmental genes of holometabolous insects may reflect a general strategy to maximize the protein production of genes expressed in bursts over short time periods, e.g., heat shock proteins. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 686-698, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Essentiality, conservation, evolutionary pressure and codon bias in bacterial genomes.

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Dilucca, Maddalena; Cimini, Giulio; Giansanti, Andrea

2018-07-15

Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than on genes that are either nonessential or peculiar to a single or a few species. In order to further assess this expectation, we study here how essentiality of a gene is connected with its degree of conservation among several unrelated bacterial species, each one characterised by its own codon usage bias. Confirming previous results on E. coli, we show the existence of a universal exponential relation between gene essentiality and conservation in bacteria. Moreover, we show that, within each bacterial genome, there are at least two groups of functionally distinct genes, characterised by different levels of conservation and codon bias: i) a core of essential genes, mainly related to cellular information processing; ii) a set of less conserved nonessential genes with prevalent functions related to metabolism. In particular, the genes in the first group are more retained among species, are subject to a stronger purifying conservative selection and display a more limited repertoire of synonymous codons. The core of essential genes is close to the minimal bacterial genome, which is in the focus of recent studies in synthetic biology, though we confirm that orthologs of genes that are essential in one species are not necessarily essential in other species. We also list a set of highly shared genes which, reasonably, could constitute a reservoir of targets for new anti-microbial drugs. Copyright © 2018 Elsevier B.V. All rights reserved.

Measurements of Voltage Harmonics in 400 kV Transmission Network

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Ryszard Pawełek

2014-06-01

Full Text Available The paper deals with the analysis of voltage harmonics measurements performed in the 400 kV transmission network. The voltage was measured by means of three transducers: resistive voltage divider, inductive measuring transformer and capacitive voltage measuring transformer. Instrument errors were estimated for measuring transformers with reference to the harmonic values obtained from the voltage divider.

Tax competition and tax harmonization in the European Union

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Danuše Nerudová

2004-01-01

Full Text Available The article deals with the problems of tax competition and harmonization within the European Union. It reveals the single difficulties connected with harmonization, identifies the problems arising from tax competition and points out the harmful tax competition as well. Single compulsory harmonized tax base in connection with prevailing tax competition in the area of tax rates is the suggested solution in the scope of direct taxation. As the solution in the area of indirect taxation could serve the introduction of “principle of origin”. This would cause remarkable administrative costs decrease not only for economic subjects but for tax authorities as well.

Prion protein gene analysis in three kindreds with fatal familial insomnia (FFI): Codon 178 mutation and codon 129 polymorphism

Energy Technology Data Exchange (ETDEWEB)

Medori, R.; Tritschler, H.J. (Universita di Bologna (Italy))

1993-10-01

Fatal familial insomnia (FFI) is a disease linked to a GAC(Asp) [yields] AAC(Asn) mutation in codon 178 of the prion protein (PrP) gene. FFI is characterized clinically by untreatable progressive insomnia, dysautonomia, and motor dysfunctions and is characterized pathologically by selective thalamic atrophy. The authors confirmed the 178[sup Asn] mutation in the PrP gene of a third FFI family of French ancestry. Three family members who are under 40 years of age and who inherited the mutation showed only reduced perfusion in the basal ganglia on single photon emission computerized tomography. Some FFI features differ from the clinical and neuropathologic findings associated with 178[sup Asn] reported elsewhere. However, additional intragenic mutations accounting for the phenotypic differences were not observed in two affected individuals. In other sporadic and familial forms of Creutzfeldt-Jakob disease and Gerstmann-Straeussler syndrome, Met or Val homozygosity at polymorphic codon 129 is associated with a more severe phenotype, younger age at onset, and faster progression. In FFI, young and old individuals at disease onset had 129[sup Met/Val]. Moreover, of five 178[sup Asn] individuals who are above age-at-onset range and who are well, two have 129[sup Met] and three have 129[sup Met/Val], suggesting that polymorphic site 129 does not modulate FFI phenotypic expression. Genetic heterogeneity and environment may play an important role in inter- and intrafamilial variability of the 178[sup Asn] mutation. 32 refs., 5 figs., 1 tab.

Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions.

Science.gov (United States)

Subramanian, Abhishek; Sarkar, Ram Rup

2015-10-01

Understanding the variations in gene organization and its effect on the phenotype across different Leishmania species, and to study differential clinical manifestations of parasite within the host, we performed large scale analysis of codon usage patterns between Leishmania and other known Trypanosomatid species. We present the causes and consequences of codon usage bias in Leishmania genomes with respect to mutational pressure, translational selection and amino acid composition bias. We establish GC bias at wobble position that governs codon usage bias across Leishmania species, rather than amino acid composition bias. We found that, within Leishmania, homogenous codon context coding for less frequent amino acid pairs and codons avoiding formation of folding structures in mRNA are essentially chosen. We predicted putative differences in global expression between genes belonging to specific pathways across Leishmania. This explains the role of evolution in shaping the otherwise conserved genome to demonstrate species-specific function-level differences for efficient survival. Copyright © 2015 Elsevier Inc. All rights reserved.

The Tax harmonization in open regionalism ; The European model

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Mouloud MELIKAOUI

2014-06-01

Full Text Available This research examines the subject of alternative regionalism or open regionalism and reality within the multilateral trading system, based on growing liberalization of trade, and the problem of compatibility between them, as well as the limits of economic policy harmonization in the framework of Open regionalism, special tax harmonization, in the light of economic and tax disparities of the Member States, with an overview of the European tax harmonization and limits. The Study concluded the importance of tax harmonization as a tool by activation of the concept of open regionalism, through facilitating capitals flows and investments between member states and reduction of the négatives phenomena of tax. It recommended the need to emphasizing on the importance of gradually harmonization for tax policy, and expand the rule of tax treaties and exchange of tax information and experiences between countries, This is in light a holistic approach to other economic policies as a the exchange rate policy and monetary policy, just as is the case in the European model.

Fractional high-harmonic combs by attosecond-precision split-spectrum pulse control

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Laux Martin

2013-03-01

Full Text Available Few-cycle laser fields enable pulse-shaping control of high-order harmonic generation by time delaying variable broadband spectral sections. We report the experimental generation of fractional (noninteger high-harmonic combs by the controlled interference of two attosecond pulse trains. Additionally the energy of the high harmonics is strongly tuned with the relative time delay. We quantify the tuning to directly result from the controlled variation of the instantaneous laser frequency at the shaped driver pulse intensity maximum.

Harmonic operation of high gain harmonic generation free electron laser

International Nuclear Information System (INIS)

Deng Haixiao; Chinese Academy of Sciences, Beijing; Dai Zhimin

2008-01-01

In high gain harmonic generation (HGHG) free electron laser (FEL), with the right choice of parameters of the modulator undulator, the dispersive section and the seed laser, one may make the spatial bunching of the electron beam density distribution correspond to one of the harmonic frequencies of the radiator radiation, instead of the fundamental frequency of the radiator radiation in conventional HGHG, thus the radiator undulator is in harmonic operation (HO) mode. In this paper, we investigate HO of HGHG FEL. Theoretical analyses with universal method are derived and numerical simulations in ultraviolet and deep ultraviolet spectral regions are given. It shows that the power of the 3rd harmonic radiation in the HO of HGHG may be as high as 18.5% of the fundamental power level. Thus HO of HGHG FEL may obtain short wavelength by using lower beam energy. (authors)

Fighting African Capital Flight: Empirics on Benchmarking Policy Harmonization

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Simplice A. Asongu

2014-06-01

Full Text Available With earthshaking and heartbreaking trends in African capital flight provided by a new database, this paper complements existing literature by answering some key policy questions on the feasibility of and timeframe for policy harmonization in the battle against the economic scourge. The goal of the paper is to study beta-convergence of capital flight across a set of 37 African countries in the period 1980-2010 and to discuss the policy implications. Three main findings are established. (1 African countries with low capital flight rates are catching-up their counterparts with higher rates, implying the feasibility ofpolicy harmonization towards fighting capital flight. (2 Petroleum-exporting and conflict-affected countries significantly play out in absolute and conditional convergences respectively. (3 Regardless of fundamental characteristics, a genuine timeframe for harmonizing policies is within a horizon of 6 to 13 years. Inother words, full (100% convergence within the specifiedhorizon is an indication that policies and regulations can be enforced without distinction of nationality or locality.

Single nucleotide polymorphisms of Helicobacter pylori dupA that lead to premature stop codons.

Science.gov (United States)

Moura, Sílvia B; Costa, Rafaella F A; Anacleto, Charles; Rocha, Gifone A; Rocha, Andreia M C; Queiroz, Dulciene M M

2012-06-01

 The detection of the putative disease-specific Helicobacter pylori marker duodenal ulcer promoting gene A (dupA) is currently based on PCR detection of jhp0917 and jhp0918 that form the gene. However, mutations that lead to premature stop codons that split off the dupA leading to truncated products cannot be evaluated by PCR. We directly sequence the complete dupA of 75 dupA-positive strains of H. pylori isolated from patients with gastritis (n = 26), duodenal ulcer (n = 29), and gastric carcinoma (n = 20), to search for frame-shifting mutations that lead to stop codon. Thirty-four strains had single nucleotide mutations in dupA that lead to premature stop codon creating smaller products than the predicted 1839 bp product and, for this reason, were considered as dupA-negative. Intact dupA was more frequently observed in strains isolated from duodenal ulcer patients (65.5%) than in patients with gastritis only (46.2%) or with gastric carcinoma (50%). In logistic analysis, the presence of the intact dupA independently associated with duodenal ulcer (OR = 5.06; 95% CI = 1.22-20.96, p = .02).  We propose the primer walking methodology as a simple technique to sequence the gene. When we considered as dupA-positive only those strains that carry dupA gene without premature stop codons, the gene was associated with duodenal ulcer and, therefore, can be used as a marker for this disease in our population. © 2012 Blackwell Publishing Ltd.

General Lp-harmonic Blaschke bodies

Indian Academy of Sciences (India)

Lutwak introduced the harmonic Blaschke combination and the harmonic Blaschke body of a star body. Further, Feng and Wang introduced the concept of the -harmonic Blaschke body of a star body. In this paper, we define the notion of general -harmonic Blaschke bodies and establish some of its properties.

Harmonic Analyzing of the Double PWM Converter in DFIG Based on Mathematical Model

Directory of Open Access Journals (Sweden)

Jing Liu

2017-12-01

Full Text Available Harmonic pollution of double fed induction generators (DFIGs has become a vital concern for its undesirable effects on power quality issues of wind generation systems and grid-connected system, and the double pulse width modulation (PWMconverter is one of the main harmonic sources in DFIGs. Thus the harmonic analysis of the converter in DFIGs is a necessary step to evaluate their harmonic pollution of DFIGs. This paper proposes a detailed harmonic modeling method to discuss the main harmonic components in a converter. In general the harmonic modeling could be divided into the low-order harmonic part (up to 30th order and the high-order harmonic part (greater than order 30 parts in general. The low-order harmonics are produced by the circuit topology and control algorithm, and the harmonic component will be different if the control strategy changes. The high-order harmonics are produced by the modulation of the switching function to the dc variable. In this paper, the low-order harmonic modeling is established according to the directions of power flow under the vector control (VC, and the high-order harmonic modeling is established by the switching function of space vector PWM and dc currents. Meanwhile, the simulations of harmonic a components in a converter are accomplished in a real time digital simulation system. The results indicate that the proposed modeling could effectively show the harmonics distribution of the converter in DFIGs.

Three types of preS1 start codon deletion variants in the natural course of chronic hepatitis B infection.

Science.gov (United States)

Choe, Won Hyeok; Kim, Hong; Lee, So-Young; Choi, Yu-Min; Kwon, So Young; Moon, Hee Won; Hur, Mina; Kim, Bum-Joon

2017-12-12

Naturally occurring hepatitis B virus variants carrying a deletion in the preS1 start codon region may evolve during long-lasting virus-host interactions in chronic hepatitis B (CHB). The aim of this study was to determine the immune phase-specific prevalent patterns of preS1 start codon deletion variants and related factors during the natural course of CHB. A total of 399 CHB patients were enrolled. Genotypic analysis of three different preS1 start codon deletion variants (classified by deletion size: 15-base pair [bp], 18-bp, and 21-bp deletion variants) was performed. PreS1 start codon deletion variants were detected in 155 of 399 patients (38.8%). The predominant variant was a 15-bp deletion in the immune-tolerance phase (18/50, 36%) and an 18-bp deletion in the immune-clearance phase (69/183, 37.7%). A 21-bp deletion was the predominant variant in the low replicative phase (3/25, 12.0%) and reactivated hepatitis Be antigen (HBeAg)-negative phase (22/141, 15.6%). The 15-bp and 18-bp deletion variants were more frequently found in HBeAg-positive patients (P start codon deletion variants changes according to the immune phases of CHB infection, and each variant type is associated with different clinical parameters. PreS1 start codon deletion variants might interact with the host immune response differently according to their variant types. © 2017 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Pulse Splitting for Harmonic Beamforming in Time-Modulated Linear Arrays

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Lorenzo Poli

2014-01-01

Full Text Available A novel strategy for harmonic beamforming in time-modulated linear arrays is proposed. The pulse splitting technique is exploited to simultaneously generate two harmonic patterns, one at the central frequency and another at a preselected harmonic of arbitrary order, while controlling the maximum level of the remaining sideband radiations. An optimization strategy based on the particle swarm optimizer is developed in order to determine the optimal parameters describing the pulse sequence used to modulate the excitation weights of the array elements. Representative numerical results are reported and discussed to point out potentialities and limitations of the proposed approach.

RESEARCH ON THE INTERNATIONAL ACCOUNTING HARMONIZATION PROCESS

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Tatiana Danescu

2016-12-01

Full Text Available During the last decades, the need of harmonization of the financial reporting frameworks has become more acute, mostly because the capital markets are not restricted anymore by country borders and capital movement has outlined the phenomenon of globalization and internationalism. A significant step in harmonizing the financial reporting was done in the process of normalization through different sets of rules and principles, recognized and applied in many states are the International Financial Reporting Standards (IFRS. The process of international recognition of these standards continues along with conceptual development which is based on epistemological research on specific markets, industries, economies open to international capital flows. In this context it becomes of interest to identify and understand generally accepted and applied accounting elements which carry forward the accounting harmonization process along with factors and circumstances that create diversity in nationally applied financial reporting frameworks.

Two-harmonic complex spectral-domain optical coherence tomography using achromatic sinusoidal phase modulation

Science.gov (United States)

Lu, Sheng-Hua; Huang, Siang-Ru; Chou, Che-Chung

2018-03-01

We resolve the complex conjugate ambiguity in spectral-domain optical coherence tomography (SD-OCT) by using achromatic two-harmonic method. Unlike previous researches, the optical phase of the fiber interferometer is modulated by an achromatic phase shifter based on an optical delay line. The achromatic phase modulation leads to a wavelength-independent scaling coefficient for the two harmonics. Dividing the mean absolute value of the first harmonic by that of the second harmonic in a B-scan interferogram directly gives the scaling coefficient. It greatly simplifies the determination of the magnitude ratio between the two harmonics without the need of third harmonic and cumbersome iterative calculations. The inverse fast Fourier transform of the complex-valued interferogram constructed with the scaling coefficient, first and second harmonics yields a full-range OCT image. Experimental results confirm the effectiveness of the proposed achromatic two-harmonic technique for suppressing the mirror artifacts in SD-OCT images.

Design of PR current control with selective harmonic compensators using Matlab

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Daniel Zammit

2017-12-01

Full Text Available This paper presents a procedure to design a Proportional Resonant (PR current controller with additional PR selective harmonic compensators for Grid Connected Photovoltaic (PV Inverters. The design of the PR current control and the harmonic compensators will be carried out using Matlab. Testing was carried out on a 3 kW Grid-Connected PV Inverter which was designed and constructed for this research. Both simulation and experimental results will be presented. Keywords: Inverters, Proportional-resonant controllers, Harmonic compensation, Photovoltaic, Matlab, SISO design tool

ACCOUNTING HARMONIZATION AND HISTORICAL COST ACCOUNTING

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Valentin Gabriel CRISTEA

2017-05-01

Full Text Available There is a huge interest in accounting harmonization and historical costs accounting, in what they offer us. In this article, different valuation models are discussed. Although one notices the movement from historical cost accounting to fair value accounting, each one has its advantages.

General Lp-harmonic Blaschke bodies

Indian Academy of Sciences (India)

Abstract. Lutwak introduced the harmonic Blaschke combination and the harmonic. Blaschke body of a star body. Further, Feng and Wang introduced the concept of the L p- harmonic Blaschke body of a star body. In this paper, we define the notion of general. L p-harmonic Blaschke bodies and establish some of its ...

Tail-extension following the termination codon is critical for release of the nascent chain from membrane-bound ribosomes in a reticulocyte lysate cell-free system.

Science.gov (United States)

Takahara, Michiyo; Sakaue, Haruka; Onishi, Yukiko; Yamagishi, Marifu; Kida, Yuichiro; Sakaguchi, Masao

2013-01-11

Nascent chain release from membrane-bound ribosomes by the termination codon was investigated using a cell-free translation system from rabbit supplemented with rough microsomal membrane vesicles. Chain release was extremely slow when mRNA ended with only the termination codon. Tail extension after the termination codon enhanced the release of the nascent chain. Release reached plateau levels with tail extension of 10 bases. This requirement was observed with all termination codons: TAA, TGA and TAG. Rapid release was also achieved by puromycin even in the absence of the extension. Efficient translation termination cannot be achieved in the presence of only a termination codon on the mRNA. Tail extension might be required for correct positioning of the termination codon in the ribosome and/or efficient recognition by release factors. Copyright © 2012. Published by Elsevier Inc.

Philosophical Presentation in Ptolemy’s Harmonics: The Timaeus as a Model for Organization

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Cristian Tolsa

2015-08-01

Full Text Available Ptolemy’s self-representation as philosopher is conventional in the Almagest but not so in Harmonics, which emulates Plato’s Timaeus and makes philosophy the result  of understanding harmonics rather than the premise.

Means of Harmonization in Religious Discourse

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Irina Ščukina

2012-12-01

Full Text Available Means of harmonization of religious discourse are considered by studying communicational behaviour (verbal and nonverbal between the religion institution and believers. The following factors defining specificity of realization of harmonization in Orthodox and other religious texts are taken into account: the communication channel between the author and the reader, a defining speech genre, the command of language (communication code, and extra-linguistic factors. It is shown that sharing the general social, historical and national experience, as well as a lexical overlapping of actors on both sides of the communication channel are the deciding elements of the harmonization process. The analysis also shows that usage of rational argumentation is more likely to lead to harmonisation in comparison to other rhetoric tools (i. e. affective ones or story-telling. Rational and unemotional sermonic discourse is perceived as a sign of respect (namely, for the listener's intelligence. Another successful and much-applied way seems to be evoking a feeling of equality, unity and/or identity between clerics and their flocks.

Harmonic Analysis on Torque Ripple of Brushless DC Motor Based on Advanced Commutation Control

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Yanpeng Ji

2018-01-01

Full Text Available This paper investigates the relationship between current, back electromotive force (back-EMF, and torque for permanent-magnet brushless DC (PM BLDC motors under advanced commutation control from the perspective of harmonics. Considering that the phase current is the influencing factor of both torque and torque ripple, this paper firstly analyzes the effects of advanced commutation on phase current and current harmonics. And then, based on the harmonics of the phase current and back-EMF, the torque harmonic expressions are deduced. The expressions reveal the relationship of harmonic order between the torque, phase current, and back-EMF and highlight the different contribution of individual torque harmonic to the total torque ripple. Finally, the proposed harmonic analysis method is verified by the experiments with different speed and load conditions.

Second-harmonic generation in second-harmonic fiber Bragg gratings.

Science.gov (United States)

Steel, M J; de Sterke, C M

1996-06-20

We consider the production of second-harmonic light in gratings resonant with the generated field, through a Green's function approach. We recover some standard results and obtain new limits for the uniform grating case. With the extension to nonuniform gratings, we find the Green's function for the second harmonic in a grating with an arbitrary phase shift at some point. We then obtain closed form approximate expressions for the generated light for phase shifts close to π/2 and at the center of the grating. Finally, comparing the uniform and phase-shifted gratings with homogeneous materials, we discuss the enhancement in generated light and the bandwidth over which it occurs, and the consequences for second-harmonic generation in optical fiber Bragg gratings.

Harmonic lasing in x-ray free electron lasers

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E. A. Schneidmiller

2012-08-01

Full Text Available Harmonic lasing in a free electron laser with a planar undulator (under the condition that the fundamental frequency is suppressed might be a cheap and efficient way of extension of wavelength ranges of existing and planned x-ray free electron laser (FEL facilities. Contrary to nonlinear harmonic generation, harmonic lasing can provide much more intense, stable, and narrow-band FEL beam which is easier to handle due to the suppressed fundamental frequency. In this paper we perform a parametrization of the solution of the eigenvalue equation for lasing at odd harmonics, and present an explicit expression for FEL gain length, taking into account all essential effects. We propose and discuss methods for suppression of the fundamental harmonic. We also suggest a combined use of harmonic lasing and lasing at the retuned fundamental wavelength in order to reduce bandwidth and to increase brilliance of x-ray beam at saturation. Considering 3rd harmonic lasing as a practical example, we come to the conclusion that it is much more robust than usually thought, and can be widely used in the existing or planned x-ray FEL (XFEL facilities. In particular, Linac Coherent Light Source (LCLS after a minor modification can lase to saturation at the 3rd harmonic up to the photon energy of 25–30 keV providing multigigawatt power level and narrow bandwidth. As for the European XFEL, harmonic lasing would allow one to extend operating range (ultimately up to 100 keV, to reduce FEL bandwidth and to increase brilliance, to enable two-color operation for pump-probe experiments, and to provide more flexible operation at different electron energies. Similar improvements can be realized in other x-ray FEL facilities with gap-tunable undulators like FLASH II, SACLA, LCLS II, etc. Harmonic lasing can be an attractive option for compact x-ray FELs (driven by electron beams with a relatively low energy, allowing the use of the standard undulator technology instead of

Harmonic Interaction Analysis in Grid Connected Converter using Harmonic State Space (HSS) Modeling

DEFF Research Database (Denmark)

Kwon, Jun Bum; Wang, Xiongfei; Bak, Claus Leth

2015-01-01

-model, are introduced to analyze these problems. However, it is found that Linear Time Invariant (LTI) base model analysis makes it difficult to analyze these phenomenon because of time varying system operation trajectories, varying output impedance seen by grid connected systems and neglected switching component......An increasing number of power electronics based Distributed Generation (DG) systems and loads generate coupled harmonic as well as non-characteristic harmonic with each other. Several methods like impedance based analysis, which is derived from conventional small signal- and average...... during the modeling process. This paper investigates grid connected converter by means of Harmonic State Space (HSS) small signal model, which is modeled from Linear Time varying Periodically (LTP) system. Further, a grid connected converter harmonic matrix is investigated to analyze the harmonic...

A Miniaturize Bandpass Filter with Harmonic Suppression Using Meandered Quarter-Wavelength Resonators

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Yun-Long Lu

2014-01-01

Full Text Available A miniaturized bandpass filter with harmonics suppression is presented. The proposed filter consists of two quarter-wavelength microstrip resonators, which are meandered for circuit size reduction. An interdigital capacitor, loading at zero-voltage point, is employed to provide the desired coupling between the resonators at operating frequency, whereas the coupling coefficient at the third harmonic is realized to be zero. Besides, the second and fourth harmonics are suppressed since λ/4 resonators are adopted. Benefiting from these properties, a miniaturized bandpass filter with the second, third, and fourth harmonics suppression was designed and implemented. The final measured and simulated results show good consistence with the theoretical counterparts.

Preferences of AAA/AAG codon recognition by modified nucleosides, τm5s2U34 and t6A37 present in tRNALys.

Science.gov (United States)

Sonawane, Kailas D; Kamble, Asmita S; Fandilolu, Prayagraj M

2017-12-27

Deficiency of 5-taurinomethyl-2-thiouridine, τm 5 s 2 U at the 34th 'wobble' position in tRNA Lys causes MERRF (Myoclonic Epilepsy with Ragged Red Fibers), a neuromuscular disease. This modified nucleoside of mt tRNA Lys , recognizes AAA/AAG codons during protein biosynthesis process. Its preference to identify cognate codons has not been studied at the atomic level. Hence, multiple MD simulations of various molecular models of anticodon stem loop (ASL) of mt tRNA Lys in presence and absence of τm 5 s 2 U 34 and N 6 -threonylcarbamoyl adenosine (t 6 A 37 ) along with AAA and AAG codons have been accomplished. Additional four MD simulations of multiple ASL mt tRNA Lys models in the context of ribosomal A-site residues have also been performed to investigate the role of A-site in recognition of AAA/AAG codons. MD simulation results show that, ASL models in presence of τm 5 s 2 U 34 and t 6 A 37 with codons AAA/AAG are more stable than the ASL lacking these modified bases. MD trajectories suggest that τm 5 s 2 U recognizes the codons initially by 'wobble' hydrogen bonding interactions, and then tRNA Lys might leave the explicit codon by a novel 'single' hydrogen bonding interaction in order to run the protein biosynthesis process smoothly. We propose this model as the 'Foot-Step Model' for codon recognition, in which the single hydrogen bond plays a crucial role. MD simulation results suggest that, tRNA Lys with τm 5 s 2 U and t 6 A recognizes AAA codon more preferably than AAG. Thus, these results reveal the consequences of τm 5 s 2 U and t 6 A in recognition of AAA/AAG codons in mitochondrial disease, MERRF.

Efficient Coproduction of Mannanase and Cellulase by the Transformation of a Codon-Optimized Endomannanase Gene from Aspergillus niger into Trichoderma reesei.

Science.gov (United States)

Sun, Xianhua; Xue, Xianli; Li, Mengzhu; Gao, Fei; Hao, Zhenzhen; Huang, Huoqing; Luo, Huiying; Qin, Lina; Yao, Bin; Su, Xiaoyun

2017-12-20

Cellulase and mannanase are both important enzyme additives in animal feeds. Expressing the two enzymes simultaneously within one microbial host could potentially lead to cost reductions in the feeding of animals. For this purpose, we codon-optimized the Aspergillus niger Man5A gene to the codon-usage bias of Trichoderma reesei. By comparing the free energies and the local structures of the nucleotide sequences, one optimized sequence was finally selected and transformed into the T. reesei pyridine-auxotrophic strain TU-6. The codon-optimized gene was expressed to a higher level than the original one. Further expressing the codon-optimized gene in a mutated T. reesei strain through fed-batch cultivation resulted in coproduction of cellulase and mannanase up to 1376 U·mL -1 and 1204 U·mL -1 , respectively.

Orthogonal Projection-Based Harmonic Signal Removal for Operational Modal Analysis

DEFF Research Database (Denmark)

Gres, Szymon; Andersen, Palle; Hoen, C.

2019-01-01

A presence of a high amplitude periodic signals in the output responses from operating structures often pose a challenge for output-only system identification and, in case of health monitoring, damage detection/localization methods. This paper introduces a pre-processing approach that removes...... the harmonic part from the output signals directly in the time domain. The new method uses orthogonal projections of the harmonic realization of the signal onto the raw time series within the stochastic subspace framework. Proposed algorithm is tested on two experimental examples. First, an aluminum plate...... excited with both random white and periodic excitations. Second, a full-scale industrial case of a ferry excited by a random environmental load with harmonic interference from a rotating machinery on-board. In both cases the proposed method removes the harmonics from the structural responses while leaving...

Input Harmonic Analysis on the Slim DC-Link Drive Using Harmonic State Space Model

DEFF Research Database (Denmark)

Yang, Feng; Kwon, Jun Bum; Wang, Xiongfei

2017-01-01

The harmonic performance of the slim dc-link adjustable speed drives has shown good performance in some studies but poor in some others. The contradiction indicates that a feasible theoretical analysis is still lacking to characterize the harmonic distortion for the slim dc-link drive. Considerin...... results of the slim dc-link drive, loaded up to 2.0 kW, are presented to validate the theoretical analysis....... variation according to the switching instant, the harmonics at the steady-state condition, as well as the coupling between the multiple harmonic impedances. By using this model, the impaction on the harmonics performance by the film capacitor and the grid inductance is derived. Simulation and experimental...

Improved production of membrane proteins in Escherichia coli by selective codon substitutions

DEFF Research Database (Denmark)

Nørholm, Morten H.H.; Toddo, Stephen; Virkki, Minttu T.I.

2013-01-01

Membrane proteins are extremely challenging to produce in sufficient quantities for biochemical and structural analysis and there is a growing demand for solutions to this problem. In this study we attempted to improve expression of two difficult-to-express coding sequences (araH and narK) for me......Membrane proteins are extremely challenging to produce in sufficient quantities for biochemical and structural analysis and there is a growing demand for solutions to this problem. In this study we attempted to improve expression of two difficult-to-express coding sequences (araH and nar......K) for membrane transporters. For both coding sequences, synonymous codon substitutions in the region adjacent to the AUG start led to significant improvements in expression, whereas multi-parameter sequence optimization of codons throughout the coding sequence failed. We conclude that coding sequences can be re...

Maximum likelihood estimation of ancestral codon usage bias parameters in Drosophila

DEFF Research Database (Denmark)

Nielsen, Rasmus; Bauer DuMont, Vanessa L; Hubisz, Melissa J

2007-01-01

: the selection coefficient for optimal codon usage (S), allowing joint maximum likelihood estimation of S and the dN/dS ratio. We apply the method to previously published data from Drosophila melanogaster, Drosophila simulans, and Drosophila yakuba and show, in accordance with previous results, that the D...

Frequency chirp of harmonic and attosecond pulses

International Nuclear Information System (INIS)

Varju, K.; Johansson, P; L'Huillier, A.L.; Mairesse, Y.; Salieres, P.

2005-01-01

Full text: We have explored in detail the first- and second-order variations of the atomic phase as a function of the laser intensity and harmonic order. This unravels the similitudes and differences existing between the chirp of individual harmonic pulses and the chirp of the attosecond pulses. We show that the two techniques XFROG and RABITT used to characterize the two chirps (respectively) converge to give the same information, namely the values of the mixed partial derivatives of the atomic phase. This underlines the common physical origin of all these phenomena and provides a unified frame for their description and understanding. Ref. 1 (author)

Comparison study among conventional, tissue harmonic and pulse inversion harmonic images to evaluate pleural effusion and ascites

International Nuclear Information System (INIS)

Chung, Hwan Hoon; Kim, Yun Hwan; Kang, Chang Ho; Park, Bum Jin; Chung, Kyoo Byung; Suh, Won Hyuck

2000-01-01

To determine the most useful sonographic technique to evaluate pleural effusion and ascites by comparing conventional, tissue harmonic and pulse inversion harmonic images. 12 patients having pleural effusion and 14 patients having ascites were included in this study. 18 patients were male and 8 patients were female. Average age was 54.8 yrs (25-77). We compared images which had been taken at the same section with 3 above mentioned sonographic techniques. Evaluation was done by 3 radiologists in consensus and grades were given to 3 techniques from 1 to 3. Evaluating points were 1) normal structures that border the fluid such as liver, peritoneal lining, pleura, 2) septation in fluid, 3) debris floating in fluid, and 4) artifacts. Pulse inversion harmonic image was the best in image quality for normal structures, followed by tissue harmonic and conventional image (p<0.05). Pulse inversion harmonic image was better than conventional image to evaluate septation in fluid (p<0.05), but there were no statistically significant difference between pulse inversion and tissue harmonic images, and tissue harmonic and conventional images. Tissue harmonic image was better than pulse inversion harmonic and conventional images to evaluate debris floating in fluid (p<0.05) but there was no statistically significant difference between these two latter techniques. Artifacts were most prominent on conventional image followed by tissue harmonic and pulse inversion harmonic image (p<0.05). Pulse inversion harmonic image was the best sonographic technique to evaluate pleural effusion or ascites, However, Tissue harmonic image was the best for evaluation of debris.

Comparison study among conventional, tissue harmonic and pulse inversion harmonic images to evaluate pleural effusion and ascites

Energy Technology Data Exchange (ETDEWEB)

Chung, Hwan Hoon; Kim, Yun Hwan; Kang, Chang Ho; Park, Bum Jin; Chung, Kyoo Byung; Suh, Won Hyuck [Korea University College of Medicine, Seoul (Korea, Republic of)

2000-12-15

To determine the most useful sonographic technique to evaluate pleural effusion and ascites by comparing conventional, tissue harmonic and pulse inversion harmonic images. 12 patients having pleural effusion and 14 patients having ascites were included in this study. 18 patients were male and 8 patients were female. Average age was 54.8 yrs (25-77). We compared images which had been taken at the same section with 3 above mentioned sonographic techniques. Evaluation was done by 3 radiologists in consensus and grades were given to 3 techniques from 1 to 3. Evaluating points were 1) normal structures that border the fluid such as liver, peritoneal lining, pleura, 2) septation in fluid, 3) debris floating in fluid, and 4) artifacts. Pulse inversion harmonic image was the best in image quality for normal structures, followed by tissue harmonic and conventional image (p<0.05). Pulse inversion harmonic image was better than conventional image to evaluate septation in fluid (p<0.05), but there were no statistically significant difference between pulse inversion and tissue harmonic images, and tissue harmonic and conventional images. Tissue harmonic image was better than pulse inversion harmonic and conventional images to evaluate debris floating in fluid (p<0.05) but there was no statistically significant difference between these two latter techniques. Artifacts were most prominent on conventional image followed by tissue harmonic and pulse inversion harmonic image (p<0.05). Pulse inversion harmonic image was the best sonographic technique to evaluate pleural effusion or ascites, However, Tissue harmonic image was the best for evaluation of debris.

An environmental signature for 323 microbial genomes based on codon adaptation indices

DEFF Research Database (Denmark)

Willenbrock, Hanni; Friis, Carsten; Juncker, Agnieszka

2006-01-01

, we show that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle, for instance soil bacteria and soil symbionts, spore formers, enteric bacteria, aquatic bacteria, and intercellular and extracellular pathogens. Conclusion...

Absolute in vivo translation rates of individual codons in Escherichia coli: The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate

DEFF Research Database (Denmark)

Sørensen, M.A.; Pedersen, Steen

1991-01-01

We have determined the absolute translation rates for four individual codons in Escherichia coli. We used our previously described system for direct measurements of in vivo translation rates using small, in-frame inserts in the lacZ gene. The inserts consisted of multiple synthetic 30 base-pair D...

Thrombosis in Hb Taybe [codons 38/39 (-ACC) (α1)

DEFF Research Database (Denmark)

Juul, Maja Bech; Vestergaard, Hanne; Petersen, Jesper

2012-01-01

Hb Taybe is a highly unstable hemoglobin (Hb) variant caused by a 3 bp deletion at codons 38/39 (-ACC) on the α1-globin gene. We report for the first time, a patient with a compound heterozygosity for Hb Taybe and a 5 bp deletion at the splice donor site of IVS-I on the α2-globin gene and ischemic...

Prophylactic thyroidectomy for asymptomatic 3-year-old boy with positive multiple endocrine neoplasia type 2A mutation (codon 634

Directory of Open Access Journals (Sweden)

Ješić Maja D.

2014-01-01

Full Text Available Introduction. The multiple endocrine neoplasia type 2A (MEN 2A syndrome, comprising medullary thyroid carcinoma (MTC, pheochromocytoma and primary hyperparathyroidism (PHPT is most frequently caused by codon 634 activating mutations of the RET (rearranged during transfection proto-oncogene on chromosome 10. For this codon-mutation carriers, earlier thyroidectomy (before the age of 5 years would be advantageous in limiting the potential for the development of MTC as well as parathyroid adenomas. Case Outline. This is a case report of 3-year-old boy from the MEN 2A family (the boy’s father and grandmother and paternal aunt in which cysteine substitutes for phenylalanine at codon 634 in exon 11 of the RET proto-oncogene, who underwent thyroidectomy solely on the basis of genetic information. A boy had no thyromegaly, thyroidal irregularities or lymphadenopathy and no abnormality on the neck ultrasound examination. The pathology finding of thyroid gland was negative for MTC. Two years after total thyroidectomy, 5-year-old boy is healthy with permanent thyroxine replacement. His serum calcitonin level is <2 pg/ml (normal <13 pg/ml, has normal serum calcium and parathyroid hormone levels and negative urinary catecholamines. Long-term follow-up of this patient is required to determine whether very early thyroidectomy improves the long-term outcome of PHPT. Conclusion. Children with familial antecedents of MEN 2A should be genetically studied for the purpose of determining the risk of MTC and assessing the possibilities of making prophylactic thyroidectomy before the age of 5 years.

Propagation effects in the generation process of high-order vortex harmonics.

Science.gov (United States)

Zhang, Chaojin; Wu, Erheng; Gu, Mingliang; Liu, Chengpu

2017-09-04

We numerically study the propagation of a Laguerre-Gaussian beam through polar molecular media via the exact solution of full-wave Maxwell-Bloch equations where the rotating-wave and slowly-varying-envelope approximations are not included. It is found that beyond the coexistence of odd-order and even-order vortex harmonics due to inversion asymmetry of the system, the light propagation effect results in the intensity enhancement of a high-order vortex harmonics. Moreover, the orbital momentum successfully transfers from the fundamental laser driver to the vortex harmonics which topological charger number is directly proportional to its order.

Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius.

Science.gov (United States)

Johnston, Christopher D; Bannantine, John P; Govender, Rodney; Endersen, Lorraine; Pletzer, Daniel; Weingart, Helge; Coffey, Aidan; O'Mahony, Jim; Sleator, Roy D

2014-01-01

It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease.

Research on Harmonic Characteristics Influence for Distribution Network with Renewable Energy

Directory of Open Access Journals (Sweden)

Huang Wei

2016-01-01

Full Text Available In order to study the influence on harmonic characteristics of distribution network with renewable energy, a simplified model of distribution network is established to analyse theory while considering the influence of cable on the system capacitive current. Establishing an actual distribution network model by Digsilent to research the harmonic characteristics impact when photovoltaic power with PV incorporated the distribution network in a variety of different access , while using constant current source model as harmonic source model which often been used in engineering practices. The simulation results show that: optimizing the access location and dispersion of PV can decrease the waveform distortion levels in distribution network and a certain number of high-order harmonic will magnify by a specific grid structure, deteriorating the distribution network power quality.

The harmonization of banking legislation in the EU

Directory of Open Access Journals (Sweden)

Shkëlqesa Çitaku

2016-03-01

Full Text Available This paper attempts to assess the current legislation of banking in the European Union. The process of unification in Europe is also followed by efforts to harmonize and unify the laws of the member states. In the field of banking industry the precondition for harmonization of laws is the integration of internal market with the free movement of capital. The regulation and supervision of banks in EU still remains fragmented. European member states still have diverse regulations concerning the role of the state. The European Commission has the important function of proposing EU legislation on financial services including banks and ensuring that EU law is properly applied throughout the EU. Banks are considered as a key industry enabling all the economic activities via depositing, crediting and arranging of payments. A number of secondary legislation has been adopted by the EU institutions to harmonize the national banking law of Member States. The principles and objectives set by the European Commission Treaty depend on four EU freedoms with the aim of effective and open market including banks. Therefore it was a continuous process of harmonization of national banking regulation via secondary law since the 70’s.

A Framework to Analyze the Stochastic Harmonics and Resonance of Wind Energy Grid Interconnection

Directory of Open Access Journals (Sweden)

Youngho Cho

2016-08-01

Full Text Available This paper addresses a modeling and analysis methodology for investigating the stochastic harmonics and resonance concerns of wind power plants (WPPs. Wideband harmonics from modern wind turbines (WTs are observed to be stochastic, associated with real power production, and they may adversely interact with the grid impedance and cause unexpected harmonic resonance, if not comprehensively addressed in the planning and commissioning of the WPPs. These issues should become more critical as wind penetration levels increase. We thus propose a planning study framework comprising the following functional steps: First, the best fitted probability density functions (PDFs of the harmonic components of interest in the frequency domain are determined. In operations planning, maximum likelihood estimations (MLEs followed by a chi-square test are used once field measurements or manufacturers’ data are available. Second, harmonic currents from the WPP are represented by randomly-generating harmonic components based on their PDFs (frequency spectrum and then synthesized for time domain simulations via inverse Fourier transform. Finally, we conduct a comprehensive assessment by including the impacts of feeder configurations, harmonic filters and the variability of parameters. We demonstrate the efficacy of the proposed study approach for a 100-MW offshore WPP consisting of 20 units of 5-MW full converter turbines, a realistic benchmark system adapted from a WPP under development in Korea and discuss lessons learned through this research.

Fine-tuning translation kinetics selection as the driving force of codon usage bias in the hepatitis A virus capsid.

Science.gov (United States)

Aragonès, Lluís; Guix, Susana; Ribes, Enric; Bosch, Albert; Pintó, Rosa M

2010-03-05

Hepatitis A virus (HAV), the prototype of genus Hepatovirus, has several unique biological characteristics that distinguish it from other members of the Picornaviridae family. Among these, the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synthesis by a mechanism similar to that of other picornaviruses. Consequently, HAV must inefficiently compete for the cellular translational machinery and this may explain its poor growth in cell culture. In this context of virus/cell competition, HAV has strategically adopted a naturally highly deoptimized codon usage with respect to that of its cellular host. With the aim to optimize its codon usage the virus was adapted to propagate in cells with impaired protein synthesis, in order to make tRNA pools more available for the virus. A significant loss of fitness was the immediate response to the adaptation process that was, however, later on recovered and more associated to a re-deoptimization rather than to an optimization of the codon usage specifically in the capsid coding region. These results exclude translation selection and instead suggest fine-tuning translation kinetics selection as the underlying mechanism of the codon usage bias in this specific genome region. Additionally, the results provide clear evidence of the Red Queen dynamics of evolution since the virus has very much evolved to re-adapt its codon usage to the environmental cellular changing conditions in order to recover the original fitness.

Characterization of Variant Creutzfeldt-Jakob Disease Prions in Prion Protein-humanized Mice Carrying Distinct Codon 129 Genotypes*

Science.gov (United States)

Takeuchi, Atsuko; Kobayashi, Atsushi; Ironside, James W.; Mohri, Shirou; Kitamoto, Tetsuyuki

2013-01-01

To date, all clinical variant Creutzfeldt-Jakob disease (vCJD) patients are homozygous for methionine at polymorphic codon 129 (129M/M) of the prion protein (PrP) gene. However, the appearance of asymptomatic secondary vCJD infection in individuals with a PRNP codon 129 genotype other than M/M and transmission studies using animal models have raised the concern that all humans might be susceptible to vCJD prions, especially via secondary infection. To reevaluate this possibility and to analyze in detail the transmission properties of vCJD prions to transgenic animals carrying distinct codon 129 genotype, we performed intracerebral inoculation of vCJD prions to humanized knock-in mice carrying all possible codon 129 genotypes (129M/M, 129M/V, or 129V/V). All humanized knock-in mouse lines were susceptible to vCJD infection, although the attack rate gradually decreased from 129M/M to 129M/V and to 129V/V. The amount of PrP deposition including florid/amyloid plaques in the brain also gradually decreased from 129M/M to 129M/V and to 129V/V. The biochemical properties of protease-resistant abnormal PrP in the brain and transmissibility of these humanized mouse-passaged vCJD prions upon subpassage into knock-in mice expressing bovine PrP were not affected by the codon 129 genotype. These results indicate that individuals with the 129V/V genotype may be more susceptible to secondary vCJD infection than expected and may lack the neuropathological characteristics observed in vCJD patients with the 129M/M genotype. Besides the molecular typing of protease-resistant PrP in the brain, transmission studies using knock-in mice carrying bovine PrP may aid the differential diagnosis of secondary vCJD infection, especially in individuals with the 129V/V genotype. PMID:23792955

Characterization of variant Creutzfeldt-Jakob disease prions in prion protein-humanized mice carrying distinct codon 129 genotypes.

Science.gov (United States)

Takeuchi, Atsuko; Kobayashi, Atsushi; Ironside, James W; Mohri, Shirou; Kitamoto, Tetsuyuki

2013-07-26

To date, all clinical variant Creutzfeldt-Jakob disease (vCJD) patients are homozygous for methionine at polymorphic codon 129 (129M/M) of the prion protein (PrP) gene. However, the appearance of asymptomatic secondary vCJD infection in individuals with a PRNP codon 129 genotype other than M/M and transmission studies using animal models have raised the concern that all humans might be susceptible to vCJD prions, especially via secondary infection. To reevaluate this possibility and to analyze in detail the transmission properties of vCJD prions to transgenic animals carrying distinct codon 129 genotype, we performed intracerebral inoculation of vCJD prions to humanized knock-in mice carrying all possible codon 129 genotypes (129M/M, 129M/V, or 129V/V). All humanized knock-in mouse lines were susceptible to vCJD infection, although the attack rate gradually decreased from 129M/M to 129M/V and to 129V/V. The amount of PrP deposition including florid/amyloid plaques in the brain also gradually decreased from 129M/M to 129M/V and to 129V/V. The biochemical properties of protease-resistant abnormal PrP in the brain and transmissibility of these humanized mouse-passaged vCJD prions upon subpassage into knock-in mice expressing bovine PrP were not affected by the codon 129 genotype. These results indicate that individuals with the 129V/V genotype may be more susceptible to secondary vCJD infection than expected and may lack the neuropathological characteristics observed in vCJD patients with the 129M/M genotype. Besides the molecular typing of protease-resistant PrP in the brain, transmission studies using knock-in mice carrying bovine PrP may aid the differential diagnosis of secondary vCJD infection, especially in individuals with the 129V/V genotype.

Harmonic Patterns in Forex Trading

OpenAIRE

Nemček, Sebastian

2013-01-01

This diploma thesis is committed to examination of validity of Harmonic Patterns in Forex trading. Scott Carney described existing and introduced new Harmonic Patterns in 1999 in his book Harmonic Trader. These patterns use the Fibonacci principle to analyze price action and to provide both bullish and bearish trading signals. The goal of this thesis is to find out whether harmonic trading strategy on selected pairs is profitable in FX market, which patterns are the most profitable and what i...

Synthesis of Variable Harmonic Impedance in Inverter-Interfaced Distributed Generation Unit for Harmonic Damping Throughout a Distribution Network

DEFF Research Database (Denmark)

Wang, Xiongfei; Blaabjerg, Frede; Chen, Zhe

2012-01-01

This paper proposes a harmonic impedance synthesis technique for voltage-controlled distributed generation inverters in order to damp harmonic voltage distortion on a distribution network. The approach employs a multiloop control scheme, where a selective harmonic load current feedforward loop...... at the dominant harmonic frequencies. Thus, the harmonic voltage drop on the grid-side inductance and the harmonic resonances throughout a distribution feeder with multiple shunt-connected capacitors can be effectively attenuated. Simulation and laboratory test results validate the performance of the proposed...

Tuvan throat singing and harmonics

Science.gov (United States)

Ruiz, Michael J.; Wilken, David

2018-05-01

Tuvan throat singing, also called overtone singing, provides for an exotic demonstration of the physics of harmonics as well as introducing an Asian musical aesthetic. A low fundamental is sung and the singer skillfully alters the resonances of the vocal system to enhance an overtone (harmonic above the fundamental). The result is that the listener hears two pitches simultaneously. Harmonics such as H8, H9, H10, and H12 form part of a pentatonic scale and are commonly selected for melody tones by Tuvan singers. A real-time spectrogram is provided in a video (Ruiz M J 2018 Video: Tuvan Throat Singing and Harmonics http://mjtruiz.com/ped/tuva/) so that Tuvan harmonics can be visualized as they are heard.

Design of 12-phase, 2-stage Harmonic Rejection Mixer for TV Tuners

Directory of Open Access Journals (Sweden)

D. Lee

2016-06-01

Full Text Available A two-stage 12-phase harmonic rejection mixer (HRM for TV tuners is proposed in order to reject the local oscillator (LO harmonics up to the ninth order. The proposed weighing scheme for 12-phase, 2-stage harmonic mixing can reduce the harmonic rejection (HR sensitivity to the amplitude error caused by irrational numbers such as . To verify this HR, the 2-stage HR circuit is designed with baseband gm weighting in order to save power and improve the HR ratios without calibration. The proposed HRM achieves the third to ninth worst HR ratios, more than 55 dB, according to Monte Carlo simulations. It consumes 6.5 mA under a 2.5 V supply voltage.

Mutations in the codon for a conserved arginine-1563 in the COL4A5 collagen gene in Alport syndrome

DEFF Research Database (Denmark)

Zhou, J; Gregory, M C; Hertz, Jens Michael

1993-01-01

for arginine to the translation stop codon TGA. In Utah kindred 2123 and in the Danish kindred A13, there was a C-->T mutation in the noncoding strand changing the same codon to CAA for glutamine. Both mutations were confirmed by allele-specific hybridization on PCR-amplified DNA from other family members....

EUROPEAN HARMONIZATION OF CONSOLIDATED FINANCIAL STATEMENTS REGULATIONS?

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Cirstea Andreea

2012-07-01

Full Text Available The purpose of this paper is to analyze the degree of formal accounting harmonization within the European Union with respect to the EC Regulation No. 1606/2002 adopted by the European Parliament and European Council on the 19th of July 2002, which regulates the application of IAS/IFRS regarding the financial reporting of listed European companies. The conclusions of the paper were drawn after the completion of a thorough analysis performed by using correlation and/ or association coefficients, namely: the Jaccard’s Correlation Coefficients, Rogers and Tanimoto Coefficient, Lance and Williams Coefficient and Binary Euclidian Distance Coefficient. The results lead us to conclude that although our first hypothesis is verified, the degree of harmonization between the accounting systems of EU Member States could be truly quantified only through an analysis of the material accounting harmonization, more precisely by analyzing the way the companies put into practice the requirements imposed through the EC Regulation No. 1606/2002.

SOLUTION OF HARMONIC OSCILLATOR OF NONLINEAR MASTER SCHRÖDINGER

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T B Prayitno

2012-02-01

Full Text Available We have computed the solution of a nonrelativistic particle motion in a harmonic oscillator potential of the nonlinear master Schrödinger equation. The equation itself is based on two classical conservation laws, the Hamilton-Jacobi and the continuity equations. Those two equations give each contribution for the definition of quantum particle. We also prove that the solution can’t be normalized.   Keywords : harmonic oscillator, nonlinear Schrödinger.

Tissue Harmonic Synthetic Aperture Imaging

DEFF Research Database (Denmark)

Rasmussen, Joachim

The main purpose of this PhD project is to develop an ultrasonic method for tissue harmonic synthetic aperture imaging. The motivation is to advance the field of synthetic aperture imaging in ultrasound, which has shown great potentials in the clinic. Suggestions for synthetic aperture tissue...... system complexity compared to conventional synthetic aperture techniques. In this project, SASB is sought combined with a pulse inversion technique for 2nd harmonic tissue harmonic imaging. The advantages in tissue harmonic imaging (THI) are expected to further improve the image quality of SASB...

Nucleotide composition of the Zika virus RNA genome and its codon usage

NARCIS (Netherlands)

van Hemert, Formijn; Berkhout, Ben

2016-01-01

RNA viruses have genomes with a distinct nucleotide composition and codon usage. We present the global characteristics of the RNA genome of Zika virus (ZIKV), an emerging pathogen within the Flavivirus genus. ZIKV was first isolated in 1947 in Uganda, caused a widespread epidemic in South and

Superstrings and harmonic superspace

International Nuclear Information System (INIS)

Kallosh, R.E.; AN SSSR, Moscow. Fizicheskij Inst.)

1987-01-01

The paper on superstrings and harmonic superspace is a contribution to the book dedicated to E.S. Fradkin on his sixtieth birthday. The purpose of the paper is to propose a description of N = 2,3 superspace which could be used for the investigation of the effective d = 10 harmonic superspace corresponding to the heterotic superstring. A description is given of the structure of semi-simple Lie algebras in the Cartan-Weyl basis, as well as the general properties of the even, compact part of harmonic superspace. The main properties of the four-dimensional N = 2 SYM theory are discussed, along with the N = 3, d = 4 super Yang-Mills theory. Finally the relation between the harmonic superspace and the heterotic E 8 x E 8 superstring is examined. (U.K.)

On the conformal equivalence of harmonic maps and exponentially harmonic maps

International Nuclear Information System (INIS)

Hong Minchun.

1991-06-01

Suppose that (M,g) and (N,h) are compact smooth Riemannian manifolds without boundaries. For m = dim M ≥3, and Φ: (M,g) → (N,h) is exponentially harmonic, there exists a smooth metric g-tilde conformally equivalent to g such that Φ: (M,g-tilde) → (N,h) is harmonic. (author). 7 refs

Policy harmonized approach for the EU agricultural sector modelling

Directory of Open Access Journals (Sweden)

G. SALPUTRA

2008-12-01

Full Text Available Policy harmonized (PH approach allows for the quantitative assessment of the impact of various elements of EU CAP direct support schemes, where the production effects of direct payments are accounted through reaction prices formed by producer price and policy price add-ons. Using the AGMEMOD model the impacts of two possible EU agricultural policy scenarios upon beef production have been analysed – full decoupling with a switch from historical to regional Single Payment scheme or alternatively with re-distribution of country direct payment envelopes via introduction of EU-wide flat area payment. The PH approach, by systematizing and harmonizing the management and use of policy data, ensures that projected differential policy impacts arising from changes in common EU policies reflect the likely actual differential impact as opposed to differences in how “common” policies are implemented within analytical models. In the second section of the paper the AGMEMOD model’s structure is explained. The policy harmonized evaluation method is presented in the third section. Results from an application of the PH approach are presented and discussed in the paper’s penultimate section, while section 5 concludes.;

Waveguide harmonic damper for klystron amplifier

International Nuclear Information System (INIS)

Kang, Y.

1998-01-01

A waveguide harmonic damper was designed for removing the harmonic frequency power from the klystron amplifiers of the APS linac. Straight coaxial probe antennas are used in a rectangular waveguide to form a damper. A linear array of the probe antennas is used on a narrow wall of the rectangular waveguide for damping klystron harmonics while decoupling the fundamental frequency in dominent TE 01 mode. The klystron harmonics can exist in the waveguide as waveguide higher-order modes above cutoff. Computer simulations are made to investigate the waveguide harmonic damping characteristics of the damper

Codon and amino-acid distribution in DNA

International Nuclear Information System (INIS)

Kim, J.K.; Yang, S.I.; Kwon, Y.H.; Lee, E.I.

2005-01-01

According to the Zipf's law, the distribution of rank-ordered frequency of words in the natural language can be modelled on the power law. In this paper, we examine the frequency distribution of 64 codons over the coding and non-coding regions of 88 DNA from EMBL and GenBank database, using exponential fitting. Also, we regard 20 amino-acids as vocabulary, perform the same frequency analysis to the same database and show that amino-acids can be used as biological meaningful words for Zipf's approach. Our analysis suggests that a natural language structure may exist not only in the coding region of DNA but in the non-coding one of DNA

Cross-constrained problems for nonlinear Schrodinger equation with harmonic potential

Directory of Open Access Journals (Sweden)

Runzhang Xu

2012-11-01

Full Text Available This article studies a nonlinear Schodinger equation with harmonic potential by constructing different cross-constrained problems. By comparing the different cross-constrained problems, we derive different sharp criterion and different invariant manifolds that separate the global solutions and blowup solutions. Moreover, we conclude that some manifolds are empty due to the essence of the cross-constrained problems. Besides, we compare the three cross-constrained problems and the three depths of the potential wells. In this way, we explain the gaps in [J. Shu and J. Zhang, Nonlinear Shrodinger equation with harmonic potential, Journal of Mathematical Physics, 47, 063503 (2006], which was pointed out in [R. Xu and Y. Liu, Remarks on nonlinear Schrodinger equation with harmonic potential, Journal of Mathematical Physics, 49, 043512 (2008].

A L2HGDH initiator methionine codon mutation in a Yorkshire terrier with L-2-hydroxyglutaric aciduria

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Farias Fabiana HG

2012-07-01

Full Text Available Abstract Background L-2-hydroxyglutaric aciduria is a metabolic repair deficiency characterized by elevated levels of L-2-hydroxyglutaric acid in urine, blood and cerebrospinal fluid. Neurological signs associated with the disease in humans and dogs include seizures, ataxia and dementia. Case presentation Here we describe an 8 month old Yorkshire terrier that presented with episodes of hyperactivity and aggressive behavior. Between episodes, the dog’s behavior and neurologic examinations were normal. A T2 weighted MRI of the brain showed diffuse grey matter hyperintensity and a urine metabolite screen showed elevated 2-hydroxyglutaric acid. We sequenced all 10 exons and intron-exon borders of L2HGDH from the affected dog and identified a homozygous A to G transition in the initiator methionine codon. The first inframe methionine is at p.M183 which is past the mitochondrial targeting domain of the protein. Initiation of translation at p.M183 would encode an N-terminal truncated protein unlikely to be functional. Conclusions We have identified a mutation in the initiation codon of L2HGDH that is likely to result in a non-functional gene. The Yorkshire terrier could serve as an animal model to understand the pathogenesis of L-2-hydroxyglutaric aciduria and to evaluate potential therapies.

Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs.

Science.gov (United States)

Mandal, Debabrata; Köhrer, Caroline; Su, Dan; Babu, I Ramesh; Chan, Clement T Y; Liu, Yuchen; Söll, Dieter; Blum, Paul; Kuwahara, Masayasu; Dedon, Peter C; Rajbhandary, Uttam L

2014-02-01

Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2(Ile)) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2(Ile) binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.

Evolution of type 2 vaccine derived poliovirus lineages. Evidence for codon-specific positive selection at three distinct locations on capsid wall.

Directory of Open Access Journals (Sweden)

Tapani Hovi

Full Text Available Partial sequences of 110 type 2 poliovirus strains isolated from sewage in Slovakia in 2003-2005, and most probably originating from a single dose of oral poliovirus vaccine, were subjected to a detailed genetic analysis. Evolutionary patterns of these vaccine derived poliovirus strains (SVK-aVDPV2 were compared to those of type 1 and type 3 wild poliovirus (WPV lineages considered to have a single seed strain origin, respectively. The 102 unique SVK-aVDPV VP1 sequences were monophyletic differing from that of the most likely parental poliovirus type 2/Sabin (PV2 Sabin by 12.5-15.6%. Judging from this difference and from the rate of accumulation of synonymous transversions during the 22 month observation period, the relevant oral poliovirus vaccine dose had been administered to an unknown recipient more than 12 years earlier. The patterns of nucleotide substitution during the observation period differed from those found in the studied lineages of WPV1 or 3, including a lower transition/transversion (Ts/Tv bias and strikingly lower Ts/Tv rate ratios at the 2(nd codon position for both purines and pyrimidines. A relatively low preference of transitions at the 2(nd codon position was also found in the large set of VP1 sequences of Nigerian circulating (cVDPV2, as well as in the smaller sets from the Hispaniola cVDPV1 and Egypt cVDPV2 outbreaks, and among aVDPV1and aVDPV2 strains recently isolated from sewage in Finland. Codon-wise analysis of synonymous versus non-synonymous substitution rates in the VP1 sequences suggested that in five codons, those coding for amino acids at sites 24, 144, 147, 221 and 222, there may have been positive selection during the observation period. We conclude that pattern of poliovirus VP1 evolution in prolonged infection may differ from that found in WPV epidemics. Further studies on sufficiently large independent datasets are needed to confirm this suggestion and to reveal its potential significance.

Power line harmonic radiation observed by the DEMETER spacecraft at 50/60Hz and low harmonics

Czech Academy of Sciences Publication Activity Database

Němec, F.; Parrot, M.; Santolík, Ondřej

2015-01-01

Roč. 120, č. 10 (2015), s. 8954-8967 ISSN 2169-9380 R&D Projects: GA ČR(CZ) GA14-31899S; GA MŠk LH12231 Institutional support: RVO:68378289 Keywords : PLHR * power line harmonic radiation * DEMETER Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 3.318, year: 2015 http://onlinelibrary.wiley.com/doi/10.1002/2015JA021682/full

The Harmonic Oscillator–A Simplified Approach

Directory of Open Access Journals (Sweden)

L. R. Ganesan

2008-01-01

Full Text Available Among the early problems in quantum chemistry, the one dimensional harmonic oscillator problem is an important one, providing a valuable exercise in the study of quantum mechanical methods. There are several approaches to this problem, the time honoured infinite series method, the ladder operator method etc. A method which is much shorter, mathematically simpler is presented here.

Over Expression of a tRNALeu Isoacceptor Changes Charging Pattern of Leucine tRNAs and Reveals New Codon Reading

DEFF Research Database (Denmark)

Sørensen, Michael Askvad; Elf, J.; Bouakaz, E.

2005-01-01

During mRNA translation, synonymous codons for one amino acid are often read by different isoaccepting tRNAs. The theory of selective tRNA charging predicts greatly varying percentages of aminoacylation among isoacceptors in cells starved for their common amino acid. It also predicts major changes...... in tRNA charging patterns upon concentration changes of single isoacceptors, which suggests a novel type of translational control of gene expression. We therefore tested the theory by measuring with Northern blots the charging of Leu-tRNAs in Escherichia coli under Leu limitation in response to over...... postulated a previously unknown common codon for tRNALeu GAG and tRNALeu UAG. Subsequently, we demonstrated that the tRNALeu GAG codon CUU is, in fact, read also by tRNALeu UAG, due to a uridine-5-oxyacetic acid modification....

Harmonic Damping in DG-Penetrated Distribution Network

DEFF Research Database (Denmark)

Lu, Jinghang; Savaghebi, Mehdi; Guerrero, Josep M.

2016-01-01

Grid background harmonics may be amplified, propagate through a long distribution feeder and even lead to power system instability. In this paper, harmonic propagation issue is investigated and mitigation of the harmonics is analyzed by using transmission line theory which has already been applied...... in power systems. It is demonstrated that a specific harmonic will not be amplified if the feeder’s length is less than one quarter of the harmonic wavelength meanwhile the terminal impedance is less than characteristic impedance. Besides, three scenarios will be considered in accordance...... with the relationship between the feeder’s length and harmonic wavelength. Harmonic suppression control strategies will be respectively designed considering 5th and 7th harmonics coexisting in the distribution line. Finally, a simulation study has been performed to verify the theoretical analysis and demonstrate...

Harmonic supergraphs. Green functions

International Nuclear Information System (INIS)

Galperin, A.; Ivanov, E.; Gievetsky, V.; Sokatchev, E.

1985-01-01

The quantization procedure in the harmonic superspace approach is worked out. Harmonic distributions are introduced and are used to construct the analytic superspace delta-functions and the Green functions for the hypermultiplet and the N=2 Yang-Mills superfields. The gauge fixing is described and the relevant Faddeev-Popov ghosts are defined. The corresponding BRST transformations are found. The harmonic superspace quantization of the N=2 gauge theory turns out to be rather simple and has many parallels with that for the standard (N=0) Yang-Mills theory. In particular, no ghosts-forghosts are needed

A pretandem harmonic buncher

International Nuclear Information System (INIS)

Lin, Qui-xun; Van Wechel, T.D.

1987-01-01

A single gap harmonic buncher has been constructed as a pretandem buncher. Over 85% of a proton dc beam has been bunched into pulses. The width (fwhm) of the pulses is 0.7 ns. The buncher is based on that built at Argonne. Changes were made to the buncher's configuration so that the buncher could be tuned to the desired four harmonic frequencies. A method of calibrating and setting the relative phases and amplitudes of the four harmonic frequencies has been used to obtain an optimum sawtooth-like bunching waveform

Harmonic Interaction Analysis in Grid-connected Converter using Harmonic State Space (HSS) Modeling

DEFF Research Database (Denmark)

Kwon, Jun Bum; Wang, Xiongfei; Blaabjerg, Frede

2017-01-01

research about the harmonic interaction. However, it is found that the Linear Time Invariant (LTI) based model analysis makes it difficult to analyze these phenomena because of the time-varying properties of the power electronic based systems. This paper investigates grid-connected converter by using......An increasing number of power electronic based Distributed Generation (DG) systems and loads generate not only characteristic harmonics but also unexpected harmonics. Several methods like impedance based analysis, which are derived from the conventional average model, are introduced to perform...

Translation Initiation from Conserved Non-AUG Codons Provides Additional Layers of Regulation and Coding Capacity

Directory of Open Access Journals (Sweden)

Ivaylo P. Ivanov

2017-06-01

Full Text Available Neurospora crassa cpc-1 and Saccharomyces cerevisiae GCN4 are homologs specifying transcription activators that drive the transcriptional response to amino acid limitation. The cpc-1 mRNA contains two upstream open reading frames (uORFs in its >700-nucleotide (nt 5′ leader, and its expression is controlled at the level of translation in response to amino acid starvation. We used N. crassa cell extracts and obtained data indicating that cpc-1 uORF1 and uORF2 are functionally analogous to GCN4 uORF1 and uORF4, respectively, in controlling translation. We also found that the 5′ region upstream of the main coding sequence of the cpc-1 mRNA extends for more than 700 nucleotides without any in-frame stop codon. For 100 cpc-1 homologs from Pezizomycotina and from selected Basidiomycota, 5′ conserved extensions of the CPC1 reading frame are also observed. Multiple non-AUG near-cognate codons (NCCs in the CPC1 reading frame upstream of uORF2, some deeply conserved, could potentially initiate translation. At least four NCCs initiated translation in vitro. In vivo data were consistent with initiation at NCCs to produce N-terminally extended N. crassa CPC1 isoforms. The pivotal role played by CPC1, combined with its translational regulation by uORFs and NCC utilization, underscores the emerging significance of noncanonical initiation events in controlling gene expression.

Exact diagonalization of the D-dimensional spatially confined quantum harmonic oscillator

Directory of Open Access Journals (Sweden)

Kunle Adegoke

2016-01-01

Full Text Available In the existing literature various numerical techniques have been developed to quantize the confined harmonic oscillator in higher dimensions. In obtaining the energy eigenvalues, such methods often involve indirect approaches such as searching for the roots of hypergeometric functions or numerically solving a differential equation. In this paper, however, we derive an explicit matrix representation for the Hamiltonian of a confined quantum harmonic oscillator in higher dimensions, thus facilitating direct diagonalization.

Evaluation of the Harmonic Impedance of Frydlant (Line 53 Power Network

Directory of Open Access Journals (Sweden)

Shehab Abdulwadood Ali

2013-01-01

Full Text Available The harmonic impedance of the power system is an important quantity, which describes the behaviour of the power system with the existence of different frequencies beside the fundamental. The harmonic study belongs to the most difficult part of the electrical measurements and calculations even by using computer software. The main problem accompanying the calculating methods is to obtain the exact data of the electrical network parameters or to know the exact operational status of the system. In this paper the harmonic impedance of Frydlant (line 53, 22~kV in Czech Republic power network was calculated by using a very specialized software and suitable for solving such calculations called "NetCalc. version 3.0" [1].

Harmonics in transmission power systems

DEFF Research Database (Denmark)

Wiechowski, Wojciech Tomasz

. The comparison shows that results obtained used both types of the cores are the same, so it is concluded that both cores can be used for harmonic measurements. Low-inductance resistors are introduced in the secondary circuits, in series with the metering and protective relaying. On those resistors, the harmonic......Some time ago, Energinet.dk, the Transmission System Operator of the 150 kV and 400 kV transmission network in Denmark, had experienced operational malfunctions of some of the measuring and protection equipment. Also an overloading of a harmonic filter has been reported, and therefore, a need...... end only so the ground is not used as a return path. A way to reduce the capacitive coupling is to provide shielding. Harmonic currents are measured using the conventional inductive voltage transformers. Both protective and metering cores were compared if they could be used for harmonic measurements...

2×1 Microstrip Patch Array Antenna with Harmonic Suppression Capability for Rectenna

Directory of Open Access Journals (Sweden)

Nur Aisyah Amir

2017-12-01

Full Text Available This paper is an extension of work originally presented in 2016 IEEE Asia-Pacific Conference on Applied Electromagnetics (APACE. A 2×1 microstrip patch array antenna integrated with photonic bandgap (PBG and stubs is designed and analyzed. The performance of the PBG and stubs structure are explained and analyzed in terms of the elimination of the resonance at the harmonic frequencies of the antenna. The proposed antenna is designed on FR-4 substrate with thickness of 1.6 mm and operated at 2.45 GHz frequency suitable for rectenna design application. From the simulated result, the first harmonic frequency (5.4 GHz, the second harmonic frequency (6.6 GHz and the third harmonic frequency (7.8 GHz are successfully suppressed. For instance, the radiation to the forward of the stubs-PBG antenna is suppressed at more than 15 dB at the second and third harmonic frequencies.

Genotyping of K-ras codons 12 and 13 mutations in colorectal cancer by capillary electrophoresis.

Science.gov (United States)

Chen, Yen-Ling; Chang, Ya-Sian; Chang, Jan-Gowth; Wu, Shou-Mei

2009-06-26

Point mutations of the K-ras gene located in codons 12 and 13 cause poor responses to the anti-epidermal growth factor receptor (anti-EGFR) therapy of colorectal cancer (CRC) patients. Besides, mutations of K-ras gene have also been proven to play an important role in human tumor progression. We established a simple and effective capillary electrophoresis (CE) method for simultaneous point mutation detection in codons 12 and 13 of K-ras gene. We combined one universal fluorescence-based nonhuman-sequence primer and two fragment-oriented primers in one tube, and performed this two-in-one polymerase chain reaction (PCR). PCR fragments included wild type and seven point mutations at codons 12 and 13 of K-ras gene. The amplicons were analyzed by single-strand conformation polymorphism (SSCP)-CE method. The CE analysis was performed by using a 1x Tris-borate-EDTA (TBE) buffer containing 1.5% (w/v) hydroxyethylcellulose (HEC) (MW 250,000) under reverse polarity with 15 degrees C and 30 degrees C. Ninety colorectal cancer patients were blindly genotyped using this developed method. The results showed good agreement with those of DNA sequencing method. The SSCP-CE was feasible for mutation screening of K-ras gene in populations.

Secondary magnetic field harmonics dependence on vacuum beam chamber geometry

Directory of Open Access Journals (Sweden)

S. Y. Shim

2013-08-01

Full Text Available The harmonic magnetic field properties due to eddy currents have been studied with respect to the geometry of the vacuum beam chamber. We derived a generalized formula enabling the precise prediction of any field harmonics generated by eddy currents in beam tubes with different cross-sectional geometries. Applying our model to study the properties of field harmonics in beam tubes with linear dipole magnetic field ramping clearly proved that the circular cross section tube generates only a dipole field from eddy currents. The elliptic tube showed noticeable magnitudes of sextupole and dipole fields. We demonstrate theoretically that it is feasible to suppress the generation of the sextupole field component by appropriately varying the tube wall thickness as a function of angle around the tube circumference. This result indicates that it is possible to design an elliptical-shaped beam tube that generates a dipole field component with zero magnitude of sextupole. In a rectangular-shaped beam tube, one of the selected harmonic fields can be prevented if an appropriate wall thickness ratio between the horizontal and vertical tube walls is properly chosen. Our generalized formalism can be used for optimization of arbitrarily complex-shaped beam tubes, with respect to suppression of detrimental field harmonics.

Multidimensional high harmonic spectroscopy

International Nuclear Information System (INIS)

Bruner, Barry D; Soifer, Hadas; Shafir, Dror; Dudovich, Nirit; Serbinenko, Valeria; Smirnova, Olga

2015-01-01

High harmonic generation (HHG) has opened up a new frontier in ultrafast science where attosecond time resolution and Angstrom spatial resolution are accessible in a single measurement. However, reconstructing the dynamics under study is limited by the multiple degrees of freedom involved in strong field interactions. In this paper we describe a new class of measurement schemes for resolving attosecond dynamics, integrating perturbative nonlinear optics with strong-field physics. These approaches serve as a basis for multidimensional high harmonic spectroscopy. Specifically, we show that multidimensional high harmonic spectroscopy can measure tunnel ionization dynamics with high precision, and resolves the interference between multiple ionization channels. In addition, we show how multidimensional HHG can function as a type of lock-in amplifier measurement. Similar to multi-dimensional approaches in nonlinear optical spectroscopy that have resolved correlated femtosecond dynamics, multi-dimensional high harmonic spectroscopy reveals the underlying complex dynamics behind attosecond scale phenomena. (paper)

Single-order laser high harmonics in XUV for ultrafast photoelectron spectroscopy of molecular wavepacket dynamics

Directory of Open Access Journals (Sweden)

Mizuho Fushitani

2016-11-01

Full Text Available We present applications of extreme ultraviolet (XUV single-order laser harmonics to gas-phase ultrafast photoelectron spectroscopy. Ultrashort XUV pulses at 80 nm are obtained as the 5th order harmonics of the fundamental laser at 400 nm by using Xe or Kr as the nonlinear medium and separated from other harmonic orders by using an indium foil. The single-order laser harmonics is applied for real-time probing of vibrational wavepacket dynamics of I2 molecules in the bound and dissociating low-lying electronic states and electronic-vibrational wavepacket dynamics of highly excited Rydberg N2 molecules.

Audibility of harmonics in 'periodic white noise'

NARCIS (Netherlands)

Duifhuis, H.; Tomesen, H.H.

1970-01-01

In a previous article (Duifhuis, 1970) results' concerning the audibility of harmonics in a periodic pulse have been presented. Each of the lower harmonics could be perceived separately, whereas the high harmonics were heard together as one complex signal. High harmonics, however, appeared to be

Probabilistic Harmonic Modeling of Wind Power Plants

DEFF Research Database (Denmark)

Guest, Emerson; Jensen, Kim H.; Rasmussen, Tonny Wederberg

2017-01-01

A probabilistic sequence domain (SD) harmonic model of a grid-connected voltage-source converter is used to estimate harmonic emissions in a wind power plant (WPP) comprised of Type-IV wind turbines. The SD representation naturally partitioned converter generated voltage harmonics into those...... with deterministic phase and those with probabilistic phase. A case study performed on a string of ten 3MW, Type-IV wind turbines implemented in PSCAD was used to verify the probabilistic SD harmonic model. The probabilistic SD harmonic model can be employed in the planning phase of WPP projects to assess harmonic...

Third harmonic current injection into highly saturated multi-phase machines

Directory of Open Access Journals (Sweden)

Klute Felix

2017-03-01

Full Text Available One advantage of multi-phase machines is the possibility to use the third harmonic of the rotor flux for additional torque generation. This effect can be maximised for Permanent Magnet Synchronous Machines (PMSM with a high third harmonic content in the magnet flux. This paper discusses the effects of third harmonic current injection (THCI on a five-phase PMSM with a conventional magnet shape depending on saturation. The effects of THCI in five-phase machines are shown in a 2D FEM model in Ansys Maxwell verified by measurement results. The results of the FEM model are analytically analysed using the Park model. It is shown in simulation and measurement that the torque improvement by THCI increases significantly with the saturation level, as the amplitude of the third harmonic flux linkage increases with the saturation level but the phase shift of the rotor flux linkage has to be considered. This paper gives a detailed analysis of saturation mechanisms of PMSM, which can be used for optimizing the efficiency in operating points of high saturations, without using special magnet shapes.

Cloning, Codon Optimization, and Expression of Yersinia intermedia Phytase Gene in E. coli.

Science.gov (United States)

Mirzaei, Maryam; Saffar, Behnaz; Shareghi, Behzad

2016-06-01

Phytate is an anti-nutritional factor in plants, which catches the most phosphorus contents and some vital minerals. Therefore, Phytase is added mainly as an additive to the monogastric animals' foods to hydrolyze phytate and increase absorption of phosphorus. Y. intermedia phytase is a new phytase with special characteristics such as high specific activity, pH stability, and thermostability. Our aim was to clone, express, and characterizea codon optimized Y. intermedia phytase gene in E. coli . The Y. intermedia phytase gene was optimized according to the codon usage in E. coli . The sequence was synthesized and sub-cloned in pET-22b (+) vector and transformed into E. coli Bl21 (DE3). The protein was expressed in the presence of IPTG at a final concentration of 1 mM at 30°C. The purification of recombinant protein was performed by Ni 2+ affinity chromatography. Phytase activity and stability were determined in various pH and temperatures. The codon optimized Y. intermedia phytase gene was sub-cloned successfully.The expression was confirmed by SDS-PAGE and Western blot analysis. The recombinant enzyme (approximately 45 kDa) was purified. Specific activity of enzyme was 3849 (U.mg -1 ) with optimal pH 5 and optimal temperature of 55°C. Thermostability (80°C for 15 min) and pH stability (3-6) of the enzyme were 56 and more than 80%, respectively. The results of the expression and enzyme characterization revealed that the optimized Y. intermedia phytase gene has a good potential to be produced commercially andto be applied in animals' foodsindustry.

Stabilization of the genome of the mismatch repair deficient Mycobacterium tuberculosis by context-dependent codon choice.

Science.gov (United States)

Wanner, Roger M; Güthlein, Carolin; Springer, Burkhard; Böttger, Erik C; Ackermann, Martin

2008-05-28

The rate at which a stretch of DNA mutates is determined by the cellular systems for DNA replication and repair, and by the nucleotide sequence of the stretch itself. One sequence feature with a particularly strong influence on the mutation rate are nucleotide repeats. Some microbial pathogens use nucleotide repeats in their genome to stochastically vary phenotypic traits and thereby evade host defense. However, such unstable sequences also come at a cost, as mutations are often deleterious. Here, we analyzed how these opposing forces shaped genome stability in the human pathogen Mycobacterium tuberculosis. M. tuberculosis lacks a mismatch repair system, and this renders nucleotide repeats particularly unstable. We found that proteins of M. tuberculosis are encoded by using codons in a context-dependent manner that prevents the emergence of nucleotide repeats. This context-dependent codon choice leads to a strong decrease in the estimated frame-shift mutation rate and thus to an increase in genome stability. These results indicate that a context-specific codon choice can partially compensate for the lack of a mismatch repair system, and helps to maintain genome integrity in this pathogen.

Simulation of a Centrifugal Pump by Using the Harmonic Balance Method

Directory of Open Access Journals (Sweden)

Franco Magagnato

2015-01-01

Full Text Available The harmonic balance method was used for the flow simulation in a centrifugal pump. Independence studies have been done to choose proper number of harmonic modes and inlet eddy viscosity ratio value. The results from harmonic balance method show good agreements with PIV experiments and unsteady calculation results (which is based on the dual time stepping method for the predicted head and the phase-averaged velocity. A detailed analysis of the flow fields at different flow rates shows that the flow rate has an evident influence on the flow fields. At 0.6Qd, some vortices begin to appear in the impeller, and at 0.4Qd some vortices have blocked the flow passage. The flow fields at different positions at 0.6Qd and 0.4Qd show how the complicated flow phenomena are forming, developing, and even disappearing. The harmonic balance method can be used for the flow simulation in pumps, showing the same accuracy as unsteady methods, but is considerably faster.

Reduction of the Harmonic Series Influences Musical Enjoyment With Cochlear Implants.

Science.gov (United States)

Nemer, John S; Kohlberg, Gavriel D; Mancuso, Dean M; Griffin, Brianna M; Certo, Michael V; Chen, Stephanie Y; Chun, Michael B; Spitzer, Jaclyn B; Lalwani, Anil K

2017-01-01

Cochlear implantation is associated with poor music perception and enjoyment. Reducing music complexity has been shown to enhance music enjoyment in cochlear implant (CI) recipients. In this study, we assess the impact of harmonic series reduction on music enjoyment. Prospective analysis of music enjoyment in normal-hearing (NH) individuals and CI recipients. Single tertiary academic medical center. NH adults (N = 20) and CI users (N = 8) rated the Happy Birthday song on three validated enjoyment modalities-musicality, pleasantness, and naturalness. Subjective rating of music excerpts. Participants listened to seven different instruments play the melody, each with five levels of harmonic reduction (Full, F3+F2+F1+F0, F2+F1+F0, F1+F0, F0). NH participants listened to the segments both with and without CI simulation. Linear mixed effect models (LME) and likelihood ratio tests were used to assess the impact of harmonic reduction on enjoyment. NH listeners without simulation rated segments with the first four harmonics (F3+F2+F1+F0) most pleasant and natural (p <0.001, p = 0.004). NH listeners with simulation rated the first harmonic alone (F0) most pleasant and natural (p <0.001, p = 0.003). Their ratings demonstrated a positive linear relationship between harmonic reduction and both pleasantness (slope estimate = 0.030, SE = 0.004, p <0.001, LME) and naturalness (slope estimate = 0.012, SE = 0.003, p = 0.003, LME). CI recipients also found the first harmonic alone (F0) to be most pleasant (p = 0.003), with a positive linear relationship between harmonic reduction and pleasantness (slope estimate = 0.029, SE = 0.008, p <0.001, LME). Harmonic series reduction increases music enjoyment in CI and NH individuals with or without CI simulation. Therefore, minimization of the harmonics may be a useful strategy for enhancing musical enjoyment among both NH and CI listeners.

Evidence for a novel coding sequence overlapping the 5'-terminal ~90 codons of the Gill-associated and Yellow head okavirus envelope glycoprotein gene

Directory of Open Access Journals (Sweden)

Atkins John F

2009-12-01

Full Text Available Abstract The genus Okavirus (order Nidovirales includes a number of viruses that infect crustaceans, causing major losses in the shrimp industry. These viruses have a linear positive-sense ssRNA genome of ~26-27 kb, encoding a large replicase polyprotein that is expressed from the genomic RNA, and several additional proteins that are expressed from a nested set of 3'-coterminal subgenomic RNAs. In this brief report, we describe the bioinformatic discovery of a new, apparently coding, ORF that overlaps the 5' end of the envelope glycoprotein encoding sequence, ORF3, in the +2 reading frame. The new ORF has a strong coding signature and, in fact, is more conserved at the amino acid level than the overlapping region of ORF3. We propose that translation of the new ORF initiates at a conserved AUG codon separated by just 2 nt from the ORF3 AUG initiation codon, resulting in a novel 86 amino acid protein.

Complex harmonic modal analysis of rotor systems

International Nuclear Information System (INIS)

Han, Dong Ju

2015-01-01

Complex harmonic analysis for rotor systems has been proposed from the strict complex modal analysis based upon Floquet theory. In this process the harmonic balance method is adopted, effectively associated with conventional eigenvalue analysis. Also, the harmonic coefficients equivalent to dFRFs in harmonic mode has been derived in practice. The modes are classified from identifying the modal characteristics, and the adaptation of harmonic balance method has been proven by comparing the results of the stability analyses from Floque theory and the eigen analysis. The modal features of each critical speed are depicted in quantitatively and qualitatively by showing that the strengths of each component of the harmonic coefficients are estimated from the order of magnitude analysis according to their harmonic patterns. This effectiveness has been verified by comparing with the numerical solutions

Harmonic Analysis Associated with the Generalized q-Bessel Operator

Directory of Open Access Journals (Sweden)

Ahmed Abouelaz

2016-01-01

Full Text Available In this article, we give a new harmonic analysis associated with the generalized q-Bessel operator. We introduce the generalized $q$-Bessel transform, the generalized q-Bessel translation and the generalized $q$-Bessel convolution product.

Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.

Science.gov (United States)

Mondal, Sunil Kanti; Kundu, Sudip; Das, Rabindranath; Roy, Sujit

2016-08-01

Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.

Some Implicit Methods for Solving Harmonic Variational Inequalities

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Muhammad Aslam Noor

2016-08-01

Full Text Available In this paper, we use the auxiliary principle technique to suggest an implicit method for solving the harmonic variational inequalities. It is shown that the convergence of the proposed method only needs pseudo monotonicity of the operator, which is a weaker condition than monotonicity.

Harmonic uniflow engine

Science.gov (United States)

Bennett, Charles L.

2016-03-22

A reciprocating-piston uniflow engine includes a harmonic oscillator inlet valve capable of oscillating at a resonant frequency for controlling the flow of working fluid into the engine. In particular, the inlet valve includes an inlet valve head and a spring arranged together as a harmonic oscillator so that the inlet valve head is moveable from an unbiased equilibrium position to a biased closed position occluding an inlet. When released, the inlet valve head undergoes a single oscillation past the equilibrium position to a maximum open position and returns to a biased return position close to the closed position to choke the flow and produce a pressure drop across the inlet valve causing the inlet valve to close. In other embodiments, the harmonic oscillator arrangement of the inlet valve enables the uniflow engine to be reversibly operated as a uniflow compressor.

Synonymous codon usage analysis of hand, foot and mouth disease viruses: A comparative study on coxsackievirus A6, A10, A16, and enterovirus 71 from 2008 to 2015.

Science.gov (United States)

Su, Weiheng; Li, Xue; Chen, Meili; Dai, Wenwen; Sun, Shiyang; Wang, Shuai; Sheng, Xin; Sun, Shixiang; Gao, Chen; Hou, Ali; Zhou, Yan; Sun, Bo; Gao, Feng; Xiao, Jingfa; Zhang, Zhewen; Jiang, Chunlai

2017-09-01

Enterovirus 71 (EV71) and coxsackievirus A16 (CVA16) have been considered major pathogens of hand, foot and mouth disease (HFMD) throughout the world for decades. In recent years, coxsackievirus A6 (CVA6) and coxsackievirus A10 (CVA10) have raised attention as two other serious pathogens of HFMD. The present study focused on the synonymous codon usage of four viruses isolated from 2008 to 2015, with particular attention on P1 (encoding capsid proteins) and P2-P3 regions (both encoding non-structural proteins) in the genomic RNA. Relative synonymous codon usage, effective number of codons, neutrality and correspondence were analyzed. The results indicated that these viruses prefer A/T at the third position in codons rather than G/C. The most frequent codons of 4 essential and 2 semi-essential amino acids, as well as a key amino acid of metabolic junctions (Glu) used in the four viruses are also the most frequently used in humans. Effective number of codons (ENC) values indicated weak codon usage bias in all the viruses. Relatively, the force of mutation pressure in the P1 region was found to be stronger than that in the P2-P3 region, and this force in the P1 region of CVA6 and EV71 was stronger than that of CVA10 and A16. The neutrality analysis results implied that mutation pressure plays a minor role in shaping codon bias of these viruses. Correspondence analysis indicated that the codon usage of EV71 strains varied much more than that of other viruses. In conclusion, the present study provides novel and comparative insight into the evolution of HFMD pathogens at the codon level. Copyright © 2017. Published by Elsevier B.V.

Genome-wide analysis of codon usage bias in Bovine Coronavirus

OpenAIRE

Castells, Mat?as; Victoria, Mat?as; Colina, Rodney; Musto, H?ctor; Cristina, Juan

2017-01-01

Background Bovine coronavirus (BCoV) belong to the genus Betacoronavirus of the family Coronaviridae. BCoV are widespread around the world and cause enteric or respiratory infections among cattle, leading to important economic losses to the beef and dairy industry worldwide. To study the relation of codon usage among viruses and their hosts is essential to understand host-pathogen interaction, evasion from host?s immune system and evolution. Methods We performed a comprehensive analysis of co...

Analysis of Harmonic Coupling and Stability in Back-to-Back Converter Systems for Wind Turbines using Harmonic State Space (HSS)

DEFF Research Database (Denmark)

Kwon, Jun Bum; Wang, Xiongfei; Bak, Claus Leth

2015-01-01

Understanding about harmonic propagation in wind turbine converter is fundamental to research the influence of these on a large network harmonic distortion. Therefore, the analysis of wind turbine converter harmonic spectrum as well as the influence of converter operating point into the network i...... connected into the large wind farm model to analyze the overall steady-state harmonic as well as harmonic stability. All theoretical modeling and analysis is verified by means of simulation and experimental results.......Understanding about harmonic propagation in wind turbine converter is fundamental to research the influence of these on a large network harmonic distortion. Therefore, the analysis of wind turbine converter harmonic spectrum as well as the influence of converter operating point into the network...... is urgently important issues in harmonic studies on wind farm. However, the conventional modeling procedure and simplified model for controller design are not enough to analyze such complicated systems. Besides, they have many limitations in terms of including a non-linear component, different operating...

High-frequency harmonic imaging of the eye

Science.gov (United States)

Silverman, Ronald H.; Coleman, D. Jackson; Ketterling, Jeffrey A.; Lizzi, Frederic L.

2005-04-01

Purpose: Harmonic imaging has become a well-established technique for ultrasonic imaging at fundamental frequencies of 10 MHz or less. Ophthalmology has benefited from the use of fundamentals of 20 MHz to 50 MHz. Our aim was to explore the ability to generate harmonics for this frequency range, and to generate harmonic images of the eye. Methods: The presence of harmonics was determined in both water and bovine vitreous propagation media by pulse/echo and hydrophone at a series of increasing excitation pulse intensities and frequencies. Hydrophone measurements were made at the focal point and in the near- and far-fields of 20 MHz and 40 MHz transducers. Harmonic images of the anterior segment of the rabbit eye were obtained by a combination of analog filtering and digital post-processing. Results: Harmonics were generated nearly identically in both water and vitreous. Hydrophone measurements showed the maximum second harmonic to be -5 dB relative to the 35 MHz fundamental at the focus, while in pulse/echo the maximum harmonic amplitude was -15dB relative to the fundamental. Harmonics were absent in the near-field, but present in the far-field. Harmonic images of the eye showed improved resolution. Conclusion: Harmonics can be readily generated at very high frequencies, and at power levels compliant with FDA guidelines for ophthalmology. This technique may yield further improvements to the already impressive resolutions obtainable in this frequency range. Improved imaging of the macular region, in particular, may provide significant improvements in diagnosis of retinal disease.

Extended Gersgorin Theorem-Based Parameter Feasible Domain to Prevent Harmonic Resonance in Power Grid

Directory of Open Access Journals (Sweden)

Tao Lin

2017-10-01

Full Text Available Harmonic resonance may cause abnormal operation and even damage of power facilities, further threatening normal and safe operation of power systems. For renewable energy generations, controlled loads and parallel reactive power compensating equipment, their operating statuses can vary frequently. Therefore, the parameters of equivalent fundamental and harmonic admittance/impedance of these components exist in uncertainty, which will change the elements and eigenvalues of harmonic network admittance matrix. Consequently, harmonic resonance in power grid is becoming increasingly more complex. Hence, intense research about prevention and suppression of harmonic resonance, particularly the parameter feasible domain (PFD which can keep away from harmonic resonance, are needed. For rapid online evaluation of PFD, a novel method without time-consuming pointwise precise eigenvalue computations is proposed. By analyzing the singularity of harmonic network admittance matrix, the explicit sufficient condition that the matrix elements should meet to prevent harmonic resonance is derived by the extended Gersgorin theorem. Further, via the non-uniqueness of similar transformation matrix (STM, a strategy to determine the appropriate STM is proposed to minimize the conservation of the obtained PFD. Eventually, the availability and advantages in computation efficiency and conservation of the method, are demonstrated through four different scale benchmarks.

Computer model for harmonic ultrasound imaging.

Science.gov (United States)

Li, Y; Zagzebski, J A

2000-01-01

Harmonic ultrasound imaging has received great attention from ultrasound scanner manufacturers and researchers. In this paper, we present a computer model that can generate realistic harmonic images. In this model, the incident ultrasound is modeled after the "KZK" equation, and the echo signal is modeled using linear propagation theory because the echo signal is much weaker than the incident pulse. Both time domain and frequency domain numerical solutions to the "KZK" equation were studied. Realistic harmonic images of spherical lesion phantoms were generated for scans by a circular transducer. This model can be a very useful tool for studying the harmonic buildup and dissipation processes in a nonlinear medium, and it can be used to investigate a wide variety of topics related to B-mode harmonic imaging.

Experimental Research on Vibrations of Double Harmonic Gear Transmission

Directory of Open Access Journals (Sweden)

Sava Ianici

2017-11-01

Full Text Available Gears transmission can be important sources of vibration in the mechanical system structures and can have a significant share in the overall vibration level. The current trend of significant increase in powers and speeds transmitted by modern mechanical systems, along with the size reduction, may cause a worsening of the behaviour of transmissions with gears in terms of vibration, especially when the optimization criteria were not respected in the design, execution and installation phase. This paper presents a study of vibrations that occur in a double harmonic gear transmission (DHGT, based on experimental research. The experimental researches revealed that in a double harmonic gear transmission the vibrations are initiated and develop in the multipara harmonics engagement of the teeth and in the kinematic couplings materialized between the wave generator and the flexible toothed wheel. These vibrations are later transmitted by means of the shafts and bearings to the transmission housing, respectively, through the walls of it, propagating in the air.

Codon and amino acid usage in two major human pathogens of genus Bartonella--optimization between replicational-transcriptional selection, translational control and cost minimization.

Science.gov (United States)

Das, Sabyasachi; Paul, Sandip; Chatterjee, Sanjib; Dutta, Chitra

2005-01-01

Intra-genomic variation in synonymous codon and amino acid usage in two human pathogens Bartonella henselae and B. quintana has been carried out through multivariate analysis. Asymmetric mutational bias, coupled with replicational-transcriptional selection, has been identified as the prime selection force behind synonymous codon selection--a characteristic of the genus Bartonella, not exhibited by any other alpha-proteobacterial genome. Distinct codon usage patterns and low synonymous divergence values between orthologous sequences of highly expressed genes from the two Bartonella species indicate that there exists a residual intra-strand synonymous codon bias in the highly expressed genes, possibly operating at the level of translation. In the case of amino acid usage, the mean hydropathy level and aromaticity are the major sources of variation, both having nearly equal impact, while strand-specific mutational pressure and gene expressivity strongly influence the inter-strand variations. In both species under study, the highly expressed gene products tend not to contain heavy and/or aromatic residues, following the cost-minimization hypothesis in spite of their intracellular lifestyle. The codon and amino acid usage in these two human pathogens are, therefore, consequences of a complex balance between replicational-transcriptional selection, translational control, protein hydropathy and cost minimization.

High-order harmonics generation from overdense plasmas

International Nuclear Information System (INIS)

Quere, F.; Thaury, C.; Monot, P.; Martin, Ph.; Geindre, J.P.; Audebert, P.; Marjoribanks, R.

2006-01-01

Complete test of publication follows. When an intense laser beam reflects on an overdense plasma generated on a solid target, high-order harmonics of the incident laser frequency are observed in the reflected beam. This process provides a way to produce XUV femtosecond and attosecond pulses in the μJ range from ultrafast ultraintense lasers. Studying the mechanisms responsible for this harmonic emission is also of strong fundamental interest: just as HHG in gases has been instrumental in providing a comprehensive understanding of basic intense laser-atom interactions, HHG from solid-density plasmas is likely to become a unique tool to investigate many key features of laser-plasma interactions at high intensities. We will present both experimental and theoretical evidence that two mechanisms contribute to this harmonic emission: - Coherent Wake Emission: in this process, harmonics are emitted by plasma oscillations in te overdense plasma, triggered in the wake of jets of Brunel electrons generated by the laser field. - The relativistic oscillating mirror: in this process, the intense laser field drives a relativistic oscillation of the plasma surface, which in turn gives rise to a periodic phase modulation of the reflected beam, and hence to the generation of harmonics of the incident frequency. Left graph: experimental harmonic spectrum from a polypropylene target, obtained with 60 fs laser pulses at 10 19 W/cm 2 , with a very high temporal contrast (10 10 ). The plasma frequency of this target corresponds to harmonics 15-16, thus excluding the CWE mechanism for the generation of harmonics of higher orders. Images on the right: harmonic spectra from orders 13 et 18, for different distances z between the target and the best focus. At the highest intensity (z=0), harmonics emitted by the ROM mechanism are observed above the 15th order. These harmonics have a much smaller spectral width then those due to CWE (below the 15th order). These ROM harmonics vanish as soon

Harmonic Detection at Initialization With Kalman Filter

DEFF Research Database (Denmark)

Hussain, Dil Muhammad Akbar; Imran, Raja Muhammad; Shoro, Ghulam Mustafa

2014-01-01

Most power electronic equipment these days generate harmonic disturbances, these devices hold nonlinear voltage/current characteristic. The harmonics generated can potentially be harmful to the consumer supply. Typically, filters are integrated at the power source or utility location to filter out...... the affect of harmonics on the supply. For the detection of these harmonics various techniques are available and one of that technique is the Kalman filter. In this paper we investigate that what are the consequences when harmonic detection system based on Kalman Filtering is initialized...

Harmonic response of coupled and uncoupled granular YBCO

International Nuclear Information System (INIS)

Torralba, Maria Veronica S; Sarmago, Roland V

2004-01-01

The harmonic responses of granular YBCO were obtained via mutual inductance measurements. Two samples, one with and another without intergranular coupling, were investigated in terms of the harmonic components of magnetization at various field amplitudes and frequencies. By comparing the behaviour of the features in the harmonics to that of the peaks in the fundamental response, we explicitly identified which features in the harmonics originate from intragranular harmonic generation and which arise due to a contribution of intergranular coupling. Harmonic responses were obtained despite the absence of vortices and even harmonics were detected in a purely AC magnetic field

Gliding and Quasi-harmonic Tremor Behaviour of Raung Volcano: November 2014 Crisis Period Case Study

Directory of Open Access Journals (Sweden)

Vico Luthfi Ipmawan

2018-01-01

Full Text Available DOI: 10.17014/ijog.5.1.13-21The seismic activity of Raung Volcano was raised on 11 November 2014. As many as 1709 tremors were recorded followed by continuous tremors appearing in late November 2014. Quasi-harmonic and gliding tremors appeared in a spectrogram on 12 November 2014. The quasi-harmonic tremors refer to tremors that have no fully harmonic form in spectrum. The gliding harmonic tremors refer to harmonic tremors that have frequency jumps with either positive or negative increment. After signal restitution processing, the Maximum Entropy Spectral Analysis (MESA method was applied in Raung recordings resulting the spectrum and the spectrogram of tremors. The quasi-harmonic tremors have the monotonic spectrum in its head and centre segment, and the harmonic one in its tails. There are twenty-four spectrums that show frequency changes between the monotonic and harmonic. The similarity between the fundamental frequency range of the monotonic and harmonic ones suggests that both signals are excited from a common resonator. The alternating of monotonic and harmonic respectively over this period is qualitatively similar with Julian’s synthetic time series about the nonlinear oscillator model. It is suggested that Raung Volcano magma pressure is sizeable to make a chaotic vibration. A pressure increasing in Raung magmatic conduit causes the increasing of P-wave velocity and makes a positive gliding frequency.

Electromagnetic cyclotron harmonic waves

International Nuclear Information System (INIS)

Ohnuma, T.; Watanabe, T.; Hamamatsu, K.

1981-09-01

Electromagnetic electron cyclotron harmonic waves just below the electron cyclotron harmonics are investigated numerically and experimentally. Backward waves which are observed to propagate nearly perpendicular to the magnetic field just below the electron cyclotron frequency in a high density magnetoplasma are confirmed to be in accord with the theoretical electromagnetic cyclotron waves. (author)

Second harmonic generation in a bounded magnetoplasma

International Nuclear Information System (INIS)

Thomas, D.G.

1975-01-01

An experimental study of second harmonic generation in a magnetized plasma contained in a cylindrical cavity resonator shows how the harmonic power varies with fundamental power, background gas pressure, and magnetization. Two cavities were designed. For each the TM010 resonance was in the S-band and the TM011 resonance in the C-band. Both frequencies were harmonically related when the d.c. discharge sustaining the plasma was adjusted to give plasma frequencies of approximately 0.7 GHz and 1.53 GHz. The experimental results show the harmonic power approximately proportional to the square of the fundamental power from 5 to 100 mw, and a decreasing function of pressure from 10 to 150 millitorr. Experiments at constant plasma frequency and varying magnetic field from 0 to 3000 Gauss show a sharp drop in harmonic power to undetectable levels when the electron cyclotron frequency approximates either the fundamental or second harmonic frequencies. These effects are attributed, respectively, to the coupling of fundamental power to other modes and to cavity detuning away from the harmonic. With the plasma frequency adjusted to maintain simultaneous resonance of fundamental and harmonic, a harmonic signal maximum occurred when the upper hybrid frequency approximated the harmonic frequency. Several anomalies, apparently related to the magnetization, background gas, and electron density distribution were observed. Otherwise, the results are qualitatively consistent with the first order theory for a cold, collisional plasma

Canine parvovirus type 2 (CPV-2) and Feline panleukopenia virus (FPV) codon bias analysis reveals a progressive adaptation to the new niche after the host jump.

Science.gov (United States)

Franzo, Giovanni; Tucciarone, Claudia Maria; Cecchinato, Mattia; Drigo, Michele

2017-09-01

Based on virus dependence from host cell machinery, their codon usage is expected to show a strong relation with the host one. Even if this association has been stated, especially for bacteria viruses, the linkage is considered to be less consistent for more complex organisms and a codon bias adaptation after host jump has never been proven. Canine parvovirus type 2 (CPV-2) was selected as a model because it represents a well characterized case of host jump, originating from Feline panleukopenia virus (FPV). The current study demonstrates that the adaptation to specific tissue and host codon bias affected CPV-2 evolution. Remarkably, FPV and CPV-2 showed a higher closeness toward the codon bias of the tissues they display the higher tropism for. Moreover, after the host jump, a clear and significant trend was evidenced toward a reduction in the distance between CPV-2 and the dog codon bias over time. This evidence was not confirmed for FPV, suggesting that an equilibrium has been reached during the prolonged virus-host co-evolution. Additionally, the presence of an intermediate pattern displayed by some strains infecting wild species suggests that these could have facilitated the host switch also by acting on codon bias. Copyright © 2017 Elsevier Inc. All rights reserved.

CodonShuffle: a tool for generating and analyzing synonymously mutated sequences

OpenAIRE

Jorge, Daniel Macedo de Melo; Mills, Ryan E.; Lauring, Adam S.

2015-01-01

Because synonymous mutations do not change the amino acid sequence of a protein, they are generally considered to be selectively neutral. Empiric data suggest, however, that a significant fraction of viral mutational fitness effects may be attributable to synonymous mutation. Bias in synonymous codon usage in viruses may result from selection for translational efficiency, mutational bias, base pairing requirements in RNA structures, or even selection against specific dinucleotides by innate i...

Current Harmonics Compensation in Microgrids Exploiting the Power Electronics Interfaces of Renewable Energy Sources

Directory of Open Access Journals (Sweden)

Ioannis Bouloumpasis

2015-03-01

Full Text Available This work presents a method of current harmonic reduction in a distorted distribution system. In order to evaluate the proposed method a grid with high-order current harmonics is assumed. The reduction of current distortion is feasible due to the pulse modulation of an active filter, which consists of a buck-boost converter connected back-to-back to a polarity swapping inverter. For a practical application, this system would be the power electronic interface of a Renewable Energy Source (RES and therefore it changes a source of harmonics to a damping harmonics system. Using the proposed method, the current Total Harmonic Distortion (THD of the grid is reduced below the acceptable limits and thus the general power quality of the system is improved. Simulations in the MATLAB/SIMULINK platform and experiments have been performed in order to verify the effectiveness of the proposed method.

Harmonic Issues Assessment on PWM VSC-Based Controlled Microgrids using Newton Methods

DEFF Research Database (Denmark)

Agundis-Tinajero, Gibran; Segundo-Ramirez, Juan; Peña-Gallardo, Rafael

2018-01-01

This paper presents the application of Newton-based methods in the time-domain for the computation of the periodic steady state solutions of microgrids with multiple distributed generation units, harmonic stability and power quality analysis. Explicit representation of the commutation process...... of the power electronic converters and closed-loop power management strategies are fully considered. Case studies under different operating scenarios are presented: grid-connected mode, islanded mode, variations in the Thevenin equivalent of the grid and the loads. Besides, the close relation between...... the harmonic distortion, steady state performance of the control systems, asymptotic stability and power quality is analyzed in order to evaluate the importance and necessity of using full models in stressed and harmonic distorted scenarios....

Sensitivity of echo enabled harmonic generation to sinusoidal electron beam energy structure

Directory of Open Access Journals (Sweden)

E. Hemsing

2017-06-01

Full Text Available We analytically examine the bunching factor spectrum of a relativistic electron beam with sinusoidal energy structure that then undergoes an echo-enabled harmonic generation (EEHG transformation to produce high harmonics. The performance is found to be described primarily by a simple scaling parameter. The dependence of the bunching amplitude on fluctuations of critical parameters is derived analytically, and compared with simulations. Where applicable, EEHG is also compared with high gain harmonic generation (HGHG and we find that EEHG is generally less sensitive to several types of energy structure. In the presence of intermediate frequency modulations like those produced by the microbunching instability, EEHG has a substantially narrower intrinsic bunching pedestal.

Intense harmonic generation from various ablation media

International Nuclear Information System (INIS)

Ozaki, T.; Elouga, L.; Suzuki, M.; Kuroda, H.; Ganeev, R.A.

2006-01-01

Complete test of publication follows. High-order harmonic generation (HHG) is a unique source of coherent extreme ultraviolet (XUV) radiation, which can produce soft x-rays within the spectral 'water-window' (between 2.3 and 4.4 nm), and ultimately short pulses with attosecond duration. However, the intensity of present-day harmonics is still low, and serious applications will need an increase of the conversion efficiency. Instead of using gas media, one can also use ablation material, produced on solid targets using a low-intensity prepulse, as the nonlinear medium to generate high-order harmonics. Recently, we have successfully demonstrated the generation of up to the 63 rd harmonic (λ = 12.6 nm) of a Ti:sapphire laser radiation using boron ablation, and a strong enhancement in the intensity of the 13 th harmonic from indium ablation. These harmonics were generated with a modest laser (10 mJ, 150 fs) and with the pre-pulse to main pulse energy ratio constant. In this paper, we perform systematic investigations of ablation harmonics, using the 200 mJ, 30 fs Ti:sapphire beam line of the Canadian Advanced Laser Light Source (ALLS) facility. ALLS allows studying ablation harmonics over wider experimental parameters, and with independent control over the pre-pulse and main pulse energies. The 10 Hz, 200 mJ Ti:sapphire beam line of ALLS is divided into two beams. Each beam has its own energy control system, which allows independent control over the energy of each beam. One of the beams is used as a pre-pulse for creating ablation, which is focused onto the solid target without pulse compression, with pulse duration of 200 ps. The second beam is used as the main pulse for harmonic generation. The main pulse is delayed in time relative to the pre-pulse by propagating through an optical delay line, and then sent through a pulse compressor. The compressed pulse duration have typical pulse duration of 30 fs FWHM, which is then focused onto the ablation medium using MgF 2

Harmonic balance approach to the periodic solutions of the (an)harmonic relativistic oscillator

International Nuclear Information System (INIS)

Belendez, Augusto; Pascual, Carolina

2007-01-01

The first-order harmonic balance method via the first Fourier coefficient is used to construct two approximate frequency-amplitude relations for the relativistic oscillator for which the nonlinearity (anharmonicity) is a relativistic effect due to the time line dilation along the world line. Making a change of variable, a new nonlinear differential equation is obtained and two procedures are used to approximately solve this differential equation. In the first the differential equation is rewritten in a form that does not contain a square-root expression, while in the second the differential equation is solved directly. The approximate frequency obtained using the second procedure is more accurate than the frequency obtained with the first due to the fact that, in the second procedure, application of the harmonic balance method produces an infinite set of harmonics, while in the first procedure only two harmonics are produced. Both approximate frequencies are valid for the complete range of oscillation amplitudes, and excellent agreement of the approximate frequencies with the exact one are demonstrated and discussed. The discrepancy between the first-order approximate frequency obtained by means of the second procedure and the exact frequency never exceeds 1.6%. We also obtained the approximate frequency by applying the second-order harmonic balance method and in this case the relative error is as low 0.31% for all the range of values of amplitude of oscillation A

mRNA secondary structure at start AUG codon is a key limiting factor for human protein expression in Escherichia coli

International Nuclear Information System (INIS)

Zhang Weici; Xiao Weihua; Wei Haiming; Zhang Jian; Tian Zhigang

2006-01-01

Codon usage and thermodynamic optimization of the 5'-end of mRNA have been applied to improve the efficiency of human protein production in Escherichia coli. However, high level expression of human protein in E. coli is still a challenge that virtually depends upon each individual target genes. Using human interleukin 10 (huIL-10) and interferon α (huIFN-α) coding sequences, we systematically analyzed the influence of several major factors on expression of human protein in E. coli. The results from huIL-10 and reinforced by huIFN-α showed that exposing AUG initiator codon from base-paired structure within mRNA itself significantly improved the translation of target protein, which resulted in a 10-fold higher protein expression than the wild-type genes. It was also noted that translation process was not affected by the retained short-range stem-loop structure at Shine-Dalgarno (SD) sequences. On the other hand, codon-optimized constructs of huIL-10 showed unimproved levels of protein expression, on the contrary, led to a remarkable RNA degradation. Our study demonstrates that exposure of AUG initiator codon from long-range intra-strand secondary structure at 5'-end of mRNA may be used as a general strategy for human protein production in E. coli

Maximal Regularity of the Discrete Harmonic Oscillator Equation

Directory of Open Access Journals (Sweden)

Airton Castro

2009-01-01

Full Text Available We give a representation of the solution for the best approximation of the harmonic oscillator equation formulated in a general Banach space setting, and a characterization of lp-maximal regularity—or well posedness—solely in terms of R-boundedness properties of the resolvent operator involved in the equation.

Harmonically excited orbital variations

International Nuclear Information System (INIS)

Morgan, T.

1985-01-01

Rephrasing the equations of motion for orbital maneuvers in terms of Lagrangian generalized coordinates instead of Newtonian rectangular cartesian coordinates can make certain harmonic terms in the orbital angular momentum vector more readily apparent. In this formulation the equations of motion adopt the form of a damped harmonic oscillator when torques are applied to the orbit in a variationally prescribed manner. The frequencies of the oscillator equation are in some ways unexpected but can nonetheless be exploited through resonant forcing functions to achieve large secular variations in the orbital elements. Two cases are discussed using a circular orbit as the control case: (1) large changes in orbital inclination achieved by harmonic excitation rather than one impulsive velocity change, and (2) periodic and secular changes to the longitude of the ascending node using both stable and unstable excitation strategies. The implications of these equations are also discussed for both artificial satellites and natural satellites. For the former, two utilitarian orbits are suggested, each exploiting a form of harmonic excitation. 5 refs

Expansion into lattice harmonics in cubic symmetries

Science.gov (United States)

Kontrym-Sznajd, G.

2018-05-01

On the example of a few sets of sampling directions in the Brillouin zone, this work shows how important the choice of the cubic harmonics is on the quality of approximation of some quantities by a series of such harmonics. These studies led to the following questions: (1) In the case that for a given l there are several independent harmonics, can one use in the expansion only one harmonic with a given l?; (2) How should harmonics be ordered: according to l or, after writing them in terms of (x4 + y4 + z4)n (x2y2z2)m, according to their degree q = n + m? To enable practical applications of such harmonics, they are constructed in terms of the associated Legendre polynomials up to l = 26. It is shown that electron momentum densities, reconstructed from experimental data for ErGa3 and InGa3, are described much better by harmonics ordered with q.

Balancing Vibrations at Harmonic Frequencies by Injecting Harmonic Balancing Signals into the Armature of a Linear Motor/Alternator Coupled to a Stirling Machine

Science.gov (United States)

Holliday, Ezekiel S. (Inventor)

2014-01-01

Vibrations at harmonic frequencies are reduced by injecting harmonic balancing signals into the armature of a linear motor/alternator coupled to a Stirling machine. The vibrations are sensed to provide a signal representing the mechanical vibrations. A harmonic balancing signal is generated for selected harmonics of the operating frequency by processing the sensed vibration signal with adaptive filter algorithms of adaptive filters for each harmonic. Reference inputs for each harmonic are applied to the adaptive filter algorithms at the frequency of the selected harmonic. The harmonic balancing signals for all of the harmonics are summed with a principal control signal. The harmonic balancing signals modify the principal electrical drive voltage and drive the motor/alternator with a drive voltage component in opposition to the vibration at each harmonic.

Explaining the harmonic sequence paradox.

Science.gov (United States)

Schmidt, Ulrich; Zimper, Alexander

2012-05-01

According to the harmonic sequence paradox, an expected utility decision maker's willingness to pay for a gamble whose expected payoffs evolve according to the harmonic series is finite if and only if his marginal utility of additional income becomes zero for rather low payoff levels. Since the assumption of zero marginal utility is implausible for finite payoff levels, expected utility theory - as well as its standard generalizations such as cumulative prospect theory - are apparently unable to explain a finite willingness to pay. This paper presents first an experimental study of the harmonic sequence paradox. Additionally, it demonstrates that the theoretical argument of the harmonic sequence paradox only applies to time-patient decision makers, whereas the paradox is easily avoided if time-impatience is introduced. ©2011 The British Psychological Society.

Synthesis of variable harmonic impedance in inverter-interfaced distributed generation unit for harmonic damping throughout a distribution network

DEFF Research Database (Denmark)

Wang, Xiongfei; Blaabjerg, Frede; Chen, Zhe

2012-01-01

This paper proposes a harmonic impedance synthesis technique for voltage-controlled distributed generation inverter in order to damp harmonic voltage distortion on a distribution network. The approach employs a multiloop control scheme, where a selective load harmonic current feedforward loop bas...

Harmonic d-tensors

Energy Technology Data Exchange (ETDEWEB)

Hohmann, Manuel [Physikalisches Institut, Universitaet Tartu (Estonia)

2016-07-01

Tensor harmonics are a useful mathematical tool for finding solutions to differential equations which transform under a particular representation of the rotation group SO(3). In order to make use of this tool also in the setting of Finsler geometry, where the objects of relevance are d-tensors instead of tensors, we construct a set of d-tensor harmonics for both SO(3) and SO(4) symmetries and show how these can be used for calculations in Finsler geometry and gravity.

Fidelity of HIS4 start codon selection influences 3-Amino-1,2,4 ...

Indian Academy of Sciences (India)

Pankaj Alone

Fidelity of HIS4 start codon selection influences 3-Amino-1,2,4-Triazole (3AT) .... media in presence or absence of 3AT and harvested at 6000xg at room ..... The overnight cultures were serially diluted (with O.D600 of 0.5, 0.05, 0.005, 0.0005,.

Mycobacterium tuberculosis Is Resistant to Isoniazid at a Slow Growth Rate by Single Nucleotide Polymorphisms in katG Codon Ser315.

Directory of Open Access Journals (Sweden)

Rose E Jeeves

Full Text Available An important aim for improving TB treatment is to shorten the period of antibiotic therapy without increasing relapse rates or encouraging the development of antibiotic-resistant strains. In any M. tuberculosis population there is a proportion of bacteria that are drug-tolerant; this might be because of pre-existing populations of slow growing/non replicating bacteria that are protected from antibiotic action due to the expression of a phenotype that limits drug activity. We addressed this question by observing populations of either slow growing (constant 69.3h mean generation time or fast growing bacilli (constant 23.1h mean generation time in their response to the effects of isoniazid exposure, using controlled and defined growth in chemostats. Phenotypic differences were detected between the populations at the two growth rates including expression of efflux mechanisms and the involvement of antisense RNA/small RNA in the regulation of a drug-tolerant phenotype, which has not been explored previously for M. tuberculosis. Genotypic analyses showed that slow growing bacilli develop resistance to isoniazid through mutations specifically in katG codon Ser315 which are present in approximately 50-90% of all isoniazid-resistant clinical isolates. The fast growing bacilli persisted as a mixed population with katG mutations distributed throughout the gene. Mutations in katG codon Ser315 appear to have a fitness cost in vitro and particularly in fast growing cultures. Our results suggest a requirement for functional katG-encoded catalase-peroxide in the slow growers but not the fast-growing bacteria, which may explain why katG codon Ser315 mutations are favoured in the slow growing cultures.

Harmonic mappings into manifolds with boundary

International Nuclear Information System (INIS)

Chen Yunmei; Musina, R.

1989-08-01

In this paper we deal with harmonic maps from a compact Riemannian manifold into a manifold with boundary. In this case, a weak harmonic map is by definition a solution to a differential inclusion. In the first part of the paper we investigate the general properties of weak harmonic maps, which can be seen as solutions to a system of elliptic differential equations. In the second part we concentrate our attention on the heat flow method for harmonic maps. The result we achieve in this context extends a result by Chen and Struwe. (author). 21 refs

Power quality issues current harmonics

CERN Document Server

Mikkili, Suresh

2015-01-01

Power Quality Issues: Current Harmonics provides solutions for the mitigation of power quality problems related to harmonics. Focusing on active power filters (APFs) due to their excellent harmonic and reactive power compensation in two-wire (single phase), three-wire (three-phase without neutral), and four-wire (three-phase with neutral) AC power networks with nonlinear loads, the text:Introduces the APF technology, describing various APF configurations and offering guidelines for the selection of APFs for specific application considerationsCompares shunt active filter (SHAF) control strategi

Harmonic engine

Science.gov (United States)

Bennett, Charles L [Livermore, CA

2009-10-20

A high efficiency harmonic engine based on a resonantly reciprocating piston expander that extracts work from heat and pressurizes working fluid in a reciprocating piston compressor. The engine preferably includes harmonic oscillator valves capable of oscillating at a resonant frequency for controlling the flow of working fluid into and out of the expander, and also preferably includes a shunt line connecting an expansion chamber of the expander to a buffer chamber of the expander for minimizing pressure variations in the fluidic circuit of the engine. The engine is especially designed to operate with very high temperature input to the expander and very low temperature input to the compressor, to produce very high thermal conversion efficiency.

Harmonic Suppressed Slot Antennas Using Rectangular/Circular Defected Ground Structures

Directory of Open Access Journals (Sweden)

Mohammad Saeid Ghaffarian

2012-01-01

Full Text Available Two wide rectangle-shaped microstrip-fed 2.6-GHz slot antennas using defected ground structures (DGSs with a low design complexity are proposed to achieve wideband harmonic suppression. To accomplish this, two rectangular DGSs (RDGSs in the first antenna and two circular DGSs (CDGSs in the second one with various dimensions are etched into the ground plane, which could have a wideband-stop characteristic. Simulated and measured reflection coefficients indicate that the two proposed structures effectively suppress the second and third harmonics up to 23 dB between 3.5 and 10.5 GHz with a maximum ripple of 2.4 dB. In addition, the radiation patterns and peak gains of the antennas can be suppressed at least 17 dB and 7.1 dBi, respectively, at the third harmonic frequency of 7.86 GHz.

Predicting Harmonic Distortion of Multiple Converters in a Power System

Directory of Open Access Journals (Sweden)

P. M. Ivry

2017-01-01

Full Text Available Various uncertainties arise in the operation and management of power systems containing Renewable Energy Sources (RES that affect the systems power quality. These uncertainties may arise due to system parameter changes or design parameter choice. In this work, the impact of uncertainties on the prediction of harmonics in a power system containing multiple Voltage Source Converters (VSCs is investigated. The study focuses on the prediction of harmonic distortion level in multiple VSCs when some system or design parameters are only known within certain constraints. The Univariate Dimension Reduction (UDR method was utilized in this study as an efficient predictive tool for the level of harmonic distortion of the VSCs measured at the Point of Common Coupling (PCC to the grid. Two case studies were considered and the UDR technique was also experimentally validated. The obtained results were compared with that of the Monte Carlo Simulation (MCS results.

Probabilistic Harmonic Calculation in Distribution Networks with Electric Vehicle Charging Stations

Directory of Open Access Journals (Sweden)

Jianxue Wang

2014-01-01

Full Text Available Integrating EV charging station into power grid will bring impacts on power system, among which the most significant one is the harmonic pollution on distribution networks. Due to the uncertainty of the EV charging process, the harmonic currents brought by EV charging stations have a random nature. This paper proposed a mathematical simulation method for studying the working status of charging stations, which considers influencing factors including random leaving factor, electricity price, and waiting time. Based on the proposed simulation method, the probability distribution of the harmonic currents of EV charging stations is obtained and used in the calculation of the probability harmonic power flow. Then the impacts of EVs and EV charging stations on distribution networks can be analyzed. In the case study, the proposed simulation and analysis method is implemented on the IEEE-34 distribution network. The influences of EV arrival rates, the penetration rate, and the accessing location of EV charging station are also investigated. Results show that this research has good potential in guiding the planning and construction of charging station.

Coherent harmonics generated by a super-short electron pulse

International Nuclear Information System (INIS)

Ding Wu

1996-01-01

A novel mechanism generating superradiance harmonics is found. In this superradiance harmonics, the temporal width of harmonics is extremely short, the ratio of high harmonic fundamental wave is much higher than the known superradiance harmonics

Dual-harmonic auto voltage control for the rapid cycling synchrotron of the Japan Proton Accelerator Research Complex

Directory of Open Access Journals (Sweden)

Fumihiko Tamura

2008-07-01

Full Text Available The dual-harmonic operation, in which the accelerating cavities are driven by the superposition of the fundamental and the second harmonic rf voltage, is useful for acceleration of the ultrahigh intensity proton beam in the rapid cycling synchrotron (RCS of Japan Proton Accelerator Research Complex (J-PARC. However, the precise and fast voltage control of the harmonics is necessary to realize the dual-harmonic acceleration. We developed the dual-harmonic auto voltage control system for the J-PARC RCS. We describe details of the design and the implementation. Various tests of the system are performed with the RCS rf system. Also, a preliminary beam test has been done. We report the test results.

Harmonic lasing in X-ray FELs

Energy Technology Data Exchange (ETDEWEB)

Schneidmiller, E.A.; Yurkov, M.V.

2012-05-15

Harmonic lasing in a free electron laser with a planar undulator (under the condition that the fundamental frequency is suppressed) might be a cheap and efficient way of extension of wavelength ranges of existing and planned X-ray FEL facilities. Contrary to nonlinear harmonic generation, harmonic lasing can provide much more intense, stable, and narrow-band FEL beam which is easier to handle due to the suppressed fundamental frequency. In this paper we perform a parametrization of the solution of the eigenvalue equation for lasing at odd harmonics, and present an explicit expression for FEL gain length, taking into account all essential effects. We propose and discuss methods for suppression of the fundamental harmonic. We also suggest a combined use of harmonic lasing and lasing at the retuned fundamental wavelength in order to reduce bandwidth and to increase brilliance of X-ray beam at saturation. Considering 3rd harmonic lasing as a practical example, we come to the conclusion that it is much more robust than usually thought, and can be widely used in the existing or planned X-ray FEL facilities. In particular, LCLS after a minor modification can lase to saturation at the 3rd harmonic up to the photon energy of 25-30 keV providing multi-gigawatt power level and narrow bandwidth. As for the European XFEL, harmonic lasing would allow to extend operating range (ultimately up to 100 keV), to reduce FEL bandwidth and to increase brilliance, to enable two-color operation for pump-probe experiments, and to provide more flexible operation at different electron energies. Similar improvements can be realized in other X-ray FEL facilities with gap-tunable undulators like FLASH II, SACLA, LCLS II, etc. Harmonic lasing can be an attractive option for compact X-ray FELs (driven by electron beams with a relatively low energy), allowing the use of the standard undulator technology instead of small-gap in-vacuum devices. Finally, in this paper we discover that in a part of the

Symmetries in physics and harmonics

International Nuclear Information System (INIS)

Kolk, D.

2006-01-01

In this book the symmetries of elementary particles are described in relation to the rules of harmonics in music. The selection rules are described in connections with harmonic intervals. Also symmetry breaking is considered in this framework. (HSI)

Multipurpose Compensation Scheme for Voltage Sag/Swell and Selective Harmonics Elimination in Distribution Systems

Directory of Open Access Journals (Sweden)

Mustafa Inci

2018-01-01

Full Text Available Voltage harmonics, sag, and swell are the most harmful disturbances in distribution systems. This paper introduces a novel effective controller method for simultaneous compensation of both voltage sag/swell and voltage harmonics by using multifunctional dynamic voltage restorer. In proposed controller method called FFT with integrated ISRF, ISRF detects the magnitudes of voltage sag/swell quickly and precisely, and FFT extracts the selective components of voltage harmonics very effectively. The proposed method integrates the superior properties of ISRF and FFT methods. FFT integrated ISRF is applied for the first time to provide the compensation of both sag/swell and selective harmonics together. The proposed system has ability to compensate symmetrical/asymmetrical sag/swell and symmetrical/asymmetrical selective harmonics which are 5th, 7th, 11th and 13th. The controlled system is modelled in PSCAD/EMDTC and compared with conventional methods. The performance results verify that the proposed method compensates voltage disturbances effectively in the system.

Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data.

Science.gov (United States)

Bao, Le; Gu, Hong; Dunn, Katherine A; Bielawski, Joseph P

2007-02-08

Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous evolutionary dynamics among codon sites. These are called fixed-effect models, and they require that all codon sites are assigned to one of several partitions which are permitted to have independent parameters for selection pressure, evolutionary rate, transition to transversion ratio or codon frequencies. For single gene analysis, partitions might be defined according to protein tertiary structure, and for multiple gene analysis partitions might be defined according to a gene's functional category. Given a set of related fixed-effect models, the task of selecting the model that best fits the data is not trivial. In this study, we implement a set of fixed-effect codon models which allow for different levels of heterogeneity among partitions in the substitution process. We describe strategies for selecting among these models by a backward elimination procedure, Akaike information criterion (AIC) or a corrected Akaike information criterion (AICc). We evaluate the performance of these model selection methods via a simulation study, and make several recommendations for real data analysis. Our simulation study indicates that the backward elimination procedure can provide a reliable method for model selection in this setting. We also demonstrate the utility of these models by application to a single-gene dataset partitioned according to tertiary structure (abalone sperm lysin), and a multi-gene dataset partitioned according to the functional category of the gene (flagellar-related proteins of Listeria). Fixed-effect models have advantages and disadvantages. Fixed-effect models are desirable when data partitions are known to exhibit significant heterogeneity or when a statistical test of such heterogeneity is desired. They have the disadvantage of requiring a priori

Unassigned Codons, Nonsense Suppression, and Anticodon Modifications in the Evolution of the Genetic Code

NARCIS (Netherlands)

P.T.S. van der Gulik (Peter); W.D. Hoff (Wouter)

2011-01-01

htmlabstractThe origin of the genetic code is a central open problem regarding the early evolution of life. Here, we consider two undeveloped but important aspects of possible scenarios for the evolutionary pathway of the translation machinery: the role of unassigned codons in early stages

Harmonic generation effect in high-Tc films

International Nuclear Information System (INIS)

Khare, Neeraj; Shrivastava, S.K.; Padmanabhan, V.P.N.; Khare, Sangeeta; Gupta, A.K.

1997-01-01

Harmonic generation in thick BPSCCO and thin YBCO films are reported. The application of an ac field (H ac > H c1 ) of frequency f causes the generation of odd harmonics of frequency (2n+1)f. The application of dc field in addition to the ac field causes the appearance of even harmonics also in the BPSCCO film. However, the appearance of even harmonics is not observed in YBCO film with high J c ∼ 1.6x10 6 A/cm 2 and appearance of second harmonic with small magnitude is observed in YBCO film with low J c ∼ 2x10 3 A/cm 2 . The variation of amplitudes of these harmonics are studied as a function of magnitude of ac and dc field and the results are explained in the framework of critical state model. A high-T c film magnetometer based on the measurement of the amplitude of second harmonic has been developed whose field sensitivity is ∼ 1.5x10 -8 T. (author)

High-harmonic generation in a dense medium

International Nuclear Information System (INIS)

Strelkov, V.V.; Platonenko, V.T.; Becker, A.

2005-01-01

The high-harmonic generation in a plasma or gas under conditions when the single-atom response is affected by neighboring ions or atoms of the medium is studied theoretically. We solve numerically the three-dimensional Schroedinger equation for a single-electron atom in the combined fields of the neighboring particles and the laser, and average the results over different random positions of the particles using the Monte Carlo method. Harmonic spectra are calculated for different medium densities and laser intensities. We observe a change of the harmonic properties due to a random variation of the harmonic phase induced by the field of the medium, when the medium density exceeds a certain transition density. The transition density is found to depend on the harmonic order, but it is almost independent of the fundamental intensity. It also differs for the two (shorter and longer) quantum paths. The latter effect leads for ionic densities in the transition regime to a narrowing of the harmonic lines and a shortening of the attosecond pulses generated using a group of harmonics

Simulation of Dynamic Behavior of the Flexible Wheel of the Double Harmonic Gear Transmission

Directory of Open Access Journals (Sweden)

Draghiţa Ianici

2014-06-01

Full Text Available The paper presents the construction and functioning of a new type the harmonic gear transmission named double harmonic gear transmission, which can be used in the construction drives of industrial robots. In the second part of this paper is presented the dynamic analysis of the double harmonic gear transmission, which is based on the results of the numerical simulations of the flexible wheel in case of its deformation with a mechanical wave generator with disc cam. Investigation of dynamic behavior of the flexible toothed wheel was performed by using the finite element method in SolidWorks Simulation software.

Harmonization of monographic standards is needed to ensure the quality of Chinese medicinal materials

Directory of Open Access Journals (Sweden)

Zhao Sandy

2009-09-01

Full Text Available Abstract This article provides an overview on the regulations of Chinese medicinal materials (CMMs in various countries and regions. Harmonization of CMM monographs would provide standards for the quality control of CMM products and play an important role in the modernization and globalization of Chinese medicine. A harmonized regulatory system would improve the quality of CMMs thereby ensuring the safety of the products and assisting Chinese medicine practitioners in their practice. The fast growing demand worldwide for traditional medicines calls for harmonized monographic standards to safeguard the safety and quality of CMM products.

Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion

Science.gov (United States)

Heinemann, Ilka U.; Rovner, Alexis J.; Aerni, Hans R.; Rogulina, Svetlana; Cheng, Laura; Olds, William; Fischer, Jonathan T.; Söll, Dieter; Isaacs, Farren J.; Rinehart, Jesse

2012-01-01

Genetically encoded phosphoserine incorporation programmed by the UAG codon was achieved by addition of engineered elongation factor and an archaeal aminoacyl-tRNA synthetase to the normal Escherichia coli translation machinery (Park (2011) Science 333, 1151). However, protein yield suffers from expression of the orthogonal phosphoserine translation system and competition with release factor 1 (RF-1). In a strain lacking RF-1, phosphoserine phosphatase, and where 7 UAG codons residing in essential genes were converted to UAA, phosphoserine incorporation into GFP and WNK4 was significantly elevated, but with an accompanying loss in cellular fitness and viability. PMID:22982858

Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11.

Science.gov (United States)

Li, Manqing; Kao, Elaine; Gao, Xia; Sandig, Hilary; Limmer, Kirsten; Pavon-Eternod, Mariana; Jones, Thomas E; Landry, Sebastien; Pan, Tao; Weitzman, Matthew D; David, Michael

2012-11-01

In mammals, one of the most pronounced consequences of viral infection is the induction of type I interferons, cytokines with potent antiviral activity. Schlafen (Slfn) genes are a subset of interferon-stimulated early response genes (ISGs) that are also induced directly by pathogens via the interferon regulatory factor 3 (IRF3) pathway. However, many ISGs are of unknown or incompletely understood function. Here we show that human SLFN11 potently and specifically abrogates the production of retroviruses such as human immunodeficiency virus 1 (HIV-1). Our study revealed that SLFN11 has no effect on the early steps of the retroviral infection cycle, including reverse transcription, integration and transcription. Rather, SLFN11 acts at the late stage of virus production by selectively inhibiting the expression of viral proteins in a codon-usage-dependent manner. We further find that SLFN11 binds transfer RNA, and counteracts changes in the tRNA pool elicited by the presence of HIV. Our studies identified a novel antiviral mechanism within the innate immune response, in which SLFN11 selectively inhibits viral protein synthesis in HIV-infected cells by means of codon-bias discrimination.

Comparative investigation of the various determinants that influence the codon and amino acid usage patterns in the genus Bifidobacterium.

Science.gov (United States)

Roy, Ayan; Mukhopadhyay, Subhasish; Sarkar, Indrani; Sen, Arnab

2015-06-01

Various strains of the genus Bifidobacterium are crucial members of the human, animal and insect gut, associated with beneficial probiotic activities. An extensive analysis on codon and amino acid usage of the GC rich genus Bifidobacterium has been executed in the present study. Multivariate statistical analysis revealed a coupled effect of GC compositional constraint and natural selection for translational efficiency to be operative in producing the observed codon usage variations. Gene expression level was inferred to be the most crucial factor governing the codon usage patterns. Amino acid usage was found to be influenced significantly by hydrophobic and aromatic character of the encoded proteins. Gene expressivity and protein energetic cost also had considerable impact on the differential mode of amino acid usage. The genus was found to strictly obey the cost-minimization hypothesis as was reflected from the amino acid usage patterns of the potential highly expressed gene products. Evolutionary analysis revealed that the highly expressed genes were candidates to extreme evolutionary selection pressure and indicated a high degree of conservation at the proteomic level. Interestingly, the complimentary strands of replication appeared to evolve under similar evolutionary constraints which might be addressed as a consequence of absence of replicational selection and lack of strand-specific asymmetry among the members of the genus. Thus, the present endeavor confers considerable know-how pertaining to the codon and amino acid usage intricacies in Bifidobacterium and might prove handy for further scientific investigations associated with the concerned domain.

Harmonic sums and polylogarithms generated by cyclotomic polynomials

Energy Technology Data Exchange (ETDEWEB)

Ablinger, Jakob; Schneider, Carsten [Johannes Kepler Univ., Linz (Austria). Research Inst. for Symbolic Computation; Bluemlein, Johannes [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany)

2011-05-15

The computation of Feynman integrals in massive higher order perturbative calculations in renormalizable Quantum Field Theories requires extensions of multiply nested harmonic sums, which can be generated as real representations by Mellin transforms of Poincare-iterated integrals including denominators of higher cyclotomic polynomials. We derive the cyclotomic harmonic polylogarithms and harmonic sums and study their algebraic and structural relations. The analytic continuation of cyclotomic harmonic sums to complex values of N is performed using analytic representations. We also consider special values of the cyclotomic harmonic polylogarithms at argument x=1, resp., for the cyclotomic harmonic sums at N{yields}{infinity}, which are related to colored multiple zeta values, deriving various of their relations, based on the stuffle and shuffle algebras and three multiple argument relations. We also consider infinite generalized nested harmonic sums at roots of unity which are related to the infinite cyclotomic harmonic sums. Basis representations are derived for weight w=1,2 sums up to cyclotomy l=20. (orig.)

Harmonic currents circulation in electrical networks simulation and analysis

Energy Technology Data Exchange (ETDEWEB)

Em-Mamlouk, W.M. [MEP, Cairo (Egypt); El-Sharkawy, M.A. [Shams Univ., Cairo (Egypt). Dept. of Electrical Power and Machines; Mostafa, H.E. [Jazan Univ., Jazan (Saudi Arabia). Electrical Dept.

2009-07-01

A detailed harmonic flow analysis for a 13-bus balanced industrial distribution system was presented. The aim of the study was to determine the influence of harmonic sources in various branches of the system on voltage and current waveforms before disruptions to the utility supply system occurred. The current harmonic contents of an adjustable speed drive (ASD) were studied under various loading conditions. The test system was simulated using a standard study test system. Harmonic effects from multiple sources were investigated, and voltage distortion on the different buses was monitored. The study demonstrated that while the harmonic loads circulated harmonic currents in all system branches, no harmonic source was directly connected to the system buses. Many of the investigated cases exceeded allowable voltage total harmonic distortion and or current total harmonic distortion standards set by the Institute of Electrical and Electronic Engineers (IEEE). It was concluded that active harmonic filters should be used to prevent the effects of harmonic current circulation at different buses on neighbouring loads within a system. 8 refs., 11 tabs., 15 figs.

Exact solution of the time-dependent harmonic plus an inverse harmonic potential with a time-dependent electromagnetic field

International Nuclear Information System (INIS)

Yuece, Cem

2003-01-01

In this paper, the problem of the charged harmonic plus an inverse harmonic oscillator with time-dependent mass and frequency in a time-dependent electromagnetic field is investigated. It is reduced to the problem of the inverse harmonic oscillator with time-independent parameters and the exact wave function is obtained

Association of the p53 codon 72 polymorphism to gastric cancer risk in a high risk population of Costa Rica

International Nuclear Information System (INIS)

Alpizar-Alpizar, Warner; Sierra, Rafaela; Cuenca, Patricia; Une, Clas; Mena, Fernando; Perez-Perez, Guillermo Ignacio

2005-01-01

Gastric cancer is the second most common cancer associated death cause worldwide. Several factors have been associated with higher risk to develop gastric cancer, among them genetic predisposition. The p53 gene has a polymorphism located at codon 72, which has been associated with higher risk of several types of cancer, including gastric cancer. The aim of this study was to determine the association of p53, codon 72 polymorphism, with the risk of gastric cancer and pre-malignant lesions in a high-risk population from Costa Rica. The genotyping was carried out by PCR-RFLP in a sample of 58 gastric cancer patients, 99 control persons and 41 individuals classified as group I and II, according to the Japanese histological classification. No association was found for p53, codon 72 polymorphism with neither the risk of gastric cancer nor the risk of less severe gastric lesions in the studied sample. Based on this study and taking into account other studies carried out with p53, codon 72 polymorphism, the role of this polymorphism in the development of gastric cancer remains unclear. De novo mutations on p53 gene produced during neoplastic development of this disease might play a greater role than germinal polymorphisms of this same gene. Other polymorphic genes have been associated with higher risk to develop gastric cancer. (author) [es

Young children's harmonic perception.

Science.gov (United States)

Costa-Giomi, Eugenia

2003-11-01

Harmony and tonality are two of the most difficult elements for young children to perceive and manipulate and are seldom taught in the schools until the end of early childhood. Children's gradual harmonic and tonal development has been attributed to their cumulative exposure to Western tonal music and their increasing experiential knowledge of its rules and principles. Two questions that are relevant to this problem are: (1) Can focused and systematic teaching accelerate the learning of the harmonic/tonal principles that seem to occur in an implicit way throughout childhood? (2) Are there cognitive constraints that make it difficult for young children to perceive and/or manipulate certain harmonic and tonal principles? A series of studies specifically addressed the first question and suggested some possible answers to the second one. Results showed that harmonic instruction has limited effects on children's perception of harmony and indicated that the drastic improvement in the perception of implied harmony noted approximately at age 9 is due to development rather than instruction. I propose that young children's difficulty in perceiving implied harmony stems from their attention behaviors. Older children have less memory constraints and more strategies to direct their attention to the relevant cues of the stimulus. Younger children focus their attention on the melody, if present in the stimulus, and specifically on its concrete elements such as rhythm, pitch, and contour rather than its abstract elements such as harmony and key. The inference of the abstract harmonic organization of a melody required in the perception of implied harmony is thus an elusive task for the young child.

Classical and multilinear harmonic analysis

CERN Document Server

Muscalu, Camil

2013-01-01

This two-volume text in harmonic analysis introduces a wealth of analytical results and techniques. It is largely self-contained and useful to graduates and researchers in pure and applied analysis. Numerous exercises and problems make the text suitable for self-study and the classroom alike. The first volume starts with classical one-dimensional topics: Fourier series; harmonic functions; Hilbert transform. Then the higher-dimensional Calderón-Zygmund and Littlewood-Paley theories are developed. Probabilistic methods and their applications are discussed, as are applications of harmonic analysis to partial differential equations. The volume concludes with an introduction to the Weyl calculus. The second volume goes beyond the classical to the highly contemporary and focuses on multilinear aspects of harmonic analysis: the bilinear Hilbert transform; Coifman-Meyer theory; Carleson's resolution of the Lusin conjecture; Calderón's commutators and the Cauchy integral on Lipschitz curves. The material in this vo...

Higher order harmonics of reactor neutron equation

International Nuclear Information System (INIS)

Li Fu; Hu Yongming; Luo Zhengpei

1996-01-01

The flux mapping method using the higher order harmonics of the neutron equation is proposed. Based on the bi-orthogonality of the higher order harmonics, the process and formulas for higher order harmonics calculation are derived via the source iteration method with source correction. For the first time, not only any order harmonics for up-to-3-dimensional geometry are achieved, but also the preliminary verification to the capability for flux mapping have been carried out

Bounce-harmonic Landau Damping of Plasma Waves

Science.gov (United States)

Anderegg, Francois

2015-11-01

We present measurement of plasma wave damping, spanning the temperature regimes of direct Landau damping, bounce-harmonic Landau damping, inter-species drag damping, and viscous damping. Direct Landau damping is dominant at high temperatures, but becomes negligible as v vph / 5 . The measurements are conducted in trapped pure ion plasmas contained in Penning-Malmberg trap, with wave-coherent LIF diagnostics of particle velocities. Our focus is on bounce harmonics damping, controlled by an applied ``squeeze'' potential, which generates harmonics in the wave potential and in the particle dynamics. A particle moving in z experiences a non-sinusoidal mode potential caused by the squeeze, producing high spatial harmonics with lower phase velocity. These harmonics are Landau damped even when the mode phase velocity vph is large compared to the thermal velocity v , since the nth harmonic is resonant with a particle bouncing at velocity vb =vph / n . Here we increase the bounce harmonics through applied squeeze potential; but some harmonics are always present in finite length systems. For our centered squeeze geometry, theory shows that only odd harmonics are generated, and predicts the Landau damping rate from vph / n . Experimentally, the squeeze potential increases the wave damping and reduces its frequency. The frequency shift occurs because the squeeze potential reduces the number of particle where the mode velocity is the largest, therefore reducing the mode frequency. We observe an increase in the damping proportional to Vs2,and a frequency reduction proportional to Vs , in quantitative agreement with theory. Wave-coherent laser induced fluorescence allows direct observation of bounce resonances on the particle distribution, here predominantly at vph / 3 . A clear increase of the bounce harmonics is visible on the particle distribution when the squeeze potential is applied. Supported by NSF Grant PHY-1414570, and DOE Grants DE-SC0002451 and DE-SC0008693.

CURRENT TRENDS IN TAX HARMONIZATION AND COMPETITION WITHIN THE EUROPEAN UNION

Directory of Open Access Journals (Sweden)

Gherman Adela-Teodora

2010-12-01

Full Text Available This article treats on the fiscal harmonization process within the European Union being indispensable for assuring loyalty in the competition on its single market, given the fact that different system of taxation had direct and powerful impact on the prices level and on chosing the location for production and distribution activities. Both direct and indirect taxation distort the four fundamental freedoms of the single market. Most of the European Unions regulations regarding fiscal harmonization resemble to the Directive regarding especially the indirect taxes: VAT, Excises. The fiscal reforms from the member states have to be conceived in such a manner that they take into account the necessity of fiscal harmonization on EU level, creating a reasonable compromise between each country's sovereignty and the desideratum of removing fiscal barriers from the normal functioning of the single market.

Understanding fifth-harmonic generation in CLBO

Science.gov (United States)

Patankar, S.; Yang, S. T.; Moody, J. D.; Bayramian, A. J.; Swadling, G. F.; Barker, D.; Datte, P.; Mennerat, G.; Norton, M.; Carr, C. W.; Begishev, I. A.; Bromage, J.; Ross, J. S.

2018-02-01

We report on results of fifth harmonic generation in Cesium Lithium Borate (CLBO) using a three-crystal cascaded frequency conversion scheme designed to study the energy balance of the final sum frequency generation stage. The experimental setup independently combines the first and fourth harmonic of a Nd:Glass laser in a 5mm thick CLBO crystal. Energy balance between the incoming and output energy is close to unity when the CLBO is out of phase matching and approximately 80% when the crystal is in phase matching. A detailed analysis of the residual fundamental and fourth harmonic energy indicates 5th harmonic light is being generated but only 26% is unaccounted for. We attribute the missing light to linear transmission loss in the CLBO oven. The ratio of the output to input energy is unity when the missing 5th harmonic is incorporated into the calculations. Two-dimensional plane wave mixing simulations show agreement with the results at lower intensities.

Harmonic Mitigation Using a Polarized Ramp-time Current-Controlled Inverter

Directory of Open Access Journals (Sweden)

Lawrence J. Borle

2010-12-01

Full Text Available This paper describes the implementation of a shunt active power filter for a three-phase four-wire system to compensate for power quality problems generated by mixed non-linear loads, which are a combination of harmonic, reactive and unbalanced components. The filter is a three-phase current-controlled voltage source inverter (CC-VSI with a filter inductor at the AC output and a DC-bus capacitor. The CC-VSI is operated to directly control the grid current to be sinusoidal and in phase with the grid voltage without sensing the load currents. The switching is controlled using polarized ramp-time current control, which is based on the concept of zero average current error (ZACE with a fixed switching frequency. The laboratory experiment results indicate that the filter is able to mitigate predominantly the harmonics, as well as the reactive power, so that the grid currents are sinusoidal, in phase with the grid voltages and symmetrical although the grid voltage contains harmonics.

Codon optimization of the HIV-1 vpu and vif genes stabilizes their mRNA and allows for highly efficient Rev-independent expression

International Nuclear Information System (INIS)

Nguyen, Kim-Lien; Llano, Manuel; Akari, Hirofumi; Miyagi, Eri; Poeschla, Eric M.; Strebel, Klaus; Bour, Stephan

2004-01-01

Two HIV-1 accessory proteins, Vpu and Vif, are notoriously difficult to express autonomously in the absence of the viral Tat and Rev proteins. We examined whether the codon bias observed in the vpu and vif genes relative to highly expressed human genes contributes to the Rev dependence and low expression level outside the context of the viral genome. The entire vpu gene as well as the 5' half of the vif gene were codon optimized and the resulting open reading frames (ORFs) (vphu and hvif, respectively) were cloned in autonomous expression vectors under the transcriptional control of the CMV promoter. Codon optimization efficiently removed the expression block observed in the native genes and allowed high levels of Rev- and Tat-independent expression of Vpu and Vif. Most of the higher protein levels detected are accounted for by enhanced steady-state levels of the mRNA encoding the optimized species. Nuclear run-on experiments show for the first time that codon optimization has no effect on the rate of transcriptional initiation or elongation of the vphu mRNA. Instead, optimization of the vpu gene was found to stabilize the vphu mRNA in the nucleus and enhance its export to the cytoplasm. This was achieved by allowing the optimized mRNA to use a new CRM1-independent nuclear export pathway. This work provides a better understanding of the molecular mechanisms underlying the process of codon optimization and introduces novel tools to study the biological functions of the Vpu and Vif proteins independently of other viral proteins

Third Harmonic Imaging using a Pulse Inversion

DEFF Research Database (Denmark)

Rasmussen, Joachim; Du, Yigang; Jensen, Jørgen Arendt

2011-01-01

The pulse inversion (PI) technique can be utilized to separate and enhance harmonic components of a waveform for tissue harmonic imaging. While most ultrasound systems can perform pulse inversion, only few image the 3rd harmonic component. PI pulse subtraction can isolate and enhance the 3rd...

Validation Techniques of network harmonic models based on switching of a series linear component and measuring resultant harmonic increments

DEFF Research Database (Denmark)

Wiechowski, Wojciech Tomasz; Lykkegaard, Jan; Bak, Claus Leth

2007-01-01

In this paper two methods of validation of transmission network harmonic models are introduced. The methods were developed as a result of the work presented in [1]. The first method allows calculating the transfer harmonic impedance between two nodes of a network. Switching a linear, series network......, as for example a transmission line. Both methods require that harmonic measurements performed at two ends of the disconnected element are precisely synchronized....... are used for calculation of the transfer harmonic impedance between the nodes. The determined transfer harmonic impedance can be used to validate a computer model of the network. The second method is an extension of the fist one. It allows switching a series element that contains a shunt branch...

Research on the influence of driving harmonic on electromagnetic field and temperature field of permanent magnet synchronous motor

Directory of Open Access Journals (Sweden)

Qiu Hongbo

2017-06-01

Full Text Available At present, the drivers with different control methods are used in most of permanent magnet synchronous motors (PMSM. A current outputted by a driver contains a large number of harmonics that will cause the PMSM torque ripple, winding heating and rotor temperature rise too large and so on. In this paper, in order to determine the influence of the current harmonics on the motor performance, different harmonic currents were injected into the motor armature. Firstly, in order to study the influence of the current harmonic on the motor magnetic field, a novel decoupling method of the motor magnetic field was proposed. On this basis, the difference of harmonic content in an air gap magnetic field was studied, and the influence of a harmonic current on the air gap flux density was obtained. Secondly, by comparing the fluctuation of the motor torque in the fundamental and different harmonic currents, the influence of harmonic on a motor torque ripple was determined. Then, the influence of different current harmonics on the eddy current loss of the motor was compared and analyzed, and the influence of the drive harmonic on the eddy current loss was obtained. Finally, by using a finite element method (FEM, the motor temperature distribution with different harmonics was obtained.

Benefits from the BESSY FEL Higher Harmonic Radiation

CERN Document Server

Goldammer, K

2005-01-01

In the FEL process, bunching and coherent radiation is produced at the fundamental frequency as well as its higher harmonics. BESSY proposes a linac-based cascaded High-Gain Harmonic-Generation (HGHG) free electron laser (FEL) multi-user facility. The BESSY soft X-ray FEL will be seeded by three lasers spanning the spectral range of 230nm to 460nm. Two to four HGHG stages downconvert the seed wavelength to the desired radiation range of 1.24nm to 51nm using higher harmonic bunching. As a surplus, higher harmonic radiation is intrinsically produced in each FEL stage. Radiation on a higher harmonic of the FEL frequency is of high interest because it yields the possibility to reduce the number of FEL stages. This paper details extensive studies of the higher harmonic content of the BESSY FEL radiation. Important aspects of FEL interaction on higher harmonics as resulting from theory and from numerical simulations are discussed. For the case of the BESSY FEL, methods for improving the harmonic content are present...

Hermitian harmonic maps into convex balls

International Nuclear Information System (INIS)

Li Zhenyang; Xi Zhang

2004-07-01

In this paper, we consider Hermitian harmonic maps from Hermitian manifolds into convex balls. We prove that there exist no non-trivial Hermitian harmonic maps from closed Hermitian manifolds into convex balls, and we use the heat flow method to solve the Dirichlet problem for Hermitian harmonic maps when the domain is compact Hermitian manifold with non-empty boundary. The case where the domain manifold is complete(noncompact) is also studied. (author)

A study of parametric instability in a harmonic gyrotron: Designs of third harmonic gyrotrons at 94 GHz and 210 GHz

International Nuclear Information System (INIS)

Saraph, G.P.; Antonsen, T.M. Jr.; Nusinovich, G.S.; Levush, B.

1995-01-01

Mode competition can present a major hurdle in achieving stable, efficient operation of a gyrotron at the cyclotron harmonics. A type of mode interaction in which three modes at different cyclotron harmonics are parametrically coupled together is analyzed here. This coupling can lead to parametric excitation or suppression of a mode; cyclic mode hopping; or the coexistence of three modes. Simulation results are presented for the parametric instability involving modes at the fundamental, second harmonic, and third harmonic of the cyclotron frequency. It is shown that the parametric excitation can lead to stable, efficient operation of a high-power gyrotron at the third harmonic. Based on this phenomenon, two practical designs are presented here for the third harmonic operation at 94 and 210 GHz. copyright 1995 American Institute of Physics

Harmonic disturbance location by applying Bayesian inference

NARCIS (Netherlands)

Ye, G.; Xiang, Y.; Cuk, V.; Cobben, J.F.G.

2016-01-01

Harmonic pollution is one of the most important power quality issues in electric power systems. Correct location of the main harmonic disturbance source is a key step to solve the problem. This paper presents a method to detect the location of harmonic disturbance source in low voltage network

Introduction to classical and quantum harmonic oscillators

CERN Document Server

Bloch, Sylvan C

2013-01-01

From conch shells to lasers . harmonic oscillators, the timeless scientific phenomenon As intriguing to Galileo as they are to scientists today, harmonic oscillators have provided a simple and compelling paradigm for understanding the complexities that underlie some of nature's and mankind's most fascinating creations. From early string and wind instruments fashioned from bows and seashells to the intense precision of lasers, harmonic oscillators have existed in various forms, as objects of beauty and scientific use. And harmonic oscillation has endured as one of science's most fascinating con

Dual aperture dipole magnet with second harmonic component

Science.gov (United States)

Praeg, Walter F.

1985-01-01

An improved dual aperture dipole electromagnet includes a second-harmonic frequency magnetic guide field winding which surrounds first harmonic frequency magnetic guide field windings associated with each aperture. The second harmonic winding and the first harmonic windings cooperate to produce resultant magnetic waveforms in the apertures which have extended acceleration and shortened reset portions of electromagnet operation.

Effect of the nucleotides surrounding the start codon on the translation of foot-and-mouth disease virus RNA.

Science.gov (United States)

Ma, X X; Feng, Y P; Gu, Y X; Zhou, J H; Ma, Z R

2016-06-01

As for the alternative AUGs in foot-and-mouth disease virus (FMDV), nucleotide bias of the context flanking the AUG(2nd) could be used as a strong signal to initiate translation. To determine the role of the specific nucleotide context, dicistronic reporter constructs were engineered to contain different versions of nucleotide context linking between internal ribosome entry site (IRES) and downstream gene. The results indicate that under FMDV IRES-dependent mechanism, the nucleotide contexts flanking start codon can influence the translation initiation efficiencies. The most optimal sequences for both start codons have proved to be UUU AUG(1st) AAC and AAG AUG(2nd) GAA.

Effect of Polymorphisms at Codon 146 of the Goat PRNP Gene on Susceptibility to Challenge with Classical Scrapie by Different Routes.

Science.gov (United States)

Papasavva-Stylianou, Penelope; Simmons, Marion Mathieson; Ortiz-Pelaez, Angel; Windl, Otto; Spiropoulos, John; Georgiadou, Soteria

2017-11-15

This report presents the results of experimental challenges of goats with scrapie by both the intracerebral (i.c.) and oral routes, exploring the effects of polymorphisms at codon 146 of the goat PRNP gene on resistance to disease. The results of these studies illustrate that while goats of all genotypes can be infected by i.c. challenge, the survival distribution of the animals homozygous for asparagine at codon 146 was significantly shorter than those of animals of all other genotypes (chi-square value, 10.8; P = 0.001). In contrast, only those animals homozygous for asparagine at codon 146 (NN animals) succumbed to oral challenge. The results also indicate that any cases of infection in non-NN animals can be detected by the current confirmatory test (immunohistochemistry), although successful detection with the rapid enzyme-linked immunosorbent assay (ELISA) was more variable and dependent on the polymorphism. Together with data from previous studies of goats exposed to infection in the field, these data support the previously reported observations that polymorphisms at this codon have a profound effect on susceptibility to disease. It is concluded that only animals homozygous for asparagine at codon 146 succumb to scrapie under natural conditions. IMPORTANCE In goats, like in sheep, there are PRNP polymorphisms that are associated with susceptibility or resistance to scrapie. However, in contrast to the polymorphisms in sheep, they are more numerous in goats and may be restricted to certain breeds or geographical regions. Therefore, eradication programs must be specifically designed depending on the identification of suitable polymorphisms. An initial analysis of surveillance data suggested that such a polymorphism in Cypriot goats may lie in codon 146. In this study, we demonstrate experimentally that NN animals are highly susceptible after i.c. inoculation. The presence of a D or S residue prolonged incubation periods significantly, and prions were detected

Transient regime in second harmonic generation

Science.gov (United States)

Szeftel, Jacob; Sandeau, Laure; Sandeau, Nicolas; Delezoide, Camille; Khater, Antoine

2013-09-01

The time growth of the electromagnetic field at the fundamental and double frequencies is studied from the very onset of the second harmonic generation (SHG) process for a set of dipoles lacking a symmetry centre and exhibiting a nonresonant coupling with a classical electromagnetic field. This approach consists first of solving the Schrödinger equation by applying a generalised Rabi rotation to the Hamiltonian describing the light-dipole interaction. This rotation has been devised for the resulting Hamiltonian to show up time-independent for both components of the electromagnetic field at the fundamental frequency and the second harmonic one. Then an energy conservation argument, derived from the Poynting theorem, is introduced to work out an additional relationship between the electromagnetic field and its associated electric polarisation. Finally this analysis yields the full time behaviour of all physical quantities of interest. The calculated results reproduce accurately both the observed spatial oscillations of the SHG intensity (Maker's fringes) and its power law dependence on the intensity of the incoming light at the fundamental frequency.

Fast harmonic field mapper

International Nuclear Information System (INIS)

Au, R.; Fowler, M.; Hanawa, H.; Riedel, J.; Qua, Z.G.

1984-01-01

In early 1983 it was decided to mount coils on arms separated by 120 degrees and buck them out so that the third harmonic dphi/dt component would be cancelled and thus the first and second field harmonics could be very accurately measured. The original intention was to do as others had done, namely, use fast ADC's to read the voltages, and computer process the result to get the Fourier components. However, because of the 100 to 1 dynamic range of the fast ADC's and the likelihood that noise would be a problem, the authors decided to do things differently. Using a fast Fourier transform analyzer was considered, but this instrument is very expensive, so they decided to use a completely electronic analog approach: The authors decided to use active bandpass filters to render the harmonic components

Contribution of single amino acid and codon substitutions to the production and secretion of a lipase by Bacillus subtilis.

Science.gov (United States)

Skoczinski, Pia; Volkenborn, Kristina; Fulton, Alexander; Bhadauriya, Anuseema; Nutschel, Christina; Gohlke, Holger; Knapp, Andreas; Jaeger, Karl-Erich

2017-09-25

Bacillus subtilis produces and secretes proteins in amounts of up to 20 g/l under optimal conditions. However, protein production can be challenging if transcription and cotranslational secretion are negatively affected, or the target protein is degraded by extracellular proteases. This study aims at elucidating the influence of a target protein on its own production by a systematic mutational analysis of the homologous B. subtilis model protein lipase A (LipA). We have covered the full natural diversity of single amino acid substitutions at 155 positions of LipA by site saturation mutagenesis excluding only highly conserved residues and qualitatively and quantitatively screened about 30,000 clones for extracellular LipA production. Identified variants with beneficial effects on production were sequenced and analyzed regarding B. subtilis growth behavior, extracellular lipase activity and amount as well as changes in lipase transcript levels. In total, 26 LipA variants were identified showing an up to twofold increase in either amount or activity of extracellular lipase. These variants harbor single amino acid or codon substitutions that did not substantially affect B. subtilis growth. Subsequent exemplary combination of beneficial single amino acid substitutions revealed an additive effect solely at the level of extracellular lipase amount; however, lipase amount and activity could not be increased simultaneously. Single amino acid and codon substitutions can affect LipA secretion and production by B. subtilis. Several codon-related effects were observed that either enhance lipA transcription or promote a more efficient folding of LipA. Single amino acid substitutions could improve LipA production by increasing its secretion or stability in the culture supernatant. Our findings indicate that optimization of the expression system is not sufficient for efficient protein production in B. subtilis. The sequence of the target protein should also be considered as an

The Methodological Background for Harmonizing Components of Sustainable Development of an Industrial City

Directory of Open Access Journals (Sweden)

Prushkivskyj Volodymyr G.

2016-11-01

Full Text Available The aim of the article is to develop a methodological background for harmonizing components of sustainable development of an industrial city. The ways of harmonization of economic, environmental and social components are studied. It is proposed to use the rule of «golden ratio» to determine the «ideal» values of the components of sustainable development. On the basis of the index method the components of sustainable development are evaluated. The comparative analysis of the actual and harmonic distribution between the sub-indices of sustainable development is performed. Based on the rule of «golden ratio» it is proved that the harmonization allows to state the existence of differences as well as to carry out a quantitative analysis. It is justified that the existence of disharmony between the components of sustainable development requires elaboration of an appropriate mechanism on the basis of redistribution of investment resources as well as other economic instruments to support the components at a certain level.

Stability and nonlinear dynamics of gyrotrons at cyclotron harmonics

International Nuclear Information System (INIS)

Saraph, G.P.; Nusinovich, G.S.; Antonsen, T.M. Jr.; Levush, B.

1992-01-01

Gyrotrons operating at higher harmonics of the cyclotron frequency can overcome the frequency limitations caused by achievable strength of the magnetic field. However, the excitation of modes at the fundamental frequency exhibit a major problem for stable operation of harmonic gyrotron at high power with high efficiency. Therefore the issues of stability of gyrotron operation at the cyclotron harmonics and nonlinear dynamics of mode interaction are of great importance. The results of the authors stability analysis and multimode simulation are presented here. A detailed nonlinear theory of steady state single mode operation at cyclotron harmonics has been presented previously, taking into account beam-wave coupling and nonlinear gain function at cyclotron harmonics. A set of equations describing low gain regime interaction of modes resonant at different cyclotron harmonics was studied before. The multifrequency time-dependent nonlinear analysis presented here is based on previous gyrotron studies and beam-wave interaction at cyclotron harmonics. The authors have determined the parameter space for stable single mode operation at the second harmonic. The nonlinear dynamics of mode evolution and mode interaction for a harmonic gyrotron is presented. A new nonlinear effect in which the parasite at the fundamental harmonic helps excite the operating mode at the second harmonic has been demonstrated

Detection of Harmonic Occurring using Kalman Filtering

DEFF Research Database (Denmark)

Hussain, Dil Muhammad Akbar; Shoro, Ghulam Mustafa; Imran, Raja Muhammed

2014-01-01

/current characteristic. These harmonics are not to be allowed to grow beyond a certain limit to avoid any grave consequence to the customer’s main supply. Filters can be implemented at the power source or utility location to eliminate these harmonics. In this paper we detect the instance at which these harmonics occur...

High order harmonic generation in rare gases

Energy Technology Data Exchange (ETDEWEB)

Budil, Kimberly Susan [Univ. of California, Davis, CA (United States)

1994-05-01

The process of high order harmonic generation in atomic gases has shown great promise as a method of generating extremely short wavelength radiation, extending far into the extreme ultraviolet (XUV). The process is conceptually simple. A very intense laser pulse (I ~10¹³-10¹⁴ W/cm²) is focused into a dense (~10¹⁷ particles/cm³) atomic medium, causing the atoms to become polarized. These atomic dipoles are then coherently driven by the laser field and begin to radiate at odd harmonics of the laser field. This dissertation is a study of both the physical mechanism of harmonic generation as well as its development as a source of coherent XUV radiation. Recently, a semiclassical theory has been proposed which provides a simple, intuitive description of harmonic generation. In this picture the process is treated in two steps. The atom ionizes via tunneling after which its classical motion in the laser field is studied. Electron trajectories which return to the vicinity of the nucleus may recombine and emit a harmonic photon, while those which do not return will ionize. An experiment was performed to test the validity of this model wherein the trajectory of the electron as it orbits the nucleus or ion core is perturbed by driving the process with elliptically, rather than linearly, polarized laser radiation. The semiclassical theory predicts a rapid turn-off of harmonic production as the ellipticity of the driving field is increased. This decrease in harmonic production is observed experimentally and a simple quantum mechanical theory is used to model the data. The second major focus of this work was on development of the harmonic "source". A series of experiments were performed examining the spatial profiles of the harmonics. The quality of the spatial profile is crucial if the harmonics are to be used as the source for experiments, particularly if they must be refocused.

The p53 codon 72 PRO/PRO genotype may be associated with initial central visual field defects in caucasians with primary open angle glaucoma.

Directory of Open Access Journals (Sweden)

Janey L Wiggs

Full Text Available Loss of vision in glaucoma is due to apoptotic retinal ganglion cell loss. While p53 modulates apoptosis, gene association studies between p53 variants and glaucoma have been inconsistent. In this study we evaluate the association between a p53 variant functionally known to influence apoptosis (codon 72 Pro/Arg and the subset of primary open angle glaucoma (POAG patients with early loss of central visual field.Genotypes for the p53 codon 72 polymorphism (Pro/Arg were obtained for 264 POAG patients and 400 controls from the U.S. and in replication studies for 308 POAG patients and 178 controls from Australia (GIST. The glaucoma patients were divided into two groups according to location of initial visual field defect (either paracentral or peripheral. All cases and controls were Caucasian with European ancestry.The p53-PRO/PRO genotype was more frequent in the U.S. POAG patients with early visual field defects in the paracentral regions compared with those in the peripheral regions or control group (p=2.7 × 10(-5. We replicated this finding in the GIST cohort (p  =7.3 × 10(-3, and in the pooled sample (p=6.6 × 10(-7 and in a meta-analysis of both the US and GIST datasets (1.3 × 10(-6, OR 2.17 (1.58-2.98 for the PRO allele.These results suggest that the p53 codon 72 PRO/PRO genotype is potentially associated with early paracentral visual field defects in primary open-angle glaucoma patients.

Pulse Compression of Phase-matched High Harmonic Pulses from a Time-Delay Compensated Monochromator

Directory of Open Access Journals (Sweden)

Ito Motohiko

2013-03-01

Full Text Available Pulse compression of single 32.6-eV high harmonic pulses from a time-delay compensated monochromator was demonstrated down to 11±3 fs by compensating the pulse front tilt. The photon flux was intensified up to 5.7×109 photons/s on target by implementing high harmonic generation under a phase matching condition in a hollow fiber used for increasing the interaction length.

HARMONIC ANALYSIS OF SVPWM INVERTER USING MULTIPLE-PULSES METHOD

Directory of Open Access Journals (Sweden)

Mehmet YUMURTACI

2009-01-01

Full Text Available Space Vector Modulation (SVM technique is a popular and an important PWM technique for three phases voltage source inverter in the control of Induction Motor. In this study harmonic analysis of Space Vector PWM (SVPWM is investigated using multiple-pulses method. Multiple-Pulses method calculates the Fourier coefficients of individual positive and negative pulses of the output PWM waveform and adds them together using the principle of superposition to calculate the Fourier coefficients of the all PWM output signal. Harmonic magnitudes can be calculated directly by this method without linearization, using look-up tables or Bessel functions. In this study, the results obtained in the application of SVPWM for values of variable parameters are compared with the results obtained with the multiple-pulses method.

Harmonic Instability Analysis of Single-Phase Grid Connected Converter using Harmonic State Space (HSS) modeling method

DEFF Research Database (Denmark)

Kwon, Jun Bum; Wang, Xiongfei; Bak, Claus Leth

2015-01-01

The increasing number of renewable energy sources at the distribution grid is becoming a major issue for utility companies, since the grid connected converters are operating at different operating points due to the probabilistic characteristics of renewable energy. Besides, typically, the harmonics...... proposes a new model of a single phase grid connected renewable energy source using the Harmonic State Space modeling approach, which is able to identify such problems and the model can be extended to be applied in the multiple connected converter analysis. The modeling results show the different harmonic...... and impedance from other renewable energy sources are not taken carefully into account in the installation and design. However, this may bring an unknown harmonic instability into the multiple power sourced system and also make the analysis difficult due to the complexity of the grid network. This paper...

Artificial optical emissions at HAARP for pump frequencies near the third and second electron gyro-harmonic

Directory of Open Access Journals (Sweden)

M. J. Kosch

2005-07-01

Full Text Available High-power high-frequency radio waves beamed into the ionosphere cause plasma turbulence, which can accelerate electrons. These electrons collide with the F-layer neutral oxygen causing artificial optical emissions identical to natural aurora. Pumping at electron gyro-harmonic frequencies has special significance as many phenomena change their character. In particular, artificial optical emissions become strongly reduced for the third and higher gyro-harmonics. The High frequency Active Auroral Research Program (HAARP facility is unique in that it can select a frequency near the second gyro-harmonic. On 25 February 2004, HAARP was operated near the third and passed through the second gyro-harmonic for the first time in a weakening ionosphere. Two novel observations are: firstly, a strong enhancement of the artificial optical emission intensity near the second gyro-harmonic, which is opposite to higher gyro-harmonics; secondly, the optical enhancement maximum occurs for frequencies just above the second gyro-harmonic. We provide the first experimental evidence for these effects, which have been predicted theoretically. In addition, irregular optical structures were created when the pump frequency was above the ionospheric critical frequency.

Keywords. Active experiments – Auroral ionosphere – Wave-particle interactions

Artificial optical emissions at HAARP for pump frequencies near the third and second electron gyro-harmonic

Directory of Open Access Journals (Sweden)

M. J. Kosch

2005-07-01

Full Text Available High-power high-frequency radio waves beamed into the ionosphere cause plasma turbulence, which can accelerate electrons. These electrons collide with the F-layer neutral oxygen causing artificial optical emissions identical to natural aurora. Pumping at electron gyro-harmonic frequencies has special significance as many phenomena change their character. In particular, artificial optical emissions become strongly reduced for the third and higher gyro-harmonics. The High frequency Active Auroral Research Program (HAARP facility is unique in that it can select a frequency near the second gyro-harmonic. On 25 February 2004, HAARP was operated near the third and passed through the second gyro-harmonic for the first time in a weakening ionosphere. Two novel observations are: firstly, a strong enhancement of the artificial optical emission intensity near the second gyro-harmonic, which is opposite to higher gyro-harmonics; secondly, the optical enhancement maximum occurs for frequencies just above the second gyro-harmonic. We provide the first experimental evidence for these effects, which have been predicted theoretically. In addition, irregular optical structures were created when the pump frequency was above the ionospheric critical frequency.Keywords. Active experiments – Auroral ionosphere – Wave-particle interactions

Analytic model of bunched beams for harmonic generation in the low-gain free electron laser regime

Directory of Open Access Journals (Sweden)

G. Penn

2006-06-01

Full Text Available One scheme for harmonic generation employs free electron lasers (FELs with two undulators: the first uses a seed laser to modulate the energy of the electron beam; following a dispersive element which acts to bunch the beam, the second undulator radiates at a higher harmonic. These processes are currently evaluated using extensive calculations or simulation codes which can be slow to evaluate and difficult to set up. We describe a simple algorithm to predict the output of a harmonic generation beam line in the low-gain FEL regime, based on trial functions for the output radiation. Full three-dimensional effects are included. This method has been implemented as a Mathematica® package, named CAMPANILE, which runs rapidly and can be generalized to include effects such as asymmetric beams and misalignments. This method is compared with simulation results using the FEL code GENESIS, both for single stages of harmonic generation and for the LUX project, a design concept for an ultrafast x-ray facility, where multiple stages upshift the input laser frequency by factors of up to 200.

Linking high harmonics from gases and solids.

Science.gov (United States)

Vampa, G; Hammond, T J; Thiré, N; Schmidt, B E; Légaré, F; McDonald, C R; Brabec, T; Corkum, P B

2015-06-25

When intense light interacts with an atomic gas, recollision between an ionizing electron and its parent ion creates high-order harmonics of the fundamental laser frequency. This sub-cycle effect generates coherent soft X-rays and attosecond pulses, and provides a means to image molecular orbitals. Recently, high harmonics have been generated from bulk crystals, but what mechanism dominates the emission remains uncertain. To resolve this issue, we adapt measurement methods from gas-phase research to solid zinc oxide driven by mid-infrared laser fields of 0.25 volts per ångström. We find that when we alter the generation process with a second-harmonic beam, the modified harmonic spectrum bears the signature of a generalized recollision between an electron and its associated hole. In addition, we find that solid-state high harmonics are perturbed by fields so weak that they are present in conventional electronic circuits, thus opening a route to integrate electronics with attosecond and high-harmonic technology. Future experiments will permit the band structure of a solid to be tomographically reconstructed.

Full-Genome Characterization and Genetic Evolution of West African Isolates of Bagaza Virus

Directory of Open Access Journals (Sweden)

Martin Faye

2018-04-01

Full Text Available Bagaza virus is a mosquito-borne flavivirus, first isolated in 1966 in Central African Republic. It has currently been identified in mosquito pools collected in the field in West and Central Africa. Emergence in wild birds in Europe and serological evidence in encephalitis patients in India raise questions on its genetic evolution and the diversity of isolates circulating in Africa. To better understand genetic diversity and evolution of Bagaza virus, we describe the full-genome characterization of 11 West African isolates, sampled from 1988 to 2014. Parameters such as genetic distances, N-glycosylation patterns, recombination events, selective pressures, and its codon adaptation to human genes are assessed. Our study is noteworthy for the observation of N-glycosylation and recombination in Bagaza virus and provides insight into its Indian origin from the 13th century. Interestingly, evidence of Bagaza virus codon adaptation to human house-keeping genes is also observed to be higher than those of other flaviviruses well known in human infections. Genetic variations on genome of West African Bagaza virus could play an important role in generating diversity and may promote Bagaza virus adaptation to other vertebrates and become an important threat in human health.

Comparative analysis of chosen transforms in the context of de-noising harmonic signals

Directory of Open Access Journals (Sweden)

Artur Zacniewski

2015-09-01

Full Text Available In the article, comparison of popular transforms used i.a. in denoising harmonical signals was presented. The division of signals submitted to mathematical analysis was shown and chosen transforms such as Short Time Fourier Transform, Wigner-Ville Distribution, Wavelet Transform and Discrete Cosine Transform were presented. Harmonic signal with white noise added was submitted for research. During research, the parameters of noise were changed to analyze the effects of using particular transform on noised signal. The importance of right choice for transform and its parameters (different for particular kind of transform was shown. Small changes in parameters or different functions used in transform can lead to considerably different results.[b]Keywords[/b]: denoising of harmonical signals, wavelet transform, discrete cosine transform, DCT

Pseudo harmonic morphisms on Riemannian polyhedra

International Nuclear Information System (INIS)

Aprodu, M.A.; Bouziane, T.

2004-10-01

The aim of this paper is to extend the notion of pseudo harmonic morphism (introduced by Loubeau) to the case when the source manifold is an admissible Riemannian polyhedron. We define these maps to be harmonic in the sense of Eells-Fuglede and pseudo-horizontally weakly conformal in our sense. We characterize them by means of germs of harmonic functions on the source polyhedron, in the sense of Korevaar-Schoen, and germs of holomorphic functions on the Kaehler target manifold. (author)

Coherent harmonic production using a two-section undulator FEL

Energy Technology Data Exchange (ETDEWEB)

Jaroszynski, D.A. [Commissariat a l`Energie, Bruyeres-le-Chatel (France); Prazeres, R.; Glotin, F. [Centre Universitaire Paris-Sud (France)] [and others

1995-12-31

We present measurements and a theoretical analysis of a new method of generating harmonic radiation in a free-electron laser oscillator with a two section undulator in a single optical cavity. To produce coherent harmonic radiation the undulator is arranged so that the downstream undulator section resonance frequency matches a harmonic of the upstream undulator. Both the fundamental and the harmonic optical fields evolve in the same optical cavity and are coupled out with different extraction fractions using a hole in one of the cavity mirrors. We present measurements that show that the optical power at the second and third harmonic can be enhanced by more than an order of magnitude in this fundamental/harmonic configuration. We compare the production of harmonic radiation of a two sectioned fundamental/harmonic undulator with that produced from a FEL operating at its highest efficiency with a step-tapered undulator, where the bunching at the end of the first section is very large. We examine, the dependence of the harmonic power on the intracavity power by adjusting the optical cavity desynchronism, {delta}L. We also examine the evolution of the fundamental and harmonic powers as a function of cavity roundtrip number to evaluate the importance of the small signal gain at the harmonic. We compare our measurements with predictions of a multi-electron numerical model that follows the evolution of fundamental and harmonic power to saturation. This fundamental/harmonic mode, of operation of the FEL may have useful applications in the production of coherent X-ray and VUV radiation, a spectral range where high reflectivity optical cavity mirrors are difficult or impossible to manufacture.

Measurement-based harmonic current modeling of mobile storage for power quality study in the distribution system

Directory of Open Access Journals (Sweden)

Wenge Christoph

2017-12-01

Full Text Available Electric vehicles (EVs can be utilized as mobile storages in a power system. The use of battery chargers can cause current harmonics in the supplied AC system. In order to analyze the impact of different EVs with regardto their number and their emission of current harmonics, a generic harmonic current model of EV types was built and implemented in the power system simulation tool PSS®NETOMAC. Based on the measurement data for different types of EVs three standardized harmonic EV models were developed and parametrized. Further, the identified harmonic models are used by the computation of load flow in a modeled, German power distribution system. As a benchmark, a case scenario was studied regarding a high market penetration of EVs in the year 2030 for Germany. The impact of the EV charging on the power distribution system was analyzed and evaluated with valid power quality standards.

Protein evolution via amino acid and codon elimination

DEFF Research Database (Denmark)

Goltermann, Lise; Larsen, Marie Sofie Yoo; Banerjee, Rajat

2010-01-01

BACKGROUND: Global residue-specific amino acid mutagenesis can provide important biological insight and generate proteins with altered properties, but at the risk of protein misfolding. Further, targeted libraries are usually restricted to a handful of amino acids because there is an exponential...... correlation between the number of residues randomized and the size of the resulting ensemble. Using GFP as the model protein, we present a strategy, termed protein evolution via amino acid and codon elimination, through which simplified, native-like polypeptides encoded by a reduced genetic code were obtained...... simultaneously), while retaining varying levels of activity. Combination of these substitutions to generate a Phe-free variant of GFP abolished fluorescence. Combinatorial re-introduction of five Phe residues, based on the activities of the respective single amino acid replacements, was sufficient to restore GFP...

Second harmonic generation imaging

CERN Document Server

2013-01-01

Second-harmonic generation (SHG) microscopy has shown great promise for imaging live cells and tissues, with applications in basic science, medical research, and tissue engineering. Second Harmonic Generation Imaging offers a complete guide to this optical modality, from basic principles, instrumentation, methods, and image analysis to biomedical applications. The book features contributions by experts in second-harmonic imaging, including many pioneering researchers in the field. Written for researchers at all levels, it takes an in-depth look at the current state of the art and possibilities of SHG microscopy. Organized into three sections, the book: Provides an introduction to the physics of the process, step-by-step instructions on how to build an SHG microscope, and comparisons with related imaging techniques Gives an overview of the capabilities of SHG microscopy for imaging tissues and cells—including cell membranes, muscle, collagen in tissues, and microtubules in live cells—by summarizing experi...

Second-harmonic imaging of semiconductor quantum dots

DEFF Research Database (Denmark)

Østergaard, John Erland; Bozhevolnyi, Sergey I.; Pedersen, Kjeld

2000-01-01

Resonant second-harmonic generation is observed at room temperature in reflection from self-assembled InAlGaAs quantum dots grown on a GaAs (001) substrate. The detected second-harmonic signal peaks at a pump wavelength of similar to 885 nm corresponding to the quantum-dot photoluminescence maximum....... In addition, the second-harmonic spectrum exhibits another smaller but well-pronounced peak at 765 nm not found in the linear experiments. We attribute this peak to the generation of second-harmonic radiation in the AlGaAs spacer layer enhanced by the local symmetry at the quantum-dot interface. We further...

Harmonic Series Meets Fibonacci Sequence

Science.gov (United States)

Chen, Hongwei; Kennedy, Chris

2012-01-01

The terms of a conditionally convergent series may be rearranged to converge to any prescribed real value. What if the harmonic series is grouped into Fibonacci length blocks? Or the harmonic series is arranged in alternating Fibonacci length blocks? Or rearranged and alternated into separate blocks of even and odd terms of Fibonacci length?

Tuvan Throat Singing and Harmonics

Science.gov (United States)

Ruiz, Michael J.; Wilken, David

2018-01-01

Tuvan throat singing, also called overtone singing, provides for an exotic demonstration of the physics of harmonics as well as introducing an Asian musical aesthetic. A low fundamental is sung and the singer skillfully alters the resonances of the vocal system to enhance an overtone (harmonic above the fundamental). The result is that the…

Localized, Non-Harmonic Active Flap Motions for Low Frequency In-Plane Rotor Noise Reduction

Science.gov (United States)

Sim, Ben W.; Potsdam, Mark; Kitaplioglu, Cahit; LeMasurier, Philip; Lorber, Peter; Andrews, Joseph

2012-01-01

A first-of-its-kind demonstration of the use of localized, non-harmonic active flap motions, for suppressing low frequency, in-plane rotor noise, is reported in this paper. Operational feasibility is verified via testing of the full-scale AATD/Sikorsky/UTRC active flap demonstration rotor in the NFAC's 40- by 80-Foot anechoic wind tunnel. Effectiveness of using localized, non-harmonic active flap motions are compared to conventional four-per-rev harmonic flap motions, and also active flap motions derived from closed-loop acoustics implementations. All three approaches resulted in approximately the same noise reductions over an in-plane three-by-three microphone array installed forward and near in-plane of the rotor in the nearfield. It is also reported that using an active flap in this localized, non-harmonic manner, resulted in no more that 2% rotor performance penalty, but had the tendency to incur higher hub vibration levels.

A System for Anesthesia Drug Administration Using Barcode Technology: The Codonics Safe Label System and Smart Anesthesia Manager.

Science.gov (United States)

Jelacic, Srdjan; Bowdle, Andrew; Nair, Bala G; Kusulos, Dolly; Bower, Lynnette; Togashi, Kei

2015-08-01

Many anesthetic drug errors result from vial or syringe swaps. Scanning the barcodes on vials before drug preparation, creating syringe labels that include barcodes, and scanning the syringe label barcodes before drug administration may help to prevent errors. In contrast, making syringe labels by hand that comply with the recommendations of regulatory agencies and standards-setting bodies is tedious and time consuming. A computerized system that uses vial barcodes and generates barcoded syringe labels could address both safety issues and labeling recommendations. We measured compliance of syringe labels in multiple operating rooms (ORs) with the recommendations of regulatory agencies and standards-setting bodies before and after the introduction of the Codonics Safe Label System (SLS). The Codonics SLS was then combined with Smart Anesthesia Manager software to create an anesthesia barcode drug administration system, which allowed us to measure the rate of scanning syringe label barcodes at the time of drug administration in 2 cardiothoracic ORs before and after introducing a coffee card incentive. Twelve attending cardiothoracic anesthesiologists and the OR satellite pharmacy participated. The use of the Codonics SLS drug labeling system resulted in >75% compliant syringe labels (95% confidence interval, 75%-98%). All syringe labels made using the Codonics SLS system were compliant. The average rate of scanning barcodes on syringe labels using Smart Anesthesia Manager was 25% (730 of 2976) over 13 weeks but increased to 58% (956 of 1645) over 8 weeks after introduction of a simple (coffee card) incentive (P < 0.001). An anesthesia barcode drug administration system resulted in a moderate rate of scanning syringe label barcodes at the time of drug administration. Further, adaptation of the system will be required to achieve a higher utilization rate.

New Evidence That Nonlinear Source-Filter Coupling Affects Harmonic Intensity and fo Stability During Instances of Harmonics Crossing Formants.

Science.gov (United States)

Maxfield, Lynn; Palaparthi, Anil; Titze, Ingo

2017-03-01

The traditional source-filter theory of voice production describes a linear relationship between the source (glottal flow pulse) and the filter (vocal tract). Such a linear relationship does not allow for nor explain how changes in the filter may impact the stability and regularity of the source. The objective of this experiment was to examine what effect unpredictable changes to vocal tract dimensions could have on fo stability and individual harmonic intensities in situations in which low frequency harmonics cross formants in a fundamental frequency glide. To determine these effects, eight human subjects (five male, three female) were recorded producing fo glides while their vocal tracts were artificially lengthened by a section of vinyl tubing inserted into the mouth. It was hypothesized that if the source and filter operated as a purely linear system, harmonic intensities would increase and decrease at nearly the same rates as they passed through a formant bandwidth, resulting in a relatively symmetric peak on an intensity-time contour. Additionally, fo stability should not be predictably perturbed by formant/harmonic crossings in a linear system. Acoustic analysis of these recordings, however, revealed that harmonic intensity peaks were asymmetric in 76% of cases, and that 85% of fo instabilities aligned with a crossing of one of the first four harmonics with the first three formants. These results provide further evidence that nonlinear dynamics in the source-filter relationship can impact fo stability as well as harmonic intensities as harmonics cross through formant bandwidths. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

Translational Control of the SigR-Directed Oxidative Stress Response in Streptomyces via IF3-Mediated Repression of a Noncanonical GTC Start Codon.

Science.gov (United States)

Feeney, Morgan A; Chandra, Govind; Findlay, Kim C; Paget, Mark S B; Buttner, Mark J

2017-06-13

The major oxidative stress response in Streptomyces is controlled by the sigma factor SigR and its cognate antisigma factor RsrA, and SigR activity is tightly controlled through multiple mechanisms at both the transcriptional and posttranslational levels. Here we show that sigR has a highly unusual GTC start codon and that this leads to another level of SigR regulation, in which SigR translation is repressed by translation initiation factor 3 (IF3). Changing the GTC to a canonical start codon causes SigR to be overproduced relative to RsrA, resulting in unregulated and constitutive expression of the SigR regulon. Similarly, introducing IF3* mutations that impair its ability to repress SigR translation has the same effect. Thus, the noncanonical GTC sigR start codon and its repression by IF3 are critical for the correct and proper functioning of the oxidative stress regulatory system. sigR and rsrA are cotranscribed and translationally coupled, and it had therefore been assumed that SigR and RsrA are produced in stoichiometric amounts. Here we show that RsrA can be transcribed and translated independently of SigR, present evidence that RsrA is normally produced in excess of SigR, and describe the factors that determine SigR-RsrA stoichiometry. IMPORTANCE In all sigma factor-antisigma factor regulatory switches, the relative abundance of the two proteins is critical to the proper functioning of the system. Many sigma-antisigma operons are cotranscribed and translationally coupled, leading to a generic assumption that the sigma and antisigma factors are produced in a fixed 1:1 ratio. In the case of sigR - rsrA , we show instead that the antisigma factor is produced in excess over the sigma factor, providing a buffer to prevent spurious release of sigma activity. This excess arises in part because sigR has an extremely rare noncanonical GTC start codon, and as a result, SigR translation initiation is repressed by IF3. This finding highlights the potential significance

Theoretical description of high-order harmonic generation in solids

International Nuclear Information System (INIS)

Kemper, A F; Moritz, B; Devereaux, T P; Freericks, J K

2013-01-01

We consider several aspects of high-order harmonic generation in solids: the effects of elastic and inelastic scattering, varying pulse characteristics and inclusion of material-specific parameters through a realistic band structure. We reproduce many observed characteristics of high harmonic generation experiments in solids including the formation of only odd harmonics in inversion-symmetric materials, and the nonlinear formation of high harmonics with increasing field. We find that the harmonic spectra are fairly robust against elastic and inelastic scattering. Furthermore, we find that the pulse characteristics can play an important role in determining the harmonic spectra. (paper)

The Virasoro algebra from harmonic superspace

International Nuclear Information System (INIS)

Saidi, E.H.; Zakkari, M.

1990-08-01

Using harmonic superspace techniques, we construct a new field realization of the Virasoro algebra. The main conformal objects are U(1) Cartan tensors instead of the U(1) Lorentz ones. The new conformal model, which admits moreover a d=2 (4,0) global supersymmetry is constructed out of the infinitely relaxed HST and FS hypermultiplets. The conformal current T 4+ together with the harmonic superspace OPE rules are given. The Virasoro algebra and the harmonic superspace Schwarzian derivative S 4+ are also derived. (author). 14 refs

A 43-level filterless CMLI with very low harmonics values

Directory of Open Access Journals (Sweden)

Mahmoud El-Bakry

2014-12-01

Full Text Available This paper introduces a 43-level asymmetric uniform step cascaded multilevel inverter (CMLI that consists of four H-bridges per phase, with different dc sources of values E, 2E, 7E and 11E. A mixed integer linear programming (MILP optimization model is applied to determine the switching angles of the CMLI power switches that can minimize the values of any undesired harmonics. Single phase and three phase cases are considered. The results show very low values of all the undesired harmonics over wide voltage ranges, which agree with the IEEE standards 519-1992 for voltage distortion limits for both the values of %THDE and %VHmax so that no output filters are needed.

Tuning protein expression using synonymous codon libraries targeted to the 5' mRNA coding region

DEFF Research Database (Denmark)

Goltermann, Lise; Borch Jensen, Martin; Bentin, Thomas

2011-01-01

intermediate expression levels of green fluorescent protein in Escherichia coli. At least in one case, no apparent effect on protein stability was observed, pointing to RNA level effects as the principal reason for the observed expression differences. Targeting a synonymous codon library to the 5' coding...

Voltage harmonic elimination with RLC based interface smoothing filter

International Nuclear Information System (INIS)

Chandrasekaran, K; Ramachandaramurthy, V K

2015-01-01

A method is proposed for designing a Dynamic Voltage Restorer (DVR) with RLC interface smoothing filter. The RLC filter connected between the IGBT based Voltage Source Inverter (VSI) is attempted to eliminate voltage harmonics in the busbar voltage and switching harmonics from VSI by producing a PWM controlled harmonic voltage. In this method, the DVR or series active filter produces PWM voltage that cancels the existing harmonic voltage due to any harmonic voltage source. The proposed method is valid for any distorted busbar voltage. The operating VSI handles no active power but only harmonic power. The DVR is able to suppress the lower order switching harmonics generated by the IGBT based VSI. Good dynamic and transient results obtained. The Total Harmonic Distortion (THD) is minimized to zero at the sensitive load end. Digital simulations are carried out using PSCAD/EMTDC to validate the performance of RLC filter. Simulated results are presented. (paper)

Three-dimensional harmonic control of a nuclear reactor

International Nuclear Information System (INIS)

Potapenko, P.T.

1989-01-01

Algorithms for neutron flux control based on harmonic three-dimensional core are considered. The essence of the considered approach includes determination of harmonics amplitudes by signals self-powered detectors placed in reactor channels and reconstruction of neutron field distribution over the reactor core volume using the data obtained. Neutron field harmonic control is shown to be reduced to independent measurement and calculation of height harmonics in channels using techniques developed for channel power control

Seeding High Gain Harmonic Generation with Laser Harmonics produced in Gases

CERN Document Server

Lambert, Guillaume; Couprie, Marie Emmanuelle; Garzella, David; Doria, Andrea; Giannessi, Luca; Hara, Toru; Kitamura, Hideo; Shintake, Tsumoru

2004-01-01

Free electron Lasers employing High Gain Harmonic generation (HGHG) schemes are very promising coherent ligth sources for the soft X-ray regime. They offer both transverse and longitudinal coherence, while Self Amplified Spontaneous Emission schemes have a longitudinal coherence limited. We propose here to seed HGHG with high harmonics produced by a Ti:Sa femtosecond laser focused on a gas jet, tuneable in the 100-10 nm spectral region. Specifities concerning the implementation of this particular laser source as a seed for HGHG are investigated. Semi analytical , numerical 1D and 3D calculations are given, for the cases of the SCSS, SPARC and ARC-EN-CIEL projects.

Recent progress of below-threshold harmonic generation

International Nuclear Information System (INIS)

Xiong, Wei-Hao; Peng, Liang-You; Gong, Qihuang

2017-01-01

The harmonics generated from the interaction of a strong laser field with atoms and molecules in the gas phase can be applied as coherent light sources and detecting techniques for structures and dynamics in matter. In the last three decades, the most prevailing experimental and theoretical studies have been focused on the high-order harmonic generation due to its applications in attosecond science. However, low-order harmonics near the ionization threshold of the target have been less explored, partially because the spectrum in this region is more complicated from both the theoretical and experimental point of view. After several pioneering investigations in the mid 1990s, near threshold harmonics (NTHs) begun to draw a great attention again because of the development of high repetition rate cavity enhanced harmonics about 10 years ago. Very recently, NTHs have attracted a lot of experimental and theoretical studies due to their potential applications as light sources and complicated mechanisms. In this topical review, we will summarize the progress of NTHs, including the early and recent experimental measurements in atoms and molecules, as well as the relevant theoretical explorations of these harmonics. (topical review)

Harmonic generation with a dual frequency pulse.

Science.gov (United States)

Keravnou, Christina P; Averkiou, Michalakis A

2014-05-01

Nonlinear imaging was implemented in commercial ultrasound systems over the last 15 years offering major advantages in many clinical applications. In this work, pulsing schemes coupled with a dual frequency pulse are presented. The pulsing schemes considered were pulse inversion, power modulation, and power modulated pulse inversion. The pulse contains a fundamental frequency f and a specified amount of its second harmonic 2f. The advantages and limitations of this method were evaluated with both acoustic measurements of harmonic generation and theoretical simulations based on the KZK equation. The use of two frequencies in a pulse results in the generation of the sum and difference frequency components in addition to the other harmonic components. While with single frequency pulses, only power modulation and power modulated pulse inversion contained odd harmonic components, with the dual frequency pulse, pulse inversion now also contains odd harmonic components.

Mutation at codon 442 in the rpoB gene of Mycobacterium leprae does not confer resistance to rifampicin.

Science.gov (United States)

Lavania, Mallika; Hena, Abu; Reja, Hasanoor; Nigam, Astha; Biswas, Nibir Kumar; Singh, Itu; Turankar, Ravindra P; Gupta, Ud; Kumar, Senthil; Rewaria, Latika; Patra, Pradip K R; Sengupta, Utpal; Bhattacharya, Basudeb

2016-03-01

Rifampicin is the major drug in the treatment of leprosy. The rifampicin resistance of Mycobacterium leprae results from a mutation in the rpoB gene, encoding the β subunit of RNA polymerase. As M. leprae is a non-cultivable organism observation of its growth using mouse food-pad (MFP) is the only Gold Standard assay used for confirmation of "in-vivo" drug resistance. Any mutation at molecular level has to be verified by MFP assay for final confirmation of drug resistance in leprosy. In the present study, M. leprae strains showing a mutation only at codon 442 Gln-His and along with mutation either at codon 424 Val-Gly or at 438 Gln-Val within the Rifampicin Resistance Determining Region (RRDR) confirmed by DNA sequencing and by high resolution melting (HRM) analysis were subjected for its growth in MFP. The M. leprae strain having the new mutation at codon 442 Gln-His was found to be sensitive to all the three drugs and strains having additional mutations at 424 Val-Gly and 438 Gln-Val were conferring resistance with Multi drug therapy (MDT) in MFP. These results indicate that MFP is the gold standard method for confirming the mutations detected by molecular techniques.

Harmonic Instability Assessment Using State-Space Modeling and Participation Analysis in Inverter-Fed Power Systems

DEFF Research Database (Denmark)

Wang, Yanbo; Wang, Xiongfei; Blaabjerg, Frede

2017-01-01

parameters on the harmonic instability of the power system. Moreover, the harmonic-frequency oscillation modes are identified, where participation analysis is presented to evaluate the contributions of different states to these modes and to further reveal how the system gives rise to harmonic instability......This paper presents a harmonic instability analysis method using state-space modeling and participation analysis in the inverter-fed ac power systems. A full-order state-space model for the droop-controlled Distributed Generation (DG) inverter is built first, including the time delay of the digital...... control system, inner current and voltage control loops, and outer droop-based power control loop. Based on the DG inverter model, an overall state-space model of a two-inverter-fed system is established. The eigenvalue-based stability analysis is then presented to assess the influence of controller...

The MSPDBL2 codon 591 polymorphism is associated with lumefantrine in vitro drug responses in Plasmodium falciparum isolates from Kilifi, Kenya.

Science.gov (United States)

Ochola-Oyier, Lynette Isabella; Okombo, John; Mwai, Leah; Kiara, Steven M; Pole, Lewa; Tetteh, Kevin K A; Nzila, Alexis; Marsh, Kevin

2015-03-01

The mechanisms of drug resistance development in the Plasmodium falciparum parasite to lumefantrine (LUM), commonly used in combination with artemisinin, are still unclear. We assessed the polymorphisms of Pfmspdbl2 for associations with LUM activity in a Kenyan population. MSPDBL2 codon 591S was associated with reduced susceptibility to LUM (P = 0.04). The high frequency of Pfmspdbl2 codon 591S in Kenya may be driven by the widespread use of lumefantrine in artemisinin combination therapy (Coartem). Copyright © 2015, Ochola-Oyier et al.

Harmonic and geometric analysis

CERN Document Server

Citti, Giovanna; Pérez, Carlos; Sarti, Alessandro; Zhong, Xiao

2015-01-01

This book presents an expanded version of four series of lectures delivered by the authors at the CRM. Harmonic analysis, understood in a broad sense, has a very wide interplay with partial differential equations and in particular with the theory of quasiconformal mappings and its applications. Some areas in which real analysis has been extremely influential are PDE's and geometric analysis. Their foundations and subsequent developments made extensive use of the Calderón–Zygmund theory, especially the Lp inequalities for Calderón–Zygmund operators (Beurling transform and Riesz transform, among others) and the theory of Muckenhoupt weights.  The first chapter is an application of harmonic analysis and the Heisenberg group to understanding human vision, while the second and third chapters cover some of the main topics on linear and multilinear harmonic analysis. The last serves as a comprehensive introduction to a deep result from De Giorgi, Moser and Nash on the regularity of elliptic partial differen...

[Harmonization of TSH Measurements.

Science.gov (United States)

Takeoka, Keiko; Hidaka, Yoh; Hishinuma, Akira; Ikeda, Katsuyoshi; Okubo, Shigeo; Tsuchiya, Tatsuyuki; Hashiguchi, Teruto; Furuta, Koh; Hotta, Taeko; Matsushita, Kazuyuki; Matsumoto, Hiroyuki; Murakami, Masami; Maekawa, Masato

2016-05-01

The measured concentration of thyroid stimulating hormone (TSH) differs depending on the reagents used. Harmonization of TSH is crucial because the decision limits are described in current clinical practice guide- lines as absolute values, e.g. 2.5 mIU/L in early pregnancy. In this study, we tried to harmonize the report- ed concentrations of TSH using the all-procedure trimmed mean. TSH was measured in 146 serum samples, with values ranging from 0.01 to 18.8 mIU/L, using 4 immunoassays. The concentration of TSH was highest with E test TOSOH and lowest with LUMIPULSE. The concentrations with each reagent were recalculated with the following formulas: E test TOSOH 0.855x-0.014; ECLusys 0.993x+0.079; ARCHITECT 1.041x- 0.010; and LUMIPULSE 1.096x-0.015. Recalculation eliminated the between-assay discrepancy. These formulas may be used until harmonization of TSH is achieved by the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC).

Discretized representations of harmonic variables by bilateral Jacobi operators

Directory of Open Access Journals (Sweden)

Andreas Ruffing

2000-01-01

Full Text Available Starting from a discrete Heisenberg algebra we solve several representation problems for a discretized quantum oscillator in a weighted sequence space. The Schrödinger operator for a discrete harmonic oscillator is derived. The representation problem for a q-oscillator algebra is studied in detail. The main result of the article is the fact that the energy representation for the discretized momentum operator can be interpreted as follows: It allows to calculate quantum properties of a large number of non-interacting harmonic oscillators at the same time. The results can be directly related to current research on squeezed laser states in quantum optics. They reveal and confirm the observation that discrete versions of continuum Schrodinger operators allow more structural freedom than their continuum analogs do.

International Cooperation in Nuclear E&T: On the Way to Nuclear Training Harmonization

International Nuclear Information System (INIS)

Filipev, I.; Karmanov, F.; Artisyuk, V.; Karezin, V.; Sushkov, P.

2016-01-01

Full text: Global use of nuclear power is likely to continue to grow in the coming decades. Some countries have chosen to invite multiple vendors for NPP technology supply. The worldwide expansion of nuclear power use and the multi-vendor paradigm inevitably lead to the need of harmonized approaches towards safety and the initial step here is harmonization of education and training (E&T) efforts between recipient and vendor countries and between vendors as well. Establishing international and regional E&T networks is the vital mechanism of the harmonization. The present paper gives an example of collaboration between Russia and the EU through achievements of ENEN-RU projects aimed at harmonization of E&T efforts in nuclear field. One of the goals of this activity is to introduce double-degree programmes in nuclear engineering in Russian and EU universities. To support this initiative ROSATOM-CICE&T is currently developing multimedia-based fundamental educational courses in Russian and English languages. The courses will be also used as the backbone for new nuclear engineering programmes in the universities of newcomer states. To provide a harmonized development of operating personnel career trajectories in these countries an applied bachelor programme for operating personnel has been developed. (author

An easy trick to a periodic solution of relativistic harmonic oscillator

Directory of Open Access Journals (Sweden)

Jafar Biazar

2014-04-01

Full Text Available In this paper, the relativistic harmonic oscillator equation which is a nonlinear ordinary differential equation is investigated by Homotopy perturbation method. Selection of a linear operator, which is a part of the main operator, is one of the main steps in HPM. If the aim is to obtain a periodic solution, this choice does not work here. To overcome this lack, a linear operator is imposed, and Fourier series of sines will be used in solving the linear equations arise in the HPM. Comparison of the results, with those of resulted by Differential Transformation and Harmonic Balance Method, shows an excellent agreement.

Harmonic Mitigation Methods in Large Offshore Wind Power Plants

DEFF Research Database (Denmark)

Kocewiak, Łukasz Hubert; Chaudhary, Sanjay; Hesselbæk, Bo

2013-01-01

Various sources of harmonic problems in large wind power plants (WPPs) and optimized harmonic mitigation methods are presented in this paper. The harmonic problems such as sources of harmonic emission and amplification as well as harmonic stability are identified. Also modern preventive...... and remedial harmonic mitigation methods in terms of passive and active filtering are described. It is shown that WPP components such as long HVAC cables and park transformers can introduce significant low-frequency resonances which can affect wind turbine control system operation and overall WPP stability...... as well as amplification of harmonic distortion. It is underlined that there is a potential in terms of active filtering in modern grid-side converters in e.g. wind turbines, STATCOMs or HVDC stations utilized in modern large WPPs. It is also emphasized that the grid-side converter controller should...

SHAF for Mitigation of Current Harmonics Using p-q Method with PI and Fuzzy Controllers

Directory of Open Access Journals (Sweden)

A. K. Panda

2011-08-01

Full Text Available Commencing with incandescent light bulb, every load today creates harmonics. Unfortunately, these loads vary with respect to their amount of harmonic content and response to problems caused by harmonics. Issue of Harmonics are of a greater concern to engineers, building designers and in industrial applications because they do more than distort voltage waveforms, they can overheat the building wiring, cause nuisance tripping, overheat transformer units, and cause random end-user equipment failures. Thus power quality has become more and more serious with each passing day. As a result active power filter (APF gains much more attention due to excellent harmonic compensation. But still the performance of the active filter seems to be in contradictions with different control techniques. The main objective of this paper is to analyse shunt active filter with fuzzy and pi controllers. To carry out the analysis, we consider active and reactive power method (p-q. Extensive simulations were carried out; simulations were performed with balance, unbalanced and non sinusoidal conditions. Simulation results validate the dynamic behaviour of fuzzy logic controller over pi controller.

Two examples of escaping harmonic maps

International Nuclear Information System (INIS)

Pereira do Valle, A.; Verjovsky, A.

1988-12-01

This paper is part of a study on the existence of special harmonic maps on complete non-compact Riemannian manifolds. We generalize the notion of escaping geodesic and prove some results on the existence of escaping harmonic maps. 11 refs, 6 figs

High-order harmonic conversion efficiency in helium

International Nuclear Information System (INIS)

Crane, J.K.

1992-01-01

Calculated results are presented for the energy, number of photons, and conversion efficiency for high-order harmonic generation in helium. The results show the maximum values that we should expect to achieve experimentally with our current apparatus and the important parameters for scaling this source to higher output. In the desired operating regime where the coherence length, given by L coh =πb/(q-1), is greater than the gas column length, l, the harmonic output can be summarized by a single equation: N q =[(π z n z b 3 τ q |d q | z )/4h]{(p/q)(2l/b) z }. N q - numbers of photons of q-th harmonic; n - atom density; b - laser confocal parameter; τ q - pulse width of harmonic radiation; q - harmonic order; p - effective order of nonlinearity. (Note the term in brackets, the phase-matching function, has been separated from the rest of the expression in order to be consistent with the relevant literature)

Vector Quantization of Harmonic Magnitudes in Speech Coding Applications—A Survey and New Technique

Directory of Open Access Journals (Sweden)

Wai C. Chu

2004-12-01

Full Text Available A harmonic coder extracts the harmonic components of a signal and represents them efficiently using a few parameters. The principles of harmonic coding have become quite successful and several standardized speech and audio coders are based on it. One of the key issues in harmonic coder design is in the quantization of harmonic magnitudes, where many propositions have appeared in the literature. The objective of this paper is to provide a survey of the various techniques that have appeared in the literature for vector quantization of harmonic magnitudes, with emphasis on those adopted by the major speech coding standards; these include constant magnitude approximation, partial quantization, dimension conversion, and variable-dimension vector quantization (VDVQ. In addition, a refined VDVQ technique is proposed where experimental data are provided to demonstrate its effectiveness.

Harmonic calculation software for industrial applications with ASDs

DEFF Research Database (Denmark)

Blaabjerg, Frede; Asiminoaei, Lucian; Hansen, Steffan

2007-01-01

This article describes the evaluation of new harmonic calculation software. By using a combination of a prestored database and new interpolation techniques the software can provide the harmonic data on real applications of a very fast speed. The harmonic results obtained with this software have a...

Audibility of high harmonics in a periodic pulse

NARCIS (Netherlands)

Duifhuis, H.

1970-01-01

A periodic pulse consisting of sufficiently narrow pulses has a frequency spectrum which contains all harmonics with equal amplitude. Owing to the limited resolving power of the hearing organ, only the low harmonics can be perceived separately. The high harmonics are heard together as one complex

Full genotyping of a highly polymorphic human gene trait by time-resolved fluorescence resonance energy transfer.

Directory of Open Access Journals (Sweden)

Edoardo Totè

Full Text Available The ability of detecting the subtle variations occurring, among different individuals, within specific DNA sequences encompassed in highly polymorphic genes discloses new applications in genomics and diagnostics. DQB1 is a gene of the HLA-II DQ locus of the Human Leukocyte Antigens (HLA system. The polymorphisms of the trait of the DQB1 gene including codons 52-57 modulate the susceptibility to a number of severe pathologies. Moreover, the donor-receiver tissue compatibility in bone marrow transplantations is routinely assessed through crossed genotyping of DQB and DQA. For the above reasons, the development of rapid, reliable and cost-effective typing technologies of DQB1 in general, and more specifically of the codons 52-57, is a relevant although challenging task. Quantitative assessment of the fluorescence resonance energy transfer (FRET efficiency between chromophores labelling the opposite ends of gene-specific oligonucleotide probes has proven to be a powerful tool to type DNA polymorphisms with single-nucleotide resolution. The FRET efficiency can be most conveniently quantified by applying a time-resolved fluorescence analysis methodology, i.e. time-correlated single-photon counting, which allows working on very diluted template specimens and in the presence of fluorescent contaminants. Here we present a full in-vitro characterization of the fluorescence responses of two probes when hybridized to oligonucleotide mixtures mimicking all the possible genotypes of the codons 52-57 trait of DQB1 (8 homozygous and 28 heterozygous. We show that each genotype can be effectively tagged by the combination of the fluorescence decay constants extrapolated from the data obtained with such probes.

Enhancement of harmonic generation using a two section undulator

International Nuclear Information System (INIS)

Prazeres, R.; Glotin, F.; Jaroszynski, D.A.; Ortega, J.M.; Rippon, C.

1999-01-01

Enhancement of the 2nd and 3rd harmonic of the wavelength of a Free-Electron Laser (FEL) has been measured when a single electron beam is crossing a two-section undulator. To produce the harmonic radiation enhancement, the undulator is arranged so that the resonance wavelength of the 2nd undulator (downstream) matches a harmonic of the 1st undulator (upstream). Both the fundamental and the harmonic optical fields evolve in the same optical cavity and are coupled out with different extraction efficiency, through a hole in one of the cavity mirrors. We present measurements that show that the optical power at the 2nd and 3rd harmonic can be enhanced, by about one order of magnitude, in two configurations: when the resonance wavelength of the 2nd undulator matches the harmonic of 1st one (harmonic configuration), or when the gap of the 2nd undulator is slightly larger than first one (step-tapered configuration). We examine the dependence of the harmonic power on the gap of the 2nd undulator. This fundamental/harmonic mode of operation of the FEL may have useful applications in the production of coherent X-ray and VUV radiation, a spectral range where high reflectivity optical cavity mirrors are difficult or impossible to manufacture

Effects of harmonic roving on pitch discrimination

DEFF Research Database (Denmark)

Santurette, Sébastien; de Kérangal, Mathilde le Gal; Joshi, Suyash Narendra

2015-01-01

Performance in pitch discrimination tasks is limited by variability intrinsic to listeners which may arise from peripheral auditory coding limitations or more central noise sources. The present study aimed at quantifying such “internal noise” by estimating the amount of harmonic roving required...... to impair pitch discrimination performance. Fundamental-frequency difference limens (F0DLs) were obtained in normal-hearing listeners with and without musical training for complex tones filtered between 1.5 and 3.5 kHz with F0s of 300 Hz (resolved harmonics) and 75 Hz (unresolved harmonics). The harmonicity...... that could be used to quantify the internal noise and provide strong constraints for physiologically inspired models of pitch perception....

Studies of harmonic generation in free electron lasers

International Nuclear Information System (INIS)

Goldammer, K.

2007-01-01

Nonlinear harmonic generation is one of the most interesting aspects of Free Electron Lasers under study today. It provides for coherent, high intensity radiation at higher harmonics of the FEL resonant frequency. The sources, numerical simulation and applications of harmonic radiation in cascaded High Gain Harmonic Generation FELs were the subject of this thesis. Harmonic emission in FELs originates from harmonic microbunching of the particles and the particular electron trajectory during FEL interaction. Numerical FEL simulation codes model these analytical equations and predict the performance of Free Electron Lasers with good accuracy. This thesis has relied heavily upon the FEL simulation code Genesis 1.3 which has been upgraded in the framework of this thesis to compute harmonic generation in a self-consistent manner. Tests against analytical predictions suggest that the harmonic power levels as well as harmonic gain lengths are simulated correctly. A benchmark with the FEL simulation code GINGER yields excellent agreement of the harmonic saturation length and saturation power. The new version of the simulation code Genesis was also tested against measurements from the VUV-FEL FLASH at DESY. The spectral power distributions of fundamental and third harmonic radiation were recorded at 25.9 nm and 8.6 nm, respectively. The relative bandwidths (FWHM) were in the range of 2 % for both the fundamental as well as the third harmonic, which was accurately reproduced by time-dependent simulations with Genesis. The new code was also used to propose and evaluate a new design for the BESSY Soft X-Ray FEL, a cascaded High Gain Harmonic Generation FEL proposed by BESSY in Berlin. The original design for the BESSY High Energy FEL line requires four HGHG stages to convert the initial seed laser wavelength of 297.5 nm down to 1.24 nm. A new scheme is proposed that makes use of fifth harmonic radiation from the first stage and reduces the number of HGHG stages to three. It

Studies of harmonic generation in free electron lasers

Energy Technology Data Exchange (ETDEWEB)

Goldammer, K.

2007-11-12

Nonlinear harmonic generation is one of the most interesting aspects of Free Electron Lasers under study today. It provides for coherent, high intensity radiation at higher harmonics of the FEL resonant frequency. The sources, numerical simulation and applications of harmonic radiation in cascaded High Gain Harmonic Generation FELs were the subject of this thesis. Harmonic emission in FELs originates from harmonic microbunching of the particles and the particular electron trajectory during FEL interaction. Numerical FEL simulation codes model these analytical equations and predict the performance of Free Electron Lasers with good accuracy. This thesis has relied heavily upon the FEL simulation code Genesis 1.3 which has been upgraded in the framework of this thesis to compute harmonic generation in a self-consistent manner. Tests against analytical predictions suggest that the harmonic power levels as well as harmonic gain lengths are simulated correctly. A benchmark with the FEL simulation code GINGER yields excellent agreement of the harmonic saturation length and saturation power. The new version of the simulation code Genesis was also tested against measurements from the VUV-FEL FLASH at DESY. The spectral power distributions of fundamental and third harmonic radiation were recorded at 25.9 nm and 8.6 nm, respectively. The relative bandwidths (FWHM) were in the range of 2 % for both the fundamental as well as the third harmonic, which was accurately reproduced by time-dependent simulations with Genesis. The new code was also used to propose and evaluate a new design for the BESSY Soft X-Ray FEL, a cascaded High Gain Harmonic Generation FEL proposed by BESSY in Berlin. The original design for the BESSY High Energy FEL line requires four HGHG stages to convert the initial seed laser wavelength of 297.5 nm down to 1.24 nm. A new scheme is proposed that makes use of fifth harmonic radiation from the first stage and reduces the number of HGHG stages to three. It

Analyzing correlation functions with tesseral and Cartesian spherical harmonics

International Nuclear Information System (INIS)

Danielewicz, Pawel; Pratt, Scott

2007-01-01

The dependence of interparticle correlations on the orientation of particle relative momentum can yield unique information on the space-time features of emission in reactions with multiparticle final states. In the present paper, the benefits of a representation and analysis of the three-dimensional correlation information in terms of surface spherical harmonics is presented. The harmonics include the standard complex tesseral harmonics and the real Cartesian harmonics. Mathematical properties of the lesser known Cartesian harmonics are illuminated. The physical content of different angular harmonic components in a correlation is described. The resolving power of different final-state effects with regard to determining angular features of emission regions is investigated. The considered final-state effects include identity interference, strong interactions, and Coulomb interactions. The correlation analysis in terms of spherical harmonics is illustrated with the cases of Gaussian and blast-wave sources for proton-charged meson and baryon-baryon pairs

Optimal Selective Harmonic Control for Power Harmonics Mitigation

DEFF Research Database (Denmark)

Zhou, Keliang; Yang, Yongheng; Blaabjerg, Frede

2015-01-01

of power harmonics. The proposed optimal SHC is of hybrid structure: all recursive SHC modules with weighted gains are connected in parallel. It bridges the real “nk+-m order RC” and the complex “parallel structure RC”. Compared to other IMP based control solutions, it offers an optimal trade-off among...

Math Model and Calculation Analysis of Inter-harmonic of Double PWM Speed Control System in Distribution Network

Directory of Open Access Journals (Sweden)

Yang Wen-Huan

2014-11-01

Full Text Available Aiming at the problem that the distribution network voltage will fluctuate because of the inter-harmonic currents injected into the network by double PWM speed control system when regulating the speed of the asynchronous motor, we established the inter-harmonic current math model of double PWM speed control system according to switching function based on a real bridge crane. The distribution law of the inter-harmonic is got by calculating the grid-side currents and their spectrum while letting the motor run at different quadrants and frequencies. The result which is verified by simulation and experiment shows that the content of the inter harmonic currents is more than that of harmonic currents in double PWM speed control system, the frequency of the inter harmonics of the grid-side current mainly focus on the scope lower than the fundamental frequency, and when the motor runs at low frequencies, the THD of the grid-side current is high. The result has verified the reason why the voltage of a bridge crane distribution system of a deepwater port in Shanghai flickers.

Azimuthal anisotropy: The higher harmonics

International Nuclear Information System (INIS)

Poskanzer, Arthur M.; STAR Collaboration

2004-01-01

We report the first observations of the fourth harmonic (v 4 ) in the azimuthal distribution of particles at RHIC. The measurement was done taking advantage of the large elliptic flow generated at RHIC. The integrated v 4 is about a factor of 10 smaller than v 2 . For the sixth (v 6 ) and eighth (v 8 ) harmonics upper limits on the magnitudes are reported

Effects of Stretching by P.N.F and Harmonic Techniques on Hamstring Flexibility

Directory of Open Access Journals (Sweden)

Hassan Shakeri

2006-01-01

Full Text Available Objective: Improving of muscle flexibility is an important issue in physiotherapy and sport sciences. There are many methods for increasing muscle length and decreasing muscle stiffness. In research findings, PNF method has been found to be better than static and ballistic methods. There is another method named Harmonic technique (introduced by E. Lederman 1997 that has been claimed to be more effective, but there is not enough documentation about this claim. Aim of this study was to compare effects of stretching by PNF and harmonic techniques on hamstring flexibility. Materials & Methods: This research is a RCT study in that 45 colledge students aged 18-35 years were arranged in three groups (Harmonic, P.N.F, and control. Subjects haven’t had any painful pathology in low-back and lower extremities for last six months. Subjects had limited hamstring length (20 degrees deficiency in Active-Knee-Extension test and hadn’t professional sport activities. Dependent variablies were muscle stiffness and hamstring length which popliteal angle in AKE test was its indirect index. In pilot study, reliability of measurement of these variables were approved. Then hamstring muscle of subjects in harmonic and PNF groups were stretched by harmonic and PNF methods for six weeks, 5 minute per day and 3d/wks, whereas control group hadn’t any exercise. Results: Findings of this study showed that in both used techniques, changes of hamstring length were significant (P=0.000, but in control group there wasn’t significant change. There wasn’t significant differences between changes of hamstring length in PNF and Harmonic groups. Only in harmonic group, muscle stiffness had significant changes (P<0.03. Conclusion: According to findings of this research, both harmonic and PNF methods equally increased length of hamstring, and harmonic technique can be used as an alternative stretching method for other techniques. Maybe harmonic technique is better than PNF

General Criterion for Harmonicity

Science.gov (United States)

Proesmans, Karel; Vandebroek, Hans; Van den Broeck, Christian

2017-10-01

Inspired by Kubo-Anderson Markov processes, we introduce a new class of transfer matrices whose largest eigenvalue is determined by a simple explicit algebraic equation. Applications include the free energy calculation for various equilibrium systems and a general criterion for perfect harmonicity, i.e., a free energy that is exactly quadratic in the external field. As an illustration, we construct a "perfect spring," namely, a polymer with non-Gaussian, exponentially distributed subunits which, nevertheless, remains harmonic until it is fully stretched. This surprising discovery is confirmed by Monte Carlo and Langevin simulations.

Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine

Science.gov (United States)

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409

Evaluation of Harmonic Content from a Tap Transformer Based Grid Connection System for Wind Power

Directory of Open Access Journals (Sweden)

S. Apelfröjd

2013-01-01

Full Text Available Simulations done in MATLAB/Simulink together with experiments conducted at the Ångströms laboratory are used to evaluate and discuss the total harmonic distortion (THD and total demand distortion (TDD of a tap transformer based grid connection system. The grid connection topology can be used with different turbine and generator topologies and is here applied on a vertical axis wind turbine (VAWT with a permanent magnet synchronous generator (PMSG and its operational scheme. The full variable-speed wind conversion system consists of a diode rectifier, DC link, IGBT inverter, LCL-filter, and tap transformer. The full variable-speed operation is enabled by the use of the different step-up ratios of the tap transformer. In the laboratory study, a full experimental setup of the system was used, a clone of the on-site PMSG driven by a motor was used, and the grid was replaced with a resistive load. With a resistive load, grid harmonics and possible unbalances are removed. The results show a TDD and THD below 5% for the full operating range and harmonic values within the limits set up by IEEE-519. Furthermore, a change in tap, going to a lower step-up ratio, results in a reduction in both THD and TDD for the same output power.

Harmonic superspaces of extended supersymmetry

International Nuclear Information System (INIS)

Ivanov, E.; Kalitzin, S.; Nguyen Ai Viet; Ogievetsky, V.

1984-01-01

The main technical apparatus of the harmonic superspace approach to extended SUSY, the calculus of harmonic variables on homogeneous spaces of the SUSY automorphism groups, is presented in detail for N=2, 3, 4. The basic harmonics for the coset manifolds G/H with G=SU(2), H=U(1); G=SU(3), H=SU(2)xU(1) and H=U(1)xU(1); G=SU(4), H=SU(3)xU(1), H=SU(2)xSU(2)xU(1), H=SU(2)xU(1)xU(1) and H=U(1)xU(1)xU(1); G=USp(2), H=SU(2)xSU(2), H=SU(2)xU(1) and H=U(1)xU(1) are tabulated a number of useful relations among them

Tunneling ionization and harmonic generation in two-color fields

International Nuclear Information System (INIS)

Kondo, K.; Kobayashi, Y.; Sagisaka, A.; Nabekawa, Y.; Watanabe, S.

1996-01-01

Tunneling ionization and harmonic generation in two-color fields were studied with a fundamental beam (ω) and its harmonics (2ω,3ω), which were generated by a 100-fs Ti:sapphire laser. Ion yields of atoms and molecules were successfully controlled by means of a change in the relative phase between ω and 3ω pulses. Two-color interference was clearly observed in photoelectron spectra and harmonic spectra. In the ω endash 2ω field even-order harmonics were observed in which the intensity was almost equal to that of the odd harmonics because of an asymmetric optical field. These results were compared with the quasi-static model for ionization and with the quantum theory for harmonic generation. copyright 1996 Optical Society of America

Extended BRS and anti-BRS symmetries in N=2 harmonic superspace

International Nuclear Information System (INIS)

Lhallabi, T.; Saidi, E.H.

1986-08-01

The full set of extended BRS and anti-BRS symmetries are derived for components of superconnection and gauge superfield using the N=2 harmonic superspace. The quantization of N=2 supersymmetric theory is developed and the proof of its gauge invariance is presented. (author)

High-order harmonic generation with short-pulse lasers

International Nuclear Information System (INIS)

Schafer, K.J.; Krause, J.L.; Kulander, K.C.

1992-12-01

Recent progress in the understanding of high-order harmonic conversion from atoms and ions exposed to high-intensity, short-pulse optical lasers is reviewed. We find that ions can produce harmonics comparable in strength to those obtained from neutral atoms, and that the emission extends to much higher order. Simple scaling laws for the strength of the harmonic emission and the maximium observable harmonic are suggested. These results imply that the photoemission observed in recent experiments in helium and neon contains contributions from ions as well as neutrals

Immune-escape mutations and stop-codons in HBsAg develop in a large proportion of patients with chronic HBV infection exposed to anti-HBV drugs in Europe

DEFF Research Database (Denmark)

Colagrossi, Luna; Hermans, Lucas E; Salpini, Romina

2018-01-01

structure of HBV genome, some immune-escape mutations or stop-codons in HBsAg can derive from drug-resistance mutations in RT. This study is aimed at gaining insight in prevalence and characteristics of immune-associated escape mutations, and stop-codons in HBsAg in chronically HBV-infected patients...

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

Directory of Open Access Journals (Sweden)

Meiler Arno

2012-09-01

Full Text Available Abstract Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

Challenges and Opportunities for Harmonizing Research Methodology

DEFF Research Database (Denmark)

van Hees, V. T.; Thaler-Kall, K.; Wolf, K. H.

2016-01-01

Objectives: Raw accelerometry is increasingly being used in physical activity research, but diversity in sensor design, attachment and signal processing challenges the comparability of research results. Therefore, efforts are needed to harmonize the methodology. In this article we reflect on how...... increased methodological harmonization may be achieved. Methods: The authors of this work convened for a two-day workshop (March 2014) themed on methodological harmonization of raw accelerometry. The discussions at the workshop were used as a basis for this review. Results: Key stakeholders were identified...... as manufacturers, method developers, method users (application), publishers, and funders. To facilitate methodological harmonization in raw accelerometry the following action points were proposed: i) Manufacturers are encouraged to provide a detailed specification of their sensors, ii) Each fundamental step...

Cohabiting with the harmonic pollution

International Nuclear Information System (INIS)

Garcia C, Antonio A

1999-01-01

The Norm IEEE 519 tries of the permissible limits of harmonic distortion in the point of common joining between the energy supplier company and the industry. However fulfilling these limits of distortion doesn't guarantee that the problem for the company has finished, on the contrary will have to counteract the effects created by the harmonic distortion toward the interior of its electric system and to cohabit with this distortion

Novel Harmonic Regularization Approach for Variable Selection in Cox’s Proportional Hazards Model

Directory of Open Access Journals (Sweden)

Ge-Jin Chu

2014-01-01

Full Text Available Variable selection is an important issue in regression and a number of variable selection methods have been proposed involving nonconvex penalty functions. In this paper, we investigate a novel harmonic regularization method, which can approximate nonconvex Lq  (1/2harmonic regularization method can be efficiently solved using our proposed direct path seeking approach, which can produce solutions that closely approximate those for the convex loss function and the nonconvex regularization. Simulation results based on the artificial datasets and four real microarray gene expression datasets, such as real diffuse large B-cell lymphoma (DCBCL, the lung cancer, and the AML datasets, show that the harmonic regularization method can be more accurate for variable selection than existing Lasso series methods.

Examining the impact of harmonic correlation on vibrational frequencies calculated in localized coordinates

Energy Technology Data Exchange (ETDEWEB)

Hanson-Heine, Magnus W. D., E-mail: magnus.hansonheine@nottingham.ac.uk [School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD (United Kingdom)

2015-10-28

Carefully choosing a set of optimized coordinates for performing vibrational frequency calculations can significantly reduce the anharmonic correlation energy from the self-consistent field treatment of molecular vibrations. However, moving away from normal coordinates also introduces an additional source of correlation energy arising from mode-coupling at the harmonic level. The impact of this new component of the vibrational energy is examined for a range of molecules, and a method is proposed for correcting the resulting self-consistent field frequencies by adding the full coupling energy from connected pairs of harmonic and pseudoharmonic modes, termed vibrational self-consistent field (harmonic correlation). This approach is found to lift the vibrational degeneracies arising from coordinate optimization and provides better agreement with experimental and benchmark frequencies than uncorrected vibrational self-consistent field theory without relying on traditional correlated methods.

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