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Sample records for codon usage analysis

  1. 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.

  2. Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes.

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    Susanta K Behura

    Full Text Available BACKGROUND: Codon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Although genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias. METHODS AND PRINCIPAL FINDINGS: Here, we use bioinformatics approaches to analyze codon usage bias and codon context patterns in a genome-wide manner among 15 dipteran and 7 hymenopteran insect species. Results show that GAA is the most frequent codon in the dipteran species whereas GAG is the most frequent codon in the hymenopteran species. Data reveals that codons ending with C or G are frequently used in the dipteran genomes whereas codons ending with A or T are frequently used in the hymenopteran genomes. Synonymous codon usage orders (SCUO vary within genomes in a pattern that seems to be distinct for each species. Based on comparison of 30 one-to-one orthologous genes among 17 species, the fruit fly Drosophila willistoni shows the least codon usage bias whereas the honey bee (Apis mellifera shows the highest bias. Analysis of codon context patterns of these insects shows that specific codons are frequently used as the 3'- and 5'-context of start and stop codons, respectively. CONCLUSIONS: Codon bias pattern is distinct between dipteran and hymenopteran insects. While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects. Also, codon context patterns vary among these species largely according to their phylogeny.

  3. Analysis of codon usage and nucleotide composition bias in polioviruses

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    Gu Yuan-xing

    2011-03-01

    Full Text Available Abstract Background Poliovirus, the causative agent of poliomyelitis, is a human enterovirus and a member of the family of Picornaviridae and among the most rapidly evolving viruses known. Analysis of codon usage can reveal much about the molecular evolution of the viruses. However, little information about synonymous codon usage pattern of polioviruses genome has been acquired to date. Methods The relative synonymous codon usage (RSCU values, effective number of codon (ENC values, nucleotide contents and dinucleotides were investigated and a comparative analysis of codon usage pattern for open reading frames (ORFs among 48 polioviruses isolates including 31 of genotype 1, 13 of genotype 2 and 4 of genotype 3. Results The result shows that the overall extent of codon usage bias in poliovirus samples is low (mean ENC = 53.754 > 40. The general correlation between base composition and codon usage bias suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in those polioviruses. Depending on the RSCU data, it was found that there was a significant variation in bias of codon usage among three genotypes. Geographic factor also has some effect on the codon usage pattern (exists in the genotype-1 of polioviruses. No significant effect in gene length or vaccine derived polioviruses (DVPVs, wild viruses and live attenuated virus was observed on the variations of synonymous codon usage in the virus genes. The relative abundance of dinucleotide (CpG in the ORFs of polioviruses are far below expected values especially in DVPVs and attenuated virus of polioviruses genotype 1. Conclusion The information from this study may not only have theoretical value in understanding poliovirus evolution, especially for DVPVs genotype 1, but also have potential value for the development of poliovirus vaccines.

  4. Analysis of Synonymous Codon Usage Bias in Chlamydia

    Institute of Scientific and Technical Information of China (English)

    Hui L(ü); Wei-Ming ZHAO; Yan ZHENG; Hong WANG; Mei QI; Xiu-Ping YU

    2005-01-01

    Chlamydiae are obligate intracellular bacterial pathogens that cause ocular and sexually transmitted diseases, and are associated with cardiovascular diseases. The analysis of codon usage may improve our understanding of the evolution and pathogenesis of Chlamydia and allow reengineering of target genes to improve their expression for gene therapy. Here, we analyzed the codon usage of C. muridarum, C.trachomatis (here indicating biovar trachoma and LGV), C. pneumoniae, and C. psittaci using the codon usage database and the CUSP (Create a codon usage table) program of EMBOSS (The European Molecular Biology Open Software Suite). The results show that the four genomes have similar codon usage patterns,with a strong bias towards the codons with A and T at the third codon position. Compared with Homo sapiens, the four chlamydial species show discordant seven or eight preferred codons. The ENC (effective number of codons used in a gene)-plot reveals that the genetic heterogeneity in Chlamydia is constrained by the G+C content, while translational selection and gene length exert relatively weaker influences. Moreover,mutational pressure appears to be the major determinant of the codon usage variation among the chlamydial genes. In addition, we compared the codon preferences of C. trachomatis with those of E. coli, yeast,adenovirus and Homo sapiens. There are 23 codons showing distinct usage differences between C. trachomatis and E. coli, 24 between C. trachomatis and adenovirus, 21 between C. trachomatis and Homo sapiens, but only six codons between C. trachomatis and yeast. Therefore, the yeast system may be more suitable for the expression of chlamydial genes. Finally, we compared the codon preferences of C. trachomatis with those of six eukaryotes, eight prokaryotes and 23 viruses. There is a strong positive correlation between the differences in coding GC content and the variations in codon bias (r=0.905, P<0.001). We conclude that the variation of codon bias

  5. Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

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    Xiuzhang Li

    2016-07-01

    Full Text Available Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59% in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C.

  6. Genome-wide analysis of the synonymous codon usage patterns in apple

    Institute of Scientific and Technical Information of China (English)

    LI Ning; SUN Mei-hong; JIANG Ze-sheng; SHU Huai-rui; ZHANG Shi-zhong

    2016-01-01

    Apple (Malus×domestica) has been proposed as an important woody plant and the major cultivated fruit trees in temperate regions. Apple whole genome sequencing has been completed, which provided an excelent opportunity for genome-wide analysis of the synonymous codon usage patterns. In this study, a multivariate bioinformatics analysis was performed to reveal the characteristics of synonymous codon usage and the main factors affecting codon bias in apple. The neutrality, correspondence, and correlation analyses were performed by CodonW and SPSS (Statistical Product and Service Solu-tions) programs, indicating that the apple genome codon usage patterns were affected by mutational pressure and selective constraint. Meanwhile, coding sequence length and the hydrophobicity of proteins could also inlfuence the codon usage patterns. In short, codon usage pattern analysis and determination of optimal codons has laid an important theoretical basis for genetic engineering, gene prediction and molecular evolution studies in apple.

  7. Comparative Analysis of Codon Usage Patterns Among Mitochondrion, Chloroplast and Nuclear Genes in Triticum aestivum L.

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    Wen-Juan Zhang; Jie Zhou; Zuo-Feng Li; Li Wang; Xun Gu; Yang Zhong

    2007-01-01

    In many organisms, the difference in codon usage patterns among genes reflects variation in local base compositional biases and the intensity of natural selection. In this study, a comparative analysis was performed to investigate the characteristics of codon bias and factors in shaping the codon usage patterns among mitochondrion,chloroplast and nuclear genes in common wheat (Triticum aestivum L.). GC contents in nuclear genes were higher than that in mitochondrion and chloroplast genes. The neutrality and correspondence analyses indicated that the codon usage in nuclear genes would be a result of relative strong mutational bias, while the codon usage patterns of rnitochondrion and chloroplast genes were more conserved in GC content and influenced by translation level.The Parity Rule 2 (PR2) plot analysis showed that pyrimidines were used more frequently than purines at the third codon position in the three genomes. In addition, using a new alterative strategy, 11, 12, and 24 triplets were defined as preferred codons in the mitochondrion, chloroplast and nuclear genes, respectively. These findings suggested that the mitochondrion, chloroplast and nuclear genes shared particularly different features of codon usage and evolutionary constraints.

  8. 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.

  9. Analysis of Codon Usage Patterns in Herbaceous Peony (Paeonia lactiflora Pall. Based on Transcriptome Data

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    Yanqing Wu

    2015-10-01

    Full Text Available Codon usage bias, which exists in many genomes, is mainly determined by mutation and selection. To elucidate the genetic features and evolutionary history of herbaceous peony (Paeonia lactiflora, a well-known symbol of prosperity in China, we examined synonymous codon usage in 24,216 reconstructed genes from the P. lactiflora transcriptome. The mean GC content was 44.4%, indicating that the nucleotide content of P. lactiflora genes is slightly AT rich and GC poor. The P. lactiflora genome has a wide range of GC3 (GC content at the third synonymous codon position distribution, with a significant correlation between GC12 and GC3. ENC (effective number of codons analysis suggested that mutational bias played a major role in shaping codon usage. Parity Rule 2 (PR2 analysis revealed that GC and AU were not used proportionally. We identified 22 “optimal codons”, most ending with an A or U. Our results suggested that nucleotide composition mutation bias and translational selection were the main driving factors of codon usage bias in P. lactiflora. These results lay the foundation for exploring the evolutionary mechanisms and heterologous expression of functionally-important proteins in P. lactiflora.

  10. Analysis of synonymous codon usage in chloroplast genome of Populus alba

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    ZHOU Meng; LONG Wei; LI Xia

    2008-01-01

    The pattern of codon usage in the chloroplast genome of Populus alba was investigated.Correspondence analysis (a commonly used multivariate statistical approach) and method of effective number of codons (ENc)-plot were conducted to analyze synonymous codon usage.The results of correspondence analysis showed that the distribution of genes on the major axis was significantly correlated with the frequency of use of G+C in synonymously variable third position of sense codon (GC3S),(r=0.349),and the positions of genes on the axis 2 and axis 3 were significantly correlated with CAI (r=-0.348,p<0.01 and r=0.602,p<0.01).The ENc for most genes was similar to that for the expected ENc based on the GC3S,but several genes with low ENC values were lying below the expected curve.All of these data indicated that codon usage was dominated by a mutational bias in chloroplast genome of P.alba.The selection in nature for translational efficiency only played a minor role in shaping codon usage in the chloroplast genome of P.alba.

  11. A Comprehensive Analysis of Codon Usage Patterns in Blunt Snout Bream (Megalobrama amblycephala Based on RNA-Seq Data

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    Xiaoke Duan

    2015-05-01

    Full Text Available Blunt snout bream (Megalobrama amblycephala is an important fish species for its delicacy and high economic value in China. Codon usage analysis could be helpful to understand its codon biology, mRNA translation and vertebrate evolution. Based on RNA-Seq data for M. amblycephala, high-frequency codons (CUG, AGA, GUG, CAG and GAG, as well as low-frequency ones (NUA and NCG codons were identified. A total of 724 high-frequency codon pairs were observed. Meanwhile, 14 preferred and 199 avoided neighboring codon pairs were also identified, but bias was almost not shown with one or more intervening codons inserted between the same pairs. Codon usage bias in the regions close to start and stop codons indicated apparent heterogeneity, which even occurs in the flanking nucleotide sequence. Codon usage bias (RSCU and SCUO was related to GC3 (GC content of 3rd nucleotide in codon bias. Six GO (Gene ontology categories and the number of methylation targets were influenced by GC3. Codon usage patterns comparison among 23 vertebrates showed species specificities by using GC contents, codon usage and codon context analysis. This work provided new insights into fish biology and new information for breeding projects.

  12. A Comparative Analysis of Synonymous Codon Usage Bias Pattern in Human Albumin Superfamily

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    Hoda Mirsafian

    2014-01-01

    Full Text Available Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life. Though the frequency of codon usage is not equal across species and within genome in the same species, the phenomenon is non random and is tissue-specific. Several factors such as GC content, nucleotide distribution, protein hydropathy, protein secondary structure, and translational selection are reported to contribute to codon usage preference. The synonymous codon usage patterns can be helpful in revealing the expression pattern of genes as well as the evolutionary relationship between the sequences. In this study, synonymous codon usage bias patterns were determined for the evolutionarily close proteins of albumin superfamily, namely, albumin, α-fetoprotein, afamin, and vitamin D-binding protein. Our study demonstrated that the genes of the four albumin superfamily members have low GC content and high values of effective number of codons (ENC suggesting high expressivity of these genes and less bias in codon usage preferences. This study also provided evidence that the albumin superfamily members are not subjected to mutational selection pressure.

  13. 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.

  14. Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins

    Indian Academy of Sciences (India)

    VISHWA JYOTI BARUAH; SIDDHARTHA SANKAR SATAPATHY; BHESH RAJ POWDEL; ROCKTOTPAL KONWARH; ALAK KUMAR BURAGOHAIN; SUVENDRA KUMAR RAY

    2016-09-01

    The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G+C% of the HEG was found to be less in comparison to the genome G+ C% in Crenarchaea, whereas reverse was the case in Euryarchaea. The preponderance of U/A ending codons that code for HEG in Crenarchaea was in sharp contrast to the C/G ended ones in Euryarchaea. The analysis revealed prevalence of U-ending codons even within the WWY (nucleotide ambiguity code) families in Crenarchaea vis-à-vis Euryarchaea, bacteria and Eukarya. No plausible interpretation of the observed disparity could be made either in the context of tRNA gene composition or genome G +C%. The results in this study attested that the preferential biasness for codons in HEG of Crenarchaea might be different from Euryarchaea. The main highlights are (i) varied CUB in the HEG and in the whole genomes in Euryarchaea and Crenarchaea. (ii) Crenarchaea was found to have some unusual optimal codons (OCs) compared to other organisms. (iii) G+ C% (and GC 3) of the HEG were different from the genome G + C% in the two phyla. (iv) Genome G + C% and tRNAgene number failed to explain CUB in Crenarchaea. (v) Translational selection is possibly responsible for A + T rich OCs in Crenarchaea.

  15. Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus

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    Wong Emily HM

    2010-08-01

    Full Text Available Abstract Background The influenza A virus is an important infectious cause of morbidity and mortality in humans and was responsible for 3 pandemics in the 20th century. As the replication of the influenza virus is based on its host's machinery, codon usage of its viral genes might be subject to host selection pressures, especially after interspecies transmission. A better understanding of viral evolution and host adaptive responses might help control this disease. Results Relative Synonymous Codon Usage (RSCU values of the genes from segment 1 to segment 6 of avian and human influenza viruses, including pandemic H1N1, were studied via Correspondence Analysis (CA. The codon usage patterns of seasonal human influenza viruses were distinct among their subtypes and different from those of avian viruses. Newly isolated viruses could be added to the CA results, creating a tool to investigate the host origin and evolution of viral genes. It was found that the 1918 pandemic H1N1 virus contained genes with mammalian-like viral codon usage patterns, indicating that the introduction of this virus to humans was not through in toto transfer of an avian influenza virus. Many human viral genes had directional changes in codon usage over time of viral isolation, indicating the effect of host selection pressures. These changes reduced the overall GC content and the usage of G at the third codon position in the viral genome. Limited evidence of translational selection pressure was found in a few viral genes. Conclusions Codon usage patterns from CA allowed identification of host origin and evolutionary trends in influenza viruses, providing an alternative method and a tool to understand the evolution of influenza viruses. Human influenza viruses are subject to selection pressure on codon usage which might assist in understanding the characteristics of newly emerging viruses.

  16. Analysis of the codon usage of the ORF2 gene of feline calicivirus.

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    Zang, Minghui; He, Wanting; Du, Fanshu; Wu, Gongjian; Wu, Bohao; Zhou, Zhenlei

    2017-10-01

    Feline calicivirus (FCV) is a highly prevalent pathogen of the domestic cat that causes acute infections of the oral and upper respiratory tract. The E region of the ORF2 protein is responsible for the induction of virus-neutralizing antibodies, thus it is important to understand the codon usage of this gene. Here, analysed 90 coding sequences of ORF2 and show that it undergoes a low codon usage bias. In addition, although mutational bias is one of the factors shaping the codon usage bias of this gene, natural selection plays a more significant role. Our results reveal part of the mechanisms driving FCV evolution, which will lay foundation for the further research of FCV. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. 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.

  18. Comparative genome sequence analysis of Sulfolobus acidocaldarius and 9 other isolates of its genus for factors influencing codon and amino acid usage.

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    Nayak, Kinshuk Chandra

    2013-01-15

    In the present study, major constraints for codon and amino acid usage of Sulfolobus acidocaldarius, Sulfolobus solfataricus, Sulfolobus tokodali, Sulfolobus islandis and 6 other isolates from islandicus species of genus Sulfolobus were investigated. Correspondence analysis revealed high significant correlation between the major trend of synonymous codon usage and gene expression level, as assessed by the "Codon Adaptation Index" (CAI). There is a significant negative correlation between Nc (Effective number of codons) and CAI demonstrating role of codon bias as an important determinant of codon usage. The significant correlation between major trend of synonymous codon usage and GC3s (G+C at third synonymous position) indicated dominant role of mutational bias in codon usage pattern. The result was further supported from SCUO (synonymous codon usage order) analysis. The amino acid usage was found to be significantly influenced by aromaticity and hydrophobicity of proteins. However, translational selection which causes a preference for codons that are most rapidly translated by current tRNA with multiple copy numbers was not found to be highly dominating for all studied isolates. Notably, 26 codons that were found to be optimally used by genes of S. acidocaldarius at higher expression level and its comparative analysis with 9 other isolates may provide some useful clues for further in vivo genetic studies on this genus.

  19. Genome landscapes and bacteriophage codon usage.

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    Julius B Lucks

    2008-02-01

    Full Text Available Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonymous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa, and L. lactis as their primary host. We use the concept of a "genome landscape," which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such as GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.

  20. Complex Codon Usage Pattern and Compositional Features of Retroviruses

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    Sourav RoyChoudhury

    2013-01-01

    Full Text Available Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition.

  1. Gender-specific selection on codon usage in plant genomes

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    Krochko Joan E

    2007-06-01

    Full Text Available Abstract Background Currently, there is little data available regarding the role of gender-specific gene expression on synonymous codon usage (translational selection in most organisms, and particularly plants. Using gender-specific EST libraries (with > 4000 ESTs from Zea mays and Triticum aestivum, we assessed whether gender-specific gene expression per se and gender-specific gene expression level are associated with selection on codon usage. Results We found clear evidence of a greater bias in codon usage for genes expressed in female than in male organs and gametes, based on the variation in GC content at third codon positions and the frequency of species-preferred codons. This finding holds true for both highly and for lowly expressed genes. In addition, we found that highly expressed genes have greater codon bias than lowly expressed genes for both female- and male-specific genes. Moreover, in both species, genes with female-specific expression show a greater usage of species-specific preferred codons for each of the 18 amino acids having synonymous codons. A supplemental analysis of Brassica napus suggests that bias in codon usage could also be higher in genes expressed in male gametophytic tissues than in heterogeneous (flower tissues. Conclusion This study reports gender-specific bias in codon usage in plants. The findings reported here, based on the analysis of 1 497 876 codons, are not caused either by differences in the biological functions of the genes or by differences in protein lengths, nor are they likely attributable to mutational bias. The data are best explained by gender-specific translational selection. Plausible explanations for these findings and the relevance to these and other organisms are discussed.

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

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    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.

  3. Correlation matrix for quartet codon usage

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    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.

  4. 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.

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

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    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.

  6. Codon Usage Bias and Determining Forces in Taenia solium Genome.

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    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.

  7. Efficient translation initiation dictates codon usage at gene start

    Science.gov (United States)

    Bentele, Kajetan; Saffert, Paul; Rauscher, Robert; Ignatova, Zoya; Blüthgen, Nils

    2013-01-01

    The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5–10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate. PMID:23774758

  8. Analysis of the relationship between genomic GC Content and patterns of base usage, codon usage and amino acid usage in prokaryotes: similar GC content adopts similar compositional frequencies regardless of the phylogenetic lineages.

    Directory of Open Access Journals (Sweden)

    Hui-Qi Zhou

    Full Text Available The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. These genomes had GC contents that ranged from 13.5% to 74.9%. We analyzed the distance of base frequencies at the three codon positions, codon frequencies, and amino acid compositions across genomes with respect to the differences in the GC content of these prokaryotic species. We found that although the phylogenetic lineages were remote among some species, a similar genomic GC content forced them to adopt similar base usage patterns at the three codon positions, codon usage patterns, and amino acid usage patterns. Our work demonstrates that in prokaryotic genomes: a base usage, codon usage, and amino acid usage change with GC content with a linear correlation; b the distance of each usage has a linear correlation with the GC content difference; and c GC content is more essential than phylogenetic lineage in determining base usage, codon usage, and amino acid usage. This work is exceptional in that we adopted intuitively graphic methods for all analyses, and we used these analyses to examine as many as 2670 prokaryotes. We hope that this work is helpful for understanding common features in the organization of microbial genomes.

  9. Evolution of synonymous codon usage in Neurospora tetrasperma and Neurospora discreta.

    Science.gov (United States)

    Whittle, C A; Sun, Y; Johannesson, H

    2011-01-01

    Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems.

  10. 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.

  11. 茶树密码子用法分析%Analysis of Codon Usage in Tea Plant (Camellia sinensis)

    Institute of Scientific and Technical Information of China (English)

    赵洋; 杨阳; 刘振; 杨培迪

    2011-01-01

    运用CodonW软件和CUSP程序对筛选的134个茶树蛋白质编码基因序列进行了分析、计算密码子使用频率,并将它与人、果蝇、酵母、大肠杆菌这4种代表性生物及拟南芥、大豆、棉花、水稻、小麦等单、双子叶植物进行比较.结果显示茶树密码子偏爱性与人、果蝇、酵母、大肠杆菌有不同程度的差异,与单子叶植物水稻、小麦的密码子使用频率差异较大,与双子叶植物拟南芥、大豆、棉花的密码子偏爱性一致,分析结果对茶树基因转化及高效表达系统的选择等具有重要指导意义.%The coding sequence of 134 selected proteins in tea plant (Camellia sinensis) were analyzed by CodonW and CUSP program in this investigation, and the frequency of codon usage which encoded amino acids was calculated and compared with four classes of representative organisms including human (Homo sapiens), yeast (Saccharomyces cerevisiae), Escherichia coli. Bacteria and fruit fly (Drosophila melanogaster). These results showed that codon preference of tea plant was differed in various degrees with these model organisms. Accomparison of codon usage frequency of tea plant with dicotyledons and monocotyledons plants including Arabidopsis thaliana, soybean (Glycine max), cotton (Gossypium hirsutum), rice (Oryza sativa), wheat (Triticum aestivum), the consequence indicated that codon usage frequency of tea plant was obviously differed from these monocotyledons such as Oryza sativa and Triticum aestivum, but had a consistency in codon preference with these dicotyledons such as Arabidopsis thaliana, Glycine max and Gossypium hirsutum. These results showed an important guidance for tea plant gene-transforming and the selection of the high-efficient expression system.

  12. 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.

  13. Codon usage in mammalian genes is biased by sequence slippage mechanisms.

    Science.gov (United States)

    Bains, W

    1993-01-01

    The codons for some conserved amino acids are found to be the same between homologous genes from different species when the statistics of codon usage would suggest that they should be different. I examine whether this 'coincidence' of codon usage could be due to genetic mechanisms homogenising the DNA around specific sites. This paper describes the further analysis of the coincident codons in 19 genes (a total of 96 homologues) for slippage. Coincident codons arise in contexts of increased sequence simplicity, and have a high chance of occurring within sequences similar to the recombination-prone minisatellite 'core' sequence. This suggests a role of genetic homogenisation in their generation.

  14. 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.

  15. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance

    Directory of Open Access Journals (Sweden)

    Zhang Zhang

    2012-03-01

    Full Text Available Abstract 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.

  16. Exploring Codon Usage Patterns of Alternatively Spliced Genes in Human Chromosome 1

    Institute of Scientific and Technical Information of China (English)

    马飞; 庄永龙; 黄颖; 李衍达

    2004-01-01

    In this study, 414 whole protein-coding sequences (238 004 codons) of alternatively spliced genes of human chromosome 1 have been employed to explore the patterns of codon usage bias among genes. Overall codon usage data analysis indicates that G- and C-ending codons are predominant in the genes. The base usage in all three codon positions suggests a selection-mutation balance. Multivariate statistical analysis reveals that the codon usage variation has a strong positive correlation with the expressivities of the genes (r=0.5790, P<0.0001). All 27 codons identified as optimal are G- and C-ending codons.Correlation analysis shows a strong negative correlation between the gene length and codon adaptation index value (r=-0.2252, P<0.0001), and a significantly positive correlation between the gene length and Nc values (r=0.1876, P<0.0001). These results suggest that the comparatively shorter genes in the genes have higher codon usage bias to maximize translational efficiency, and selection may also contribute to the reduction of highly expressed proteins.

  17. Species based synonymous codon usage in fusion protein gene of Newcastle disease virus.

    Directory of Open Access Journals (Sweden)

    Chandra Shekhar Kumar

    Full Text Available Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV has also been reported from many non-avian species. The NDV fusion protein (F is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species.

  18. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage

    DEFF Research Database (Denmark)

    Yang, Ziheng; Nielsen, Rasmus

    2008-01-01

    Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection. They are thus incapable of inferring whether mutation or selection is responsible for evolution at silent sites. Here we...... to examine the null hypothesis that codon usage is due to mutation bias alone, not influenced by natural selection. Application of the test to the mammalian data led to rejection of the null hypothesis in most genes, suggesting that natural selection may be a driving force in the evolution of synonymous...... codon usage in mammals. Estimates of selection coefficients nevertheless suggest that selection on codon usage is weak and most mutations are nearly neutral. The sensitivity of the analysis on the assumed mutation model is discussed....

  19. Characterization of Synonymous Codon Usage Bias in the Pseudorabies Virus US1 Gene

    Institute of Scientific and Technical Information of China (English)

    Meili Li; Zhiyao Zhao; Jianhong Chen; Bingyun Wang; Zi Li; Jian Li; Mingsheng Cai

    2012-01-01

    In the present study,we examined the codon usage bias between pseudorabies virus (PRV) US1 gene and the US1-like genes of 20 reference alphaherpesviruses.Comparative analysis showed noticeable disparities of the synonymous codon usage bias in the 21 alphaherpesviruses,indicated by codon adaptation index,effective number of codons (ENc) and GC3s value.The codon usage pattern of PRV US1 gene was phylogenetically conserved and similar to that of the US1-like genes of the genus Varicellovirus of alphaherpesvirus,with a strong bias towards the codons with C and G at the third codon position.Cluster analysis of codon usage pattern of PRV US1 gene with its reference alphaherpesviruses demonstrated that the codon usage bias of US1-like genes of 21 alphaherpesviruses had a very close relation with their gene functions.ENc-plot revealed that the genetic heterogeneity in PRV US1 gene and the 20 reference alphaherpesviruses was constrained by G+C content,as well as the gene length.In addition,comparison of codon preferences in the US1 gene of PRV with those of E.coli,yeast and human revealed that there were 50 codons showing distinct usage differences between PRV and yeast,49 between PRV and human,but 48 between PRV and E.coli.Although there were slightly fewer differences in codon usages between E.coli and PRV,the difference is unlikely to be statistically significant,and experimental studies are necessary to establish the most suitable expression system for PRV US1.In conclusion,these results may improve our understanding of the evolution,pathogenesis and functional studies of PRV,as well as contributing to the area of herpesvirus research or even studies with other viruses.

  20. Characterization of codon usage bias in the dUTPase gene of duck enteritis virus

    Institute of Scientific and Technical Information of China (English)

    Lichan Zhao; Anchun Cheng; Mingshu Wang; Guiping Yuan; Mingsheng Cai

    2008-01-01

    A comparative analysis of the codon usage bias in the newly discovered dUTPase gene(Assigned Accession No.:DQ4861491 of the duck enteritis virus(DEV)and the dUTPase gene of 32 reference herpesviruses was performed.The results indicated that the DEV dUT-Pase gene encodes a protein of 477 amino acids,which includes five conserved motifs with a 3-1-2-4-5 arrangement.The codon adap-tation index(CAI),effective number of codons(ENC),and GC3s values indicated synonymous codon usage bias in the dUTPase gene of herpesviruses,and this synonymous bias was correlated with host evolution.The codon usage pattens of the DEV dUTPase gene were phylogenetically conserved and similar to that of the dUTPase genes of the avian alphaherpesvirus.Although codon usage in each micro-orgamsm was different,there were no strain-specific differences among them.Sixty-one codons in the predicted polypeptide.with a strong bias towards A and T at the third codon position,were used.Comparison of the codon usage in the dUTPase gene of different organisms revealed that there were 19 codons showing distinct codon usage differences between the DEV and Escherichia coli dUTPase genes;16 between the DEV and yeast dUTPase genes;and 15 between the DEV and human dUTPase genes.Analysis of variance(ANOVA) showed significant differences between the DEV and yeast dUTPase genes(r=0.536,P<0.01).The extent of codon usage bias in the DEV dUTPase gene was highly correlated with the gene expression level,therefore the results may provide usefu information for gene classification and functional studies.

  1. Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses.

    Science.gov (United States)

    Velazquez-Salinas, Lauro; Zarate, Selene; Eschbaumer, Michael; Pereira Lobo, Francisco; Gladue, Douglas P; Arzt, Jonathan; Novella, Isabel S; Rodriguez, Luis L

    2016-01-01

    Arboviruses (arthropod borne viruses) have life cycles that include both vertebrate and invertebrate hosts with substantial differences in vector and host specificity between different viruses. Most arboviruses utilize RNA for their genetic material and are completely dependent on host tRNAs for their translation, suggesting that virus codon usage could be a target for selection. In the current study we analyzed the relative synonymous codon usage (RSCU) patterns of 26 arboviruses together with 25 vectors and hosts, including 8 vertebrates and 17 invertebrates. We used hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify trends in codon usage. HCA demonstrated that the RSCU of arboviruses reflects that of their natural hosts, but not that of dead-end hosts. Of the two major components identified by PCA, the first accounted for 62.1% of the total variance, and among the 59 codons analyzed in this study, the leucine codon CTG had the highest correlation with the first principal component, however isoleucine had the highest correlation during amino acid analysis. Nucleotide and dinucleotide composition were the variables that explained most of the total codon usage variance. The results suggest that the main factors driving the evolution of codon usage in arboviruses is based on the nucleotide and dinucleotide composition present in the host. Comparing codon usage of arboviruses and potential vector hosts can help identifying potential vectors for emerging arboviruses.

  2. Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses

    Science.gov (United States)

    Velazquez-Salinas, Lauro; Zarate, Selene; Eschbaumer, Michael; Pereira Lobo, Francisco; Gladue, Douglas P.; Arzt, Jonathan; Novella, Isabel S.; Rodriguez, Luis L.

    2016-01-01

    Arboviruses (arthropod borne viruses) have life cycles that include both vertebrate and invertebrate hosts with substantial differences in vector and host specificity between different viruses. Most arboviruses utilize RNA for their genetic material and are completely dependent on host tRNAs for their translation, suggesting that virus codon usage could be a target for selection. In the current study we analyzed the relative synonymous codon usage (RSCU) patterns of 26 arboviruses together with 25 vectors and hosts, including 8 vertebrates and 17 invertebrates. We used hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify trends in codon usage. HCA demonstrated that the RSCU of arboviruses reflects that of their natural hosts, but not that of dead-end hosts. Of the two major components identified by PCA, the first accounted for 62.1% of the total variance, and among the 59 codons analyzed in this study, the leucine codon CTG had the highest correlation with the first principal component, however isoleucine had the highest correlation during amino acid analysis. Nucleotide and dinucleotide composition were the variables that explained most of the total codon usage variance. The results suggest that the main factors driving the evolution of codon usage in arboviruses is based on the nucleotide and dinucleotide composition present in the host. Comparing codon usage of arboviruses and potential vector hosts can help identifying potential vectors for emerging arboviruses. PMID:27455096

  3. Complex Mutation and Weak Selection together Determined the Codon Usage Bias in Bryophyte Mitochondrial Genomes

    Institute of Scientific and Technical Information of China (English)

    Bin Wang; Jing Liu; Liang Jin; Xue-Ying Feng; Jian-Qun Chen

    2010-01-01

    Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usagepatterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright's Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to finetune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary,complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes.

  4. Factors affecting mito-nuclear codon usage interactions in the OXPHOS system of Drosophila melanogaster

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Codon usage bias varies considerably among genomes and even within the genes of the same genome.In eukaryotic organisms,energy production in the form of oxidative phosphorylation(OXPHOS)is the only process under control of both nuclear and mitochondrial genomes.Although factors affecting codon usage in a single genome have been studied,this has not occurred when both interactional genomes are involved.Consequently, we investigated whether or not other factors influence codon usage of coevolved genes.We used Drosophila melanogaster as a model organism.Our χ2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system was significantly different (χ2=7945.16,P<0.01).A plot of effective number of codons against GC3s content of nuclear genes showed that few genes lie on the expected curve,indicating that codon usage was random.Correspondence analysis indicated a significant correlation between axis 1 and codon adaptation index(R=0.947,P<0.01)in every nuclear gene sequence.Thus,codon usage bias of nuclear genes appeared to be affected by translational selection.Correlation between axis 1 coordinates and GC content(R=0.814.P<0.01)indicated that the codon usage of nuclear genes was also affected by GC composition.Analysis of mitochondrial genes did not reveal a significant correlation between axis 1 and any parameter.Statistical analyses indicated that codon usages of both nDNA and mtDNA were subjected to context-dependent mutations.

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

    Directory of Open Access Journals (Sweden)

    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.

  6. The effect of multiple evolutionary selections on synonymous codon usage of genes in the Mycoplasma bovis genome.

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    Jian-hua Zhou

    Full Text Available Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains' genomes were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05, the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally

  7. Looking into the genome of Thermosynechococcus elongatus (thermophilic cyanobacteria) with codon selection and usage perspective.

    Science.gov (United States)

    Prabha, Ratna; Singh, Dhananjaya P; Rai, Anil

    2015-01-01

    Genome analysis of thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 revealed factors ruling choices of codons in this organism. Multiple parameters like Nc, GC3s, RSCU, Codon Adaptation Index (CAI), optimal and rare codons, codon-pair context and amino acid usage were analysed and compositional constraint was identified as major factor. Wide range of Nc values for the same GC3 content suggested the role of translational selection. Mutational bias is suggested at synonymous position. Among optimal codons for translation, most were GC-ending. Seven codons (AGA, AGG, AUA, UAA, UAG, UCA and UGA) were found to have least occurrence in the entire genome and except stop codons all were A-ending (exception AGG). Most widely used codon-pair in the genome are G-ending or C-ending and A-ending or U-ending codons make pair with G-ending or C-ending codons. Amino acids which are largely distributed in T. elongatus tend to use G-ending or C-ending codons most frequently. Findings showed cumulative role of translational selection, translational accuracy and gene expression levels with mutational bias as key player in codon selection pattern of this organism.

  8. Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea).

    Science.gov (United States)

    Chen, Haixia; Sun, Shichun; Norenburg, Jon L; Sundberg, Per

    2014-01-01

    The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested 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 and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.

  9. Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea.

    Directory of Open Access Journals (Sweden)

    Haixia Chen

    Full Text Available The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested 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 and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes.

  10. Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation

    Directory of Open Access Journals (Sweden)

    Guiming Liu

    2010-01-01

    Full Text Available The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak.

  11. The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern

    Directory of Open Access Journals (Sweden)

    Ma Ming-ren

    2011-12-01

    Full Text Available Abstract Background Hepatitis B virus (HBV infection is one of the main human health problem and causes a large-scale of patients chronic infection worldwide.. As the replication of HBV depends on its host cell system, codon usage pattern for the viral gene might be susceptible to two main selections, namely mutation pressure and translation selection. In this case, a deeper investigation between HBV evolution and host adaptive response might assist control this disease. Result Relative synonymous codon usage (RSCU values for the whole HBV coding sequence were studied by Principal component analysis (PCA. The characteristics of the synonymous codon usage patterns, nucleotide contents and the comparison between ENC values of the whole HBV coding sequence indicated that the interaction between virus mutation pressure and host translation selection exists in the processes of HBV evolution. The synonymous codon usage pattern of HBV is a mixture of coincidence and antagonism to that of host cell. But the difference of genetic characteristic of HBV failed to be observed to its different epidemic areas or subtypes, suggesting that geographic factor is limited to influence the evolution of this virus, while genetic characteristic based on HBV genotypes could be divided into three groups, namely (i genotyps A and E, (ii genotype B, (iii genotypes C, D and G. Conclusion Codon usage patterns from PCA for identification of evolutionary trends in HBV provide an alternative approach to understand the evolution of HBV. Further more, a combined selection of mutation pressure with translation selection on codon usage might shed a light on understanding the evolutionary trends of HBV genotypes.

  12. 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...

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

    Science.gov (United States)

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

    2017-09-18

    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.

  14. Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species

    Indian Academy of Sciences (India)

    Qingpo Liu; Qingzhong Xue

    2005-04-01

    A detailed comparison was made of codon usage of chloroplast genes with their host (nuclear) genes in the four angiosperm species Oryza sativa, Zea mays, Triticum aestivum and Arabidopsis thaliana. The average GC content of the entire genes, and at the three codon positions individually, was higher in nuclear than in chloroplast genes, suggesting different genomic organization and mutation pressures in nuclear and chloroplast genes. The results of Nc-plots and neutrality plots suggested that nucleotide compositional constraint had a large contribution to codon usage bias of nuclear genes in O. sativa, Z. mays, and T. aestivum, whereas natural selection was likely to be playing a large role in codon usage bias in chloroplast genomes. Correspondence analysis and chi-test showed that regardless of the genomic environment (species) of the host, the codon usage pattern of chloroplast genes differed from nuclear genes of their host species by their AU-richness. All the chloroplast genomes have predominantly A- and/or U-ending codons, whereas nuclear genomes have G-, C- or U-ending codons as their optimal codons. These findings suggest that the chloroplast genome might display particular characteristics of codon usage that are different from its host nuclear genome. However, one feature common to both chloroplast and nuclear genomes in this study was that pyrimidines were found more frequently than purines at the synonymous codon position of optimal codons.

  15. Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens

    Directory of Open Access Journals (Sweden)

    Lang Daniel

    2005-03-01

    Full Text Available Abstract Background The moss Physcomitrella patens is an emerging plant model system due to its high rate of homologous recombination, haploidy, simple body plan, physiological properties as well as phylogenetic position. Available EST data was clustered and assembled, and provided the basis for a genome-wide analysis of protein encoding genes. Results We have clustered and assembled Physcomitrella patens EST and CDS data in order to represent the transcriptome of this non-seed plant. Clustering of the publicly available data and subsequent prediction resulted in a total of 19,081 non-redundant ORF. Of these putative transcripts, approximately 30% have a homolog in both rice and Arabidopsis transcriptome. More than 130 transcripts are not present in seed plants but can be found in other kingdoms. These potential "retained genes" might have been lost during seed plant evolution. Functional annotation of these genes reveals unequal distribution among taxonomic groups and intriguing putative functions such as cytotoxicity and nucleic acid repair. Whereas introns in the moss are larger on average than in the seed plant Arabidopsis thaliana, position and amount of introns are approximately the same. Contrary to Arabidopsis, where CDS contain on average 44% G/C, in Physcomitrella the average G/C content is 50%. Interestingly, moss orthologs of Arabidopsis genes show a significant drift of codon fraction usage, towards the seed plant. While averaged codon bias is the same in Physcomitrella and Arabidopsis, the distribution pattern is different, with 15% of moss genes being unbiased. Species-specific, sensitive and selective splice site prediction for Physcomitrella has been developed using a dataset of 368 donor and acceptor sites, utilizing a support vector machine. The prediction accuracy is better than those achieved with tools trained on Arabidopsis data. Conclusion Analysis of the moss transcriptome displays differences in gene structure, codon

  16. 人类1号染色体可变剪接与普通剪接基因同义密码子的使用分析I.同义密码子偏爱使用分析%Synonymous Codon Usage of Both Alternatively and Commonly Spliced Genes in Human Chromosome 1 I:Synonymous Codon Usage Bias Analysis

    Institute of Scientific and Technical Information of China (English)

    陈学平; 武耀廷; 郭家明; 张成; 马飞

    2004-01-01

    It is already clear that alternative splicing has an extremely important role in expanding the protein diversity. Comparative study of the codon usage patterns of alternatively and commonly spliced genes may thereby be necessary. In this paper, the patterns of codon usage bias of two kinds of human genes, alternatively spliced genes and commonly spliced genes, were formulated through analyzing 344 non-redundant protein coding sequences from alternatively spliced genes (188183 codons) and 386 from commonly spliced genes (223116 codons) in human chromosome 1. Overall codon usage data analysis indicated that the alternatively spliced genes showed a stronger codon usage bias than commonly spliced genes. Very extensive heterogeneity of G+C content in silent third codon position (GC3s) was evident among these genes, and GC3s content of alternatively spliced genes was higher than that of commonly spliced genes. G- or C-ending codons were more abundant in alternatively spliced genes than commonly spliced genes in human chromosome 1. The causation of differences created could be explained by pre-mRNA structural characteristics of alternatively spliced genes influencing their codon usage bias.%人类1号染色体可变剪接(选择性剪接)基因344非冗余蛋白质编码序列(188183密码子)和普通剪接(非可变剪接)基因的386蛋白质编码序列(223116密码子)被用于研究人类密码子使用偏爱模式.全部密码子使用数据分析表明,人类可变剪接基因密码子的偏爱水平显著高于普通剪接基因.在人类1号染色体基因中,密码子第三位置的G+C含量有很大的异质性(0.24~0.95),并且可变剪接基因密码子第三位置平均G+C含量(64.66%)大于普通剪接基因(59.97%).Nc值对GC3s图显示密码子偏爱使用除了受核苷酸组成制约外,其它的因子可能也影响密码子的使用变化.此外,可变剪接基因中以G 或C结尾的密码子比普通剪接基因出现的频率高.密码子使

  17. Evolution of codon usage in Zika virus genomes is host and vector specific.

    Science.gov (United States)

    Butt, Azeem Mehmood; Nasrullah, Izza; Qamar, Raheel; Tong, Yigang

    2016-10-12

    The codon usage patterns of viruses reflect the evolutionary changes that allow them to optimize their survival and adapt their fitness to the external environment and, most importantly, their hosts. Here we report the genotype-specific codon usage patterns of Zika virus (ZIKV) strains from the current and previous outbreaks. Several genotype-specific and common codon usage traits were noted in the ZIKV coding sequences, indicating their independent evolutionary origins from a common ancestor. The overall influence of natural selection was more profound than that of mutation pressure, acting on a specific set of viral genes in the Asian-genotype ZIKV strains from the recent outbreak. An interplay between codon adaptation and deoptimization may have allowed the virus to adapt to multiple host and vectors and is reported for the first time in ZIKV genomes. Combining our codon analysis with geographical data on Aedes populations in the Americas suggested that ZIKV has evolved host- and vector-specific codon usage patterns to maintain successful replication and transmission chains within multiple hosts and vectors.

  18. Pangenome evidence for higher codon usage bias and stronger translational selection in core genes of Escherichia coli

    Directory of Open Access Journals (Sweden)

    Shixiang Sun

    2016-08-01

    Full Text Available Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias.

  19. Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli.

    Science.gov (United States)

    Sun, Shixiang; Xiao, Jingfa; Zhang, Huiyong; Zhang, Zhang

    2016-01-01

    Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias.

  20. Analysis on codon usage frequency in bovine milk protein%牛乳蛋白的遗传密码子使用频率分析

    Institute of Scientific and Technical Information of China (English)

    刘晶; 于浩; 杨润军; 鲍永华; 李俊雅; 戴蕴平; 赵志辉

    2011-01-01

    研究牛乳蛋白不同氨基酸的密码子使用频率对利用乳腺生物反应器表达目标蛋白过程中密码子的优化具有重要意义.本试验运用ENBOSS的CHIPS和SMS中的密码子使用工具对7种牛乳蛋白编码的基因进行了分析,并将这7个编码序列拼接在一起进行了乳蛋白全基因组的密码子偏爱性研究,同时与绵羊、猪及小鼠的乳蛋白密码子偏爱性进行了比较.结果表明:牛乳蛋白的CHIPS分析Nc值为51.867,αs1-CN、αs2-2-CN、β-CN、κ-CN、α-LB、β-IG、LTF的Nc值分别为52.005、49.967、48.746、58.113、55.514、36.274、47.646,编码牛乳蛋白氨基酸的密码子出现频率较均一;牛乳蛋白V、A、R、I、T、L、Q、P等氨基酸的密码子使用频率与其他物种有较大差异.牛乳蛋白的密码予偏爱性与绵羊最为接近.%In order to analyze bovine milk protein codon preference,7 coding sequences and the whole genome of bovine milk proteins were analyzed by CHIPS of EMBOSS and codon usage of SMS. The results were compared with codon usage of sheep,pig,and mouse milk protein. The results showed that the Nc value of all milk proteins in bovine and αs1- CN,αs2- CN,β- CN,κ- CN,α-LB,β-LG,LTF are 52. 005,49. 967,48. 746,58. 113,55. 514,36. 274,47. 646, respectively. Alternative codons for V, A, R, I, T, L, Q, P amino acids in bovine milk protein are distinctly different comparing with those of other species. It could be concluded that Nc value demonstrated that the codon usage frequency of bovine milk protein was comparatively uniform. Codon preference of bovine milk protein was the most close to that of sheep.

  1. Factors Influencing the Synonymous Codon and Amino Acid Usage Bias in AT-rich Pseudomonas aeruginosa Phage PhiKZ

    Institute of Scientific and Technical Information of China (English)

    K. SAU; S. SAU; S. C. MANDAL; T. C. GHOSH

    2005-01-01

    To reveal how the AT-rich genome of bacteriophage PhiKZ has been shaped in order to carry out its growth in the GC-rich host Pseudomonas aeruginosa, synonymous codon and amino acid usage bias of PhiKZ was investigated and the data were compared with that of P. aeruginosa. It was found that synonymous codon and amino acid usage of PhiKZ was distinct from that of P. aeruginosa. In contrast to P. aeruginosa, the third codon position of the synonymous codons of PhiKZ carries mostly A or T base; codon usage bias in PhiKZ is dictated mainly by mutational bias and, to a lesser extent, by translational selection. A cluster analysis of the relative synonymous codon usage values of 16 myoviruses including PhiKZ shows that PhiKZ is evolutionary much closer to Escherichia coli phage T4. Further analysis reveals that the three factors of mean molecular weight, aromaticity and cysteine content are mostly responsible for the variation of amino acid usage in PhiKZ proteins, whereas amino acid usage of P. aeruginosa proteins is mainly governed by grand average of hydropathicity, aromaticity and cysteine content. Based on these observations, we suggest that codons of the phage-like PhiKZ have evolved to preferentially incorporate the smaller amino acid residues into their proteins during translation, thereby economizing the cost of its development in GC-rich P. aeruginosa.

  2. A critical analysis of codon optimization in human therapeutics.

    Science.gov (United States)

    Mauro, Vincent P; Chappell, Stephen A

    2014-11-01

    Codon optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. Applications for codon optimization include recombinant protein drugs and nucleic acid therapies, including gene therapy, mRNA therapy, and DNA/RNA vaccines. However, recent reports indicate that codon optimization can affect protein conformation and function, increase immunogenicity, and reduce efficacy. We critically review this subject, identifying additional potential hazards including some unique to nucleic acid therapies. This analysis highlights the evolved complexity of codon usage and challenges the scientific bases for codon optimization. Consequently, codon optimization may not provide the optimal strategy for increasing protein production and may decrease the safety and efficacy of biotech therapeutics. We suggest that the use of this approach is reconsidered, particularly for in vivo applications. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Impact of bias discrepancy and amino acid usage on estimates of the effective number of codons used in a gene, and a test for selection on codon usage

    DEFF Research Database (Denmark)

    Fuglsang, Anders

    2007-01-01

    The effective number of codons (Nc) used in a gene is one of the most commonly used measures of synonymous codon usage bias, owing much of its popularity to the fact that it is species independent and that simulation studies have shown that it is less dependent of gene length than other measures....... that exists for Buchnera sp. APS and Borrelia burgdorferi....

  4. Development of the BestCodon software for calculating diversified codon usages%开发可统计任意密码子用法的软件BestCodon

    Institute of Scientific and Technical Information of China (English)

    余劲聪; 方柏山

    2011-01-01

    密码子偏好是自然现象,分析密码子的用法可以优化表达基因,即密码子优化,从而调节目的基因在特定宿主中的表达水平.现有密码子用法分析软件多数只限于单个密码子,适用于密码子对和密码子三联体的较少见.本文提出1种可统计任意密码子用法的软件结构,开发出1个密码子用法统计软件"BestCodon",拥有序列检查和密码子用法统计2个模块.检查模块可代替人工校对,剔除输入序列中非规范字符,为后续分析提供正确的、符合规范的数据.统计模块根据用户指定的密码子组合类型,结果返回特定的密码子用法表.本文还探讨序列检查和密码子用法统计中计算机的运算特性,结果表明该软件检查1条长达150000 bp的序列仪耗时约0.2 s,而从中统计密码子十联体的用法仅耗时约0.1 g.%Codon bias is the universal phenomenon in the nature.Optimizing the genetic expression can be available based on comparative analysis of the related codon usages, as codon optimization, by which regulating the expression level of target genes will be achieved.Most of existed software for counting codon usages is simply competent for single codon usage.Few of them can count codon pair or codon triplet usages.In this study,therefore, the software architecture that satisfies the requirement for calculating diversified codon usages has been presented and the codon usage counting software named "BestCodon" has been developed, which consists of the Sequences Checking Module (SCM) and the Codon Usage Counting Module (CUCM).The illegal characters potentially existed in the input sequences would be eliminated through SC instead of manual proofreading.Then the checked sequences are applicable to the follow-up processes.With the type of user-defined codon combination, the required codon usage table (CUT) can be gained by CUCM.Operating characteristics of checking sequence and counting codon usage and were discussed

  5. 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.

  6. Patterns of synonymous codon usage bias in chloroplast genomes of seed plants

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Codon usage in chloroplast genome of six seed plants (Arabidopsis thaliana, Populus alba, Zea mays, Triticum aestivum,Pinus koraiensis and Cycas taitungensis) was analyzed to find general patterns of codon usage in chloroplast genomes of seed plants.The results show that chloroplast genomes of the six seed plants had similar codon usage patterns, with a strong bias towards a high representation of NNA and NNT codons. In chloroplast genomes of the six seed plants, the effective number of codons (ENC) for most genes was similar to that of the expected ENC based on the GC content at the third codon position, but several genes with low ENC values were laying below the expected curve. All of these data indicate that codon usage was dominated by a mutational bias in chloroplast genomes of seed plants and that selection appeared to be limited to a subset of genes and to only subtly affect codon us-age. Meantime, four, six, eight, nine, ten and 12 codons were defined as the optimal codons in chloroplast genomes of the six seed plants.

  7. Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

    Directory of Open Access Journals (Sweden)

    Dou Yong-xi

    2011-10-01

    Full Text Available Abstract Background Porcine reproductive and respitatory syndrome virus (PRRSV is a recently emerged pathogen and severely affects swine populations worldwide. The replication of PRRSV is tightly controlled by viral gene expression and the codon usage of translation initiation region within each gene could potentially regulate the translation rate. Therefore, a better understanding of the codon usage pattern of the initiation translation region would shed light on the regulation of PRRSV gene expression. Results In this study, the codon usage in the translation initiation region and in the whole coding sequence was compared in PRRSV ORF1a and ORFs2-7. To investigate the potential role of codon usage in affecting the translation initiation rate, we established a codon usage model for PRRSV translation initiation region. We observed that some non-preferential codons are preferentially used in the translation initiation region in particular ORFs. Although some positions vary with codons, they intend to use codons with negative CUB. Furthermore, our model of codon usage showed that the conserved pattern of CUB is not directly consensus with the conserved sequence, but shaped under the translation selection. Conclusions The non-variation pattern with negative CUB in the PRRSV translation initiation region scanned by ribosomes is considered the rate-limiting step in the translation process.

  8. Analysis of Synonymous Codon Usage in Aeropyrum pernix K1 and Other Crenarchaeota Microorganisms%嗜热泉生古细菌及其他泉古菌同义密码子使用偏向性分析

    Institute of Scientific and Technical Information of China (English)

    江澎; 孙啸; 陆祖宏

    2007-01-01

    In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms (I.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639). The results indicated that the synonymous codon usage in A. Pernix K1 was less biased, which was highly correlated with the GC3s value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. Pernix K1, P. Aerophilum str. IM2, and S. Acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the living environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. Pernix K1 and S. Acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. Aerophilum str. IM2 genomes.%比较分析了嗜热泉生古细菌(Aeropyrum pernix K1)和其他两种系统发育相关的泉古菌[嗜气菌(Pyrobaculum aerophilum str.IM2)和嗜硫菌(Sulfolobus acidocaldarius DSM 639)]的同义密码子使用偏向性.结果表明嗜热泉生古细菌(Aeropyrumpernix K1)的密码子偏向性很小,并且与GC3s成高度的相关性.这3种泉古菌的密码子使用模式在进化上很保守.与基因的功能对密码子使用的影响相比,这些泉古菌密码子的使用偏向性更是由其物种所决定的.嗜热泉生古细菌(A.pernix K1),嗜气菌(P. aerophilum str.IM2)和嗜硫菌(S. acidocaldarius DSM 639)生存在不同的极限环境中.推测正是这些极限环境决定了这些泉古菌的密码子使用偏向性模式.此外在这些泉古菌的基因组中并没有发现其正义链和反义链的密码子使用偏

  9. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.

    Science.gov (United States)

    Thiele, Ines; Fleming, Ronan M T; Que, Richard; Bordbar, Aarash; Diep, Dinh; Palsson, Bernhard O

    2012-01-01

    Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. Here, we present the first integrated stoichiometric multiscale model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655, which describes the sequence-specific synthesis and function of almost 2000 gene products at molecular detail. We added linear constraints, which couple enzyme synthesis and catalysis reactions. Comparison with experimental data showed improvement of growth phenotype prediction with the multiscale model over E. coli's metabolic model alone. Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. We addressed the question of whether the bias in synonymous codon usage could affect the growth phenotype and environmental niches that an organism can occupy. We created two classes of in silico strains, one with more biased codon usage and one with more equilibrated codon usage than the wildtype. The reduced growth phenotype in biased strains was caused by tRNA supply shortage, indicating that expansion of tRNA gene content or tRNA codon recognition allow E. coli to respond to changes in codon usage bias. Our analysis suggests that in order to maximize growth and to adapt to new environmental niches, codon usage and tRNA content must co-evolve. These results provide further evidence for the mutation-selection-drift balance theory of codon usage bias. This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors.

  10. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.

    Directory of Open Access Journals (Sweden)

    Ines Thiele

    Full Text Available Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. Here, we present the first integrated stoichiometric multiscale model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655, which describes the sequence-specific synthesis and function of almost 2000 gene products at molecular detail. We added linear constraints, which couple enzyme synthesis and catalysis reactions. Comparison with experimental data showed improvement of growth phenotype prediction with the multiscale model over E. coli's metabolic model alone. Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. We addressed the question of whether the bias in synonymous codon usage could affect the growth phenotype and environmental niches that an organism can occupy. We created two classes of in silico strains, one with more biased codon usage and one with more equilibrated codon usage than the wildtype. The reduced growth phenotype in biased strains was caused by tRNA supply shortage, indicating that expansion of tRNA gene content or tRNA codon recognition allow E. coli to respond to changes in codon usage bias. Our analysis suggests that in order to maximize growth and to adapt to new environmental niches, codon usage and tRNA content must co-evolve. These results provide further evidence for the mutation-selection-drift balance theory of codon usage bias. This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors.

  11. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes

    Directory of Open Access Journals (Sweden)

    Kleinhofs Andris

    2004-06-01

    Full Text Available Abstract Background Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported. Results Based on an informatics method (SCUO we developed previously using Shannon informational theory and maximum entropy theory, we investigated the quantitative relationship between codon usage bias and GC composition. The regression based on 70 bacterial and 16 archaeal genomes showed that in bacteria, SCUO = -2.06 * GC3 + 2.05*(GC32 + 0.65, r = 0.91, and that in archaea, SCUO = -1.79 * GC3 + 1.85*(GC32 + 0.56, r = 0.89. We developed an analytical model to quantify synonymous codon usage bias by GC compositions based on SCUO. The parameters within this model were inferred by inspecting the relationship between codon usage bias and GC composition across 70 bacterial and 16 archaeal genomes. We further simplified this relationship using only GC3. This simple model was supported by computational simulation. Conclusions The synonymous codon usage bias could be simply expressed as 1+ (p/2log2(p/2 + ((1-p/2log2((l-p/2, where p = GC3. The software we developed for measuring SCUO (codonO is available at http://digbio.missouri.edu/~wanx/cu/codonO.

  12. Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

    Directory of Open Access Journals (Sweden)

    Suzuki Haruo

    2007-01-01

    Full Text Available G + C composition at the third codon position (GC3 is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from 0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.

  13. Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria

    Directory of Open Access Journals (Sweden)

    Haruo Suzuki

    2007-07-01

    Full Text Available G + C composition at the third codon position (GC3 is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from −0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.

  14. Nucleotide composition bias and codon usage trends of gene populations in Mycoplasma capricolum subsp. capricolum and M. agalactiae

    Indian Academy of Sciences (India)

    Xiao-Xia Ma; Yu-Ping Feng; Jia-Ling Bai; De-Rong Zhang; Xin-Shi Lin; Zhong-Ren Ma

    2015-06-01

    Because of the low GC content of the gene population, amino acids of the two mycoplasmas tend to be encoded by synonymous codons with an A or T end. Compared with the codon usage of ovine, Mycoplasma capricolum and M. agalactiae tend to select optimal codons, which are rare codons in ovine. Due to codon usage pattern caused by genes with key biological functions, the overall codon usage trends represent a certain evolutionary direction in the life cycle of the two mycoplasmas. The overall codon usage trends of a gene population of M. capricolum subsp. capricolum can be obviously separated from other mycoplasmas, and the overall codon usage trends of M. agalactiae are highly similar to those of M. bovis. These results partly indicate the independent evolution of the two mycoplasmas without the limits of the host cell’s environment. The GC and AT skews estimate nucleotide composition bias at different positions of nucleotide triplets and the protein consideration caused by the nucleotide composition bias at codon positions 1 and 2 largely take part in synonymous codon usage patterns of the two mycoplasmas. The correlation between the codon adaptation index and codon usage variation indicates that the effect of codon usage on gene expression in M. capricolum subsp. capricolum is opposite to that of M. agalactiae, further suggesting independence of the evolutionary process influencing the overall codon usage trends of gene populations of mycoplasmas.

  15. Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish.

    Science.gov (United States)

    Mishima, Yuichiro; Tomari, Yukihide

    2016-03-17

    The control of mRNA stability plays a central role in regulating gene expression. In metazoans, the earliest stages of development are driven by maternally supplied mRNAs. The degradation of these maternal mRNAs is critical for promoting the maternal-to-zygotic transition of developmental programs, although the underlying mechanisms are poorly understood in vertebrates. Here, we characterized maternal mRNA degradation pathways in zebrafish using a transcriptome analysis and systematic reporter assays. Our data demonstrate that ORFs enriched with uncommon codons promote deadenylation by the CCR4-NOT complex in a translation-dependent manner. This codon-mediated mRNA decay is conditional on the context of the 3' UTR, with long 3' UTRs conferring resistance to deadenylation. These results indicate that the combined effect of codon usage and 3' UTR length determines the stability of maternal mRNAs in zebrafish embryos. Our study thus highlights the codon-mediated mRNA decay as a conserved regulatory mechanism in eukaryotes.

  16. Codon Usage Bias and Determining Forces in Green Plant Mitochondrial Genomes

    Institute of Scientific and Technical Information of China (English)

    Bin Wang; Jing Yuan; Jing Liu; Liang Jin; Jian-Qun Chen

    2011-01-01

    The phenomenon of codon usage bias has been observed in a wide range of organisms. As organisms evolve, how their codon usage pattern change is still an intriguing question. In this article, we focused on the green plant mitochondrial genomes to analyze the codon usage patterns in different lineages,and more importantly, to investigate the possible change of determining forces during the plant evolution. Two patterns were observed between the separate lineages of green plants: Chlorophyta and Streptophyta. In Chlorophyta lineages, their codon usages showed substantial variation (from strongly A, T-biased to strongly G, C-biased); while in Streptophyta lineages, especially in the land plants, the overall codon usages are interestingly stable. Further, based on the Nc-GC3s plots and Akashi's scaled XZ-tests, we found that lineages within Chlorophyta exhibit much stronger evidence of deviating from neutrality; while lineages within Streptophyta rarely do so. Such differences, together with previous reports based on the chloroplast data, suggests that after plants colonized the land, their codon usages in organellar genomes are more reluctant to be shaped by selection force.

  17. Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids

    NARCIS (Netherlands)

    Rispe, C.; Delmotte, F.; Ham, van R.C.H.J.; Moya, A.

    2004-01-01

    We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of Buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in Escherichia coli, a close free-living relative. We sought to discriminate genes

  18. Heterologous Proteins Production in Escherichia coli: An Investigation on the Effect of Codon Usage and Expression Host Optimization

    Directory of Open Access Journals (Sweden)

    Hasan Mirzahoseini

    2011-01-01

    Full Text Available Objective: The production of heterologous proteins in Escherichia coli is strongly affectedby codon bias. This phenomenon occurs when the codon usage of mRNA coding for theforeign protein differs from that of the bacterium. The ribosome pauses upon encounteringa rare codon and may detach from mRNA, thereby the yield of recombinant protein productionreduces. The aim of this study is to investigate the effect of these codon numbersreductions on the recombinant protein production.Materials and Methods: Since most amino acids are encoded by more than one codon,codons were changed in order to their usage in a special host such as E. coli without anytransformation in amino acids sequence. Silent mutations in 5' codons of human basicfibroblast growth factor cDNA carried out by site-directed mutagenesis and the expressionlevel of the recombinant protein is analyzed by means of sodium dodecyl sulfate polyacrylamidegel electrophoresis (SDS-PAGE and Western blot.Results: Expression level in mutant and wild-type genes indicated a considerable difference.In contrast with the remarkable bands of wild-type gene in all the strains particularly in codonplus strain, there were no significant bands related to mutant gene in SDS-PAGE analysis.Conclusion: Because of the same conditions of mutant and wild-type genes during thetranslation and transcription, this significant difference may relate to mRNA efficiency fortranslation. Our results indicate that increased stability of 5' mRNA secondary structuresin E. coli prevents efficient translation initiation. Furthermore, wild-type gene significantbands in codon plus strain support the hypothesis that the possible elimination of translationalpauses that increase translation rate leads to over expression.

  19. Analysis of Codon Usage Between Different Citrus Species%不同种类柑橘的密码子用法分析

    Institute of Scientific and Technical Information of China (English)

    胡桂兵; 张上隆; 徐昌杰; 林顺权

    2006-01-01

    采用高频密码子分析法,对甜橙Citrus sinensis、温州蜜柑C. unshiu、葡萄柚C. paradisi和柠檬C. limon等4种柑橘的蛋白质编码基因序列(codon DNA sequence,CDS)进行了分析,计算出了柑橘同义密码子相对使用频率(relative frequency of synonymous codon,RFSC),确定出了4种柑橘的高频率密码子,发现不同种类柑橘偏爱密码子稍有差别.

  20. Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates.

    Science.gov (United States)

    Doherty, Aoife; McInerney, James O

    2013-10-01

    Synonymous codon usage patterns are shaped by a balance between mutation, drift, and natural selection. To date, detection of translational selection in vertebrates has proven to be a challenging task, obscured by small long-term effective population sizes in larger animals and the existence of isochores in some species. The consensus is that, in such species, natural selection is either completely ineffective at overcoming mutational pressures and genetic drift or perhaps is effective but so weak that it is not detectable. The aim of this research is to understand the interplay between mutation, selection, and genetic drift in vertebrates. We observe that although variation in mutational bias is undoubtedly the dominant force influencing codon usage, translational selection acts as a weak additional factor influencing synonymous codon usage. These observations indicate that translational selection is a widespread phenomenon in vertebrates and is not limited to a few species.

  1. Transfer RNA gene numbers may not be completely responsible for the codon usage bias in asparagine, isoleucine, phenylalanine, and tyrosine in the high expression genes in bacteria.

    Science.gov (United States)

    Satapathy, Siddhartha Sankar; Dutta, Malay; Buragohain, Alak Kumar; Ray, Suvendra Kumar

    2012-08-01

    It is generally believed that the effect of translational selection on codon usage bias is related to the number of transfer RNA genes in bacteria, which is more with respect to the high expression genes than the whole genome. Keeping this in the background, we analyzed codon usage bias with respect to asparagine, isoleucine, phenylalanine, and tyrosine amino acids. Analysis was done in seventeen bacteria with the available gene expression data and information about the tRNA gene number. In most of the bacteria, it was observed that codon usage bias and tRNA gene number were not in agreement, which was unexpected. We extended the study further to 199 bacteria, limiting to the codon usage bias in the two highly expressed genes rpoB and rpoC which encode the RNA polymerase subunits β and β', respectively. In concordance with the result in the high expression genes, codon usage bias in rpoB and rpoC genes was also found to not be in agreement with tRNA gene number in many of these bacteria. Our study indicates that tRNA gene numbers may not be the sole determining factor for translational selection of codon usage bias in bacterial genomes.

  2. Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals.

    NARCIS (Netherlands)

    Parmley, J.L.; Hurst, L.D.

    2007-01-01

    In mammals there is a bias in amino acid usage near splice sites that is explained, in large part, by the high density of exonic splicing enhancers (ESEs) in these regions. Is there a similar bias for the relative use of synonymous codons, and can any such bias be predicted by their abundance in ESE

  3. Effect of exonic splicing regulation on synonymous codon usage in alternatively spliced exons of Dscam

    Directory of Open Access Journals (Sweden)

    Takahashi Aya

    2009-08-01

    Full Text Available Abstract Background Synonymous codon usage is typically biased towards translationally superior codons in many organisms. In Drosophila, genomic data indicates that translationally optimal codons and splice optimal codons are mostly mutually exclusive, and adaptation to translational efficiency is reduced in the intron-exon boundary regions where potential exonic splicing enhancers (ESEs reside. In contrast to genomic scale analyses on large datasets, a refined study on a well-controlled set of samples can be effective in demonstrating the effects of particular splice-related factors. Down syndrome cell adhesion molecule (Dscam has the largest number of alternatively spliced exons (ASEs known to date, and the splicing frequency of each ASE is accessible from the relative abundance of the transcript. Thus, these ASEs comprise a unique model system for studying the effect of splicing regulation on synonymous codon usage. Results Codon Bias Indices (CBI in the 3' boundary regions were reduced compared to the rest of the exonic regions among 48 and 33 ASEs of exon 6 and 9 clusters, respectively. These regional differences in CBI were affected by splicing frequency and distance from adjacent exons. Synonymous divergence levels between the 3' boundary region and the remaining exonic region of exon 6 ASEs were similar. Additionally, another sensitive comparison of paralogous exonic regions in recently retrotransposed processed genes and their parental genes revealed that, in the former, the differences in CBI between what were formerly the central regions and the boundary regions gradually became smaller over time. Conclusion Analyses of the multiple ASEs of Dscam allowed direct tests of the effect of splice-related factors on synonymous codon usage and provided clear evidence that synonymous codon usage bias is restricted by exonic splicing signals near the intron-exon boundary. A similar synonymous divergence level between the different exonic

  4. Analysis of characteristic of codon usage in Ref gene of Eucommia ulmoides%杜仲Ref基因密码子偏好性分析

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    杜仲是世界上唯一的硬橡胶树种,是能够替代三叶橡胶的最具开发潜力的胶源植物.本研究以杜仲胶合成下游途径Ref基因为研究对象,运用CodonW和CUSPS等研究Ref基因的密码子组成特点及使用偏好性.研究结果表明,杜仲Ref基因的GC含量为49%,密码子第三位碱基的GC含量为59%;杜仲Ref基因有28个偏好使用的密码子,其中约60%(17个)的密码子以G/C结尾;与大肠杆菌、酵母、拟南芥和烟草的基因组密码子使用偏好性比较,杜仲与拟南芥基因组密码子的使用偏性更为接近,拟南芥更适合作为Ref转基因的受体.本研究为预测杜仲Ref基因的异源表达,适宜表达系统的选择以及Ref基因密码子的改造以提高其在宿主中的表达,进行有效的基因功能验证提供理论参考.

  5. Synonymous codon usage affects the expression of wild type and F508del CFTR.

    Science.gov (United States)

    Shah, Kalpit; Cheng, Yi; Hahn, Brian; Bridges, Robert; Bradbury, Neil A; Mueller, David M

    2015-03-27

    The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel composed of 1480 amino acids. The major mutation responsible for cystic fibrosis results in loss of amino acid residue, F508 (F508del). Loss of F508 in CFTR alters the folding pathway resulting in endoplasmic-reticulum-associated degradation. This study investigates the role of synonymous codon in the expression of CFTR and CFTR F508del in human HEK293 cells. DNA encoding the open reading frame (ORF) for CFTR containing synonymous codon replacements was expressed using a heterologous vector integrated into the genome. The results indicate that the codon usage greatly affects the expression of CFTR. While the promoter strength driving expression of the ORFs was largely unchanged and the mRNA half-lives were unchanged, the steady-state levels of the mRNA varied by as much as 30-fold. Experiments support that this apparent inconsistency is attributed to nonsense mediated decay independent of exon junction complex. The ratio of CFTR/mRNA indicates that mRNA containing native codons was more efficient in expressing mature CFTR as compared to mRNA containing synonymous high-expression codons. However, when F508del CFTR was expressed after codon optimization, a greater percentage of the protein escaped endoplasmic-reticulum-associated degradation resulting in considerable levels of mature F508del CFTR on the plasma membrane, which showed channel activity. These results indicate that codon usage has an effect on mRNA levels and protein expression, for CFTR, and likely on chaperone-assisted folding pathway, for F508del CFTR.

  6. The preferential codon usages in variable and constant regions of immunoglobulin genes are quite distinct from each other.

    Science.gov (United States)

    Miyata, T; Hayashida, H; Yasunaga, T; Hasegawa, M

    1979-12-20

    The pattern of codon utilization in the variable and constant regions of immunoglobulin genes are compared. It is shown that, in these regions, codon utilizations are quite distinct from one another: For most degenerate codons, there is a selective bias that prefers C and/or G ending codons to U and/or A ending codons in the constant region compared with the bias in the variable region. This would strongly suggest that, in immunoglobulin genes, the bias in code word usage is determined by other factors than those concerning with the translational mechanism such as tRNA availability and codon-anticodon interaction. A possibility is also suggested that this differance of code word usage between them is due to the existence of secondary structure in the constant region but not in the variable region.

  7. Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.

    Science.gov (United States)

    Qi, Yueying; Xu, Wenjing; Xing, Tian; Zhao, Mingming; Li, Nana; Yan, Li; Xia, Guangmin; Wang, Mengcheng

    2015-01-01

    Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation-induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.

  8. Synonymous codon usage bias in plant mitochondrial genes is associated with intron number and mirrors species evolution.

    Directory of Open Access Journals (Sweden)

    Wenjing Xu

    Full Text Available Synonymous codon usage bias (SCUB is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes.

  9. Bicluster pattern of codon context usages between flavivirus and vector mosquito Aedes aegypti: relevance to infection and transcriptional response of mosquito genes.

    Science.gov (United States)

    Behura, Susanta K; Severson, David W

    2014-10-01

    The mosquito Aedes aegypti is the primary vector of dengue virus (DENV) infection in most of the subtropical and tropical countries. Besides DENV, yellow fever virus (YFV) is also transmitted by A. aegypti. Susceptibility of A. aegypti to West Nile virus (WNV) has also been confirmed. Although studies have indicated correlation of codon bias between flaviviridae and their animal/insect hosts, it is not clear if codon sequences have any relation to susceptibility of A. aegypti to DENV, YFV and WNV. In the current study, usages of codon context sequences (codon pairs for neighboring amino acids) of the vector (A. aegypti) genome as well as the flaviviral genomes are investigated. We used bioinformatics methods to quantify codon context bias in a genome-wide manner of A. aegypti as well as DENV, WNV and YFV sequences. Mutual information statistics was applied to perform bicluster analysis of codon context bias between vector and flaviviral sequences. Functional relevance of the bicluster pattern was inferred from published microarray data. Our study shows that codon context bias of DENV, WNV and YFV sequences varies in a bicluster manner with that of specific sets of genes of A. aegypti. Many of these mosquito genes are known to be differentially expressed in response to flaviviral infection suggesting that codon context sequences of A. aegypti and the flaviviruses may play a role in the susceptible interaction between flaviviruses and this mosquito. The bias in usages of codon context sequences likely has a functional association with susceptibility of A. aegypti to flaviviral infection. The results from this study will allow us to conduct hypothesis-driven tests to examine the role of codon context bias in evolution of vector-virus interactions at the molecular level.

  10. 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...

  11. Environmental shaping of codon usage and functional adaptation across microbial communities.

    Science.gov (United States)

    Roller, Masa; Lucić, Vedran; Nagy, István; Perica, Tina; Vlahovicek, Kristian

    2013-10-01

    Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.

  12. Ribosome collisions and Translation efficiency: Optimization by codon usage and mRNA destabilization

    DEFF Research Database (Denmark)

    Mitarai, Namiko; Sneppen, Kim; Pedersen, Steen

    2008-01-01

    Individual mRNAs are translated by multiple ribosomes that initiate translation with an interval of a few seconds. The ribosome speed is codon dependent, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modeling the stochastic translation...... process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations/s) and the time (1 s) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome...... collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of m...

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

    Directory of Open Access Journals (Sweden)

    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.

  14. Codon usage in genome of Listeria monocytogenes EGD-e%单增李斯特菌EGD-e基因组的密码子使用分析

    Institute of Scientific and Technical Information of China (English)

    罗雪莲; 王海印; 叶长芸

    2011-01-01

    目的 以单增李斯特菌EGD-e为研究对象,分析其密码子使用模式及影响因素.方法 利用Codon W在线工具分析单增李斯特菌EGD-e基因组的密码子使用情况;利用对应分析、ENC绘图(Nc-plot)等推测影响单增李斯特菌EGD-e密码子偏性的因素;利用高表达优越密码子分析法确定单增李斯特菌EGD-e基因组的主要偏爱密码子.结果 单增李斯特菌EGD-e基因组中G+C含量仅为37%,偏爱使用以U或A结尾的密码子;对应分析显示第1条向量轴与G+C(R=-0.182,P<0.01)、CAI(R=-0.740,P<0.01)呈显著相关,且与后者的相关程度明显高于前者.结论 单增李斯特菌EGD-e基因组的密码子使用具有一定的偏性;推测基因的表达水平是影响单增李斯特菌EGD-e基因组密码子使用的主要因素.同时,基因组密码子使用偏性还受到碱基组成的影响,而基因长度对密码子的使用偏性影响不大.最后确定了UUC、UUA等27个密码子为单增李斯特菌EGD-e的最优密码子.这些结果将为进一步研究单增李斯特菌的基因组学提供基础.%Objective To analyze the codon usage patterns and related factors by taking Listeria monocytogenes EGD-e as subject. Methods The codon usage patterns of Listeria monocytogenes was analyzed with EGD-e Online Codon W software; the factors in codon usage of Listeria monocytogenes EGD-e was presumed by using correspondence analysis and Nc-plot; the major preference codons in genome of Listeria monocytogenes EGD-e was defined by using highexpression codon. Results The GC content in the genome of Listeria monocytogenes EGD-e was only 37%, and the codon ended with U or A was used frequently; correspondence analysis showed that there was a significant correlation (R= -0. 182, P<0. 01) between the gene position on the first axis and G +C content and a significant correlation (R = -0. 740, P <0. 01 ) between the gene position on the first axis and CAI. Moreover, the correlation with the

  15. 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

    in the mutation rate from C to T. However, neither a reduction in the strength of selection nor a change in the mutational pattern can alone explain all of the data observed in the D. melanogaster lineage. For example, we also confirm previous results showing that the Notch locus has experienced positive....... melanogaster lineage has experienced a reduction in the selection for optimal codon usage. However, the D. melanogaster lineage has also experienced a change in the biological mutation rates relative to D. simulans, in particular, a relative reduction in the mutation rate from A to G and an increase...... selection for previously classified unpreferred mutations....

  16. General trends in selectively driven codon usage biases in the domain archaea.

    Science.gov (United States)

    Iriarte, Andrés; Jara, Eugenio; Leytón, Lucía; Diana, Leticia; Musto, Héctor

    2014-10-01

    Since the advent of rapid techniques for sequencing DNA in the mid 70's, it became clear that all codons coding for the same amino acid are not used according to neutral expectations. In the last 30 years, several theories were proposed for explaining this fact. However, the most important concepts were the result of analyses carried out in Bacteria, and unicellular and multicellular eukaryotes like mammals (in other words, in two of the three Domains of life). In this communication, we study the main forces that shape codon usage in Archaeae under an evolutionary perspective. This is important because, as known, the orthologous genes related with the informational system in this Domain (replication, transcription and translation) are more similar to eukaryotes than to Bacteria. Our results show that the effect of selection acting at the level of translation is present in the Domain but mainly restricted to only a phylum (Euryarchaeota) and therefore is not as extended as in Bacteria. Besides, we describe the phylogenetic distribution of translational optimal codons and estimate the effect of selection acting at the level of accuracy. Finally, we discuss these results under some peculiarities that characterize this Domain.

  17. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.

    Directory of Open Access Journals (Sweden)

    Premal Shah

    2010-09-01

    Full Text Available Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  18. Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.

    Science.gov (United States)

    Shah, Premal; Gilchrist, Michael A

    2010-09-16

    Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on tRNA competition and intra-ribosomal kinetics, we show that this assumption can be violated when tRNA abundances are positively correlated across the genetic code. Examining the distribution of tRNA abundances across 73 bacterial genomes from 20 different genera, we find a consistent positive correlation between tRNA abundances across the genetic code. This work challenges one of the fundamental assumptions made in over 30 years of research on CUB that codons with higher tRNA abundances have lower missense error rates and that missense errors are the primary selective force responsible for CUB.

  19. DNA G+C content of the third codon position and codon usage biases of human genes.

    Science.gov (United States)

    Sueoka, N; Kawanishi, Y

    2000-12-30

    The human genome, as in other eukaryotes, has a wide heterogeneity in the DNA base composition. The evolutionary basis for this heterogeneity has been unknown. A previous study of the human genome (846 genes analyzed) has shown that, in the major range of the G+C content in the third codon position (0.25-0.75), biases from the Parity Rule 2 (PR2) among the synonymous codons of the four-codon amino acids are similar except in the highest G+C range (Sueoka, N., 1999. Translation-coupled violation of Parity Rule 2 in human genes is not the cause of heterogeneity of the DNA G+C content of third codon position. Gene 238, 53-58.). PR2 is an intra-strand rule where A=T and G=C are expected when there are no biases between the two complementary strands of DNA in mutation and selection rates (substitution rates). In this study, 14,026 human genes were analyzed. In addition, the third codon positions of two-codon amino acids were analyzed. New results show the following: (a) The G+C contents of the third codon position of human genes are scattered in the G+C range of 0.22-0.96 in the third codon position. (b) The PR2 biases are similar in the range of 0.25-0.75, whereas, in the high G+C range (0.75-0.96; 13% of the genes), the PR2-bias fingerprints are different from those of the major range. (c) Unlike the PR2 biases, the G+C contents of the third codon position for both four-codon and two-codon amino acids are all correlated almost perfectly with the G+C content of the third codon position over the total G+C ranges. These results support the notion that the directional mutation pressure, rather than the directional selection pressure, is mainly responsible for the heterogeneity of the G+C content of the third codon position.

  20. Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation.

    Science.gov (United States)

    Gilchrist, Michael A; Shah, Premal; Zaretzki, Russell

    2009-12-01

    Codon usage bias (CUB) has been documented across a wide range of taxa and is the subject of numerous studies. While most explanations of CUB invoke some type of natural selection, most measures of CUB adaptation are heuristically defined. In contrast, we present a novel and mechanistic method for defining and contextualizing CUB adaptation to reduce the cost of nonsense errors during protein translation. Using a model of protein translation, we develop a general approach for measuring the protein production cost in the face of nonsense errors of a given allele as well as the mean and variance of these costs across its coding synonyms. We then use these results to define the nonsense error adaptation index (NAI) of the allele or a contiguous subset thereof. Conceptually, the NAI value of an allele is a relative measure of its elevation on a specific and well-defined adaptive landscape. To illustrate its utility, we calculate NAI values for the entire coding sequence and across a set of nonoverlapping windows for each gene in the Saccharomyces cerevisiae S288c genome. Our results provide clear evidence of adaptation to reduce the cost of nonsense errors and increasing adaptation with codon position and expression. The magnitude and nature of this adaptation are also largely consistent with simulation results in which nonsense errors are the only selective force driving CUB evolution. Because NAI is derived from mechanistic models, it is both easier to interpret and more amenable to future refinement than other commonly used measures of codon bias. Further, our approach can also be used as a starting point for developing other mechanistically derived measures of adaptation such as for translational accuracy.

  1. Is there a close relationship between synonymous codon bias and codon-anticodon binding strength in human genes?

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Synonymous codon bias has been examined in 78 human genes (19967 codons) and measured by relative synonymous codon usage (RSCU). Relative frequencies of all kinds of dinucleotides in 2,3 or 3,4 codon positions have been calculated, and codon-anticodon binding strength has been estimated by the stacking energies of codon-anticodon bases in Watson-Crick pairs. The data show common features in synonymous codon bias for all codon families in human genes: all C-ending codons, which possess the strongest co-don-anticodon binding energies, are the most favored codons in almost all codon families, and those codons with medium codon-anticodon binding energies are avoided. Data analysis suggests that besides isochore and genome signature , codon-anticodon binding strength may be closely related to syn-onymous codon choice in human genes. The join-effect of these factors on human genes results in the common features in codon bias.

  2. Optimization protein productivity of human interleukin-2 through codon usage, gene copy number and intracellular tRNA concentration in CHO cells.

    Science.gov (United States)

    Ou, Kua-Chun; Wang, Chih-Yang; Liu, Kuan-Ting; Chen, Yi-Ling; Chen, Yi-Chen; Lai, Ming-Derg; Yen, Meng-Chi

    2014-11-14

    Transfer RNA (tRNA) abundance is one of the critical factors for the enhancement of protein productivity in prokaryotic and eukaryotic hosts. Gene copy number of tRNA and tRNA codon usage bias are generally used to match tRNA abundance of protein-expressing hosts and to optimize the codons of recombinant proteins. Because sufficient concentration of intracellular tRNA and optimized codons of recombinant proteins enhanced translation efficiency, we hypothesized that sufficient supplement of host's tRNA improved protein productivity in mammalian cells. First, the small tRNA sequencing results of CHO-K1 cells showed moderate positive correlation with gene copy number and codon usage bias. Modification of human interleukin-2 (IL-2) through codons with high gene copy number and high codon usage bias (IL-2 HH, modified on Leu, Thr, Glu) significantly increased protein productivity in CHO-K1 cells. In contrast, modification through codons with relatively high gene copy number and low codon usage bias (IL-2 HL, modified on Ala, Thr, Val), or relatively low gene copy number and low codon usage bias (IL-2 LH, modified on Ala, Thr, Val) did not increase IL-2 productivity significantly. Furthermore, supplement of the alanine tRNA or threonine tRNA increased IL-2 productivity of IL-2 HL. In summary, we revealed a potential strategy to enhance productivity of recombinant proteins, which may be applied in production of protein drug or design of DNA vaccine.

  3. Analysis of Codon Usage Pattern ofPaeonia lactiflora Genes Regulating Flower Color and Its Influence Factors%芍药花色调控基因的密码子使用模式及其影响因素分析

    Institute of Scientific and Technical Information of China (English)

    吴彦庆; 赵大球; 陶俊

    2016-01-01

    Objective] The quality ofPaeonia lactiflora flower color affects its ornamental value and the commercial value of ornamental plants. This study aims to understand the codon usage pattern of genes regulating flower color and probe into the main factors affecting the formation of codon bias, which has important biological significance for mRNA translation, design of transgenes, the prediction ofexpression level and functions of new genes, and studies of molecular biology and evolution, etc.[Method]In a previous study, 6,345 differential genes were screened out by transcriptome sequencing of a flower color chimaera cultivar “Jinhui” with a consistent genetic background red outer-petal and yellow inner-petal, followed by a further filtering analysis according to the principle of CDS sequence characteristics and greater than 300 bp. We finally obtained 2,234 genes as our research object. Mobyle software was used to calculate different parameters for the codon usage, such as GC content, average GC content of the first and second positions (GC12), GC content of the third position (GC3s), effective number of codon (ENC), codon adaptation index (CAI), and relative synonymous codon usage (RSCU). Further analysis of a neutrality plot (GC12 vs. GC3), anENC-GC3s plot, and a Parity Rule 2 (PR2) plot were performed. Additionally, we probed into the influence of mutational pressure and translational selection by a multivariate statistical analysis. Finally, we took 5% CAI value as high-expression and low-expression sample groups, then calculated the RSCU value, and analyzed the significant difference to determine the optimal codons by a chi-square test.[Result]The results showed that the GC content at the third position of codons was 46.37%. The GC content of most genes was mainly distributed between 30% and 55%. Neutrality analysis showed that there was a significant positive correlation (R2=0.202,P<0.01) between GC3s and GC12 value. TheENC-plot showed most of the genes on or

  4. Co-evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas.

    Science.gov (United States)

    Salinas, Thalia; Duby, Francéline; Larosa, Véronique; Coosemans, Nadine; Bonnefoy, Nathalie; Motte, Patrick; Maréchal-Drouard, Laurence; Remacle, Claire

    2012-09-01

    Mitochondria from diverse phyla, including protozoa, fungi, higher plants, and humans, import tRNAs from the cytosol in order to ensure proper mitochondrial translation. Despite the broad occurrence of this process, our understanding of tRNA import mechanisms is fragmentary, and crucial questions about their regulation remain unanswered. In the unicellular green alga Chlamydomonas, a precise correlation was found between the mitochondrial codon usage and the nature and amount of imported tRNAs. This led to the hypothesis that tRNA import might be a dynamic process able to adapt to the mitochondrial genome content. By manipulating the Chlamydomonas mitochondrial genome, we introduced point mutations in order to modify its codon usage. We find that the codon usage modification results in reduced levels of mitochondrial translation as well as in subsequent decreased levels and activities of respiratory complexes. These effects are linked to the consequential limitations of the pool of tRNAs in mitochondria. This indicates that tRNA mitochondrial import cannot be rapidly regulated in response to a novel genetic context and thus does not appear to be a dynamic process. It rather suggests that the steady-state levels of imported tRNAs in mitochondria result from a co-evolutive adaptation between the tRNA import mechanism and the requirements of the mitochondrial translation machinery.

  5. Preferential codon usage and two types of repetitive motifs in the fibroin gene of the Chinese oak silkworm, Antheraea pernyi.

    Science.gov (United States)

    Yukuhiro, K; Kanda, T; Tamura, T

    1997-02-01

    In this paper we describe the peculiar structures and preferential codon usage found in wild silkworm fibroin genes. We determined a 1350 bp nucleotide sequence from the Chinese oak silkworm, Antheraea pernyi. The deduced amino acid sequence was partitioned into thirteen polyalanine-containing repetitive motifs, which was one of the characteristics of Antheraea fibroins. Eleven of these arrays can be classified into two types of motifs depending on difference in amino acid sequences following polyalanine. Repetitive motifs structurally similar to those of A. pernyi were detected in a homologue of the Japanese oak silkworm, Antheraea yamamai. The most remarkable feature of this study was preferential codon usage, especially seen in alanine synonymous codons within both homologues of Antheraea: isocodon GCA most frequently occurred in alanine isocodons. In contrast, GCU isocodon was the most abundant in Bombyx mori fibroin heavy chain that lacks polyalanine arrays. This result strongly suggests different modes of selective constraint between the two types of fibroin gene. The similar finding that GCA isocodon was most frequent in two dragline silk sequences of the spider, Nephila clavipes, is consistent with our results because of the repetitive polyalanine-containing arrays seen in spider dragline silk.

  6. Genomic characteristics comparisons of 12 food-related filamentous fungi in tRNA gene set, codon usage and amino acid composition.

    Science.gov (United States)

    Chen, Wanping; Xie, Ting; Shao, Yanchun; Chen, Fusheng

    2012-04-10

    Filamentous fungi are widely exploited in food industry due to their abilities to secrete large amounts of enzymes and metabolites. The recent availability of fungal genome sequences has provided an opportunity to explore the genomic characteristics of these food-related filamentous fungi. In this paper, we selected 12 representative filamentous fungi in the areas of food processing and safety, which were Aspergillus clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, A. terreus, Monascus ruber, Neurospora crassa, Penicillium chrysogenum, Rhizopus oryzae and Trichoderma reesei, and did the comparative studies of their genomic characteristics of tRNA gene distribution, codon usage pattern and amino acid composition. The results showed that the copy numbers greatly differed among isoaccepting tRNA genes and the distribution seemed to be related with translation process. The results also revealed that genome compositional variation probably constrained the base choice at the third codon, and affected the overall amino acid composition but seemed to have little effect on the integrated physicochemical characteristics of overall amino acids. The further analysis suggested that the wobble pairing and base modification were the important mechanisms in codon-anticodon interaction. In the scope of authors' knowledge, it is the first report about the genomic characteristics analysis of food-related filamentous fungi, which would be informative for the analysis of filamentous fungal genome evolution and their practical application in food industry. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Equine schlafen 11 restricts the production of equine infectious anemia virus via a codon usage-dependent mechanism.

    Science.gov (United States)

    Lin, Yue-Zhi; Sun, Liu-Ke; Zhu, Dan-Tong; Hu, Zhe; Wang, Xue-Feng; Du, Cheng; Wang, Yu-Hong; Wang, Xiao-Jun; Zhou, Jian-Hua

    2016-08-01

    Human schlafen11 is a novel restriction factor for HIV-1 based on bias regarding relative synonymous codon usage (RSCU). Here, we report the cloning of equine schlafen11 (eSLFN11) and the characteristics of its role in restricting the production of equine infectious anemia virus (EIAV), a retrovirus similar to HIV-1. Overexpression of eSLFN11 inhibited EIAV replication, whereas knockdown of endogenous eSLFN11 by siRNA enhanced the release of EIAV from its principal target cell. Notably, although eSLFN11 significantly suppressed expression of viral Gag protein and EIAV release into the culture medium, the levels of intracellular viral early gene proteins Tat and Rev and viral genomic RNA were unaffected. Coincidently, similar altered patterns of codon usage bias were observed for both the early and late genes of EIAV. Therefore, our data suggest that eSLFN11 restricts EIAV production by impairing viral mRNA translation via a mechanism that is similar to that employed by hSLFN11 for HIV-1. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. In Arabidopsis thaliana codon volatility scores reflect GC3 composition rather than selective pressure

    Directory of Open Access Journals (Sweden)

    O'Connell Mary J

    2012-07-01

    Full Text Available Abstract Background Synonymous codon usage bias has typically been correlated with, and attributed to translational efficiency. However, there are other pressures on genomic sequence composition that can affect codon usage patterns such as mutational biases. This study provides an analysis of the codon usage patterns in Arabidopsis thaliana in relation to gene expression levels, codon volatility, mutational biases and selective pressures. Results We have performed synonymous codon usage and codon volatility analyses for all genes in the A. thaliana genome. In contrast to reports for species from other kingdoms, we find that neither codon usage nor volatility are correlated with selection pressure (as measured by dN/dS, nor with gene expression levels on a genome wide level. Our results show that codon volatility and usage are not synonymous, rather that they are correlated with the abundance of G and C at the third codon position (GC3. Conclusions Our results indicate that while the A. thaliana genome shows evidence for synonymous codon usage bias, this is not related to the expression levels of its constituent genes. Neither codon volatility nor codon usage are correlated with expression levels or selective pressures but, because they are directly related to the composition of G and C at the third codon position, they are the result of mutational bias. Therefore, in A. thaliana codon volatility and usage do not result from selection for translation efficiency or protein functional shift as measured by positive selection.

  9. Synonymous codon usage in different protein secondary structural classes of human genes: Implication for increased non-randomness of GC3 rich genes towards protein stability

    Indian Academy of Sciences (India)

    Pamela Mukhopadhyay; Surajit Basak; Tapash Chandra Ghosh

    2007-08-01

    The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected frequencies of 59 codons at the level of individual synonymous families in the four different protein secondary structural classes. It was observed that synonymous codon families show non-randomness in codon usage in four different secondary structural classes. However, when the genes were classified according to their GC3 levels there was an increase in non-randomness in high GC3 group of genes. The non-randomness in codon usage was further tested among the same protein secondary structures belonging to four different protein folding classes of high GC3 group of genes. The results show that in each of the protein secondary structural unit there exist some synonymous family that shows class specific codonusage pattern. Moreover, there is an increased non-random behaviour of synonymous codons in sheet structure of all secondary structural classes in high GC3 group of genes. Biological implications of these results have been discussed.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  12. Web Usage Analysis: New Science Indicators and Co-usage

    CERN Document Server

    Polanco, Xavier; Besagni, Dominique

    2008-01-01

    A new type of statistical analysis of the science and technical information (STI) in the Web context is produced. We propose a set of indicators about Web users, visualized bibliographic records, and e-commercial transactions. In addition, we introduce two Web usage factors. Finally, we give an overview of the co-usage analysis. For these tasks, we introduce a computer based system, called Miri@d, which produces descriptive statistical information about the Web users' searching behaviour, and what is effectively used from a free access digital bibliographical database. The system is conceived as a server of statistical data which are carried out beforehand, and as an interactive server for online statistical work. The results will be made available to analysts, who can use this descriptive statistical information as raw data for their indicator design tasks, and as input for multivariate data analysis, clustering analysis, and mapping. Managers also can exploit the results in order to improve management and d...

  13. Semantic Session Analysis for Web Usage Mining

    Institute of Scientific and Technical Information of China (English)

    ZHANG Hui; SONG Hantao; XU Xiaomei

    2007-01-01

    A semantic session analysis method partitioning Web usage logs is presented. Semantic Web usage log preparation model enhances usage logs with semantic. The Markov chain model based on ontology semantic measurement is used to identifying which active session a request should belong to. The competitive method is applied to determine the end of the sessions.Compared with other algorithms, more successful sessions are additionally detected by semantic outlier analysis.

  14. [Comparison of protective properties of the smallpox DNA-vaccine based on the variola virus A30L gene and its variant with modified codon usage].

    Science.gov (United States)

    Maksiutov, R A; Shchelkunov, S N

    2011-01-01

    Efficacy of candidate DNA-vaccines based on the variola virus natural gene A30L and artificial gene A30Lopt with modified codon usage, optimized for expression in mammalian cells, was tested. The groups of mice were intracutaneously immunized three times with three-week intervals with candidate DNA-vaccines: pcDNA_A30L or pcDNA_A30Lopt, and in three weeks after the last immunization all mice in the groups were intraperitoneally infected by the ectromelia virus K1 strain in 10 LD50 dose for the estimation of protection. It was shown that the DNA-vaccines based on natural gene A30L and codon-optimized gene A30Lopt elicited virus, thereby neutralizing the antibody response and protected mice from lethal intraperitoneal challenge with the ectromelia virus with lack of statistically significant difference.

  15. Synonymous Codon Usage Bias and Overexpression of a Synthetic Gene Encoding Interferon α2b in Yeast

    Institute of Scientific and Technical Information of China (English)

    Bin FANG; Bu-feng LIANG; Guang-yuan HE

    2007-01-01

    To achieve higher level expression of Interferon α2b (IFN-α2b) in methylotrophic yeast (Pichia pastoris), a cDNA fragment coding for the mature IFN-α2b was designed and synthesized based on the synonymous codon bias of P. pastoris and optimized G+C content. The synthetic IFN-α2b was inserted into the secreted expression vector pPICZαA, and then integrated into P. pastoris GS115 genome by electroporation. Multi-copy integrants in the Mut+ recombinant P. pastoris strain were screened by high concentrations of Zeocin. 120 hours culturing allowed expression of the IFN-α2b transformant up to 810 mg/L as detected by SDS-PAGE and quantitative methods. In addition, Western blot analysis showed that the recombinant proteins had immunogenicity. The significant antiviral activity of the recombinant IFN-α2b protein was verified by WISH/ VSV system, which was 3.3×105 IU/mL.

  16. Optimized codon usage enhances the expression and immunogenicity of DNA vaccine encoding Taenia solium oncosphere TSOL18 gene.

    Science.gov (United States)

    Wang, Yuan-Yuan; Chang, Xue-Lian; Tao, Zhi-Yong; Wang, Xiao-Li; Jiao, Yu-Meng; Chen, Yong; Qi, Wen-Juan; Xia, Hui; Yang, Xiao-Di; Sun, Xin; Shen, Ji-Long; Fang, Qiang

    2015-07-01

    Cysticercosis due to larval cysts of Taenia solium, is a serious public health problem affecting humans in numerous regions worldwide. The oncospheral stage-specific TSOL18 antigen is a promising candidate for an anti-cysticercosis vaccine. It has been reported that the immunogenicity of the DNA vaccine may be enhanced through codon optimization of candidate genes. The aim of the present study was to further increase the efficacy of the cysticercosis DNA vaccine; therefore, a codon optimized recombinant expression plasmid pVAX1/TSOL18 was developed in order to enhance expression and immunogenicity of TSOL18. The gene encoding TSOL18 of Taenia solium was optimized, and the resulting opt-TSOL18 gene was amplified and expressed. The results of the present study showed that the codon-optimized TSOL18 gene was successfully expressed in CHO-K1 cells, and immunized mice vaccinated with opt-TSOL18 recombinant expression plasmids demonstrated opt‑TSOL18 expression in muscle fibers, as determined by immunohistochemistry. In addition, the codon-optimized TSOL18 gene produced a significantly greater effect compared with that of TSOL18 and active spleen cells were markedly stimulated in vaccinated mice. 3H-thymidine incorporation was significantly greater in the opt-TSOL18 group compared with that of the TSOL18, pVAX and blank control groups (P<0.01). In conclusion, the eukaryotic expression vector containing the codon-optimized TSOL18 gene was successfully constructed and was confirmed to be expressed in vivo and in vitro. The expression and immunogenicity of the codon-optimized TSOL18 gene were markedly greater compared with that of the un-optimized gene. Therefore, these results may provide the basis for an optimized TSOL18 gene vaccine against cysticercosis.

  17. Empirical codon substitution matrix

    Directory of Open Access Journals (Sweden)

    Gonnet Gaston H

    2005-06-01

    Full Text Available Abstract Background Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic increase in genomic data enabled construction of empirical matrices, researchers relied on parameterized models of codon evolution. Here we present the first empirical codon substitution matrix entirely built from alignments of coding sequences from vertebrate DNA and thus provide an alternative to parameterized models of codon evolution. Results A set of 17,502 alignments of orthologous sequences from five vertebrate genomes yielded 8.3 million aligned codons from which the number of substitutions between codons were counted. From this data, both a probability matrix and a matrix of similarity scores were computed. They are 64 × 64 matrices describing the substitutions between all codons. Substitutions from sense codons to stop codons are not considered, resulting in block diagonal matrices consisting of 61 × 61 entries for the sense codons and 3 × 3 entries for the stop codons. Conclusion The amount of genomic data currently available allowed for the construction of an empirical codon substitution matrix. However, more sequence data is still needed to construct matrices from different subsets of DNA, specific to kingdoms, evolutionary distance or different amount of synonymous change. Codon mutation matrices have advantages for alignments up to medium evolutionary distances and for usages that require DNA such as ancestral reconstruction of DNA sequences and the calculation of Ka/Ks ratios.

  18. Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda

    Directory of Open Access Journals (Sweden)

    Mun Hua Tan

    2017-03-01

    Full Text Available Background Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters and Caridea (true shrimps are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information. Methods Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements. Results We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders. Discussion Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

  19. 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.

  20. Advantages of a mechanistic codon substitution model for evolutionary analysis of protein-coding sequences.

    Directory of Open Access Journals (Sweden)

    Sanzo Miyazawa

    Full Text Available BACKGROUND: A mechanistic codon substitution model, in which each codon substitution rate is proportional to the product of a codon mutation rate and the average fixation probability depending on the type of amino acid replacement, has advantages over nucleotide, amino acid, and empirical codon substitution models in evolutionary analysis of protein-coding sequences. It can approximate a wide range of codon substitution processes. If no selection pressure on amino acids is taken into account, it will become equivalent to a nucleotide substitution model. If mutation rates are assumed not to depend on the codon type, then it will become essentially equivalent to an amino acid substitution model. Mutation at the nucleotide level and selection at the amino acid level can be separately evaluated. RESULTS: The present scheme for single nucleotide mutations is equivalent to the general time-reversible model, but multiple nucleotide changes in infinitesimal time are allowed. Selective constraints on the respective types of amino acid replacements are tailored to each gene in a linear function of a given estimate of selective constraints. Their good estimates are those calculated by maximizing the respective likelihoods of empirical amino acid or codon substitution frequency matrices. Akaike and Bayesian information criteria indicate that the present model performs far better than the other substitution models for all five phylogenetic trees of highly-divergent to highly-homologous sequences of chloroplast, mitochondrial, and nuclear genes. It is also shown that multiple nucleotide changes in infinitesimal time are significant in long branches, although they may be caused by compensatory substitutions or other mechanisms. The variation of selective constraint over sites fits the datasets significantly better than variable mutation rates, except for 10 slow-evolving nuclear genes of 10 mammals. An critical finding for phylogenetic analysis is that

  1. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events.

    Science.gov (United States)

    Chartier, Matthieu; Gaudreault, Francis; Najmanovich, Rafael

    2012-06-01

    An increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. This large-scale analysis was performed using the whole Pfam database covering over 70% of the known protein sequence universe. Our program Sherlocc, detects statistically relevant conserved rare codon clusters and produces a user-friendly HTML output. Statistically significant rare codon clusters were detected in a multitude of Pfam protein families. The most statistically significant rare codon clusters were predominantly identified in N-terminal Pfam families. Many of the longest rare codon clusters are found in membrane-related proteins which are required to interact with other proteins as part of their function, for example in targeting or insertion. We identified some cases where rare codon clusters can play a regulating role in the folding of catalytically important domains. Our results support the existence of a widespread functional role for rare codon clusters across species. Finally, we developed an online filter-based search interface that provides access to Sherlocc results for all Pfam families. The Sherlocc program and search interface are open access and are available at http://bcb.med.usherbrooke.ca

  2. Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness

    Science.gov (United States)

    Villanueva, Eneko; Martí-Solano, Maria; Fillat, Cristina

    2016-06-01

    Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development.

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

    Science.gov (United States)

    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.

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

    Directory of Open Access Journals (Sweden)

    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

  5. Codon Adaptation of Plastid Genes

    Science.gov (United States)

    Suzuki, Haruo; Morton, Brian R.

    2016-01-01

    Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes. PMID:27196606

  6. Codon Adaptation of Plastid Genes.

    Directory of Open Access Journals (Sweden)

    Haruo Suzuki

    Full Text Available Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes.

  7. WWW portal usage analysis using genetic algorithms

    Directory of Open Access Journals (Sweden)

    Ondřej Popelka

    2009-01-01

    Full Text Available The article proposes a new method suitable for advanced analysis of web portal visits. This is part of retrieving information and knowledge from web usage data (web usage mining. Such information is necessary in order to gain better insight into visitor’s needs and generally consumer behaviour. By le­ve­ra­ging this information a company can optimize the organization of its internet presentations and offer a better end-user experience. The proposed approach is using Grammatical evolution which is computational method based on genetic algorithms. Grammatical evolution is using a context-free grammar in order to generate the solution in arbitrary reusable form. This allows us to describe visitors’ behaviour in different manners depending on desired further processing. In this article we use description with a procedural programming language. Web server access log files are used as source data.The extraction of behaviour patterns can currently be solved using statistical analysis – specifically sequential analysis based methods. Our objective is to develop an alternative algorithm.The article further describes the basic algorithms of two-level grammatical evolution; this involves basic Grammatical Evolution and Differential Evolution, which forms the second phase of the computation. Grammatical evolution is used to generate the basic structure of the solution – in form of a part of application code. Differential evolution is used to find optimal parameters for this solution – the specific pages visited by a random visitor. The grammar used to conduct experiments is described along with explanations of the links to the actual implementation of the algorithm. Furthermore the fitness function is described and reasons which yield to its’ current shape. Finally the process of analyzing and filtering the raw input data is described as it is vital part in obtaining reasonable results.

  8. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events

    Science.gov (United States)

    Chartier, Matthieu; Gaudreault, Francis; Najmanovich, Rafael

    2012-01-01

    Motivation: An increasing amount of evidence from experimental and computational analysis suggests that rare codon clusters are functionally important for protein activity. Most of the studies on rare codon clusters were performed on a limited number of proteins or protein families. In the present study, we present the Sherlocc program and how it can be used for large scale protein family analysis of evolutionarily conserved rare codon clusters and their relation to protein function and structure. This large-scale analysis was performed using the whole Pfam database covering over 70% of the known protein sequence universe. Our program Sherlocc, detects statistically relevant conserved rare codon clusters and produces a user-friendly HTML output. Results: Statistically significant rare codon clusters were detected in a multitude of Pfam protein families. The most statistically significant rare codon clusters were predominantly identified in N-terminal Pfam families. Many of the longest rare codon clusters are found in membrane-related proteins which are required to interact with other proteins as part of their function, for example in targeting or insertion. We identified some cases where rare codon clusters can play a regulating role in the folding of catalytically important domains. Our results support the existence of a widespread functional role for rare codon clusters across species. Finally, we developed an online filter-based search interface that provides access to Sherlocc results for all Pfam families. Availability: The Sherlocc program and search interface are open access and are available at http://bcb.med.usherbrooke.ca Contact: rafael.najmanovich@usherbrooke.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22467916

  9. p53 codon 72 polymorphism and liver cancer susceptibility: A meta-analysis of epidemiologic studies

    Institute of Scientific and Technical Information of China (English)

    Xi Chen; Fei Liu; Bo Li; Yong-Gang Wei; Lv-Nan Yan; Tian-Fu Wen

    2011-01-01

    AIM: To evaluate the association between p53 codon 72 polymorphism and liver cancer risk by means of meta-analysis.METHODS: Two investigators independently searched the Medline, Embase and Chinese Biomedicine databas-es. Summary odds ratios and 95% CI for p53 codon 72 polymorphism and liver cancer were calculated in .xed-effects model (Mantel-Haenszel method) and random-effects model (DerSimonian and Laird method) when appropriate.RESULTS: This meta-analysis included 1115 liver can-cer cases and 1778 controls. The combined results based on all studies showed that there was a statisti-cally signi.cant link between Pro/Pro genotype and liver cancer, but not between Arg/Arg or Pro/Arg genotype and liver cancer. When stratifying for race, similar re-sults were obtained, i.e. patients with liver cancer had a signi.cantly higher frequency of Pro/Pro genotype than non-cancer patients among Asians. After stratifying the various studies by control source, gender, family history of liver cancer and chronic hepatitis virus infection, we found that (1) patients among hospital-based studies had a significantly higher frequency of Pro/Pro and a signi.cantly lower frequency of Arg/Arg genotype than individuals without cancer; (2) female patients with liver cancer had a significantly lower frequency of Arg/Arg and a higher frequency of Pro/Arg+Pro/Pro genotypes than female individuals without cancer; (3) subgroup analyses for family history of liver cancer did not re-veal any signi.cant association between p53 codon 72 polymorphism and liver cancer development; and (4) patients with negative hepatitis virus infection had a sig-ni.cantly higher frequency of Pro/Pro and a signi.cantly lower frequency of Arg/Arg genotype than individuals without cancer.CONCLUSION: This meta-analysis suggests that the p53 codon 72 polymorphism may be associated with liver cancer among Asians.

  10. P53 codon 72 polymorphism and ovarian cancer risk: a meta-analysis

    Institute of Scientific and Technical Information of China (English)

    Zhizhong Zhang; Cuangbo Fu; Meilin Wang; Na Tong; Shizhi Wang; Zhengdong Zhang

    2008-01-01

    Objective: p53 is a tumor suppressor gene and is involved in the etiology of ovarian cancer. Studies investigating the associations between the p53 codon 72 polymorphism and ovarian cancer risk showed conflicting results. We performed this meta-analysis from eligible studies to evaluate this purported relationship. Methods: This meta-analysis was performed from 9 case-control studies, including 825 ovarian cases and 1073 controls. The fixed and random effect models were used to estimate the odds ratios(ORs) for various contrasts of this polymorphism. Results: The combined results based on all studies showed that a significantly decreased risk was associated with the variant Pro/Pro genotype, compared with Arg/Pro+Arg/Arg genotypes(OR, 0.70; 95%CI, 0.51-0.95). When stratifying the studies by ethnicity, we found that individuals with the variant genotype Pro/Pro had a significantly decreased risk of ovarian cancer compared with Arg/Arg genotype(OR, 0.43; 95%CI, 0.20-0.89) and Arg/Pro+Arg/Arg genotypes(OR, 0.61; 95%CI, 0.37-0.99) among Africans. Conclusion: This meta-analysis suggests that the p53 codon 72 polymorphism may contribute to genetic susceptibility to ovarian cancer. More studies based on larger sample size should be performed to confirm the findings.

  11. An Analysis of Electronic-Mail Usage.

    Science.gov (United States)

    Fang, K.

    1998-01-01

    Describes a study that established a measure and model for use in predicting and explaining electronic mail systems as an example of computer-mediated communication technologies usage and choice. The results indicated that all of the eight hypotheses showed significant correlation between criterion and predictor variates, supported by different…

  12. Analysis of Usage Patterns in Large Multimedia Websites

    Science.gov (United States)

    Singh, Rahul; Bhattarai, Bibek

    User behavior in a website is a critical indicator of the web site's usability and success. Therefore an understanding of usage patterns is essential to website design optimization. In this context, large multimedia websites pose a significant challenge for comprehension of the complex and diverse user behaviors they sustain. This is due to the complexity of analyzing and understanding user-data interactions in media-rich contexts. In this chapter we present a novel multi-perspective approach for usability analysis of large media rich websites. Our research combines multimedia web content analysis with elements of web-log analysis and visualization/visual mining of web usage metadata. Multimedia content analysis allows direct estimation of the information-cues presented to a user by the web content. Analysis of web logs and usage-metadata, such as location, type, and frequency of interactions provides a complimentary perspective on the site's usage. The entire set of information is leveraged through powerful visualization and interactive querying techniques to provide analysis of usage patterns, measure of design quality, as well as the ability to rapidly identify problems in the web-site design. Experiments on media rich sites including the SkyServer - a large multimedia web-based astronomy information repository demonstrate the efficacy and promise of the proposed approach.

  13. COMPARISON ANALYSIS OF WEB USAGE MINING USING PATTERN RECOGNITION TECHNIQUES

    Directory of Open Access Journals (Sweden)

    Nanhay Singh

    2013-07-01

    Full Text Available Web usage mining is the application of data mining techniques to better serve the needs of web-based applications on the web site. In this paper, we analyze the web usage mining by applying the pattern recognition techniques on web log data. Pattern recognition is defined as the act of taking in raw data and making an action based on the ‘category’ of the pattern. Web usage mining is divided into three partsPreprocessing, Pattern discovery and Pattern analysis. Further, this paper intended with experimental work in which web log data is used. We have taken the web log data from the “NASA” web server which is analyzed with “Web Log Explorer”. Web Log Explorer is a web usage mining tool which plays the vital role to carry out this work.

  14. Mutation analysis of codons 345 and 347 of rhodopsin gene in Indian retinitis pigmentosa patients

    Indian Academy of Sciences (India)

    Madhurima Dikshit; Rakhi Agarwal

    2001-08-01

    More than 100 mutations have been reported till date in the rhodopsin gene in patients with retinitis pigmentosa. The present study was undertaken to detect the reported rhodopsin gene point mutations in Indian retinitis pigmentosa patients. We looked for presence or absence of codon 345 and 347 mutations in exon 5 of the gene using the technique of allele-specific polymerase chain reaction by designing primers for each mutation. We have examined 100 patients from 76 families irrespective of genetic categories. Surprisingly, in our sample the very widely reported highly frequent mutations of codon 347 (P → S/A/R/Q/L/T) were absent while the codon 345 mutation V → M was seen in three cases in one family (autosomal dominant form) and in one sporadic case (total two families). This is the first report on codon 345 and 347 mutation in Indian retinitis pigmentosa subjects.

  15. MRI usage in a pediatric emergency department: an analysis of usage and usage trends over 5 years

    Energy Technology Data Exchange (ETDEWEB)

    Scheinfeld, Meir H. [Montefiore Medical Center, Albert Einstein College of Medicine, Department of Radiology, Division of Emergency Radiology, Bronx, NY (United States); Moon, Jee-Young; Wang, Dan [Albert Einstein College of Medicine, Department of Epidemiology and Population Health, Bronx, NY (United States); Fagan, Michele J. [Montefiore Medical Center, Albert Einstein College of Medicine, Department of Pediatrics, Division of Emergency Medicine, Bronx, NY (United States); Davoudzadeh, Reubin [Montefiore Medical Center, Department of Radiology, Bronx, NY (United States); Taragin, Benjamin H. [Montefiore Medical Center, Albert Einstein College of Medicine, Department of Radiology, Division of Pediatric Radiology, Bronx, NY (United States)

    2017-03-15

    Magnetic resonance imaging (MRI) usage has anecdotally increased due to the principles of ALARA and the desire to Image Gently. Aside from a single abstract in the emergency medicine literature, pediatric emergency department MRI usage has not been described. Our objective was to determine whether MRI use is indeed increasing at a high-volume urban pediatric emergency department with 24/7 MRI availability. Also, we sought to determine which exams, time periods and demographics influenced the trend. Institutional Review Board exemption was obtained. Emergency department patient visit and exam data were obtained from the hospital database for the 2011-2015 time period. MRI usage data were normalized using emergency department patient visit data to determine usage rates. The z-test was used to compare MRI use by gender. The chi-square test was used to test for trends in MRI usage during the study period and in patient age. MRI usage for each hour and each weekday were tabulated to determine peak and trough usage times. MRI usage rate per emergency department patient visit was 0.36%. Headache, pain and rule-out appendicitis were the most common indications for neuroradiology, musculoskeletal and trunk exams, respectively. Usage in female patients was significantly greater than in males (0.42% vs. 0.29%, respectively, P<0.001). Usage significantly increased during the 5-year period (P<0.001). Use significantly increased from age 3 to 17 (0.011% to 1.1%, respectively, P<0.001). Sixty percent of exams were performed after-hours, the highest volume during the 10 p.m. hour and lowest between 4 a.m. and 9 a.m. MRI use was highest on Thursdays and lowest on Sundays (MRI on 0.45% and 0.22% of patients, respectively). MRI use in children increased during the study period, most notably in females, on weekdays and after-hours. (orig.)

  16. Synonymous codon changes in the oncogenes of the cottontail rabbit papillomavirus lead to increased oncogenicity and immunogenicity of the virus

    Science.gov (United States)

    Cladel, Nancy M.; Budgeon, Lynn R.; Hu, Jiafen; Balogh, Karla K.; Christensen, Neil D.

    2013-01-01

    Papillomaviruses use rare codons with respect to the host. The reasons for this are incompletely understood but among the hypotheses is the concept that rare codons result in low protein production and this allows the virus to escape immune surveillance. We changed rare codons in the oncogenes E6 and E7 of the cottontail rabbit papillomavirus to make them more mammalian-like and tested the mutant genomes in our in vivo animal model. While the amino acid sequences of the proteins remained unchanged, the oncogenic potential of some of the altered genomes increased dramatically. In addition, increased immunogenicity, as measured by spontaneous regression, was observed as the numbers of codon changes increased. This work suggests that codon usage may modify protein production in ways that influence disease outcome and that evaluation of synonymous codons should be included in the analysis of genetic variants of infectious agents and their association with disease. PMID:23433866

  17. The mobile devices and its mobile learning usage analysis

    OpenAIRE

    Jacob, S. M.; Issac, B.

    2014-01-01

    The usage of mobile devices for mobile learning is becoming increasingly popular. There is a new brand of students in the universities now-a-days who are easily connected to technology and innovative mobile devices. We attempt to do an analysis on a survey done with university students on mobile device usage for mobile learning purposes. This is to find the learning trends within the student community so that some of these popular practices could be encouraged to enhance learning among the st...

  18. A codon-usage variant in the (GGN){sub n} trinucleotide polymorphism of the androgen receptor gene as an aid in the prenatal diagnosis of ambiguous genitalia due to partial androgen insensitivity

    Energy Technology Data Exchange (ETDEWEB)

    Lumbroso, R.; Vasiliou, M.; Beitel, L.K. [McGill Univ., Montreal, Quebec (Canada)] [and others

    1994-09-01

    Exon 1 at the X-linked androgen receptor (AR) locus encodes an N-terminal modulatory domain that contains two large homopolyamino acid tracts: (CAG;glutamine;Gln){sub 11-33} and (GGN;Glycine;Cly){sub 15-27}. Certain AR mutations cause partial androgen insensitivity (PAI) with frank genital ambiguity that may engender appreciable parental anxiety and patient morbidity. If the AR mutation in a PAI family is unknown, the AR`s intragenic trinucleotide repeat polymorphisms may be used for prenatal diagnosis. However, intergenerational instability of repeat-size may be worrisome, particularly when the information alleles differ by only a few repeats. Here, we report the discovery of a codon-usage (silent substitution) variant in the GGN repeat, and describe its use as a source of complementary information for prenatal diagnosis. The standard sense sequence of the (GGN){sub n} tract is (GGT){sub 3} GGG(GGT){sub 2} (GGC){sub 9-21}. On 4 of 27 X chromosomes we noted that the internal GGT sequence was expanded to 3 or 4 repeats. We used an internal (GGT){sub 4} repeat in a total (GGN){sub 24} tract together with a (CAG){sub 20} tract to distinguish an X chromosome with a mutant AR allele from another X chromosome, bearing a normal allele, that had an internal (GGT){sub 2} repeat in a total (GGN){sub 23} tract together with a (CAG){sub 21} tract. Subsequently, we found the base change leading to a pathogenic amino acid substitution (M779I) in codon 6 of the mutant AR gene in an affected maternal aunt and the fetus at risk. This confirmed the prenatal diagnosis based on the intragenic trinucleotide repeat polymorphisms, and it strengthened the prediction of external genital ambiguity using our previous experience with M779I in another family.

  19. Usage Bibliometrics

    Science.gov (United States)

    Kurtz, Michael J.; Bollen, Johan

    2010-01-01

    Scholarly usage data provides unique opportunities to address the known shortcomings of citation analysis. However, the collection, processing and analysis of usage data remains an area of active research. This article provides a review of the state-of-the-art in usage-based informetric, i.e. the use of usage data to study the scholarly process.

  20. The Factors Shaping Synonymous Codon Usage in the Genome of Burkholderia mallei%影响鼻疽伯克霍尔德氏菌基因组密码子用法的因素分析

    Institute of Scientific and Technical Information of China (English)

    赵胜; 张琴; 陈智华; 赵益新; 钟金城

    2007-01-01

    鼻疽伯克霍尔德氏菌(Burkholderia malei ATCC 23344)的基因组密码子使用受多种因素的影响,本研究根据该菌的完整基因组序列,运用多元统计分析和对应分析的方法,探讨了鼻疽伯克霍尔德氏菌全基因组序列密码子的使用模式和影响密码子使用的因素.结果表明基因表达水平的高低是影响密码子使用的主要因素;基因组中编码区的碱基组成、蛋白质的疏水性和基因的长度对密码子的使用也有一定的影响,但影响力不及基因的表达水平.同时,通过比较高表达的基因、低表达的基因密码子使用情况,GCG和CUC等21个密码子被确定为鼻疽伯克霍尔德氏菌的主要偏爱密码子.以上结果对鼻疽伯克霍尔德氏菌的密码子用法研究、在分子水平上研究物种进化、基因组中未知基因的预测、开放阅读框的判断、功能基因的表达以及鼻疽病疫苗的研发等工作都提供了理论基础,具有较强的指导作用.%Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention.In this study,the main factors shaping codon usage in the genome of B.mallei ATCC 23344 were firstly reported.The results showed that the primary trend in codon usage variation in the B.mallei is due to translational selection;while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences.At the same development of a vaccine to prevent glanders.

  1. [Codon optimization and eukaryotic expression analysis of the analgesic peptide gene BmK AngM1 from Buthus martensii Karsch].

    Science.gov (United States)

    Yang, Jin-ling; Gao, Li-li; Zhu, Ping; Hou, Qi; Wang, Fen; Yu, Wen-bo; Nie, Tao

    2012-10-01

    Codon bias is an important factor which influences heterologous gene expression. Optimizing codon sequence could improve expression level of heterologous gene. In order to improve the expression level of BmK AngM1 gene encoding the analgesic peptide from Buthus martensii Karsch in Pichia pastoris, the codon-optimized BmK AngM1 gene according to its cDNA sequence and the preference codon usage of P. pastoris were cloned into expression vector pPIC9K and then transformed into P. pastoris. The expersion of recombinant BmK AngM1 (rBmK AngM1) was inducced by methanol in the medium, and the expression level of the optimized BmK AngM1 gene was 3.7 times of the native one. These results suggested that the expression of BmK AngM1 in P. pastoris could be successfully improved by codon optimization.

  2. Stop Codon Reassignment in the Wild

    Energy Technology Data Exchange (ETDEWEB)

    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

  3. Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation1[OPEN

    Science.gov (United States)

    Chan, Hui-Ting; Williams-Carrier, Rosalind; Barkan, Alice

    2016-01-01

    Codon optimization based on psbA genes from 133 plant species eliminated 105 (human clotting factor VIII heavy chain [FVIII HC]) and 59 (polio VIRAL CAPSID PROTEIN1 [VP1]) rare codons; replacement with only the most highly preferred codons decreased transgene expression (77- to 111-fold) when compared with the codon usage hierarchy of the psbA genes. Targeted proteomic quantification by parallel reaction monitoring analysis showed 4.9- to 7.1-fold or 22.5- to 28.1-fold increase in FVIII or VP1 codon-optimized genes when normalized with stable isotope-labeled standard peptides (or housekeeping protein peptides), but quantitation using western blots showed 6.3- to 8-fold or 91- to 125-fold increase of transgene expression from the same batch of materials, due to limitations in quantitative protein transfer, denaturation, solubility, or stability. Parallel reaction monitoring, to our knowledge validated here for the first time for in planta quantitation of biopharmaceuticals, is especially useful for insoluble or multimeric proteins required for oral drug delivery. Northern blots confirmed that the increase of codon-optimized protein synthesis is at the translational level rather than any impact on transcript abundance. Ribosome footprints did not increase proportionately with VP1 translation or even decreased after FVIII codon optimization but is useful in diagnosing additional rate-limiting steps. A major ribosome pause at CTC leucine codons in the native gene of FVIII HC was eliminated upon codon optimization. Ribosome stalls observed at clusters of serine codons in the codon-optimized VP1 gene provide an opportunity for further optimization. In addition to increasing our understanding of chloroplast translation, these new tools should help to advance this concept toward human clinical studies. PMID:27465114

  4. OCPAT: an online codon-preserved alignment tool for evolutionary genomic analysis of protein coding sequences

    Directory of Open Access Journals (Sweden)

    Grossman Lawrence I

    2007-09-01

    Full Text Available Abstract Background Rapidly accumulating genome sequence data from multiple species offer powerful opportunities for the detection of DNA sequence evolution. Phylogenetic tree construction and codon-based tests for natural selection are the prevailing tools used to detect functionally important evolutionary change in protein coding sequences. These analyses often require multiple DNA sequence alignments that maintain the correct reading frame for each collection of putative orthologous sequences. Since this feature is not available in most alignment tools, codon reading frames often must be checked manually before evolutionary analyses can commence. Results Here we report an online codon-preserved alignment tool (OCPAT that generates multiple sequence alignments automatically from the coding sequences of any list of human gene IDs and their putative orthologs from genomes of other vertebrate tetrapods. OCPAT is programmed to extract putative orthologous genes from genomes and to align the orthologs with the reading frame maintained in all species. OCPAT also optimizes the alignment by trimming the most variable alignment regions at the 5' and 3' ends of each gene. The resulting output of alignments is returned in several formats, which facilitates further molecular evolutionary analyses by appropriate available software. Alignments are generally robust and reliable, retaining the correct reading frame. The tool can serve as the first step for comparative genomic analyses of protein-coding gene sequences including phylogenetic tree reconstruction and detection of natural selection. We aligned 20,658 human RefSeq mRNAs using OCPAT. Most alignments are missing sequence(s from at least one species; however, functional annotation clustering of the ~1700 transcripts that were alignable to all species shows that genes involved in multi-subunit protein complexes are highly conserved. Conclusion The OCPAT program facilitates large-scale evolutionary and

  5. Nomenclature, symbols, units and their usage in spectrochemical analysis

    CERN Document Server

    Zhou, Yong

    2013-01-01

    International Union of Pure and Applied Chemistry: Nomenclature, Symbols, Units and their Usage in Spectrochemical Analysis-III: Analytical Flame Spectroscopy and Associated Non-Flame Procedures covers the analytical application of flame spectroscopy and related procedures, which is not encompassed in the first two parts of the series. Parts I and II of the series deal with general recommendations. Section 1 of this document presents a classification of the methods and instruments used in the different branches of analytical flame spectroscopy. Section 2 lists terms and symbols for common quan

  6. Functional analysis of recombinant codon-optimized bovine neutrophil β-defensin

    Directory of Open Access Journals (Sweden)

    Shahrzad Aghaei

    2016-09-01

    Full Text Available Defensins are cationic antimicrobial peptides with a broad range of activities against bacteria and fungi. In the present study, the entire coding sequence of codon-optimized Bovine Neutrophil β-Defensin 2 (BNBD2 was designed and placed upstream of Trx coding sequence into the pET-48b (+ vector. Furthermore, the codon-optimized pelB signal sequences were also added to the upstream of BNBD2 for periplasmic localization. The periplasmic sorting of recombinant β-Defensin 2 was evaluated by osmotic shock and SDS–PAGE on the released proteins. Moreover, the expression of BNBD2-Trx fusion protein was confirmed by the Western blotting technique. Next, the purification of recombinant protein was achieved by Ni++ affinity chromatography. BNBD2 was also separated from Trx by chemical cleavage with formic acid. Finally, both of the antibacterial and antifungal activities of the purified protein were examined. Overall, the results indicated successful periplasmic production of BNBD2 protein, which showed antifungal activity against some of Aspergillus species as well as the antibacterial activity, expressed as successfully suppressed growth of Escherichia coli and Staphylococcus aureus.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Mannose-binding lectin codon 54 gene polymorphism and vulvovaginal candidiasis: a systematic review and meta-analysis.

    Science.gov (United States)

    Nedovic, Bojan; Posteraro, Brunella; Leoncini, Emanuele; Ruggeri, Alberto; Amore, Rosarita; Sanguinetti, Maurizio; Ricciardi, Walter; Boccia, Stefania

    2014-01-01

    Mannose-binding lectin (MBL) plays a key role in the human innate immune response. It has been shown that polymorphisms in the MBL2 gene, particularly at codon 54 (variant allele B; wild-type allele designated as A), impact upon host susceptibility to Candida infection. This systematic review and meta-analysis were performed to assess the association between MBL2 codon 54 genotype and vulvovaginal candidiasis (VVC) or recurrent VVC (RVVC). Studies were searched in MEDLINE, SCOPUS, and ISI Web of Science until April 2013. Five studies including 704 women (386 cases and 318 controls) were part of the meta-analysis, and pooled ORs were calculated using the random effects model. For subjects with RVVC, ORs of AB versus AA and of BB versus AA were 4.84 (95% CI 2.10-11.15; P for heterogeneity = 0.013; I(2) = 68.6%) and 12.68 (95% CI 3.74-42.92; P for heterogeneity = 0.932, I(2) = 0.0%), respectively. For subjects with VVC, OR of AB versus AA was 2.57 (95% CI 1.29-5.12; P for heterogeneity = 0.897; I (2) = 0.0%). This analysis indicates that heterozygosity for the MBL2 allele B increases significantly the risk for both diseases, suggesting that MBL may influence the women's innate immunity in response to Candida.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. Preferred and avoided codon pairs in three domains of life

    Directory of Open Access Journals (Sweden)

    Tenson Tanel

    2008-10-01

    Full Text Available Abstract Background Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons – neighboring nucleotides and neighboring codons – can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserved the codon context preferences in different organisms are. We analyzed 138 organisms (bacteria, archaea and eukaryotes to find conserved patterns of codon pairs. Results After removing the effects of single codon usage and dipeptide biases we discovered a set of neighboring codons for which avoidances or preferences were conserved in all three domains of life. Such biased codon pairs could be divided into subtypes on the basis of the nucleotide patterns that influence the bias. The most frequently avoided type of codon pair was nnUAnn. We discovered that 95.7% of avoided nnUAnn type patterns contain out-frame UAA or UAG triplets on the sense and/or antisense strand. On average, nnUAnn codon pairs are more frequently avoided in ORFeomes than in genomes. Thus we assume that translational selection plays a major role in the avoidance of these codon pairs. Among the preferred codon pairs, nnGCnn was the major type. Conclusion Translational selection shapes codon pair usage in protein coding sequences by rules that are common to all three domains of life. The most frequently avoided codon pairs contain the patterns nnUAnn, nnGGnn, nnGnnC, nnCGCn, GUCCnn, CUCCnn, nnCnnA or UUCGnn. The most frequently preferred codon pairs contain the patterns nnGCnn, nnCAnn or nnUnCn.

  11. On ribosome load, codon bias and protein abundance.

    Directory of Open Access Journals (Sweden)

    Stefan Klumpp

    Full Text Available Different codons encoding the same amino acid are not used equally in protein-coding sequences. In bacteria, there is a bias towards codons with high translation rates. This bias is most pronounced in highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of translational mechanisms. Here, we investigate the effect of evolutionary forces on codon usage. The relation between codon bias and protein abundance is quantitatively analyzed based on the hypothesis that codon bias evolved to ensure the efficient usage of ribosomes, a precious commodity for fast growing cells. An explicit fitness landscape is formulated based on bacterial growth laws to relate protein abundance and ribosomal load. The model leads to a quantitative relation between codon bias and protein abundance, which accounts for a substantial part of the observed bias for E. coli. Moreover, by providing an evolutionary link, the ribosome load model resolves the apparent conflict between the observed relation of protein abundance and codon bias in natural sequences and the lack of such dependence in a synthetic gfp library. Finally, we show that the relation between codon usage and protein abundance can be used to predict protein abundance from genomic sequence data alone without adjustable parameters.

  12. Statistical analysis: the need, the concept, and the usage

    Directory of Open Access Journals (Sweden)

    Naduvilath Thomas

    1998-01-01

    Full Text Available In general, better understanding of the need and usage of statistics would benefit the medical community in India. This paper explains why statistical analysis is needed, and what is the conceptual basis for it. Ophthalmic data are used as examples. The concept of sampling variation is explained to further corroborate the need for statistical analysis in medical research. Statistical estimation and testing of hypothesis which form the major components of statistical inference are construed. Commonly reported univariate and multivariate statistical tests are explained in order to equip the ophthalmologist with basic knowledge of statistics for better understanding of research data. It is felt that this understanding would facilitate well designed investigations ultimately leading to higher quality practice of ophthalmology in our country.

  13. Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags.

    Science.gov (United States)

    Ahmad, Touqeer; Sablok, Gaurav; Tatarinova, Tatiana V; Xu, Qiang; Deng, Xiu-Xin; Guo, Wen-Wu

    2013-04-01

    Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid.

  14. Genome-wide analysis of chimpanzee genes with premature termination codons

    Directory of Open Access Journals (Sweden)

    Cavelier Lucia

    2009-01-01

    Full Text Available Abstract Background Premature termination codons (PTCs cause mRNA degradation or a truncated protein and thereby contribute to the transcriptome and proteome divergence between species. Here we present the first genome-wide study of PTCs in the chimpanzee. By comparing the human and chimpanzee genome sequences we identify and characterize genes with PTCs, in order to understand the contribution of these mutations to the transcriptome diversity between the species. Results We have studied a total of 13,487 human-chimpanzee gene pairs and found that ~8% were affected by PTCs in the chimpanzee. A majority (764/1,109 of PTCs were caused by insertions or deletions and the remaining part was caused by substitutions. The distribution of PTC genes varied between chromosomes, with Y having the highest proportion. Furthermore, the density of PTC genes varied on a megabasepair scale within chromosomes and we found the density to be correlated both with indel divergence and proximity to the telomere. Within genes, PTCs were more common close to the 5' and 3' ends of the amino acid sequence. Gene Ontology classification revealed that olfactory receptor genes were over represented among the PTC genes. Conclusion Our results showed that the density of PTC genes fluctuated across the genome depending on the local genomic context. PTCs were preferentially located in the terminal parts of the transcript, which generally have a lower frequency of functional domains, indicating that selection was operating against PTCs at sites central to protein function. The enrichment of GO terms associated with olfaction suggests that PTCs may have influenced the difference in the repertoire of olfactory genes between humans and chimpanzees. In summary, 8% of the chimpanzee genes were affected by PTCs and this type of variation is likely to have an important effect on the transcript and proteomic divergence between humans and chimpanzees.

  15. Analysis of OTR Codon Bias and Cluster in 13 Mammal Species%13种哺乳动物OTR密码子使用偏性及其聚类分析

    Institute of Scientific and Technical Information of China (English)

    张之一; 陈蕾; 薛慧良; 徐金会; 徐来祥

    2012-01-01

    Objective To study the codon bias of oxytocin receptor (OTR) gene in 13 mammal species, to explore its impacting factors and the phylogenetic relationships by clustering the codon bias. Methods Bias indexes of RSCU, CBI and ENC were calculated and the relevant analysis of several potential impacting factors was performed. SPASS 15.0 software was used for the clustering analysis of the codon bias, in which the relative synonymous eodon usage was taken as the variable. Results and Conclusion 1 ) CUG, GUG, GCC, UUC, AUC, CGC were found to be the frequently used codon;2)The number of GC located on the third of codon is the main factor that affects the eodon bias of OTR gene in mammalians, the number of GC in genes is the secondary factor, and aromatic amino acid content and hydrophobic protein level have little effect on the codon bias;3 ) For the genes with the same functions, the codon bias indexes are similar among species with close genetic relationship except for some special species.%目的研究13种哺乳动物催产素受体基因(OTR)密码子使用偏性,并探讨其影响因素;通过对偏性情况进行聚类分析,研究其与系统发育的关系.方法计算RSCU,CBI,ENC等密码子偏性指标,与可能的几种影响因素做相关性分析,采用SPASS15.0软件,以相对同义密码子使用度为变量对偏性情况进行聚类分析.结果与结论1)CUG,GUG,GCC,UUC,AUC,CGC为哺乳动物OTR使用频率较高的密码子;2)密码子第3位碱基的GC含量是影响哺乳动物OTR密码子偏性的主要因素,基因的GC含量次之,而芳香族氨基酸的含量和蛋白疏水水平对其密码子使用偏性的影响不大;3)对于功能相同的基因,亲缘关系相近的物种密码子使用偏性指标较接近,但某些物种仍有一定差异.

  16. A visual analysis of the usage efficiency of library books

    Institute of Scientific and Technical Information of China (English)

    LIU; Kan; LIU; Ping

    2008-01-01

    The monographic collections in academic libraries have undergone a period of tremendous growth in volume,in subject diversity,and in formats during the recent several decades.Readers may find it difficult to prioritize which book(s)should be borrowed for a specific purpose.The log data of book loan record may serve as a visible indicator for the more sought-after books by the readers.This paper describes our experimental efforts in exploring various visual techniques to analyze the borrowing patterns of the monographic works in a university library setting.The visual analysis is thought to provide an effective way to extract the book usage information,which may yield new insights into a host of other related technical as well as user behavior issues.Initial experiment has demonstrated that the proposed approach as articulated in this article can actually benefit end-users as well as library collection development personnel in their endeavor of book selections with effective measure.

  17. The Methods of Sensitivity Analysis and Their Usage for Analysis of Multicriteria Decision

    Directory of Open Access Journals (Sweden)

    Rūta Simanavičienė

    2011-08-01

    Full Text Available In this paper we describe the application's fields of the sensitivity analysis methods. We pass in review the application of these methods in multiple criteria decision making, when the initial data are numbers. We formulate the problem, which of the sensitivity analysis methods is more effective for the usage in the decision making process.Article in Lithuanian

  18. Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria

    Science.gov (United States)

    Satapathy, Siddhartha Sankar; Powdel, Bhesh Raj; Buragohain, Alak Kumar; Ray, Suvendra Kumar

    2016-01-01

    The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the ‘optimal codons’ (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms. PMID:27426467

  19. Increased incidence of rare codon clusters at 5' and 3' gene termini:implications for function

    Directory of Open Access Journals (Sweden)

    Clark Patricia L

    2010-02-01

    Full Text Available Abstract Background The process of translation can be affected by the use of rare versus common codons within the mRNA transcript. Results Here, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes predicted to be secreted show significant enrichment in 5' rare codon clusters, but not 3' rare codon clusters. Surprisingly, no correlation between 5' mRNA structure and rare codon usage was observed. Conclusions Potential functional roles for the enrichment of rare codons at terminal positions are explored.

  20. 栖热菌噬茵体TSP4密码子偏嗜性及其对基因异源表达的影响%Codon usage bias of Thermus phage TSP4 and its effect on protein heterologous expression

    Institute of Scientific and Technical Information of China (English)

    薛寒; 张琦; 李秋鹏; 季秀玲; 魏云林; 林连兵

    2012-01-01

    为了探索噬菌体TSP4、栖热菌模式菌株Thermus thermophilusHB27中6种蛋白编码序列和Escherichi- coli基因组遗传密码子使用偏嗜性,探索TSP4基因密码子偏嗜性对其基因异源表达的影响本研究利用生物学软件Editseq和RSCU算法统计噬菌体TSP4密码子使用频率并分析其偏嗜性,与栖热菌HB27的同源基因以及常温菌E.coli基因组的密码子使用偏嗜性进行对比分析.结果显示,噬菌体TSP4与栖热菌HB27优势密码子相似度高达85%,而与E-coli的相似性仅有65%.为了验证分析结果,选取TSP4基因组中一个潜在分子伴侣基因序列在E捌iB12I和EcoliRosetta(补充了BL21菌株中缺失的6个稀有密码子)中进行异源表达.噬菌体TSP4与其宿主菌HB27之间密码子高相似性说明在长期的进化过程中TSP4在基因水平上形成对宿主的一种适应性机制.异源表达结果显示,分子伴侣基因在EcoliBL21中未见明显表达,但在Rosetta中高效表达,说明Rosetta中补充的6个稀有密码子明显有助于分子伴侣基因的表达,该结果也进一步证明密码子偏嗜性是否一致在很大程度上影响基因的表达.%This study is to analyze the codon usage bias of six protein - coding sequences in the genomes of phage TSP4, Thermus thermophilus HB27 and Escherichia coli, and to investigate the effects of codon bias on the heterologous expression of TSP4 genes. Biological software Editseq and algorithm of RSCU were used to analyze the frequency of synonymous codon usage of TSP4 genes to obtain an index of codon usage bias, which-was further compared with that of Thermus HB27 and E. coli homologous genes. The results showed that, based on these com- pared sequences ,TSP4 shared 85% similarity of codon usage frequency with Thermus HB27 but only 65% with E. coli. Higher similarity between phage TSP4 and HB27 indicated that TSP4 might possess an adaptation mecha- nism at the genetic

  1. The Role of TP53 Gene Codon 72 Polymorphism in Leukemia: A PRISMA-Compliant Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Ruan, Xiao-Lan; Li, Sheng; Meng, Xiang-Yu; Geng, Peiliang; Gao, Qing-Ping; Ao, Xu-Bin

    2015-09-01

    The purpose of this meta-analysis was aimed to evaluate the association of tumor protein p53 (TP53) gene codon 72 polymorphism with leukemia susceptibility. We searched PubMed to identify relevant studies, and 16 case-control studies from 14 published articles were identified as eligible studies, including 2062 leukemia patients and 5826 controls. After extracting data, odds ratio (OR) with the corresponding 95% confidence interval (95%CI) was applied to assess the association between TP53 codon 72 polymorphism and leukemia susceptibility. The meta-analysis was performed with the Comprehensive Meta-Analysis software, version 2.2. Overall, no significant association between TP53 codon 72 polymorphism and leukemia susceptibility was found in this meta-analysis (Pro vs Arg: OR = 1.05, 95%CI = 0.90-1.21; Pro/Pro vs Arg/Arg: OR = 1.13, 95%CI = 0.84-1.52; Arg/Pro vs Arg/Arg: OR = 0.94, 95%CI = 0.76-1.15; [Pro/Pro + Arg/Pro] vs Arg/Arg: OR = 0.99, 95%CI = 0.80-1.21; Pro/Pro vs [Arg/Arg + Arg/Pro]: OR = 1.19, 95%CI = 0.93-1.51). Similar results were also found in subgroup analysis by ethnicity, source of controls, and types of leukemia (either acute myeloid leukemia or acute lymphocytic leukemia). Our meta-analysis demonstrates that TP53 codon 72 polymorphism may not be a risk factor for acute leukemia; however, due to the limitations of this study, it should be verified in future studies.

  2. Pyrosequencing analysis for mutations in embB codon306 among clinical mycobacterium tuberculosis isolates from Qingdao, China.

    Science.gov (United States)

    Zhang, Huaqiang; Chen, Xiaoguang; Wang, Zhongdong; Ren, Zhisheng; Wu, Jie; Sun, Haiyan; Bai, Xue

    2015-01-01

    In this study, our objectives was to analyze the molecular characteristics of mutation at embB codon306 in Mycobacterium tuberculosis in Qingdao by pyrosequencing technology, and to assess the value of embB codon306 used as a molecular marker to diagnose multidrug resistant (MDR) TB strains. Pyrosequencing was used to detect mutations at embB codon306 among M. tuberculosis isolates from tuberculosis (TB) patients in Qingdao. The correlation between embB306 mutation and MDR phenotype was evaluated by comparing with conventional drug susceptibility testing results. 60.9% of MDR strains and 15.2% of non-MDR strains carried embB306 mutation, respectively. The percentage of MDR-TB harboring embB306 mutation was significantly higher than that of non- MDR-TB (χ(2)=15.09, P Pyrosequencing should be a good diagnostic tool for MDR-TB in Qingdao.

  3. Cueing the Virtual Storyteller: Analysis of cue phrase usage in fairy tales

    NARCIS (Netherlands)

    Penning, Manon; Theune, Mariët; Busemann, S.

    2007-01-01

    An existing taxonomy of Dutch cue phrases, designed for use in story generation, was validated by analysing cue phrase usage in a corpus of classical fairy tales. The analysis led to some adaptations of the original taxonomy.

  4. USAGE OF DISSIMILARITY MEASURES AND MULTIDIMENSIONAL SCALING FOR LARGE SCALE SOLAR DATA ANALYSIS

    Data.gov (United States)

    National Aeronautics and Space Administration — USAGE OF DISSIMILARITY MEASURES AND MULTIDIMENSIONAL SCALING FOR LARGE SCALE SOLAR DATA ANALYSIS Juan M Banda, Rafal Anrgyk ABSTRACT: This work describes the...

  5. TP53 codon 72 polymorphism and cervical cancer : a pooled analysis of individual data from 49 studies

    NARCIS (Netherlands)

    Klug, Stefanie J.; Ressing, Meike; Koenig, Jochem; Abba, Martin C.; Agorastos, Theodoros; Brenna, Sylvia M. F.; Ciotti, Marco; Das, B. R.; Del Mistro, Annarosa; Dybikowska, Aleksandra; Giuliano, Anna R.; Gudleviciene, Zivile; Gyllensten, Ulf; Haws, Andrea L. F.; Helland, Aslaug; Herrington, C. Simon; Hildesheim, Alan; Humbey, Olivier; Jee, Sun H.; Kim, Jae Weon; Madeleine, Margaret M.; Menczer, Joseph; Ngan, Hextan Y. S.; Nishikawa, Akira; Niwa, Yoshimitsu; Pegoraro, Rosemary; Pillai, M. R.; Ranzani, Gulielmina; Rezza, Giovanni; Rosenthal, Adam N.; Roychoudhury, Susanta; Saranath, Dhananjaya; Schmitt, Virginia M.; Sengupta, Sharmila; Settheetham-Ishida, Wannapa; Shirasawa, Hiroshi; Snijders, Peter J. F.; Stoler, Mark H.; Suarez-Rincon, Angel E.; Szarka, Krisztina; Tachezy, Ruth; Ueda, Masatsugu; van der Zee, Ate G. J.; Doeberitz, Magnus von Knebel; Wu, Ming-Tsang; Yamashita, Tsuyoshi; Zehbe, Ingeborg; Blettner, Maria

    2009-01-01

    Background Cervical cancer is caused primarily by human papillomaviruses (HPV). The polymorphism rs1042522 at codon 72 of the TP53 tumour-suppressor gene has been investigated as a genetic cofactor. More than 80 studies were done between 1998 and 2006, after it was initially reported that women who

  6. Usage of a Responsible Gambling Tool: A Descriptive Analysis and Latent Class Analysis of User Behavior.

    Science.gov (United States)

    Forsström, David; Hesser, Hugo; Carlbring, Per

    2016-09-01

    Gambling is a common pastime around the world. Most gamblers can engage in gambling activities without negative consequences, but some run the risk of developing an excessive gambling pattern. Excessive gambling has severe negative economic and psychological consequences, which makes the development of responsible gambling strategies vital to protecting individuals from these risks. One such strategy is responsible gambling (RG) tools. These tools track an individual's gambling history and supplies personalized feedback and might be one way to decrease excessive gambling behavior. However, research is lacking in this area and little is known about the usage of these tools. The aim of this article is to describe user behavior and to investigate if there are different subclasses of users by conducting a latent class analysis. The user behaviour of 9528 online gamblers who voluntarily used a RG tool was analysed. Number of visits to the site, self-tests made, and advice used were the observed variables included in the latent class analysis. Descriptive statistics show that overall the functions of the tool had a high initial usage and a low repeated usage. Latent class analysis yielded five distinct classes of users: self-testers, multi-function users, advice users, site visitors, and non-users. Multinomial regression revealed that classes were associated with different risk levels of excessive gambling. The self-testers and multi-function users used the tool to a higher extent and were found to have a greater risk of excessive gambling than the other classes.

  7. Aeromonas phages encode tRNAs for their overused codons.

    Science.gov (United States)

    Prabhakaran, Ramanandan; Chithambaram, Shivapriya; Xia, Xuhua

    2014-01-01

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

  8. The analysis of animal faeces as a tool to monitor antibiotic usage

    NARCIS (Netherlands)

    Berendsen, B.J.A.; Wegh, R.S.; Memelink, J.; Zuidema, T.; Stolker, A.A.M.

    2015-01-01

    The analysis of antibiotics in animal faeces is important to obtain more insight in the possible formation of bacterial resistance in the animals¿ gut, to learn about the dissemination of antibiotics to the environment, to monitor trends in antibiotic usage and to detect the illegal and off-label us

  9. The analysis of animal faeces as a tool to monitor antibiotic usage

    NARCIS (Netherlands)

    Berendsen, B.J.A.; Wegh, R.S.; Memelink, J.; Zuidema, T.; Stolker, A.A.M.

    2015-01-01

    The analysis of antibiotics in animal faeces is important to obtain more insight in the possible formation of bacterial resistance in the animals¿ gut, to learn about the dissemination of antibiotics to the environment, to monitor trends in antibiotic usage and to detect the illegal and off-label

  10. A Statistical Analysis of College Biochemistry Textbooks in China: The Statuses on the Publishing and Usage

    Science.gov (United States)

    Zhou, Ping; Wang, Qinwen; Yang, Jie; Li, Jingqiu; Guo, Junming; Gong, Zhaohui

    2015-01-01

    This study aimed to investigate the statuses on the publishing and usage of college biochemistry textbooks in China. A textbook database was constructed and the statistical analysis was adopted to evaluate the textbooks. The results showed that there were 945 (~57%) books for theory teaching, 379 (~23%) books for experiment teaching and 331 (~20%)…

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

    Science.gov (United States)

    We have previously identified the mycobacterial high G+C codon usage bias as a limiting factor in heterologous expression of MAP proteins from Lb.salivarius, and demonstrated that codon optimisation of a synthetic coding gene greatly enhances MAP protein production. Here, we effectively demonstrate ...

  12. Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli

    National Research Council Canada - National Science Library

    Menzella, Hugo G

    2011-01-01

    Variations in codon usage between species are one of the major causes affecting recombinant protein expression levels, with a significant impact on the economy of industrial enzyme production processes...

  13. Analysis of polymorphisms in codons 11, 72 and 248 of TP53 in Brazilian women with breast cancer.

    Science.gov (United States)

    Almeida, B C; Kleine, J P F O; Camargo-Kosugi, C M; Lisboa, M R; França, C N; França, J P; Silva, I D C G

    2016-02-22

    The association between TP53 gene polymorphisms and breast cancer (BC) in Brazilian women is a controversial topic. In this cross-sectional study, we evaluated the association between clinical pathological variables and three polymorphisms (TP53*11, TP53*72, and TP53*248) in BC patients and controls. Genomic DNA was extracted from the blood cells of 393 participants; the cancer-free control subjects were 26-72 years old (41 ± 11.03) and the BC patients were 28-80 years old (51 ± 10.70). We used standard polymerase chain reaction-restriction fragment length polymorphism and confirmed the results by genetic sequencing. In TP53*11, there was 100% homozygous Glu distribution in both groups. TP53*72 showed genotypic distribution: in the control group, there was 16.10% homozygous Pro, and 42.44% heterozygous and 41.46% homozygous Arg; in the BC group, there was 15.43% homozygous Pro, and 42.55% heterozygous and 42.02% homozygous Arg. The relative frequency of each allele was 0.37% for Pro and 0.63% for Arg in the control group, and 0.37% for Pro and 0.63% for Arg in the BC group. The nuclear grade (P = 0.0084) and adapted histological grade (P = 0.0265) were associated with TP53*72. The distribution of the codon 72 genotypes did not deviate from Hardy-Weinberg equilibrium in either group. In TP53*248, there was 100% homozygous Arg distribution in both groups. In codon 72, the Arg allele is the most prevalent in Brazilian women. TP53*72 may be associated with susceptibility to BC, although more studies are required to evaluate the profile of Brazilian women with BC.

  14. Random harmonic analysis program, L221 (TEV156). Volume 1: Engineering and usage

    Science.gov (United States)

    Miller, R. D.; Graham, M. L.

    1979-01-01

    A digital computer program capable of calculating steady state solutions for linear second order differential equations due to sinusoidal forcing functions is described. The field of application of the program, the analysis of airplane response and loads due to continuous random air turbulence, is discussed. Optional capabilities including frequency dependent input matrices, feedback damping, gradual gust penetration, multiple excitation forcing functions, and a static elastic solution are described. Program usage and a description of the analysis used are presented.

  15. 芍药查尔酮异构酶基因(CHI)克隆、密码子偏好性分析以及蛋白结构功能预测%Cloning,Codon Usage Bias and Protein Structure and Function Prediction of CHI Gene in Paeonia lactiflora

    Institute of Scientific and Technical Information of China (English)

    吴彦庆; 赵大球; 王静; 陶俊

    2016-01-01

    In order to enrich basic data in Paeonia lactiflora CHI gene,the CDS region of Paeonia lactiflora CHI gene was cloned by RACE technology,further codon usage was analyzed by EMBOSS software,then the struc-ture and function of CHI protein was predicted by bioinformatics software and online databases.Results indicated that,the 898 bp full-length cDNA of CHI of Paeonia lactiflora(GenBank No.:JN1 19872 )was obtained.Paeonia lactiflora CHI gene has certain preference of codon usage with the terminal base A or U.There were twenty-eight bi-ased codons(RSCU >1 ),whose biased strongly codons were UUG,UGU,CAU,AGA,AGG and CGG(RSCU≥2). In codon usage frequency,the differences between CHI gene and Saccharomyces,E.coli genomes were more than Arabidopsis genome.CHI was non-transmembrane and hydrophilic protein with no signal peptide,which located mostly in cytoplasm(45.0%)and microbody(42.5%)by the result of subcellular level prediction and does not be-long to the secretory protein.CHI protein had no glycosylation sites and fourteen phosphorylation sites,including a PKC kinase located in 20th amino acid.Additionally,it had one conservative domain named chalcone.The seconda-ry structure of CHI protein contained 39% α-helices,20% extended strand,13% β-turn and 27% random coil. Tertiary structure presented an inversion bouquet by beta sandwich folding.In this study,we found one conservative domain responsible for catalytic activity of isomerase and an specific protein kinases PKC site,which will provide advantageous basic data for further studying CHI gene function.Moreover,the eukaryotic Saccharomyces expression systems may be more suitable for the expression of CHI gene.%为了丰富芍药 CHI 基因研究的基础数据,首先利用 RACE 技术对芍药 CHI 基因的 CDS 区进行克隆,并通过EMBOSS 软件分析序列的密码子偏好性,其次利用生物信息学软件和在线数据库对芍药 CHI 进行蛋白结构与功能预测。结

  16. Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias

    Directory of Open Access Journals (Sweden)

    Dusan Kunec

    2016-01-01

    Full Text Available Codon pair bias is a remarkably stable characteristic of a species. Although functionally uncharacterized, robust virus attenuation was achieved by recoding of viral proteins using underrepresented codon pairs. Because viruses replicate exclusively inside living cells, we posited that their codon pair preferences reflect those of their host(s. Analysis of many human viruses showed, however, that the encoding of viruses is influenced only marginally by host codon pair preferences. Furthermore, examination of codon pair preferences of vertebrate, insect, and arthropod-borne viruses revealed that the latter do not utilize codon pairs overrepresented in arthropods more frequently than other viruses. We found, however, that codon pair bias is a direct consequence of dinucleotide bias. We conclude that codon pair bias does not play a major role in the encoding of viral proteins and that virus attenuation by codon pair deoptimization has the same molecular underpinnings as attenuation based on an increase in CpG/TpA dinucleotides.

  17. Codon optimality is a major determinant of mRNA stability.

    Science.gov (United States)

    Presnyak, Vladimir; Alhusaini, Najwa; Chen, Ying-Hsin; Martin, Sophie; Morris, Nathan; Kline, Nicholas; Olson, Sara; Weinberg, David; Baker, Kristian E; Graveley, Brenton R; Coller, Jeff

    2015-03-12

    mRNA degradation represents a critical regulated step in gene expression. Although the major pathways in turnover have been identified, accounting for disparate half-lives has been elusive. We show that codon optimality is one feature that contributes greatly to mRNA stability. Genome-wide RNA decay analysis revealed that stable mRNAs are enriched in codons designated optimal, whereas unstable mRNAs contain predominately non-optimal codons. Substitution of optimal codons with synonymous, non-optimal codons results in dramatic mRNA destabilization, whereas the converse substitution significantly increases stability. Further, we demonstrate that codon optimality impacts ribosome translocation, connecting the processes of translation elongation and decay through codon optimality. Finally, we show that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function. This work demonstrates that codon optimization exists as a mechanism to finely tune levels of mRNAs and, ultimately, proteins.

  18. Analysis on Beijing’s Policy of Restricting Motor Vehicle Usage

    Institute of Scientific and Technical Information of China (English)

    LIU Jian; ZUO Xiaoxuan

    2012-01-01

    Along with the increase of car ownership,the problem of traffic congestion has appeared more and more serious since the 1990s in Beijing.In order to deal with the problem of traffic congestion,the policy of restricting motor vehicle usage,as a measure of transportation demand management by decreasing the total number of on-road motor vehicles,was firstly implemented in 2006 in trial,which continued from 2008 during the period of Olympic Games up to day.Starting with an analysis on policy motivation,this paper describes the practices of restricting motor vehicle usage in Beijing since 2006,analyzes the effects on the performance of the city’s transportation,and concludes after a comparative analysis that,in spite of the positive effects on relieving the traffic congestion,the policy of restricting motor vehicle usage could only constitute a temporary measure of traffic demand management,rather than a fundamental one,because the comprehensive effects would decrease along with the continuous growth of motor vehicle possession.

  19. The exploration & forensic analysis of computer usage data in the elderly.

    Science.gov (United States)

    Hatt, William J; Vanbaak, Edward A; Jimison, Holly B; Hagler, Stuart; Hayes, Tamara L; Pavel, Misha; Kaye, Jeffery

    2009-01-01

    Unobtrusive in-home computer monitoring could one day be used to deliver cost-effective diagnostic information about the cognitive abilities of the elderly. This could allow for early detection of cognitive impairment and would additionally be coupled with the cost advantages that are associated with a semi-automated system. Before using the computer usage data to draw conclusions about the participants, we first needed to investigate the nature of the data that was collected. This paper represents a forensics style analysis of the computer usage data that is being collected as part of a larger study of cognitive decline, and focuses on the isolation and removal of non user-generated activities that were recorded by our computer monitoring software (CMS).

  20. Analysis of blocking rate and bandwidth usage of mobile IPTV services in wireless cellular networks.

    Science.gov (United States)

    Li, Mingfu

    2014-01-01

    Mobile IPTV services over wireless cellular networks become more and more popular, owing to the significant growth in access bandwidth of wireless cellular networks such as 3G/4G and WiMAX. However, the spectrum resources of wireless cellular networks is rare. How to enhance the spectral efficiency of mobile networks becomes an important issue. Unicast, broadcast, and multicast are the most important transport schemes for offering mobile IPTV services over wireless cellular networks. Therefore, bandwidth usages and blocking rates of unicast, broadcast, and multicast IPTV services were analyzed and compared in this paper. Simulations were also conducted to validate the analytical results. Numerical results demonstrate that the presented analysis is correct, and multicast scheme achieves the best bandwidth usage and blocking rate performance, relative to the other two schemes.

  1. Analysis of Codon Bias of MC1R Gene in Pig (Sus scrofa)%猪黑皮质素受体1基因密码子偏好分析

    Institute of Scientific and Technical Information of China (English)

    肖红卫; 刘西梅; 郑新民; 华文君; 李莉; 张立苹; 毕延震; 华再东

    2013-01-01

    遗传密码子是生命信息的基本遗传单位,每种氨基酸对应1~6个同义密码子。特定物种在长期进化中形成了适应自身基因环境的密码子使用偏好。运用CHIPS、CUPS和CodonW程序分析猪黑皮质素受体1基因密码子偏好,并与牛、羊、小鼠、人等多种动物的黑皮质素受体1基因密码子偏好进行比较,以期为转基因动物育种提供依据。结果表明,猪偏好使用以C、G结尾的密码子(96.88%),且在整个编码区序列中G+C含量(67.81%)大于A+T(32.19%),该基因在猪体内表达水平很高(CAI=0.849),并且发现,猪的密码子偏好性与牛、犬等动物类似,明显不同于鲀、雀、獾、大猩猩等动物。要实现目的基因在猪MC1R基因中进行定点整合并成功表达和尽可能地提高其表达量,需对目的基因的部分密码子进行改造。%Genetic codon is the basic hereditary unit of life information , and each amino acid is corresponding to 1~6 synony-mous codons.Specific organisms formed codon bias in long -term evolution to adapt their genetic environment .In this paper, the codon bias of MC1R gene in the pig was analyzed by Codon W , CHIPS and CUSP programs , and it was compared with that in vari-ous animals, such as cattle, sheep, mice, human etc., so as to provide a basis for transgenic animals breeding .The results showed that the pig preferred to use the codons ending with C and G (96.88%), the content of G+C (67.81%) was higher than that of A+T (32.19%) in the whole coding sequence , and MC1R gene in the pig had very high expression level (CAI=0.849).It was also found that the codon usage bias of the pig was similar to that of cattle , dog and so on , while it was obviously different from that of Takifugu rubripes, Taeniopygia guttata, Sarcophilus harrisii, Gorilla gorilla etc..In order to realize the site-specific integration of target gene into pig MC1R gene as well as its

  2. New insights into the interplay between codon bias determinants in plants.

    Science.gov (United States)

    Camiolo, S; Melito, S; Porceddu, A

    2015-12-01

    Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  3. Genomic composition factors affect codon usage in porcine genome

    African Journals Online (AJOL)

    j.khobondo

    2015-01-28

    Jan 28, 2015 ... evolutionary biology, providing insight to the actions of ... of studying the degeneracy of genetic code, which ... and evolution, and adaptation to micro environment. The ..... molecular functions are controlled by several factors.

  4. Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes

    Science.gov (United States)

    McManus, Donald Peter; Blair, David

    2004-01-01

    Sequences of the complete protein-coding portions of the mitochondrial (mt) genome were analysed for 6 species of cestodes (including hydatid tapeworms and the pork tapeworm) and 5 species of trematodes (blood flukes and liver- and lung-flukes). A near-complete sequence was also available for an additional trematode (the blood flukeSchistosoma malayensis). All of these parasites belong to a large flatworm taxon named the Neodermata. Considerable variation was found in the base composition of the protein-coding genes among these neodermatans. This variation was reflected in statistically-significant differences in numbers of each inferred amino acid between many pairs of species. Both convergence and divergence in nucleotide, and hence amino acid, composition was noted among groups within the Neodermata. Considerable variation in skew (unequal representation of complementary bases on the same strand) was found among the species studied. A pattern is thus emerging of diversity in the mt genome in neodermatans that may cast light on evolution of mt genomes generally. PMID:15591833

  5. Genomic composition factors affect codon usage in porcine genome

    DEFF Research Database (Denmark)

    Khobondo, J O; Okeno, Tobias O; Kahi, A K

    2015-01-01

    is feebly related to nucleotide composition (GC%, GC3, CDS length). This study can be explored for designing degenerate primers, necessitate selecting appropriate hosts expression systems to manipulate the expression of target genes in vivo or in vitro and improve the accuracy of gene prediction from...

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

    Directory of Open Access Journals (Sweden)

    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.

  7. Analysis of synonymous codon usage in Shigella flexneri 2a strain 301 and other Shigella and Escherichia coli strains

    National Research Council Canada - National Science Library

    Luo, Xue Lian; Xu, Jian Guo; Ye, Chang Yun

    2011-01-01

    ... pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure...

  8. Analysis of first-year college chemistry students' knowledge about and usage of text

    Science.gov (United States)

    Pentecost, Thomas Crawford

    This study analyzed the usage of textbooks by 58 students in a first-year college chemistry course, the students' approaches to studying, and their knowledge about science reading. Student success in the course was measured by the final exam score. To analyze students' textbook usage the Science Reading Strategy Survey (SRSS) was developed. The SRSS allowed students' usage of the textbook to be categorized into one of three groups: methodical/linear use, efficient use, and making connections/deep use. Seventy-one percent of chemistry students were categorized as using the textbook in a deep/making connections manner, while 15% reported text usage that was categorized as efficient and 11% reported a methodical/linear approach to text use. The students' approaches to studying were determined by using the Study Process Questionnaire (SPQ). The internal structure of the SPQ was confirmed by factor analysis. Forty-three percent of students adopted an achieving approach and 41% approached their studies with a surface approach. Only 7.1% of students had a deep approach to learning. The disconnect between approach (SPQ) and reading strategies (SRSS) could be due to the students finding their general chemistry textbook a valuable resource for getting through a difficult subject they are not strongly motivated to learn. Student's knowledge about reading science text was measured by the Index of Science Reading Awareness (ISRA). This was the first time this instrument had been used with college students. The ISRA was analyzed and the instrument was used to measure students' knowledge about science reading strategies and their general knowledge about science reading and text. The majority, 62%, of first-year chemistry students possess comprehensive knowledge about science reading strategies and science text. The remainder of students had surface knowledge and no students in this study were found to have an incomplete knowledge. There was no correlation between the student

  9. Usage Automata

    Science.gov (United States)

    Bartoletti, Massimo

    Usage automata are an extension of finite stata automata, with some additional features (e.g. parameters and guards) that improve their expressivity. Usage automata are expressive enough to model security requirements of real-world applications; at the same time, they are simple enough to be statically amenable, e.g. they can be model-checked against abstractions of program usages. We study here some foundational aspects of usage automata. In particular, we discuss about their expressive power, and about their effective use in run-time mechanisms for enforcing usage policies.

  10. Organizational culture, creative behavior, and information and communication technology (ICT) usage: a facet analysis.

    Science.gov (United States)

    Carmeli, Abraham; Sternberg, Akiva; Elizur, D

    2008-04-01

    Despite the prominence of organizational culture (OC), this concept is controversial and its structure has yet to be systematically analyzed. This study develops a three-pronged formal definitional framework on the basis of facet theory (FT) and explores behavior modality, referent, and object. This facet analysis (FA) of OC accounts successfully for variation in both creative behavior at work and the usage of information and communication technologies (ICTs). An analysis of data collected from 230 employees in the financial industry indicates that a radex structure was obtained for work and ICT. The behavior modality facet ordered the space from center to periphery, and referents facet relates to the direction angles away from the origin.

  11. Analysis of the Optimum Usage of Slag for the Compressive Strength of Concrete.

    Science.gov (United States)

    Lee, Han-Seung; Wang, Xiao-Yong; Zhang, Li-Na; Koh, Kyung-Taek

    2015-03-18

    Ground granulated blast furnace slag is widely used as a mineral admixture to replace partial Portland cement in the concrete industry. As the amount of slag increases, the late-age compressive strength of concrete mixtures increases. However, after an optimum point, any further increase in slag does not improve the late-age compressive strength. This optimum replacement ratio of slag is a crucial factor for its efficient use in the concrete industry. This paper proposes a numerical procedure to analyze the optimum usage of slag for the compressive strength of concrete. This numerical procedure starts with a blended hydration model that simulates cement hydration, slag reaction, and interactions between cement hydration and slag reaction. The amount of calcium silicate hydrate (CSH) is calculated considering the contributions from cement hydration and slag reaction. Then, by using the CSH contents, the compressive strength of the slag-blended concrete is evaluated. Finally, based on the parameter analysis of the compressive strength development of concrete with different slag inclusions, the optimum usage of slag in concrete mixtures is determined to be approximately 40% of the total binder content. The proposed model is verified through experimental results of the compressive strength of slag-blended concrete with different water-to-binder ratios and different slag inclusions.

  12. Determinants of open educational resources usage. Temporal and spatial analysis of an example open educational re - source portal usage

    Directory of Open Access Journals (Sweden)

    Bogdan Galwas

    2012-12-01

    Full Text Available The article analyzes the behavior of users of open educational resources. These behaviors are different from those that have been tested and reported in the literature for computer-aided learning systems. This difference is due to the fact that users of open information resources are not subject to any system of obligation. Their participation in the learning system is entirely voluntary, and that their knowledge at the end of education is not controlled. The only motivation for the study and is interest in the shared knowledge as such. The observation of customer behavior such spontaneous open educational offer is much more difficult than the analysis of the behavior of students using e-learning in typical blended learning models, when the pupil or student is assessed by the teacher supervising the learning process. Therefore, as described in the work lasted four years observing the behavior of Internet users use created by the author of educational resource development is different from those with which we have most to do scientific research in e-learning. This observation, in spite of its separate character, may be the first step to create a model of how to use open knowledge.

  13. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families.

    Science.gov (United States)

    De La Torre, Amanda R; Lin, Yao-Cheng; Van de Peer, Yves; Ingvarsson, Pär K

    2015-03-05

    The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.

  14. DNA sequence analysis proves Hb M-Milwaukee-2 is due to beta-globin gene codon 92 (CAC-->TAC), the presumed mutation of Hb M-Hyde Park and Hb M-Akita.

    Science.gov (United States)

    Hutt, P J; Pisciotta, A V; Fairbanks, V F; Thibodeau, S N; Green, M M

    1998-01-01

    Among the causes of congenital methemoglobinemia, Hb M-Milwaukee-2 was one of the earliest described, in a patient who also had Hb E trait. The structure of Hb M-Milwaukee-2 has been elusive. DNA sequence analysis, as here reported, proves that this hemoglobin variant is due to the mutation CAC-->TAC at codon 92 of the beta-globin gene, corresponding to the substitution of tyrosine for histidine. This mutation is identical with that presumed to be the cause of Hb M-Hyde Park and Hb M-Akita. In addition, the DNA mutation of Hb E, GAG-->AAG at codon 26, was confirmed in this case.

  15. RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq.

    Directory of Open Access Journals (Sweden)

    Yafang Li

    Full Text Available Alternative splicing is an important biological process in the generation of multiple functional transcripts from the same genomic sequences. Differential analysis of splice junctions (SJs and intron retentions (IRs is helpful in the detection of alternative splicing events. In this study, we conducted differential analysis of SJs and IRs by use of DEXSeq, a Bioconductor package originally designed for differential exon usage analysis in RNA-seq data analysis. We set up an analysis pipeline including mapping of RNA-seq reads, the preparation of count tables of SJs and IRs as the input files, and the differential analysis in DEXSeq. We analyzed the public RNA-seq datasets generated from RNAi experiments on Drosophila melanogaster S2-DRSC cells to deplete RNA-binding proteins (GSE18508. The analysis confirmed previous findings on the alternative splicing of the trol and Ant2 (sesB genes in the CG8144 (ps-depletion experiment and identified some new alternative splicing events in other RNAi experiments. We also identified IRs that were confirmed in our SJ analysis. The proposed method used in our study can output the genomic coordinates of differentially used SJs and thus enable sequence motif search. Sequence motif search and gene function annotation analysis helped us infer the underlying mechanism in alternative splicing events. To further evaluate this method, we also applied the method to public RNA-seq data from human breast cancer (GSE45419 and the plant Arabidopsis (SRP008262. In conclusion, our study showed that DEXSeq can be adapted to differential analysis of SJs and IRs, which will facilitate the identification of alternative splicing events and provide insights into the molecular mechanisms of transcription processes and disease development.

  16. RNA-Seq Analysis of Differential Splice Junction Usage and Intron Retentions by DEXSeq

    Science.gov (United States)

    Li, Yafang; Rao, Xiayu; Mattox, William W.; Amos, Christopher I.; Liu, Bin

    2015-01-01

    Alternative splicing is an important biological process in the generation of multiple functional transcripts from the same genomic sequences. Differential analysis of splice junctions (SJs) and intron retentions (IRs) is helpful in the detection of alternative splicing events. In this study, we conducted differential analysis of SJs and IRs by use of DEXSeq, a Bioconductor package originally designed for differential exon usage analysis in RNA-seq data analysis. We set up an analysis pipeline including mapping of RNA-seq reads, the preparation of count tables of SJs and IRs as the input files, and the differential analysis in DEXSeq. We analyzed the public RNA-seq datasets generated from RNAi experiments on Drosophila melanogaster S2-DRSC cells to deplete RNA-binding proteins (GSE18508). The analysis confirmed previous findings on the alternative splicing of the trol and Ant2 (sesB) genes in the CG8144 (ps)-depletion experiment and identified some new alternative splicing events in other RNAi experiments. We also identified IRs that were confirmed in our SJ analysis. The proposed method used in our study can output the genomic coordinates of differentially used SJs and thus enable sequence motif search. Sequence motif search and gene function annotation analysis helped us infer the underlying mechanism in alternative splicing events. To further evaluate this method, we also applied the method to public RNA-seq data from human breast cancer (GSE45419) and the plant Arabidopsis (SRP008262). In conclusion, our study showed that DEXSeq can be adapted to differential analysis of SJs and IRs, which will facilitate the identification of alternative splicing events and provide insights into the molecular mechanisms of transcription processes and disease development. PMID:26327458

  17. Vertebrate codon bias indicates a highly GC-rich ancestral genome.

    Science.gov (United States)

    Nabiyouni, Maryam; Prakash, Ashwin; Fedorov, Alexei

    2013-04-25

    Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences.

  18. Analysis of physicochemical and structural properties determining HIV-1 coreceptor usage.

    Directory of Open Access Journals (Sweden)

    Katarzyna Bozek

    Full Text Available The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage. As an alternative to costly phenotypic assays, computational methods aim at predicting virus tropism based on the sequence and structure of the V3 loop of the virus gp120 protein. Here we present a numerical descriptor of the V3 loop encoding its physicochemical and structural properties. The descriptor allows for structure-based prediction of HIV tropism and identification of properties of the V3 loop that are crucial for coreceptor usage. Use of the proposed descriptor for prediction results in a statistically significant improvement over the prediction based solely on V3 sequence with 3 percentage points improvement in AUC and 7 percentage points in sensitivity at the specificity of the 11/25 rule (95%. We additionally assessed the predictive power of the new method on clinically derived 'bulk' sequence data and obtained a statistically significant improvement in AUC of 3 percentage points over sequence-based prediction. Furthermore, we demonstrated the capacity of our method to predict therapy outcome by applying it to 53 samples from patients undergoing Maraviroc therapy. The analysis of structural features of the loop informative of tropism indicates the importance of two loop regions and their physicochemical properties. The regions are located on opposite strands of the loop stem and the respective features are predominantly charge-, hydrophobicity- and structure-related. These regions are in close proximity in the bound conformation of the loop potentially forming a site determinant for the coreceptor binding. The method is available via server under http://structure.bioinf.mpi-inf.mpg.de/.

  19. In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein.

    Science.gov (United States)

    Carlini, David B; Stephan, Wolfgang

    2003-01-01

    The evolution of codon bias, the unequal usage of synonymous codons, is thought to be due to natural selection for the use of preferred codons that match the most abundant species of isoaccepting tRNA, resulting in increased translational efficiency and accuracy. We examined this hypothesis by introducing 1, 6, and 10 unpreferred codons into the Drosophila alcohol dehydrogenase gene (Adh). We observed a significant decrease in ADH protein production with number of unpreferred codons, confirming the importance of natural selection as a mechanism leading to codon bias. We then used this empirical relationship to estimate the selection coefficient (s) against unpreferred synonymous mutations and found the value (s >or= 10(-5)) to be approximately one order of magnitude greater than previous estimates from population genetics theory. The observed differences in protein production appear to be too large to be consistent with current estimates of the strength of selection on synonymous sites in D. melanogaster. PMID:12586711

  20. What Influences Geography Teachers' Usage of Geographic Information Systems? A Structural Equation Analysis

    Science.gov (United States)

    Lay, Jinn-Guey; Chi, Yu-Lin; Hsieh, Yeu-Sheng; Chen, Yu-Wen

    2013-01-01

    Understanding the usage of the geographic information system (GIS) among geography teachers is a crucial step in evaluating the current dissemination of GIS knowledge and skills in Taiwan's educational system. The primary contribution of this research is to further our understanding of the factors that affect teachers' GIS usage. The structural…

  1. The Family of Object-Related Depictives in English and Spanish: Towards a Usage-Based Constructionist Analysis

    Science.gov (United States)

    Gonzalvez-Garcia, Francisco

    2009-01-01

    Drawing on naturally-occurring data extracted from the British National Corpus (BNC) and the Corpus de Referencia del Espanol Actual (CREA) in conjunction with data elicited from native speakers by means of questionnaires, this paper provides a bottom-up, usage-based analysis of instances of depictive secondary predicates involving mainly verba…

  2. Clustering Educational Digital Library Usage Data: A Comparison of Latent Class Analysis and K-Means Algorithms

    Science.gov (United States)

    Xu, Beijie; Recker, Mimi; Qi, Xiaojun; Flann, Nicholas; Ye, Lei

    2013-01-01

    This article examines clustering as an educational data mining method. In particular, two clustering algorithms, the widely used K-means and the model-based Latent Class Analysis, are compared, using usage data from an educational digital library service, the Instructional Architect (IA.usu.edu). Using a multi-faceted approach and multiple data…

  3. Clustering Educational Digital Library Usage Data: A Comparison of Latent Class Analysis and K-Means Algorithms

    Science.gov (United States)

    Xu, Beijie; Recker, Mimi; Qi, Xiaojun; Flann, Nicholas; Ye, Lei

    2013-01-01

    This article examines clustering as an educational data mining method. In particular, two clustering algorithms, the widely used K-means and the model-based Latent Class Analysis, are compared, using usage data from an educational digital library service, the Instructional Architect (IA.usu.edu). Using a multi-faceted approach and multiple data…

  4. The Analysis of the Usage And Perspectives of Renewable Energy Sources in Lithuania

    Directory of Open Access Journals (Sweden)

    Dominykas Vasarevičius

    2011-08-01

    Full Text Available The paper presents the current situation with the renewable energy sources in Lithuania. An overview of legislation promoting the production and usage of renewable energy in Lithuania is presented. Renewable energy production methods suitable for Lithuanian conditions, their advantages and disadvantages are discussed. It is shown that there is no any promotion from the state for usage of solar energy in private households. The potential of solar energy usage is determined. In order to show the effectiveness of solar thermal energy utilization under similar climatic conditions presented the example of promotion policy model and its results in Poland.Article in Lithuanian

  5. An initial log analysis of usage patterns on a research networking system.

    Science.gov (United States)

    Boland, Mary Regina; Trembowelski, Sylvia; Bakken, Suzanne; Weng, Chunhua

    2012-08-01

    Usage data for research networking systems (RNSs) are valuable but generally unavailable for understanding scientific professionals' information needs and online collaborator seeking behaviors. This study contributes a method for evaluating RNSs and initial usage knowledge of one RNS obtained from using this method. We designed a log for an institutional RNS, defined categories of users and tasks, and analyzed correlations between usage patterns and user and query types. Our results show that scientific professionals spend more time performing deep Web searching on RNSs than generic Google users and we also show that retrieving scientist profiles is faster on an RNS than on Google (3.5 seconds vs. 34.2 seconds) whereas organization-specific browsing on a RNS takes longer than on Google (117.0 seconds vs. 34.2 seconds). Usage patterns vary by user role, e.g., faculty performed more informational queries than administrators, which implies role-specific user support is needed for RNSs.

  6. Analysis of Log File Data to Understand Mobile Service Context and Usage Patterns

    Directory of Open Access Journals (Sweden)

    Bernhard Klein

    2013-09-01

    Full Text Available Several mobile acceptance models exist today that focus on user interface handling and usage frequency evaluation. Since mobile applications reach much deeper into everyday life, it is however important to better consider user behaviour for the service evaluation. In this paper we introduce the Behaviour Assessment Model (BAM, which is designed to gaining insights about how well services enable, enhance and replace human activities. More specifically, the basic columns of the evaluation framework concentrate on (1 service actuation in relation to the current user context, (2 the balance between service usage effort and benefit, and (3 the degree to which community knowledge can be exploited. The evaluation is guided by a process model that specifies individual steps of data capturing, aggregation, and final assessment. The BAM helps to gain stronger insights regarding characteristic usage hotspots, frequent usage patterns, and leveraging of networking effects showing more realistically the strengths and weaknesses of mobile services

  7. Codon-optimized antibiotic resistance gene improves efficiency of transient transformation in Frankia

    Indian Academy of Sciences (India)

    Ken-ichi Kucho; Kentaro Kakoi; Masatoshi Yamaura; Mari Iwashita; Mikiko Abe; Toshiki Uchiumi

    2013-11-01

    Frankia is a unique actinobacterium having abilities to fix atmospheric dinitrogen and to establish endosymbiosis with trees, but molecular bases underlying these interesting characteristics are poorly understood because of a lack of stable transformation system. Extremely high GC content of Frankia genome (> 70%) can be a hindrance to successful transformation. We generated a synthetic gentamicin resistance gene whose codon usage is optimized to Frankia (fgmR) and evaluated its usefulness as a selection marker using a transient transformation system. Success rate of transient transformation and cell growth in selective culture were significantly increased by use of fgmR instead of a native gentamicin resistance gene, suggesting that codon optimization improved translation efficiency of the marker gene and increased antibiotic resistance. Our result shows that similarity in codon usage pattern is an important factor to be taken into account when exogenous transgenes are expressed in Frankia cells.

  8. Transcription attenuation in Salmonella typhimurium: the significance of rare leucine codons in the leu leader.

    Science.gov (United States)

    Carter, P W; Bartkus, J M; Calvo, J M

    1986-11-01

    The leucine operon of Salmonella typhimurium is controlled by a transcription attenuation mechanism. Four adjacent leucine codons within a 160-nucleotide leu leader RNA are thought to play a central role in this mechanism. Three of the four codons are CUA, a rarely used leucine codon within enteric bacteria. To determine whether the nature of the leucine codon affects the regulation of the leucine operon, we used oligonucleotide-directed mutagenesis to first convert one CUA of the leader to CUG and then convert all three CUA codons to CUG. CUG is the most frequently used leucine codon in enteric bacteria. A mutant having (CUA)2CUGCUC in place of (CUA)3CUC has an altered response to leucine limitation, requiring a slightly higher degree of limitation to effect derepression. Changing (CUA)3CUC to (CUG)3CUC has more dramatic effects upon operon expression. First, the basal level of expression is lowered to the point that the mutant grows more slowly than the parent in a minimal medium lacking leucine. Second, the response of the mutant to a leucine limitation is dramatically altered such that even a strong limitation elicits only a modest degree of derepression. If the mutant is grown under conditions of leucyl-tRNA limitation rather than leucine limitation, complete derepression can be achieved, but only at a much higher degree of limitation than for the wild-type operon. These results provide a clear-cut example of codon usage having a dramatic effect upon gene expression.

  9. Expanding Bicycle-Sharing Systems: Lessons Learnt from an Analysis of Usage.

    Science.gov (United States)

    Zhang, Ying; Thomas, Tom; Brussel, M J G; van Maarseveen, M F A M

    2016-01-01

    Bike-sharing programs, with initiatives to increase bike use and improve accessibility of urban transit, have received increasing attention in growing number of cities across the world. The latest generation of bike-sharing systems has employed smart card technology that produces station-based data or trip-level data. This facilitates the studies of the practical use of these systems. However, few studies have paid attention to the changes in users and system usage over the years, as well as the impact of system expansion on its usage. Monitoring the changes of system usage over years enables the identification of system performance and can serve as an input for improving the location-allocation of stations. The objective of this study is to explore the impact of the expansion of a bicycle-sharing system on the usage of the system. This was conducted for a bicycle-sharing system in Zhongshan (China), using operational usage data of different years following system expansion. To this end, we performed statistical and spatial analyses to examine the changes in both users and system usage between before and after the system expansion. The findings show that there is a big variation in users and aggregate usage following the system expansion. However, the trend in spatial distribution of demand shows no substantial difference over the years, i.e. the same high-demand and low-demand areas appear. There are decreases in demand for some old stations over the years, which can be attributed to either the negative performance of the system or the competition of nearby new stations. Expanding the system not only extends the original users' ability to reach new areas but also attracts new users to use bike-sharing systems. In the conclusions, we present and discuss the findings, and offer recommendations for the further expansion of system.

  10. The Evaluation of p53 Polymorphism at Codon 72 and Association With Breast Cancer in Iran: A Systematic Review and Meta-analysis

    Science.gov (United States)

    Soleimani, Abozar; Rahmani, Yousef; Farshchian, Negin; Delpisheh, Ali; Khassi, Kivan; Shahmohammadi, Afshar; Amirifard, Nasrin

    2016-01-01

    Background Breast cancer is the most common cancer among women in Iran and the world. Multiple environmental factors and genetic variations such as genetic polymorphisms are of its main causes. p53 gene plays an important role in conserving and sustaining the genome as a tumor suppressing gene. Change and polymorphism at codon 72 of p53 gene are correlated with increased risk of lung, mouth, endometrial, prostate, and colorectal cancers, and could be considered an indicator of susceptibility to breast cancer. Methods Twelve studies (1,190 cases and 1,145 control studies with evaluation of three types of Arg/Arg, Arg/Pro, and Pro/Pro genotypes) have been conducted using keywords, such as polymorphism at codon 72, gene p53 polymorphisms, and the relation between polymorphisms and breast cancer, from databases in Iran, including Magiran, Medlibe, Sid, and Iranmedex, as well as Latin databases such as PubMed, Google Scholar, Science Direct, and Scopus. Results The OR for Arg/Arg is 1.58 (95% CI: 2.45 to 1.01), the OR for Arg/Pro is 0.75 (95% CI: 1.10 to 0.51), and the OR for Pro/Pro is 0.62 (95% CI: 0.93 to 0.42). p53 gene polymorphism at codon 72 is statistically significant in Arg/Arg and Pro/Pro genotypes. Conclusions Arg/Arg genotype can be considered as a risk factor for breast cancer, and Pro/Pro genotype can be accounted for as a protective factor against breast cancer. PMID:28053964

  11. Advanced mathematical on-line analysis in nuclear experiments. Usage of parallel computing CUDA routines in standard root analysis

    Directory of Open Access Journals (Sweden)

    Grzeszczuk A.

    2015-01-01

    Full Text Available Compute Unified Device Architecture (CUDA is a parallel computing platform developed by Nvidia for increase speed of graphics by usage of parallel mode for processes calculation. The success of this solution has opened technology General-Purpose Graphic Processor Units (GPGPUs for applications not coupled with graphics. The GPGPUs system can be applying as effective tool for reducing huge number of data for pulse shape analysis measures, by on-line recalculation or by very quick system of compression. The simplified structure of CUDA system and model of programming based on example Nvidia GForce GTX580 card are presented by our poster contribution in stand-alone version and as ROOT application.

  12. Computational complexity and memory usage for multi-frontal direct solvers used in p finite element analysis

    KAUST Repository

    Calo, Victor M.

    2011-05-14

    The multi-frontal direct solver is the state of the art for the direct solution of linear systems. This paper provides computational complexity and memory usage estimates for the application of the multi-frontal direct solver algorithm on linear systems resulting from p finite elements. Specifically we provide the estimates for systems resulting from C0 polynomial spaces spanned by B-splines. The structured grid and uniform polynomial order used in isogeometric meshes simplifies the analysis.

  13. A new measure to study phylogenetic relations in the brown algal order Ectocarpales: The ``codon impact parameter"

    Indian Academy of Sciences (India)

    Smarajit Das; Jayprokas Chakrabarti; Zhumur Ghosh; Satyabrata Sahoo; Bibekanand Mallick

    2005-12-01

    We analyse forty-seven chloroplast genes of the large subunit of RuBisCO, from the algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base-bias defines our score called the codon-impact-parameter. This score is used to obtain phylogenetic relations amongst the 47 Ectocarpales. We compare our classification with the ones done earlier.

  14. Engineers and the Web: an analysis of real life gaps in information usage

    NARCIS (Netherlands)

    Kraaijenbrink, Jeroen

    2007-01-01

    Engineers face a wide range of gaps when trying to identify, acquire, and utilize information from the Web. To be able to avoid creating such gaps, it is essential to understand them in detail. This paper reports the results of a study of the real life gaps in information usage processes of 17 engin

  15. An Analysis: The Usage of Metadiscourse in Argumentative Writing by Malaysian Tertiary Level of Students

    Science.gov (United States)

    Anwardeen, Nor Hafizah; Luyee, Eunice Ong; Gabriel, Joanna Indra; Kalajahi, Seyed Ali Rezvani

    2013-01-01

    This paper analyzes the results of a corpus-based study on the usage of metadiscourse in argumentative writing by Malaysian college students. The aims of the study is to examine the frequency and distribution of metadiscourse used by the particular students in argumentative writing as well as to analyze the errors that made by the particular…

  16. An Analysis of Research Trends in Articles on Video Usage in Medical Education

    Science.gov (United States)

    Taslibeyaz, Elif; Aydemir, Melike; Karaman, Selcuk

    2017-01-01

    Using technology in medical education has drawn the attention of researchers in the last several years. Especially, videos have been found to promote effective learning in medical education. This study aims to examine general trends and results of articles investigating video usage in medical education and published in SSCI and ERIC journals from…

  17. Quantitative Analysis of the Usage of the COSMOS Science Education Portal

    Science.gov (United States)

    Sotiriou, Sofoklis; Bogner, Franz X.; Neofotistos, George

    2011-01-01

    A quantitative method of mapping the web usage of an innovative educational portal is applied to analyze the behaviour of users of the COSMOS Science Education Portal. The COSMOS Portal contains user-generated resources (that are uploaded by its users). It has been designed to support a science teacher's search, retrieval and access to both,…

  18. Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models.

    Directory of Open Access Journals (Sweden)

    Andreas Zwick

    Full Text Available BACKGROUND: In a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy. METHODOLOGY/PRINCIPAL FINDINGS: The hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2 are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neither compositional heterogeneity at the level of nucleotides nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately coded amino acids is a major source of non-phylogenetic signal. CONCLUSIONS: The incongruity in support between amino-acid and nucleotide analyses of the forementioned arthropod data set is resolved by showing that "standard" 20-amino-acid analyses yield lower node support specifically when serine provides crucial signal. Separate coding of Ser1 and Ser2 residues yields support commensurate with that found by degenerated nucleotides, without introducing phylogenetic artifacts. While exclusion of all serine data leads to reduced support for serine-sensitive nodes, these nodes are still recovered in the ML topology

  19. Natural selection retains overrepresented out-of-frame stop codons against frameshift peptides in prokaryotes

    Directory of Open Access Journals (Sweden)

    Tse Herman

    2010-09-01

    Full Text Available Abstract Background Out-of-frame stop codons (OSCs occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated with frameshift events can be reduced. Given such a functional significance, we expect statistically overrepresented OSCs in coding sequences as a result of a widespread selection. Accordingly, we examined available prokaryotic genomes to look for evidence of this selection. Results The complete genome sequences of 990 prokaryotes were obtained from NCBI GenBank. We found that low G+C content coding sequences contain significantly more OSCs and G+C content at specific codon positions were the principal determinants of OSC usage bias in the different reading frames. To investigate if there is overrepresentation of OSCs, we modeled the trinucleotide and hexanucleotide biases of the coding sequences using Markov models, and calculated the expected OSC frequencies for each organism using a Monte Carlo approach. More than 93% of 342 phylogenetically representative prokaryotic genomes contain excess OSCs. Interestingly the degree of OSC overrepresentation correlates positively with G+C content, which may represent a compensatory mechanism for the negative correlation of OSC frequency with G+C content. We extended the analysis using additional compositional bias models and showed that lower-order bias like codon usage and dipeptide bias could not explain the OSC overrepresentation. The degree of OSC overrepresentation was found to correlate negatively with the optimal growth temperature of the organism after correcting for the G+C% and AT skew of the coding sequence. Conclusions The present study uses approaches with statistical rigor to show that OSC overrepresentation is a widespread phenomenon among prokaryotes. Our results support the hypothesis that OSCs carry functional significance and have been selected in the course of

  20. Battery Energy Storage System battery durability and reliability under electric utility grid operations: Analysis of 3 years of real usage

    Science.gov (United States)

    Dubarry, Matthieu; Devie, Arnaud; Stein, Karl; Tun, Moe; Matsuura, Marc; Rocheleau, Richard

    2017-01-01

    Battery Energy Storage Systems (BESSs) show promise to help renewable energy sources integration onto the grid. These systems are expected to last for a decade or more, but the actual battery degradation under different real world conditions is still largely unknown. In this paper we analyze 3 years of usage of a lithium titanate BESS installed and in operation on an island power system in Hawai'i. The BESS was found to be operational 90% of the time and stored a cumulative 1.5 GWh of energy, which represents more than 5000 equivalent full cycles on the cells. This paper presents a statistical analysis of the BESS usage, develops a representative duty cycle, and provides an initial estimate of BESS degradation. The battery duty cycle was characterized based on 5 parameters: pulses duration, pulses intensity (current), SOC swing range, SOC event ramp rate, and temperature.

  1. Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity.

    Science.gov (United States)

    Hense, Winfried; Anderson, Nathan; Hutter, Stephan; Stephan, Wolfgang; Parsch, John; Carlini, David B

    2010-02-01

    Although most amino acids can be encoded by more than one codon, the synonymous codons are not used with equal frequency. This phenomenon is known as codon bias and appears to be a universal feature of genomes. The translational selection hypothesis posits that the use of optimal codons, which match the most abundant species of isoaccepting tRNAs, results in increased translational efficiency and accuracy. Previous work demonstrated that the experimental reduction of codon bias in the Drosophila alcohol dehydrogenase (Adh) gene led to a significant decrease in ADH protein expression. In this study we performed the converse experiment: we replaced seven suboptimal leucine codons that occur naturally in the Drosophila melanogaster Adh gene with the optimal codon. We then compared the in vivo ADH activities imparted by the wild-type and mutant alleles. The introduction of optimal leucine codons led to an increase in ADH activity in third-instar larvae. In adult flies, however, the introduction of optimal codons led to a decrease in ADH activity. There is no evidence that other selectively constrained features of the Adh gene, or its rate of transcription, were altered by the synonymous replacements. These results are consistent with translational selection for codon bias being stronger in the larval stage and suggest that there may be a selective conflict over optimal codon usage between different developmental stages.

  2. Does health insurance ensure equitable health outcomes? An analysis of hospital services usage in urban India.

    Science.gov (United States)

    Dutta, Mousumi; Husain, Zakir

    2013-01-01

    In this paper, we examine the relationship between socio-economic status (SES) and the usage of in-patient services, and analyze the impact of introducing health insurance in India - a major developing country with poor health outcomes. In contrast to results of similar works undertaken for developed countries, our results reveal that the positive relation between usage of in-patient services and SES persists even in the presence of health insurance. This implies that health insurance is unable to eliminate the inequities in accessing healthcare services that stem from disparities in SES. In fact, insurance aggravates inequity in the healthcare market. The study is based on unit-level data from the 2005-06 Morbidity and Health Care Survey undertaken by National Sample Survey Organization.

  3. Analysis of Internet Usage Intensity in Iraq: An Ordered Logit Model

    Directory of Open Access Journals (Sweden)

    Almas Heshmati

    2013-06-01

    Full Text Available Intensity of Internet use is significantly influenced by government policies, people’s levels of income, education, employment and general development and economic conditions. Iraq has very low Internet usage levels compared to the region and the world. This study uses an ordered logit model to analyse the intensity of Internet use in Iraq. The results showed that economic reasons (internet cost and income level were key cause for low level usage intensity rates. About 68% of the population revealed that Internet access at homes is costly. Thus, it is no wonder that Internet cafés is the most commonly used mode of Internet use followed by broadband and dial-up connections. Iraq has to develop proper strategies to enhance the rate of Internet use in the country. These strategies need to focus on decreasing internet access prices, increasing awareness about the importance of the technology and internet education in schools and universities.

  4. Preservice Drug Usage Among Naval Recruits: A 5-Year Trend Analysis

    Science.gov (United States)

    1976-09-01

    depressants , and 6 percent used narcotics. Fisher noted wide differences Lmonp the services, with Army and Marine Corps personnel reporting nearly...collections.’ The drop of 4 percentage points reported in the use of peyote, psilocybin , and mescaline between 1971 and 1975 resulted in a significant overall...significant increase in usage of amphetamines and barbiturates, a significant decrease in peyote/ psilocybin /mescaline and opium/codeine[i and no

  5. Discovering and understanding android sensor usage behaviors with data flow analysis

    KAUST Repository

    Liu, Xing

    2017-03-20

    Today’s Android-powered smartphones have various embedded sensors that measure the acceleration, orientation, light and other environmental conditions. Many functions in the third-party applications (apps) need to use these sensors. However, embedded sensors may lead to security issues, as the third-party apps can read data from these sensors without claiming any permissions. It has been proven that embedded sensors can be exploited by well designed malicious apps, resulting in leaking users’ privacy. In this work, we are motivated to provide an overview of sensor usage patterns in current apps by investigating what, why and how embedded sensors are used in the apps collected from both a Chinese app. market called “AppChina” and the official market called “Google Play”. To fulfill this goal, We develop a tool called “SDFDroid” to identify the used sensors’ types and to generate the sensor data propagation graphs in each app. We then cluster the apps to find out their sensor usage patterns based on their sensor data propagation graphs. We apply our method on 22,010 apps collected from AppChina and 7,601 apps from Google Play. Extensive experiments are conducted and the experimental results show that most apps implement their sensor related functions by using the third-party libraries. We further study the sensor usage behaviors in the third-party libraries. Our results show that the accelerometer is the most frequently used sensor. Though many third-party libraries use no more than four types of sensors, there are still some third-party libraries registering all the types of sensors recklessly. These results call for more attentions on better regulating the sensor usage in Android apps.

  6. Annual Energy Usage Reduction and Cost Savings of a School: End-Use Energy Analysis

    Directory of Open Access Journals (Sweden)

    Aiman Roslizar

    2014-01-01

    Full Text Available Buildings are among the largest consumers of energy. Part of the energy is wasted due to the habits of users and equipment conditions. A solution to this problem is efficient energy usage. To this end, an energy audit can be conducted to assess the energy efficiency. This study aims to analyze the energy usage of a primary school and identify the potential energy reductions and cost savings. A preliminary audit was conducted, and several energy conservation measures were proposed. The energy conservation measures, with reference to the MS1525:2007 standard, were modelled to identify the potential energy reduction and cost savings. It was found that the school’s usage of electricity exceeded its need, incurring an excess expenditure of RM 2947.42. From the lighting system alone, it was found that there is a potential energy reduction of 5489.06 kWh, which gives a cost saving of RM 2282.52 via the improvement of lighting system design and its operating hours. Overall, it was found that there is a potential energy reduction and cost saving of 20.7% when the energy conservation measures are earnestly implemented. The previous energy intensity of the school was found to be 50.6 kWh/m2/year, but can theoretically be reduced to 40.19 kWh/mm2/year.

  7. Analysis Clustering of Electricity Usage Profile Using K-Means Algorithm

    Science.gov (United States)

    Amri, Yasirli; Lailatul Fadhilah, Amanda; Fatmawati; Setiani, Novi; Rani, Septia

    2016-01-01

    Electricity is one of the most important needs for human life in many sectors. Demand for electricity will increase in line with population and economic growth. Adjustment of the amount of electricity production in specified time is important because the cost of storing electricity is expensive. For handling this problem, we need knowledge about the electricity usage pattern of clients. This pattern can be obtained by using clustering techniques. In this paper, clustering is used to obtain the similarity of electricity usage patterns in a specified time. We use K-Means algorithm to employ clustering on the dataset of electricity consumption from 370 clients that collected in a year. Result of this study, we obtained an interesting pattern that there is a big group of clients consume the lowest electric load in spring season, but in another group, the lowest electricity consumption occurred in winter season. From this result, electricity provider can make production planning in specified season based on pattern of electricity usage profile.

  8. Screen media usage, sleep time and academic performance in adolescents: clustering a self-organizing maps analysis.

    Science.gov (United States)

    Peiró-Velert, Carmen; Valencia-Peris, Alexandra; González, Luis M; García-Massó, Xavier; Serra-Añó, Pilar; Devís-Devís, José

    2014-01-01

    Screen media usage, sleep time and socio-demographic features are related to adolescents' academic performance, but interrelations are little explored. This paper describes these interrelations and behavioral profiles clustered in low and high academic performance. A nationally representative sample of 3,095 Spanish adolescents, aged 12 to 18, was surveyed on 15 variables linked to the purpose of the study. A Self-Organizing Maps analysis established non-linear interrelationships among these variables and identified behavior patterns in subsequent cluster analyses. Topological interrelationships established from the 15 emerging maps indicated that boys used more passive videogames and computers for playing than girls, who tended to use mobile phones to communicate with others. Adolescents with the highest academic performance were the youngest. They slept more and spent less time using sedentary screen media when compared to those with the lowest performance, and they also showed topological relationships with higher socioeconomic status adolescents. Cluster 1 grouped boys who spent more than 5.5 hours daily using sedentary screen media. Their academic performance was low and they slept an average of 8 hours daily. Cluster 2 gathered girls with an excellent academic performance, who slept nearly 9 hours per day, and devoted less time daily to sedentary screen media. Academic performance was directly related to sleep time and socioeconomic status, but inversely related to overall sedentary screen media usage. Profiles from the two clusters were strongly differentiated by gender, age, sedentary screen media usage, sleep time and academic achievement. Girls with the highest academic results had a medium socioeconomic status in Cluster 2. Findings may contribute to establishing recommendations about the timing and duration of screen media usage in adolescents and appropriate sleep time needed to successfully meet the demands of school academics and to improve

  9. Another(’s perspective on subjectivity in causal connectives: a usage-based analysis of volitional causal relations

    Directory of Open Access Journals (Sweden)

    Ninke Stukker

    2009-06-01

    connectives strongly specialize in one specific causality category, but also that their use is not restricted to the causality categories they are prototypically associated with. If we assume that the meaning of causal connectives can adequately be described with reference to well-defined conceptual categories – how can we explain that variation in the actual usage of connectives occurs? We focus on volitional causal coherence relations, which count as the prototypical usage context of the Dutch causal connective daarom “that’s why”. Volitional causal relations can alternatively be marked with the connective dus “so” which is prototypically used in epistemic causal relations. Our hypothesis is that volitional causal relations marked with daarom vs. dus systematically differ in terms of subjectivity. We discuss a model of analysis that contains multiple operationalizations of subjectivity and distinguishes between different levels of complexity (sub-clause, clause, and discourse. We find that volitional causal relations with dus contain subjective elements more often than volitional causal relations with daarom. We interpret this patterning within a usage-based theoretical framework, and propose to analyze cases of volitional dus as non-prototypical instantiations of dus’s inherent subjective, prototypically epistemic meaning.

  10. Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.

    Science.gov (United States)

    Pechmann, Sebastian; Frydman, Judith

    2013-02-01

    The choice of codons can influence local translation kinetics during protein synthesis. Whether codon preference is linked to cotranslational regulation of polypeptide folding remains unclear. Here, we derive a revised translational efficiency scale that incorporates the competition between tRNA supply and demand. Applying this scale to ten closely related yeast species, we uncover the evolutionary conservation of codon optimality in eukaryotes. This analysis reveals universal patterns of conserved optimal and nonoptimal codons, often in clusters, which associate with the secondary structure of the translated polypeptides independent of the levels of expression. Our analysis suggests an evolved function for codon optimality in regulating the rhythm of elongation to facilitate cotranslational polypeptide folding, beyond its previously proposed role of adapting to the cost of expression. These findings establish how mRNA sequences are generally under selection to optimize the cotranslational folding of corresponding polypeptides.

  11. Usage and Dose Response of a Mobile Acceptance and Commitment Therapy App: Secondary Analysis of the Intervention Arm of a Randomized Controlled Trial

    Science.gov (United States)

    Lappalainen, Raimo; Välkkynen, Pasi; Sairanen, Essi; Lappalainen, Päivi; Karhunen, Leila; Peuhkuri, Katri; Korpela, Riitta; Kolehmainen, Marjukka; Ermes, Miikka

    2016-01-01

    Background Mobile phone apps offer a promising medium to deliver psychological interventions. A mobile app based on Acceptance and Commitment Therapy (ACT) was developed and studied in a randomized controlled trial (RCT). Objective To study usage metrics of a mobile ACT intervention and dose-response relationship between usage and improvement in psychological flexibility. Methods An RCT was conducted to investigate the effectiveness of different lifestyle interventions for overweight people with psychological stress. This paper presents a secondary analysis of the group that received an 8-week mobile ACT intervention. Most of the analyzed 74 participants were female (n=64, 86%). Their median age was 49.6 (interquartile range, IQR 45.4-55.3) years and their mean level of psychological flexibility, measured with the Acceptance and Action Questionnaire II, was 20.4 (95% confidence interval 18.3-22.5). Several usage metrics describing the intensity of use, usage of content, and ways of use were calculated. Linear regression analyses were performed to study the dose-response relationship between usage and the change in psychological flexibility and to identify the usage metrics with strongest association with improvement. Binary logistic regression analyses were further used to assess the role of usage metrics between those who showed improvement in psychological flexibility and those who did not. In addition, associations between usage and baseline participant characteristics were studied. Results The median number of usage sessions was 21 (IQR 11.8-35), the number of usage days was 15 (IQR 9.0-24), and the number of usage weeks was 7.0 (IQR 4.0-8.0). The participants used the mobile app for a median duration of 4.7 (IQR 3.2-7.2) hours and performed a median of 63 (IQR 46-98) exercises. There was a dose-response relationship between usage and the change in psychological flexibility. The strongest associations with psychological flexibility (results adjusted with gender

  12. Investigation and analysis of oncologists' knowledge of morphine usage in cancer pain treatment

    Directory of Open Access Journals (Sweden)

    Liu W

    2014-05-01

    Full Text Available Weiran Liu,1,* Shumin Xie,2,* Lin Yue,3,* Jiahao Liu,2 Stephanie Mu-Lian Woo,4 Weilin Liu,2 Adam R Miller,5 Jing Zhang,6 Lijun Huang,7 Lei Zhang8,*1Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Department of Anesthesia, Tianjin, People's Republic of China; 2The Xiangya Medical School of Central-South University, Changsha, People's Republic of China; 3Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Outpatient Service, Tianjin, People's Republic of China; 4Harvard University, Cambridge, MA, USA; 5Indiana University School of Medicine, Indianapolis, IN, USA; 6Tianjin Medical University, Tianjin, People's Republic of China; 7Hunan Provincial Tumor Hospital, Department of Lymphoma and Hematology, Changsha, People's Republic of China; 8Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Lung Cancer Center, Department of Thoracic Surgery, Tianjin, People's Republic of China *These authors contributed equally to this paperPurpose: To examine oncologists' knowledge of cancer pain and morphine's clinical application in the People's Republic of China. In addition, this study analyzes and discusses the negative factors that currently affect the clinical application of morphine.Patients and methods: A questionnaire survey was given to a random sample of 150 oncologists from Tianjin Medical University Cancer Institute and Hospital. The statistical results were analyzed and processed using SPSS version 21.0 and Matlab version 2012a statistical software. Single-factor analysis of variance, Kruskal–Wallis nonparametric test, and independent samples t-test were adopted to analyze the difference in knowledge scores of morphine usage. The study

  13. Expression and analysis of a split premature termination codon in FGG responsible for congenital afibrinogenemia: escape from RNA surveillance mechanisms in transfected cells.

    Science.gov (United States)

    Neerman-Arbez, Marguerite; Germanos-Haddad, Myrna; Tzanidakis, Konstantinos; Vu, Dung; Deutsch, Samuel; David, Armelle; Morris, Michael A; de Moerloose, Philippe

    2004-12-01

    Congenital afibrinogenemia, the most severe form of fibrinogen deficiency, is characterized by the complete absence of fibrinogen. The disease is caused by mutations in 1 of the 3 fibrinogen genes FGG, FGA, and FGB, clustered on the long arm of human chromosome 4. The majority of cases are due to null mutations in the FGA gene although one would expect the 3 genes to be equally implicated. However, most patients studied so far are white, and therefore the identification of causative mutations in non-European families is necessary to establish if this finding holds true in all ethnic groups. In this study, we report the identification of a novel nonsense mutation (Arg134Xaa) in the FGG gene responsible for congenital afibrinogenemia in 10 patients from Lebanon. Expression studies in COS-7 cells demonstrated that the Arg134Xaa codon, which is encoded by adjacent exons (TG-intron 4-A) affected neither mRNA splicing nor stability, but led to the production of an unstable, severely truncated fibrinogen gamma chain that is not incorporated into a functional fibrinogen hexamer.

  14. VIRTIS on board Rosetta: cryocoolers usage analysis in support of Comet phases observations

    Science.gov (United States)

    Giuppi, Stefano; Politi, Romolo; Capria, Maria Teresa; Piccioni, Giuseppe; De Sanctis, Maria Cristina; Erard, Stéphane; Tosi, Federico; Capaccioni, Fabrizio; Filacchione, Gianrico

    Rosetta is a planetary cornerstone mission of the European Space Agency (ESA). It is devoted to the study of minor bodies of our solar system and it will be the first mission ever to land on a comet (the Jupiter-family comet 67P/Churyumov-Gerasimenko). VIRTIS-M is a sophisticated imaging spectrometer that combines two data channels in one compact instrument, respectively for the visible and the infrared range (0.25-5.0 μm). VIRTIS-H is devoted to infrared spectroscopy (2.5-5.0 μm) with high spectral resolution. Since the satellite will be inside the tail of the comet during one of the most important phases of the mission, it would not be appropriate to use a passive cooling system, due to the high flux of contaminants on the radiator. Therefore the IR sensors are cooled by two Stirling cycle cryocoolers. This paper focuses on the usage of VIRTIS cryocoolers from the beginning of the Rosetta mission till spacecraft hibernation in order to optimize their usage. After a description of the cryocooler used in the mission, a detailed information about time usage and power consumption is provided. On the basis of previous experiences with this kind of cryocoolers it has been made an estimation of the remaining working life of the VIRTIS coolers operating in Rosetta mission. Moreover an estimation of the minimum time between a cryocooler switch off and on again has been carried out in order to preserve the coolers working life.

  15. Analysis of Server Log by Web Usage Mining for Website Improvement

    Directory of Open Access Journals (Sweden)

    Navin Kumar Tyagi

    2010-07-01

    Full Text Available Web server logs stores click stream data which can be useful for mining purposes. The data is stored as a result of user's access to a website. Web usage mining an application of data mining can be used to discover user access patterns from weblog data. The obtained results are used in different applications like, site modifications, business intelligence, system improvement and personalization. In this study, we have analyzed the log files of smart sync software web server to get information about visitors; top errors which can be utilized by system administrator and web designer to increase the effectiveness of the web site.

  16. Codon information value and codon transition-probability distributions in short-term evolution

    Science.gov (United States)

    Jiménez-Montaño, M. A.; Coronel-Brizio, H. F.; Hernández-Montoya, A. R.; Ramos-Fernández, A.

    2016-07-01

    To understand the way the Genetic Code and the physical-chemical properties of coded amino acids affect accepted amino acid substitutions in short-term protein evolution, taking into account only overall amino acid conservation, we consider an underlying codon-level model. This model employs codon pair-substitution frequencies from an empirical matrix in the literature, modified for single-base mutations only. Ordering the degenerated codons according to their codon information value (Volkenstein, 1979), we found that three-fold and most of four-fold degenerated codons, which have low codon values, were best fitted to rank-frequency distributions with constant failure rate (exponentials). In contrast, almost all two-fold degenerated codons, which have high codon values, were best fitted to rank-frequency distributions with variable failure rate (inverse power-laws). Six-fold degenerated codons are considered to be doubly assigned. The exceptional behavior of some codons, including non-degenerate codons, is discussed.

  17. HPC Usage Behavior Analysis and Performance Estimation with Machine Learning Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hao [ORNL; You, Haihang [ORNL; Hadri, Bilel [ORNL; Fahey, Mark R [ORNL

    2012-01-01

    Most researchers with little high performance computing (HPC) experience have difficulties productively using the supercomputing resources. To address this issue, we investigated usage behaviors of the world s fastest academic Kraken supercomputer, and built a knowledge-based recommendation system to improve user productivity. Six clustering techniques, along with three cluster validation measures, were implemented to investigate the underlying patterns of usage behaviors. Besides manually defining a category for very large job submissions, six behavior categories were identified, which cleanly separated the data intensive jobs and computational intensive jobs. Then, job statistics of each behavior category were used to develop a knowledge-based recommendation system that can provide users with instructions about choosing appropriate software packages, setting job parameter values, and estimating job queuing time and runtime. Experiments were conducted to evaluate the performance of the proposed recommendation system, which included 127 job submissions by users from different research fields. Great feedback indicated the usefulness of the provided information. The average runtime estimation accuracy of 64.2%, with 28.9% job termination rate, was achieved in the experiments, which almost doubled the average accuracy in the Kraken dataset.

  18. Codon Bias and Mutability in HIV Sequences

    CERN Document Server

    Waelbroeck, H

    1997-01-01

    A survey of the patterns of synonymous codon preferences in the HIV env gene reveals a relation between the codon bias and the mutability requirements in different regions in the protein. At hypervariable regions in $gp120$, one finds a greater proportion of codons that tend to mutate non-synonymously, but to a target that is similar in hydrophobicity and volume. We argue that this strategy results from a compromise between the selective pressure placed on the virus by the induced immune response, which favours amino acid substitutions in the complementarity determining regions, and the negative selection against missense mutations that violate structural constraints of the env protein.

  19. Agricultural policy and its impact on fuel usage: Empirical evidence from farm household analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Hung-Hao [Department of Agricultural Economics, National Taiwan University, No. 1, Roosevelt Rd., Sec. 4, Taipei 10617 (China); Mishra, Ashok K. [Department of Agricultural Economics and Agribusiness, Louisiana State University, Ag Center (United States); Livingston, Michael [Production Economics and Technology Branch, Economic Research Service, US Department of Agriculture, 1800 M Street NW, Washington, DC 20036-5831 (United States)

    2011-01-15

    Off-farm work is a growing reality in the US agricultural sector as a whole. Another staple program in the US agriculture is the use of crop insurance. This paper assesses hitherto unaddressed issues of fuel consumption and hence pollution generated by farm households associated with off-farm work and crop insurance. We applied a quantile regression method on a unique national farm-level survey data to address the fuel consumption issues. Results indicate that off-farm work by operators tends to decrease fuel expenses. In contrast, households with crop insurance had higher fuel consumption thereby increasing fuel usage. Finally, our study shows that the net effect of these two activities resulted in an increase in the pollution level. (author)

  20. Analysis of Brain Tumors Due to the Usage of Mobile Phones

    Directory of Open Access Journals (Sweden)

    SOOBIA SAEED

    2017-07-01

    Full Text Available The impact of cellular phone radiation on human health is the subject of current mindfulness and is an outcome of the huge increase in phone usage throughout the world. Phones use electromagnetic radiation in the microwave range. The issue is associated with wireless use for 50 minutes and above. The excessive use of mobile phone may cause brain tumors. Nowadays the most commonly developed brain tumor type is GBM (Glioblastoma in multiform and Malignant Astrocytoma. In this paper, we focus on the causes of brain tumor (cancer due to the cell phone as this increase in glucose metabolism. The aim of the study is to address the aforementioned problems associated with the cell phone. MATLAB programming to detect a brain tumor has been used. We have conducted MRI (Magnetic Resonance Imaging study to get the best images and results.

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Conservation of CFTR codon frequency through primates suggests synonymous mutations could have a functional effect.

    Science.gov (United States)

    Pizzo, Lucilla; Iriarte, Andrés; Alvarez-Valin, Fernando; Marín, Mónica

    2015-05-01

    Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system, with a prevalence of about 1:3000 people. Cystic fibrosis is caused by mutations in CFTR gene, which lead to a defective function of the chloride channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Up-to-date, more than 1900 mutations have been reported in CFTR. However for an important proportion of them, their functional effects and the relation to disease are still not understood. Many of these mutations are silent (or synonymous), namely they do not alter the encoded amino acid. These synonymous mutations have been considered as neutral to protein function. However, more recent evidence in bacterial and human proteins has put this concept under revision. With the aim of understanding possible functional effects of synonymous mutations in CFTR, we analyzed human and primates CFTR codon usage and divergence patterns. We report the presence of regions enriched in rare and frequent codons. This spatial pattern of codon preferences is conserved in primates, but this cannot be explained by sequence conservation alone. In sum, the results presented herein suggest a functional implication of these regions of the gene that may be maintained by purifying selection acting to preserve a particular codon usage pattern along the sequence. Overall these results support the idea that several synonymous mutations in CFTR may have functional importance, and could be involved in the disease.

  3. Codon Constraints on Closed 2D Shapes,

    Science.gov (United States)

    2014-09-26

    yields the "vase" of Rubin’s famous figure-ground illusion observed as erly as 1819 by Turton .] Thus, knowing which side is figure determines the...inflections), then the segment is designated as a type 0 codon (see Fig. 4). Those with two zeroes are called type 2 codons. If a segment has exactly one...34: Marr, D. (1976) Early processing of visual information. Phil. Trans. Roy. Soc. Lond., 275:483-524. Marr, D. (1982) Vision: A Computational

  4. SPATIAL AND TEMPORAL ANALYSIS OF HUMAN MOVEMENTS AND APPLICATIONS FOR DISASTER RESPONSE MANAGEMENT UTILIZING CELL PHONE USAGE DATA

    Directory of Open Access Journals (Sweden)

    M. Yasumiishi

    2015-07-01

    Full Text Available As cell phone usage becomes a norm in our daily lives, analysis and application of the data has become part of various research fields. This study focuses on the application of cell phone usage data to disaster response management. Cell phones work as a communication link between emergency responders and victims during and after a major disaster. This study recognizes that there are two kinds of disasters, one with an advance warning, and one without an advance warning. Different movement distance between a day with a blizzard (advanced warning and a normal weather day was identified. In the scenario of a day with an extreme event without advanced warning (earthquake, factors that alter the phone users' movements were analyzed. Lastly, combining both cases, a conceptual model of human movement factors is proposed. Human movements consist of four factors that are push factors, movement-altering factors, derived attributes and constraint factors. Considering each category of factors in case of emergency, it should be necessary that we prepare different kinds of emergency response plans depending on the characteristics of a disaster.

  5. Bibliometrical analysys on the scientific outcome attending the usage of the accelerometer in physical activity level gauge (2010-2014

    Directory of Open Access Journals (Sweden)

    Ricardo Manuel Santos Labrador

    2015-09-01

    Full Text Available This essay provides with the data obtained via the bibliometric analysis of the works on the usage of the accelerometer as a physical activity gauge, both at national and international level, ranging from 2010 to 2014. The main purpose is to know which the scientific output has been, concerning the usage of the accelerometer such an instrument of physical activity’s quantification. The data have been extracted from the Scopus Data Base, and the number of articles on this topic raises to 2207. The keywords used in the search were: accelerometer and physical activity. The scientific output, magazines, authors, institutions, countries, and regions, have been escrutinized by years, identifying the most productive ones. The national and international outcomes reveal the most significant features to be the following: the widespread employment of the accelerometer in different scientific areas, and the growing recognition of some authors, magazines, countries and organisations as a benchmark in the field. Furthermore, it's important to stress the differences between scientific outcome at national and international level, where it's noticeable a steady growth lacking locally.

  6. Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity

    Science.gov (United States)

    Yang, Yang; Liu, Fan; Franc, Vojtech; Halim, Liem Andhyk; Schellekens, Huub; Heck, Albert J. R.

    2016-01-01

    Many biopharmaceutical products exhibit extensive structural micro-heterogeneity due to an array of co-occurring post-translational modifications. These modifications often effect the functionality of the product and therefore need to be characterized in detail. Here, we present an integrative approach, combining two advanced mass spectrometry-based methods, high-resolution native mass spectrometry and middle-down proteomics, to analyse this micro-heterogeneity. Taking human erythropoietin and the human plasma properdin as model systems, we demonstrate that this strategy bridges the gap between peptide- and protein-based mass spectrometry platforms, providing the most complete profiling of glycoproteins. Integration of the two methods enabled the discovery of three undescribed C-glycosylation sites on properdin, and revealed in addition unexpected heterogeneity in occupancies of C-mannosylation. Furthermore, using various sources of erythropoietin we define and demonstrate the usage of a biosimilarity score to quantitatively assess structural similarity, which would also be beneficial for profiling other therapeutic proteins and even plasma protein biomarkers. PMID:27824045

  7. An Analysis of WhatsApp Usage for Communication Between Consulting and Emergency Physicians.

    Science.gov (United States)

    Gulacti, Umut; Lok, Ugur; Hatipoglu, Sinan; Polat, Haci

    2016-06-01

    The aim of this study was to evaluate WhatsApp messenger usage for communication between consulting and emergency physicians. A retrospective, observational study was conducted in the emergency department (ED) of a tertiary care university hospital between January 2014 and June 2014. A total of 614 consultations requested by using the WhatsApp application were evaluated, and 519 eligible consultations were included in the study. The WhatsApp messages that were transferred to consultant physicians consisted of 510 (98.3%) photographic images, 517 (99.6%) text messages, 59 (11.3%) videos, and 10 (1.9%) voice messages. Consultation was most frequently requested from the orthopedics clinic (n = 160, 30.8%). The majority of requested consultations were terminated only by evaluation via WhatsApp messages. (n = 311, 59.9%). Most of the consulting physicians were outside of the hospital or were mobile at the time of the consultation (n = 292, 56.3%). The outside consultation request rate was significantly higher for night shifts than for day shifts (p = .004), and the majority of outside consultation request were concluded by only WhatsApp application (p WhatsApp is useful a communication tool between physicians, especially for ED consultants who are outside the hospital, because of the ability to transfer large amounts of clinical and radiological data during a short period of time.

  8. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli

    Science.gov (United States)

    Napolitano, Michael G.; Landon, Matthieu; Gregg, Christopher J.; Lajoie, Marc J.; Govindarajan, Lakshmi; Mosberg, Joshua A.; Kuznetsov, Gleb; Goodman, Daniel B.; Vargas-Rodriguez, Oscar; Isaacs, Farren J.; Söll, Dieter; Church, George M.

    2016-01-01

    The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 “recalcitrant” AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable. To evaluate synonymous and nonsynonymous alternatives to essential AGRs further, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild-type allele, allowing us to evaluate exhaustively the fitness impact of all 64 codon alternatives. Using this method, we confirmed the relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes. PMID:27601680

  9. The incorrect usage of singular spectral analysis and discrete wavelet transform in hybrid models to predict hydrological time series

    Science.gov (United States)

    Du, Kongchang; Zhao, Ying; Lei, Jiaqiang

    2017-09-01

    In hydrological time series prediction, singular spectrum analysis (SSA) and discrete wavelet transform (DWT) are widely used as preprocessing techniques for artificial neural network (ANN) and support vector machine (SVM) predictors. These hybrid or ensemble models seem to largely reduce the prediction error. In current literature researchers apply these techniques to the whole observed time series and then obtain a set of reconstructed or decomposed time series as inputs to ANN or SVM. However, through two comparative experiments and mathematical deduction we found the usage of SSA and DWT in building hybrid models is incorrect. Since SSA and DWT adopt 'future' values to perform the calculation, the series generated by SSA reconstruction or DWT decomposition contain information of 'future' values. These hybrid models caused incorrect 'high' prediction performance and may cause large errors in practice.

  10. Versatile dual reporter gene systems for investigating stop codon readthrough in plants.

    Directory of Open Access Journals (Sweden)

    Nga T Lao

    Full Text Available BACKGROUND: Translation is most often terminated when a ribosome encounters the first in-frame stop codon (UAA, UAG or UGA in an mRNA. However, many viruses (and some cellular mRNAs contain "stop" codons that cause a proportion of ribosomes to terminate and others to incorporate an amino acid and continue to synthesize a "readthrough", or C-terminally extended, protein. This dynamic redefinition of codon meaning is dependent on specific sequence context. METHODOLOGY: We describe two versatile dual reporter systems which facilitate investigation of stop codon readthrough in vivo in intact plants, and identification of the amino acid incorporated at the decoded stop codon. The first is based on the reporter enzymes NAN and GUS for which sensitive fluorogenic and histochemical substrates are available; the second on GST and GFP. CONCLUSIONS: We show that the NAN-GUS system can be used for direct in planta measurements of readthrough efficiency following transient expression of reporter constructs in leaves, and moreover, that the system is sufficiently sensitive to permit measurement of readthrough in stably transformed plants. We further show that the GST-GFP system can be used to affinity purify readthrough products for mass spectrometric analysis and provide the first definitive evidence that tyrosine alone is specified in vivo by a 'leaky' UAG codon, and tyrosine and tryptophan, respectively, at decoded UAA, and UGA codons in the Tobacco mosaic virus (TMV readthrough context.

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

    Directory of Open Access Journals (Sweden)

    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.

  12. Factors Affecting Radiologist's PACS Usage.

    Science.gov (United States)

    Forsberg, Daniel; Rosipko, Beverly; Sunshine, Jeffrey L

    2016-12-01

    The purpose of this study was to determine if any of the factors radiologist, examination category, time of week, and week effect PACS usage, with PACS usage defined as the sequential order of computer commands issued by a radiologist in a PACS during interpretation and dictation. We initially hypothesized that only radiologist and examination category would have significant effects on PACS usage. Command logs covering 8 weeks of PACS usage were analyzed. For each command trace (describing performed activities of an attending radiologist interpreting a single examination), the PACS usage variables number of commands, number of command classes, bigram repetitiveness, and time to read were extracted. Generalized linear models were used to determine the significance of the factors on the PACS usage variables. The statistical results confirmed the initial hypothesis that radiologist and examination category affect PACS usage and that the factors week and time of week to a large extent have no significant effect. As such, this work provides direction for continued efforts to analyze system data to better understand PACS utilization, which in turn can provide input to enable optimal utilization and configuration of corresponding systems. These continued efforts were, in this work, exemplified by a more detailed analysis using PACS usage profiles, which revealed insights directly applicable to improve PACS utilization through modified system configuration.

  13. 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

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

    Directory of Open Access Journals (Sweden)

    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

  15. Single molecule analysis of replicated DNA reveals the usage of multiple KSHV genome regions for latent replication.

    Directory of Open Access Journals (Sweden)

    Subhash C Verma

    2011-11-01

    Full Text Available Kaposi's sarcoma associated herpesvirus (KSHV, an etiologic agent of Kaposi's sarcoma, Body Cavity Based Lymphoma and Multicentric Castleman's Disease, establishes lifelong latency in infected cells. The KSHV genome tethers to the host chromosome with the help of a latency associated nuclear antigen (LANA. Additionally, LANA supports replication of the latent origins within the terminal repeats by recruiting cellular factors. Our previous studies identified and characterized another latent origin, which supported the replication of plasmids ex-vivo without LANA expression in trans. Therefore identification of an additional origin site prompted us to analyze the entire KSHV genome for replication initiation sites using single molecule analysis of replicated DNA (SMARD. Our results showed that replication of DNA can initiate throughout the KSHV genome and the usage of these regions is not conserved in two different KSHV strains investigated. SMARD also showed that the utilization of multiple replication initiation sites occurs across large regions of the genome rather than a specified sequence. The replication origin of the terminal repeats showed only a slight preference for their usage indicating that LANA dependent origin at the terminal repeats (TR plays only a limited role in genome duplication. Furthermore, we performed chromatin immunoprecipitation for ORC2 and MCM3, which are part of the pre-replication initiation complex to determine the genomic sites where these proteins accumulate, to provide further characterization of potential replication initiation sites on the KSHV genome. The ChIP data confirmed accumulation of these pre-RC proteins at multiple genomic sites in a cell cycle dependent manner. Our data also show that both the frequency and the sites of replication initiation vary within the two KSHV genomes studied here, suggesting that initiation of replication is likely to be affected by the genomic context rather than the DNA

  16. Comparing Usage and Cost- Effectiveness Analysis of English Printed and Electronic Books for University of Tehran

    OpenAIRE

    Davoud Haseli; Nader Naghshineh; fatemeh Fahimnia

    2014-01-01

    Libraries operate in a competitive environment, and this is essentially needed to prove its benefits for stockholders, and continuously evaluate and compare advantages for printed and electronic resources. In these cases, economic evaluation methods such as cost- effectiveness analysis, is one of the best methods, because of a comprehensive study of the use and cost of library sources. The purpose of this study is to discovery of use and cost- effectiveness analysis of English printed and ebo...

  17. Effect of the Flanking Sequence Architecture of Translation Initiation AUG Codon on Gene Expression Level in Rice

    Institute of Scientific and Technical Information of China (English)

    LIU Qing-po; TAN Jun; XUE Qing-zhong

    2004-01-01

    The relationship between the codon usage bias, gene expression level and the AUG context (from -20 to +6 positions relative to the initiator AUG codon) was examined in 541unigene sequences of rice. A significant correlation for CAI values (codon adaptation index) was observed at five nucleotide positions (-19, -18, -9, -4, +5), eight (-19, -18,-14, -9, -6, -4, -1, +5) for CPP (codon preference parameter), and seven (-18, -16, -15,-9, -7, -1, + 6) for mRNA abundance in the flanking sequence of the initiator AUG codon respectively, but a significantly positive correlation for both CAI and CPP at two positions (-4 and +5), indicating that both those positions are evolutionally under the natural selection constraint at the translational level. By site-directed mutagenesis at seven specific positions (-18, -16, -15, -9, -7, -1 and + 6) for allergenic protein that had the highest mRNA abundance in this study, its expression level decreased dramatically 63.3 and 72.5% respectively, indicating the importance of those 7 positions for gene expression. A highly positive correlation (r= 0.625, P< 0.01) between AUGCAI and GC content in the flanking sequence of the initiator AUG codon showed a more effective higher GC content on translation initiation efficiency. The strong preference for G or C at those 8 positions (-6, -5, -3, -2, -1, +4, +5 and +6) in the AUG context suggested that an important factor in modulation of the translation efficiency, as well as synonymous codon usage bias, particularly in highly expressed genes.

  18. Tracing specific synonymous codon-secondary structure correlations through evolution.

    Science.gov (United States)

    Oresic, Matej; Dehn, Michael; Korenblum, Daniel; Shalloway, David

    2003-04-01

    We previously showed that GAU codons are preferred (relative to synonymous GAC codons) for encoding aspartates specifically at the N-termini of alpha-helices in human, but not in E. coli, proteins. To test if this difference reflected a general difference between eucaryotes and procaryotes, we now extended the analysis to include the proteins and coding sequences of mammals, vertebrates, S. cerevisiae, and plants. We found that the GAU-alpha-helix correlation is also strong in non-human mammalian and vertebrate proteins but is much weaker or insignificant in S. cerevisiae and plants. The vertebrate correlations are of sufficient strength to enhance alpha-helix N-terminus prediction. Additional results, including the observation that the correlation is significantly enhanced when proteins that are known to be correctly expressed in recombinant procaryotic systems are excluded, suggest that the correlation is induced at the level of protein translation and folding and not at the nucleic acid level. To the best of our knowledge, it is not explicable by the canonical picture of protein expression and folding, suggesting the existence of a novel evolutionary selection mechanism. One possible explanation is that some alpha-helix N-terminal GAU codons may facilitate correct co-translational folding in vertebrates.

  19. The effects of codon context on in vivo translation speed.

    Directory of Open Access Journals (Sweden)

    Fabienne F V Chevance

    2014-06-01

    Full Text Available We developed a bacterial genetic system based on translation of the his operon leader peptide gene to determine the relative speed at which the ribosome reads single or multiple codons in vivo. Low frequency effects of so-called "silent" codon changes and codon neighbor (context effects could be measured using this assay. An advantage of this system is that translation speed is unaffected by the primary sequence of the His leader peptide. We show that the apparent speed at which ribosomes translate synonymous codons can vary substantially even for synonymous codons read by the same tRNA species. Assaying translation through codon pairs for the 5'- and 3'- side positioning of the 64 codons relative to a specific codon revealed that the codon-pair orientation significantly affected in vivo translation speed. Codon pairs with rare arginine codons and successive proline codons were among the slowest codon pairs translated in vivo. This system allowed us to determine the effects of different factors on in vivo translation speed including Shine-Dalgarno sequence, rate of dipeptide bond formation, codon context, and charged tRNA levels.

  20. Usage of Cellulose Diacetate as Sorption Material for Fluorescent Analysis of PAH

    Directory of Open Access Journals (Sweden)

    Tamara I. Gubina

    2014-09-01

    Full Text Available Solid-phase matrices made of cellulose diacetate (CDA as films and fibers were prepared. The CDA film matrices were found to be characterized by a negative value of the surface potential (–32 ± 2 mV while the fibers had positive ones (+419 ± 1 mV. The possibility of using these matrices as sorption materials for luminescence analysis of polycyclic hydrocarbons in water-ethanol and micellar media is shown. Modification of such polymeric CDA matrices with surfactants of various natures improves their sorptive capacity and hydrocarbon recovery, and increases the sensitivity of luminescent analysis.

  1. 玉米黑粉菌CYP51稀有密码子和mRNA二级结构分析及与杀菌剂戊唑醇分子对接%0Analysis of Rare Codon and mRNA Structure About Ustilago maydis CYP51 and Molecular Docking With Fungicide Tebuconazole

    Institute of Scientific and Technical Information of China (English)

    李书祥; 韩睿; 袁利玲; 熊丽; 袁永泽; 杨江科; 闫云君; 刘德立

    2011-01-01

    usage database (http//:www.kazusa.or.jp/coden) was used for the analysis of rare codon and software RNAStructure 4.5 was employed to study the mRNA secondary structure of translation initiation region. The results showed that rare codons rate in UmCYP51 gene is only 4.63%, the Rosetta (DE3) strain expressing some rare codons is not suitable for the protein expression of UmCYP51. Only the lowest energy of mRNA structure for pET32-Um-35 can obtained protein expression. These results are compatible with the experiments. Moreover, to design novel antifungal compounds against UmCYP51, based on the recently determined X-ray crystal structure human CYP51, a three-dimensional structure model of UmCYP51 was built through homology modeling using MODELLER 9V7 program. After refinement of the energy minimization and MD simulation using GROMACS 4.0.3 package, the UmCYP51 model was evaluated by PROCHECK Ramachandran plot statistics that indicated the designed model was in good quality. Commercial fungicide tebuconazole was docked into the model protein using Autodock 4.2.3 program to form the binding pattern of inhibitor with UmCYP51. The docking conformation of tebuconazole in the active site of UmCYPSl showed that the N-4 of the triazole ring was bound to heme iron with a distance about 0.245 nm. The hydroxy group of tebuconazole formed hydrogen-bonding interaction with the oxygen atom of carbonyl group for Ala265 with a distance about 0.245 nm. The mechanism of inhibitory activity of tebuconazole against UmCYP51 obtained from this study could aid in designing new antifungal compounds targeting this enzyme.

  2. An analysis of the inter-relationship between savings product usage ...

    African Journals Online (AJOL)

    Although the impact of the financial crisis was not as severe in ... Possible reasons for customers' dissatisfaction with the financial industry and products ... in the financial services industry based on their level of satisfaction with savings ...... delivering service quality of banks: an application of dominance analysis in modified.

  3. Usage of Latent Class Analysis in Diagnostic Microbiology in the Absence of Gold Standard Test

    Directory of Open Access Journals (Sweden)

    Gul Bayram Abiha

    2016-12-01

    Full Text Available The evaluation of performance of various tests diagnostic tests in the absence of gold standard is an important problem. Latent class analysis (LCA is a statistical analysis method known for many years, especially in the absence of a gold standard for evaluation of diagnostic tests so that LCA has found its wide application area. During the last decade, LCA method has widely used in for determining sensivity and specifity of different microbiological tests. It has investigated in the diagnosis of mycobacterium tuberculosis, mycobacterium bovis, human papilloma virus, bordetella pertussis, influenza viruses, hepatitis E virus (HEV, hepatitis C virus (HCV and other various viral infections. Researchers have compared several diagnostic tests for the diagnosis of different pathogens with LCA. We aimed to evaluate performance of latent class analysis method used microbiological diagnosis in various diseases in several researches. When we took into account all of these tests' results, we suppose that LCA is a good statistical analysis method to assess different test performances in the absence of gold standard. [Archives Medical Review Journal 2016; 25(4.000: 467-488

  4. Comparing Usage and Cost- Effectiveness Analysis of English Printed and Electronic Books for University of Tehran

    Directory of Open Access Journals (Sweden)

    Davoud Haseli

    2014-09-01

    The result showed that the use of English printed books has different in four subject areas of Engineering, Sciences, Social and Behavioral Sciences, and Humanities, unlike English ebooks. The average of use of the printed books in Social and behavioral sciences Was 1.09, and it shows the most among all, and for Sciences, was only 0.14, this is the minimum among. 20 percent of English printed books have been used and the mean for total printed books was 0.77. 52 percent of ebooks have been used, and the average of use of ebooks was 5.16, respectively. So the use and cost- effectiveness analysis of English ebooks are more than English print books. The uses statistics and cost analysis showed that cost per use for English printed books is 787168 Rial and for ebooks is 80,388.

  5. GAP-ANALYSIS METHODS USAGE FOR DISTRIBUTION LOGISTICS SYSTEM EFFICIENCY APPRAISAL

    OpenAIRE

    Markovskiy Vladimir Andreevich

    2012-01-01

    The article is dedicated to the appraisal of distribution logistics system efficiency problem, which is induced by lack of coordination of its elements. The aim of the article is to determine criteria for lack of logistics distribution systems efficiency. Novelty of the article is in applying GAP-analysis method to logistics distribution macrosystems, which allowed to propose a calculation method for informing about the presence of gaps in the logistics system. It is revea...

  6. Is Toscana A Formal Concept Analysis Based Solution In Web Usage Mining?

    Directory of Open Access Journals (Sweden)

    Dan-Andrei SITAR-TĂUT

    2012-01-01

    Full Text Available Analyzing large amount of data come from web logs represents a complex, but challenging nowadays problem with implication in various fields, thing that lets open a way for theoretically infinite approaches an implementations. The main goal of our paper represents the possibility of applying the formal concept analysis as viable solution of sustaining the web mining process, based on a technological open-source solution called TOSCANA.

  7. Heat Recovery in a Pasta Factory. Pinch Analysis Leads to Optimal Heat Pump Usage.

    OpenAIRE

    Staine, Frédéric; Favrat, Daniel; Krummenacher, Pierre

    1994-01-01

    In the previous issue of the IEA Heat Pump Centre Newsletter (Vol, 12, No.3, pp. 29-31), an article by these authors described the use of pinch analysis (also known as pinch technology) in a buildings application. This article describes a similar procedure for integrating a heat pump into a pasta production process. Many industrial processes, and particularly those dealing with drying, are characterized by an overabundance of low- grade heat which often cannot be effi...

  8. Heat Recovery in a Pasta Factory. Pinch Analysis Leads to Optimal Heat Pump Usage.

    OpenAIRE

    Staine, Frédéric; Favrat, Daniel; Krummenacher, Pierre

    1994-01-01

    In the previous issue of the IEA Heat Pump Centre Newsletter (Vol, 12, No.3, pp. 29-31), an article by these authors described the use of pinch analysis (also known as pinch technology) in a buildings application. This article describes a similar procedure for integrating a heat pump into a pasta production process. Many industrial processes, and particularly those dealing with drying, are characterized by an overabundance of low- grade heat which often cannot be effi...

  9. Analyzing PACS Usage Patterns by Means of Process Mining: Steps Toward a More Detailed Workflow Analysis in Radiology.

    Science.gov (United States)

    Forsberg, Daniel; Rosipko, Beverly; Sunshine, Jeffrey L

    2016-02-01

    In this paper, statistical analysis and techniques from process mining are employed to analyze interaction patterns originating from radiologists reading medical images in a picture archiving and communication system (PACS). Event logs from 1 week of data, corresponding to 567 cases of single-view chest radiographs read by 14 radiologists, were analyzed. Statistical analysis showed that the numbers of commands and command types used by the radiologists per case only have a slightly positive correlation with the time to read a case (0.31 and 0.55, respectively). Further, one way ANOVA showed that the factors time of day, radiologist and specialty were significant for the number of commands per case, whereas radiologist was also significant for the number of command types, but with no significance of any of the factors on time to read. Applying process mining to the event logs of all users showed that a seemingly "simple" examination (single-view chest radiographs) can be associated with a highly complex interaction process. However, repeating the process discovery on each individual radiologist revealed that the initially discovered complex interaction process consists of one group of radiologists with individually well-structured interaction processes and a second smaller group of users with progressively more complex usage patterns. Future research will focus on metrics to describe derived interaction processes in order to investigate if one set of interaction patterns can be considered as more efficient than another set when reading radiological images in a PACS.

  10. Bayesian comparisons of codon substitution models.

    Science.gov (United States)

    Rodrigue, Nicolas; Lartillot, Nicolas; Philippe, Hervé

    2008-11-01

    In 1994, Muse and Gaut (MG) and Goldman and Yang (GY) proposed evolutionary models that recognize the coding structure of the nucleotide sequences under study, by defining a Markovian substitution process with a state space consisting of the 61 sense codons (assuming the universal genetic code). Several variations and extensions to their models have since been proposed, but no general and flexible framework for contrasting the relative performance of alternative approaches has yet been applied. Here, we compute Bayes factors to evaluate the relative merit of several MG and GY styles of codon substitution models, including recent extensions acknowledging heterogeneous nonsynonymous rates across sites, as well as selective effects inducing uneven amino acid or codon preferences. Our results on three real data sets support a logical model construction following the MG formulation, allowing for a flexible account of global amino acid or codon preferences, while maintaining distinct parameters governing overall nucleotide propensities. Through posterior predictive checks, we highlight the importance of such a parameterization. Altogether, the framework presented here suggests a broad modeling project in the MG style, stressing the importance of combining and contrasting available model formulations and grounding developments in a sound probabilistic paradigm.

  11. Data pre-processing for web log mining: Case study of commercial bank website usage analysis

    Directory of Open Access Journals (Sweden)

    Jozef Kapusta

    2013-01-01

    Full Text Available We use data cleaning, integration, reduction and data conversion methods in the pre-processing level of data analysis. Data processing techniques improve the overall quality of the patterns mined. The paper describes using of standard pre-processing methods for preparing data of the commercial bank website in the form of the log file obtained from the web server. Data cleaning, as the simplest step of data pre-processing, is non–trivial as the analysed content is highly specific. We had to deal with the problem of frequent changes of the content and even frequent changes of the structure. Regular changes in the structure make use of the sitemap impossible. We presented approaches how to deal with this problem. We were able to create the sitemap dynamically just based on the content of the log file. In this case study, we also examined just the one part of the website over the standard analysis of an entire website, as we did not have access to all log files for the security reason. As the result, the traditional practices had to be adapted for this special case. Analysing just the small fraction of the website resulted in the short session time of regular visitors. We were not able to use recommended methods to determine the optimal value of session time. Therefore, we proposed new methods based on outliers identification for raising the accuracy of the session length in this paper.

  12. An Analysis of Citizen Science Based Research: Usage and Publication Patterns.

    Science.gov (United States)

    Follett, Ria; Strezov, Vladimir

    2015-01-01

    The use of citizen science for scientific discovery relies on the acceptance of this method by the scientific community. Using the Web of Science and Scopus as the source of peer reviewed articles, an analysis of all published articles on "citizen science" confirmed its growth, and found that significant research on methodology and validation techniques preceded the rapid rise of the publications on research outcomes based on citizen science methods. Of considerable interest is the growing number of studies relying on the re-use of collected datasets from past citizen science research projects, which used data from either individual or multiple citizen science projects for new discoveries, such as for climate change research. The extent to which citizen science has been used in scientific discovery demonstrates its importance as a research approach. This broad analysis of peer reviewed papers on citizen science, that included not only citizen science projects, but the theory and methods developed to underpin the research, highlights the breadth and depth of the citizen science approach and encourages cross-fertilization between the different disciplines.

  13. Extracting Usage Patterns and the Analysis of Tag Connection Dynamics within Collaborative Tagging Systems

    Directory of Open Access Journals (Sweden)

    Daniel MICAN

    2013-01-01

    Full Text Available Collaborative tagging has become a very popular way of annotation, thanks to the fact that any entity may be labeled by any individual based on his own reason. In this paper we present the results of the case study carried out on the basis of data gathered at different time intervals from the social tagging system developed and implemented on Întelepciune.ro. Analyzing collective data referring to the way in which community members associate different tags, we have observed that between tags, links are formed which become increasingly stable with the passing of time. Following the application of methodology specific to network analysis, we have managed to extract information referring to tag popularity, their influence within the network and the degree to which a tag depends upon another. As such, we have succeeded in determining different semantic structures within the collective tagging system and see their evolution at different stages in time. Furthermore, we have pictured the way in which tag rec-ommendations can be executed and that they can be integrated within recommendation sys-tems. Thus, we will be able to identify experts and trustworthy content based on different cat-egories of interest.

  14. [Pharmaco-economic analysis of NSAID usage in Gastroenterology Department of Tuzla Clinic].

    Science.gov (United States)

    Skrbo, Armin; Sober, Miroslav; Skrbo, Selma; Omerhodzić, Alma; Zunić, Lejla

    2005-01-01

    Pharmacoeconomics is young rapidly developing science that uses economic, clinical and epidemiologic methods. It studies adequate use of therapeutics giving guidelines towards rational utilization of the resources in health care. Pharmacoeconomics indentifies estimates and compares costs and clinical outcomes of different strategies giving the best solution: optimal cost/benefit ratio. These studies can be used to estimate existing programs and plan the new ones. The aim of this paper was to carry out pharmacoeconomic study on the non-steroid anti-inflamatory drugs (NSAID) use in canton Tuzla, to compare costs of medication with highly selective cyclooxygenase 2 (COX-2) inhibitors and nonselective NSAIDs and to calculate medication costs of the bleeding from upper parts of gastrointestinal tract. Study covers period from January to April 2004. Meta-analysis of selected clinical studies on safe and efficiency of NSAIDs was simultaneously conducted. Our results show that hospital treatment costs of the high-risk patients group significantly exceeds their potential medication costs with highly selective COX-2 inhibitors. Simultaneous use of non-selective NSAIDs with antacids has justification only in the low-risk group with mild gastrointestinal disturbances.

  15. A Discrete Analysis of Demography and Elec tronic banking usage in Nigeria

    Directory of Open Access Journals (Sweden)

    TITUS CHUKWUEMEZIE O KEKE

    2014-08-01

    Full Text Available This research seeks to determine which demographic sub-group has the greatest tendency to use electronic banking since different sub-groups reflect differences in mix and types of banking services used. It was based on a discrete analysis using both Binary Logistic Regression (BLR and Multinomial Logistic Regression (MLR. Seven demographic variables: gender, age, income, marital status, ethnicity, occupation and education were used. The results of the study show that males and graduates are more inclined to use e-banking. It also shows that traders and respondents in technical/administrative occupation are less inclined while students/apprentices and clerical workers are more inclined to use e-banking. In terms of the consumers’ ethnic background in electronic banking, the study found out that the Igbo and Yoruba ethnic groups have higher and positive probability of using e-banking while the Hausa/Fulashow less probability. With respect to marital status, this study shows that singles have the highest probability to use e-banking. Married/divorced people also show positive disposition to use e-banking. The implication of this study is that market segmentation is a key element of product management.

  16. From Cookies to Cooks: Insights on Dietary Patterns via Analysis of Web Usage Logs

    CERN Document Server

    West, Robert; Horvitz, Eric

    2013-01-01

    Nutrition is a key factor in people's overall health. Hence, understanding the nature and dynamics of population-wide dietary preferences over time and space can be valuable in public health. To date, studies have leveraged small samples of participants via food intake logs or treatment data. We propose a complementary source of population data on nutrition obtained via Web logs. Our main contribution is a spatiotemporal analysis of population-wide dietary preferences through the lens of logs gathered by a widely distributed Web-browser add-on, using the access volume of recipes that users seek via search as a proxy for actual food consumption. We discover that variation in dietary preferences as expressed via recipe access has two main periodic components, one yearly and the other weekly, and that there exist characteristic regional differences in terms of diet within the United States. In a second study, we identify users who show evidence of having made an acute decision to lose weight. We characterize the...

  17. Analysis of the impact of recreational trail usage for prioritising management decisions: a regression tree approach

    Science.gov (United States)

    Tomczyk, Aleksandra; Ewertowski, Marek; White, Piran; Kasprzak, Leszek

    2016-04-01

    The dual role of many Protected Natural Areas in providing benefits for both conservation and recreation poses challenges for management. Although recreation-based damage to ecosystems can occur very quickly, restoration can take many years. The protection of conservation interests at the same as providing for recreation requires decisions to be made about how to prioritise and direct management actions. Trails are commonly used to divert visitors from the most important areas of a site, but high visitor pressure can lead to increases in trail width and a concomitant increase in soil erosion. Here we use detailed field data on condition of recreational trails in Gorce National Park, Poland, as the basis for a regression tree analysis to determine the factors influencing trail deterioration, and link specific trail impacts with environmental, use related and managerial factors. We distinguished 12 types of trails, characterised by four levels of degradation: (1) trails with an acceptable level of degradation; (2) threatened trails; (3) damaged trails; and (4) heavily damaged trails. Damaged trails were the most vulnerable of all trails and should be prioritised for appropriate conservation and restoration. We also proposed five types of monitoring of recreational trail conditions: (1) rapid inventory of negative impacts; (2) monitoring visitor numbers and variation in type of use; (3) change-oriented monitoring focusing on sections of trail which were subjected to changes in type or level of use or subjected to extreme weather events; (4) monitoring of dynamics of trail conditions; and (5) full assessment of trail conditions, to be carried out every 10-15 years. The application of the proposed framework can enhance the ability of Park managers to prioritise their trail management activities, enhancing trail conditions and visitor safety, while minimising adverse impacts on the conservation value of the ecosystem. A.M.T. was supported by the Polish Ministry of

  18. Energy Usage Analysis System

    Data.gov (United States)

    General Services Administration — The EUAS application is a web based system which serves Energy Center of Expertise, under the Office of Facilitates Management and Service Programs. EUAS is used for...

  19. Stop codon reassignments in the wild.

    Science.gov (United States)

    Ivanova, Natalia N; Schwientek, Patrick; Tripp, H James; Rinke, Christian; Pati, Amrita; Huntemann, Marcel; Visel, Axel; Woyke, Tanja; Kyrpides, Nikos C; Rubin, Edward M

    2014-05-23

    The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs of metagenomic data for stop codon reassignment events, we detected recoding in a substantial fraction of the >1700 environmental samples examined. We observed extensive opal and amber stop codon reassignments in bacteriophages and of opal in bacteria. Our data indicate that bacteriophages can infect hosts with a different genetic code and demonstrate phage-host antagonism based on code differences. The abundance and diversity of genetic codes present in environmental organisms should be considered in the design of engineered organisms with altered genetic codes in order to preclude the exchange of genetic information with naturally occurring species.

  20. Investigations of oligonucleotide usage variance within and between prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J.; Skjerve, E.; Ussery, David

    2008-01-01

    Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di-to tetranucleotides). We wanted to assess the statistical information potential...... was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i. e., information in prokaryotic genomes is encoded in short oligonucleotides. Oligonucleotide usage varied more within AT-rich and host-associated genomes than...... in GC-rich and free-living genomes, and this variation was mainly located in non-coding regions. Bias (selectional pressure) in tetranucleotide usage correlated with GC content, and coding regions were more biased than non-coding regions. Non-coding regions were also found to be approximately 5.5% more...

  1. Four-base codon-mediated incorporation of non-natural amino acids into proteins in a eukaryotic cell-free translation system.

    Science.gov (United States)

    Taira, Hikaru; Fukushima, Masaharu; Hohsaka, Takahiro; Sisido, Masahiko

    2005-05-01

    Various four-base codons have been shown to work for the introduction of non-natural amino acids into proteins in an Escherichia coli cell-free translation system. Here, a four-base codon-mediated non-natural mutagenesis was applied to a eukaryotic rabbit reticulocyte cell-free translation system. Mutated streptavidin mRNAs containing four-base codons were prepared and added to a rabbit reticulocyte lysate in the presence of tRNAs that were aminoacylated with a non-natural amino acid and had the corresponding four-base anticodons. A Western blot analysis of translation products indicated that the four-base codons CGGU, CGCU, CCCU, CUCU, CUAU, and GGGU were efficiently decoded by the aminoacyl-tRNAs having the corresponding four-base anticodons. In contrast, the four-base codons AGGU, AGAU, CGAU, UUGU, UCGU, and ACGU were not decoded. The stop codon-derived four-base codons UAGU, UAAU, and UGAU were found to be inefficient, whereas the amber codon UAG and opal codon UGA were efficient for the incorporation of non-natural amino acids. The application of the expanded genetic code in a eukaryotic cell-free system opens the possibility of a four-base codon-mediated incorporation of non-natural amino acids into proteins in living eukaryotic cells.

  2. Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) markers.

    Science.gov (United States)

    Heikrujam, Monika; Kumar, Jatin; Agrawal, Veena

    2015-09-01

    To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT) polymorphism and CAAT box-derived polymorphism (CBDP) were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males). Comparatively, CBDP markers proved to be more effective than SCoT markers in terms of percentage polymorphism as the former detecting an average of 53.4% and the latter as 49.4%. The Polymorphic information content (PIC) value and marker index (MI) of CBPD were 0.43 and 1.10, respectively which were higher than those of SCoT where the respective values of PIC and MI were 0.38 and 1.09. While comparing male and female genotype populations, the former showed higher variation in respect of polymorphic percentage and PIC, MI and Rp values over female populations. Nei's diversity (h) and Shannon index (I) were calculated for each genotype and found that the genotype "MS F" (in both markers) was highly diverse and genotypes "Q104 F" (SCoT) and "82-18 F" (CBDP) were least diverse among the female genotype populations. Among male genotypes, "32 M" (CBDP) and "MS M" (SCoT) revealed highest h and I values while "58-5 M" (both markers) was the least diverse. Jaccard's similarity co-efficient of SCoT markers ranged from 0.733 to 0.922 in female genotypes and 0.941 to 0.746 in male genotype population. Likewise, CBDP data analysis also revealed similarity ranging from 0.751 to 0.958 within female genotypes and 0.754 to 0.976 within male genotype populations thereby, indicating genetically diverse Jojoba population. Employing the NTSYS (Numerical taxonomy and multivariate analysis system) Version 2.1 software, both the markers generated dendrograms which revealed that all the Jojoba genotypes were clustered into two major groups, one group consisting of

  3. Genetic diversity analysis among male and female Jojoba genotypes employing gene targeted molecular markers, start codon targeted (SCoT polymorphism and CAAT box-derived polymorphism (CBDP markers

    Directory of Open Access Journals (Sweden)

    Monika Heikrujam

    2015-09-01

    Full Text Available To detect genetic variations among different Simmondsia chinensis genotypes, two gene targeted markers, start codon targeted (SCoT polymorphism and CAAT box-derived polymorphism (CBDP were employed in terms of their informativeness and efficiency in analyzing genetic relationships among different genotypes. A total of 15 SCoT and 17 CBDP primers detected genetic polymorphism among 39 Jojoba genotypes (22 females and 17 males. Comparatively, CBDP markers proved to be more effective than SCoT markers in terms of percentage polymorphism as the former detecting an average of 53.4% and the latter as 49.4%. The Polymorphic information content (PIC value and marker index (MI of CBPD were 0.43 and 1.10, respectively which were higher than those of SCoT where the respective values of PIC and MI were 0.38 and 1.09. While comparing male and female genotype populations, the former showed higher variation in respect of polymorphic percentage and PIC, MI and Rp values over female populations. Nei's diversity (h and Shannon index (I were calculated for each genotype and found that the genotype “MS F” (in both markers was highly diverse and genotypes “Q104 F” (SCoT and “82–18 F” (CBDP were least diverse among the female genotype populations. Among male genotypes, “32 M” (CBDP and “MS M” (SCoT revealed highest h and I values while “58-5 M” (both markers was the least diverse. Jaccard's similarity co-efficient of SCoT markers ranged from 0.733 to 0.922 in female genotypes and 0.941 to 0.746 in male genotype population. Likewise, CBDP data analysis also revealed similarity ranging from 0.751 to 0.958 within female genotypes and 0.754 to 0.976 within male genotype populations thereby, indicating genetically diverse Jojoba population. Employing the NTSYS (Numerical taxonomy and multivariate analysis system Version 2.1 software, both the markers generated dendrograms which revealed that all the Jojoba genotypes were clustered into two major

  4. Usage Analysis of Web 2.0 and Library 2.0 Tools by Librarians in Kwara State Academic Libraries

    Science.gov (United States)

    Tella, Adeyinka; Soluoku, Taofeeqat

    2016-01-01

    This study analysed the usage of Web 2.0 and Library 2.0 tools by librarians in Kwara State academic libraries. A sample of 40 librarians was surveyed through total enumeration sampling technique from four different tertiary education institutions libraries in Kwara State, Nigeria. Questionnaire was used for the collection of data. The collected…

  5. An Ethnographic Analysis of Adolescent Sexual Minority Website Usage: Exploring Notions of Information Seeking and Sexual Identity Development

    Science.gov (United States)

    Sulfridge, Rocky M.

    2012-01-01

    This dissertation explores the website usage of adolescent sexual minorities, examining notions of information seeking and sexual identity development. Sexual information seeking is an important element within human information behavior and is uniquely problematic for young sexual minorities. Utilizing a contemporary gay teen website, this…

  6. A Comparative Analysis of Social Media Usage and Academic Performance in Public and Private Senior High Schools

    Science.gov (United States)

    Mingle, Jeffrey; Adams, Musah; Adjei, E. A.

    2016-01-01

    The study comparatively analyzed social media usage and academic performance in public and private senior high schools. The issue of social media and academic performance has been a very debatable topic with regard to its effect. This study further explores the relation between private and public schools in relation to social media use and…

  7. Evaluating Business Models for E-Books through Usage Data Analysis: A Case Study from the University of Westminster

    Science.gov (United States)

    Grigson, Anna

    2009-01-01

    The University of Westminster began collecting and analyzing vendor usage reports since starting their e-book collections in 2004. They have used the results both to monitor the use of the collections and to calculate basic cost-per-use metrics that have informed decisions on whether to renew particular resources. In 2008, they sought to extend…

  8. Analysis of China’s Aluminum Usage in the Transport Industry in 2009—Part Ⅱ

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    <正>Ⅱ. Aluminum Use in Railway Transport Railway transport vehicles include railway rolling stock and urban light rail transport vehicles. In recent years, with the rapid development of domestic transport industry, aluminum usage in railway transport vehicles has made significant breakthrough.

  9. An Ethnographic Analysis of Adolescent Sexual Minority Website Usage: Exploring Notions of Information Seeking and Sexual Identity Development

    Science.gov (United States)

    Sulfridge, Rocky M.

    2012-01-01

    This dissertation explores the website usage of adolescent sexual minorities, examining notions of information seeking and sexual identity development. Sexual information seeking is an important element within human information behavior and is uniquely problematic for young sexual minorities. Utilizing a contemporary gay teen website, this…

  10. Codon optimization of genes for efficient protein expression in mammalian cells by selection of only preferred human codons.

    Science.gov (United States)

    Inouye, Satoshi; Sahara-Miura, Yuiko; Sato, Jun-ichi; Suzuki, Takahiro

    2015-05-01

    A simple design method for codon optimization of genes to express a heterologous protein in mammalian cells is described. Codon optimization was performed by choosing only codons preferentially used in humans and with over 60% GC content, and the method was named the "preferred human codon-optimized method." To test our simple rule for codon optimization, the preferred human codon-optimized genes for six proteins containing photoproteins (aequorin and clytin II) and luciferases (Gaussia luciferase, Renilla luciferase, and firefly luciferases from Photinus pyralis and Luciola cruciata) were chemically synthesized and transiently expressed in Chinese hamster ovary-K1 cells. All preferred human codon-optimized genes showed higher luminescence activity than the corresponding wild-type genes. Our simple design method could be used to improve protein expression in mammalian cells efficiently. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Characterization and expression of codon optimized soybean phytase gene in E. coli.

    Science.gov (United States)

    Singh, Pritee; Punjabi, Mansi; Jolly, Monica; Rai, R D; Sachdev, Archana

    2013-12-01

    Phytic acid, the major storage form of phosphorus in plant seeds is degraded by the phytases to yield inositol and free phosphate, contributing thereby to the improved bioavailability of phytate phosphorus and essential minerals in plant foods and simultaneous reduction in phosphorus pollution of the terrestrial and aquatic ecosystems. As a possible strategy for altering seed phytate levels, the approach involving reduction of phytate content by ectopically expressing endogenous phytase gene during seed development of soybean (Glycine max L. cv. Pusa-20) was attempted in the present study. Semi-quantitative RT-PCR revealed the maximum expression of phytase gene transcripts in germinating cotyledons (approximately 10 days after germinations), compared to other vegetative tissues. A full-length phytase cDNA was amplified from the germinating seedlings by splicing by overlap extension (SOE)-PCR and its sequence analysis revealed an open-reading-frame of 1644 bp, including an N terminal signal peptide of 28 amino acids. Predicted amino acid sequence (547-aa) of molecular mass 62 kDa on alignment with related purple acid phosphatases in other plants shared five conserved domains and seven invariant amino acids involved in coordination of the metals in the binuclear center of purple acid phosphatases. Owing to a large number of E. coli low-usage codons in soybean phytase gene, the modified gene was cloned into a prokaryotic expression vector pET-28a (+) and its expression in E. coli was confirmed by SDS-PAGE and Western blot analysis. Bioassay of the crude expression product in E. coli revealed a functional phytase gene, showing a great potential for developing low phytate transgenic soybean through its seed-specific overexpression in the early stages of seed development.

  12. Analysis of Static and Dynamic E-Reference Content at a Multi-Campus University Shows, that Updated Content is Associated with Greater Annual Usage

    Directory of Open Access Journals (Sweden)

    Laura Costello

    2016-03-01

    Full Text Available Objective – To discover whether there is a difference in use over time between dynamically updated and changing subscription e-reference titles and collections, and static purchased e-reference titles and collections. Design – Case study. Setting – A multi-campus Canadian university with 9,200 students enrolled in both graduate and undergraduate programs. Subjects – E-reference book packages and individual e-reference titles. Methods – The author compared data from individual e-reference books and packages. First, individual subscription e-reference books that periodically added updated content were compared to individually purchased e-reference books that remained static after purchase. The author then compared two e-reference book packages that provided new and updated content to two static e-reference book packages. The author compared data from patron usage to new content added over time using regression analysis. Main Results – As the library acquired e-reference titles, dynamic title subscriptions added to the collection were associated with 2,246 to 4,635 views per subscription while static title additions were associated with 8 to 123 views per purchase. The author also found that there was a strong linear relationship between views and dynamic titles added to the collection (R2=0.79 and a very weak linear relationship (R2=0.18 with views when static titles are added to the collection. Regression analysis of dynamic e-reference collections revealed that the number of titles added to each collection was strongly associated with views of the material (R2=0.99, while static e-reference collections were less strongly linked (R2=0.43. Conclusion – Dynamic e-reference titles and collections experienced increases in usage each year while static titles and collections experienced decreases in usage. This indicates that collections and titles that offer new content to users each year will continue to see growth in usage while static

  13. TP53 codon 72 polymorphism in pigmentary phenotypes

    Indian Academy of Sciences (India)

    Kárita Antunes Costa; Lidia Andreu Guillo

    2012-03-01

    The p53 protein exerts different cellular functions, and recent findings have demonstrated its influence on the cascade of skin pigmentation during UV exposure. Among TP53 gene polymorphisms, the most studied is the G to C transversion in exon 4 at codon 72, which results in three distinct genotypes, Arg/Arg, Pro/Pro and Arg/Pro, each one encoding different p53 isoforms. Therefore, this study aimed to determine the relationship between TP53 codon 72 polymorphism and skin protection against sunburn. Genomic DNA was extracted from peripheral blood samples and genotyping was performed by PCR and confirmed by restriction enzyme digestion. The genotype frequency was 50% for Arg/Arg and 14.6% for Pro/Pro genotype. The frequency of heterozygous subjects was 35.4%. In our population, p53 genotypes were in Hardy–Weinberg (HW) equilibrium ($\\chi^{2}_{\\text{HM}}$ < 3.84), showing a predominance of arginine allele (total Arg allele frequency of 68%). No significant association between p53 genotype and skin colour, hair or eye colour and susceptibility to sun exposure was found. However, further analysis demonstrated a significant association between the genotype Pro/Pro and blue/green eyes among participants who presented redness (=0.016). Our findings indicate susceptibility to sun exposure when this phenotype (eye colour) occurs simultaneously with Pro/Pro genotype.

  14. 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.

  15. To Use or Not to Use: Computer-Assisted Qualitative Data Analysis Software Usage among Early-Career Sociologists in Croatia

    Directory of Open Access Journals (Sweden)

    Petra Rodik

    2015-01-01

    Full Text Available In this article we critically analyse the usage of computer-assisted qualitative data analysis software (CAQDAS among early-career sociology researchers in Croatia. In Croatia, the CAQDAS community is very small and is dominated by problems of great expectations coming from early-career researchers. This is elaborated through a case study that addresses issues of spread and availability of CAQDAS, opportunity for its usage, reasons why early-career researchers decide to use it or not and grounds for their decisions for use of a particular software package. The perceived advantages and limitations of CAQDAS are analysed and some misconceptions about CAQDAS are contextualised and related to the dominant quantitative research framework in Croatian sociology. The broadening of the number of qualitative researchers in the sociological community in Croatia, together with more educational programmes on CAQDAS, which would highlight reflexive usage of software, open perspectives for strengthening of qualitative research in Croatia. URN: http://nbn-resolving.de/urn:nbn:de:0114-fqs1501127

  16. 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.

  17. A 2-D graphical representation of protein sequences based on nucleotide triplet codons

    Science.gov (United States)

    Bai, Fenglan; Wang, Tianming

    2005-09-01

    Graphical representation of DNA provides a simple way of viewing, sorting and comparing various gene structures. A 2-D graphical representation of protein sequences based on nucleotide triplet codons has been derived for similarity analysis of protein sequences. This approach is based on a graphical representation of triplets of DNA in which the interior of the left half plane of the complex plane is used to accommodate 64 sites for the 64 codons. We associate a directed curve, numerical value, or matrix with a protein as a descriptor. The approach is illustrated on the Homo sapiens X-linked nuclear protein (ATRX) gene.

  18. Definite Article Usage across Varieties of English

    Science.gov (United States)

    Wahid, Ridwan

    2013-01-01

    This paper seeks to explore the extent of definite article usage variation in several varieties of English based on a classification of its usage types. An annotation scheme based on Hawkins and Prince was developed for this purpose. Using matching corpus data representing Inner Circle varieties and Outer Circle varieties, analysis was made on…

  19. Codon optimization of Candida rugosa lip1 gene for improving expression in Pichia pastoris and biochemical characterization of the purified recombinant LIP1 lipase.

    Science.gov (United States)

    Chang, Shu-Wei; Lee, Guan-Chiun; Shaw, Jei-Fu

    2006-02-08

    An important industrial enzyme, Candida rugosa lipase (CRL) possesses several different isoforms encoded by the lip gene family (lip1-lip7), in which the recombinant LIP1 is the major form of the CRL multigene family. Previously, 19 of the nonuniversal serine codons (CTG) of the lip1 gene hav been successfully converted into universal serine codons (TCT) by overlap extension PCR-based multiple-site-directed mutagenesis to express an active recombinant LIP1 in the yeast Pichia pastoris. To improve the expression efficiency of recombinant LIP1 in P. pastoris, a regional synthetic gene fragment of lip1 near the 5' end of a transcript has been constructed to match P. pastoris-preferred codon usage for simple scale-up fermentation. The present results show that the production level (152 mg/L) of coLIP1 (codon-optimized LIP1) has an overall improvement of 4.6-fold relative to that (33 mg/L) of non-codon-optimized LIP1 with only half the cultivation time of P. pastoris. This finding demonstrates that the regional codon optimization the lip1 gene fragment at the 5' end can greatly increase the expression level of recombinant LIP1 in the P. pastoris system. More distinct biochemical properties of the purified recombinant LIP1 for further industrial applications are also determined and discussed in detail.

  20. Usage Record Format Recommendation

    CERN Document Server

    Nilsen, J.K.; Muller-Pfeerkorn, R

    2013-01-01

    For resources to be shared, sites must be able to exchange basic accounting and usage data in a common format. This document describes a common format which enables the exchange of basic accounting and usage data from different resources. This record format is intended to facilitate the sharing of usage information, particularly in the area of the accounting of jobs, computing, memory, storage and cloud usage but with a structure that allows an easy extension to other resources. This document describes the Usage Record components both in natural language form and annotated XML. This document does not address how these records should be used, nor does it attempt to dictate the format in which the accounting records are stored. Instead, it denes a common exchange format. Furthermore, nothing is said regarding the communication mechanisms employed to exchange the records, i.e. transport layer, framing, authentication, integrity, etc.

  1. Comparative analysis of different AES implementation techniques for efficient resource usage and better performance of an FPGA

    Directory of Open Access Journals (Sweden)

    Umer Farooq

    2017-07-01

    Full Text Available Over the past few years, cryptographic algorithms have become increasingly important. Advanced Encryption Standard (AES algorithm was introduced in early 2000. It is widely adopted because of its easy implementation and robust security. In this work, AES is implemented on FPGA using five different techniques. These techniques are based on optimized implementation of AES on FPGA by making efficient resource usage of the target device. Experimental results obtained are quite varying in nature. They range from smallest (suitable for area critical application to fastest (suitable for performance critical applications implementation. Finally, technique making efficient usage of resources leads to frequency of 886.64 MHz and throughput of 113.5 Gb/s with moderate resource consumption on a Spartan-6 device. Furthermore, comparison between proposed technique and existing work shows that our technique has 32% higher frequency, while consuming 2.63× more slice LUTs, 8.33× less slice registers, and 12.59× less LUT-FF pairs.

  2. Correlation between prion protein gene codon 129 polymorphism and late-onset Alzheimer's disease

    Institute of Scientific and Technical Information of China (English)

    Hairong Qian; Luning Wang; Xiaokun Qi; Jianwei Liu; Jing Liu; Ling Ye; Hengge Xie; Wei Wang; Feng Qiu

    2009-01-01

    BACKGROUND:Studies addressing the correlation between prion protein gene codon 129 polymorphism,Alzheimer's disease,and cognitive disorders have mainly focused on Caucasians.However,prion protein gene codon 129 polymorphism is thought to also affect the Chinese Han and Wei populations.OBJECTIVE:To analyze the differences of prion protein gene codon 129 distribution among the elderly Chinese Han,East Asian,and Caucasian populations,and to study the correlation between prion protein gene codon 129 distribution and late-onset Alzheimer's disease.DESIGN,TIME AND SETTING:A gene polymorphism analysis was performed in the Institute of Geriatrics,General Hospital of Chinese PLA between January 2006 and January 2007.PARTICIPANTS:A total of 152 elderly Chinese Han people were selected from the Beijing Troop Cadre's Sanitarium.Among them,60 patients with late-onset Alzheimer's disease,with a mean age of (82±7) years (range 67-94 years) and disease course of (5.9±4.4) years,comprising 44 males with a mean age of (83±7) years and 16 females with a mean age of (78±7) years,were selected for the case group.An additional 92 healthy elderly subjects,with a mean of (76±9) years (range 60-94 years),comprising 76 males with a mean age of (77±9) years and 16 females with a mean age of (70±8) years,were selected for the control group.There were no significant differences in age and gender between the two groups (P>0.05).METHODS:DNA was extracted from peripheral blood leukocytes using routine phenol/chloroform methodology.Prion protein gene codon 129 polymorphism and ApoE polymorphism were measured using PCR-restriction fragment length polymorphism.The ApoEε allele was considered the standard for analyzing correlations between prion protein gene codon 129 polymorphism and late-onset Alzheimer's disease.MAIN OUTCOME MEASURES:Prion protein gene codon 129 distribution;correlation between genotypic frequency and allele frequency of prion protein gene codon 129 with Alzheimer

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

    Science.gov (United States)

    2016-09-20

    case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives...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...17. Gingold H, et al. (2014) A dual program for translation regulation in cellular pro- liferation and differentiation. Cell 158(6):1281–1292. 18

  4. Two new beta0-thalassemic mutations: a deletion (-CC) at codon 142 or overlapping codons 142-143, and an insertion (+T) at codon 45 or overlapping codons 44-45/45-46 of the beta-globin gene.

    Science.gov (United States)

    Lacan, Philippe; Aubry, Martine; Couprie, Nicole; Francina, Alain

    2007-01-01

    We report here two new beta(0)-thalassemic mutations. In the first case, a deletion of two nucleotides (-CC) at codon 142 was found in a French Caucasian woman. In the second case, an insertion of a single nucleotide (+T) at codon 45 was found in a Turkish girl. In both cases, no dominant thalassemia-like phenotype was observed.

  5. An Analysis of the Relationship Between Co-regulation and Interaction Proteins based on Novel 4-Dim Codons Method%基于创新的四维密码方法分析共调控与蛋白互作关系

    Institute of Scientific and Technical Information of China (English)

    宿菲; 张帆; 吴超; 肖雪; 宿晟阳; 李霞

    2008-01-01

    Objective To dig co-regulation and interaction proteins pairs,and to investigate the association tendency of co-regulation and proteins interaction based on novel 4-D codons method.Methods A novel association method based on 4-D codons is proposed,and is used to 2000 correlative colon carcinoma genes.Results Interacting-protein pairs,in which the proteins are co-regulated,tend to be more significant than at random,The more intense,the co-regulated is getting,the more distinct the interacting proteins tending to be co-regulated is.Conclusion According to the association analysis method based on 4-D codons,the article analyzes the association tendency between co-regulation and protein interacting.%目的 基于创新的四维密码子的方法挖掘共调控且互作的基因对,研究共调控与蛋白互作之间的关联趋势.方法 我们提出了创新的基于四维密码子的关联分析方法,并把此方法应用于与结肠癌相关的2000个疾病基因.结果 发现共调控的互作蛋白对比随机情况下显著;随着共调控强度的增强,蛋白间互作趋势越来越明显.结论 基于创新的四维密码子的关联分析方法,能够研究共调控与蛋白互作的关联趋势.

  6. Reduction of computer usage costs in predicting unsteady aerodynamic loadings caused by control surface motions: Analysis and results

    Science.gov (United States)

    Rowe, W. S.; Sebastian, J. D.; Petrarca, J. R.

    1979-01-01

    Results of theoretical and numerical investigations conducted to develop economical computing procedures were applied to an existing computer program that predicts unsteady aerodynamic loadings caused by leading and trailing edge control surface motions in subsonic compressible flow. Large reductions in computing costs were achieved by removing the spanwise singularity of the downwash integrand and evaluating its effect separately in closed form. Additional reductions were obtained by modifying the incremental pressure term that account for downwash singularities at control surface edges. Accuracy of theoretical predictions of unsteady loading at high reduced frequencies was increased by applying new pressure expressions that exactly satisified the high frequency boundary conditions of an oscillating control surface. Comparative computer result indicated that the revised procedures provide more accurate predictions of unsteady loadings as well as providing reduction of 50 to 80 percent in computer usage costs.

  7. 基于SAS的Web使用日志用户聚类分析%User Cluster Analysis of Web Usages Logs Based on SAS

    Institute of Scientific and Technical Information of China (English)

    欧阳烽

    2013-01-01

    The user cluster Analysis of Web Usages Logs based on SAS is the data of Web Usages Logs for data conversion, get-ting the user transaction table which is pre-formed after the handling of the corresponding data, then making the user cluster anal-ysis through the SAS data mining tools. Digital resources are reasonably procured and managed according to the demands of dif-ferent users on digital resources. Personalized services can be provided for different users.%基于SAS的Web使用日志用户聚类分析,即通过SAS数据挖掘工具将由Web使用日志数据经过数据转换和数据预处理后形成的用户事务表数据运用不同的方法进行聚类分析,以达到根据不同类别用户的需求对数字资源进行合理的采购和管理,为用户提供个性化服务的目的。

  8. High frequency of the HRAS oncogene codon 12 mutation in Macedonian patients with urinary bladder cancer

    Directory of Open Access Journals (Sweden)

    Sasho Panov

    2004-01-01

    Full Text Available Point mutations at codon 12 of the HRAS (v-Ha-ras Harvey rat sarcoma viral oncogene homolog oncogene are one of the best defined and widely studied molecular genetic events in transitional cell carcinoma (TCC of the urinary bladder. The aim of this study was to use the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP analysis of paraffin-embedded tissue-derived DNA to determine the frequency of the HRAS oncogene G ->T codon 12 mutation in TCC patients being treated at the University Urology Clinic in Skopje, Republic of Macedonia. DNA isolated from paraffin-embedded tissue (PET surgically removed TCC specimens of 62 (81.58% out of 76 patients were successfully amplified, the remaining 14 (18.42% showing compromised DNA integrity. The codon 12 mutation of the HRAS oncogene was found in 24 (38.71% out of 62 successfully tested TCC urinary bladder samples. No significant relationship between the mutation frequency and the histopathological grade of tumor differentiation was detected (chi² = 0.044; p = 0.978. The relatively high frequency of mutations found in our study was comparable with some of the previously reported data obtained by this and/or other PCR-based methods. This highly sensitive and specific PCR-RFLP analysis was demonstrated to be a suitable method for the detection of mutations at codon 12 of the HRAS oncogene in PET samples of urinary bladder TCC.

  9. Differences in smartphone usage

    DEFF Research Database (Denmark)

    Gustarini, Mattia; Scipioni, Marcello Paolo; Fanourakis, Marios

    2016-01-01

    We analyze the users’ intimacy to investigate the differences in smartphone usage, considering the user’s location and number and kind of people physically around the user. With a first user study we (1) validate the intimacy concept, (2) evaluate its correlation to smartphone usage features and (3......-time features are predictive for the intimacy, and other smartphone-based features can improve the intimacy prediction accuracy....

  10. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences

    Directory of Open Access Journals (Sweden)

    Bauer Margarete

    2004-10-01

    Full Text Available Abstract Background In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge of basic biological processes. The central problem of this so called metagenome-approach is that the cloned fragments often lack suitable phylogenetic marker genes, rendering the identification of clones that are likely to originate from the same genome difficult or impossible. In such cases, the analysis of intrinsic DNA-signatures like tetranucleotide frequencies can provide valuable hints on fragment affiliation. With this application in mind, the TETRA web-service and the TETRA stand-alone program have been developed, both of which automate the task of comparative tetranucleotide frequency analysis. Availability: http://www.megx.net/tetra Results TETRA provides a statistical analysis of tetranucleotide usage patterns in genomic fragments, either via a web-service or a stand-alone program. With respect to discriminatory power, such an analysis outperforms the assignment of genomic fragments based on the (G+C-content, which is a widely-used sequence-based measure for assessing fragment relatedness. While the web-service is restricted to the calculation of correlation coefficients between tetranucleotide usage patterns of submitted DNA sequences, the stand-alone program generates a much more detailed output, comprising all raw data and graphical plots. The stand-alone program is controlled via a graphical user interface and can batch-process a multitude of sequences. Furthermore, it comes with pre-computed tetranucleotide usage patterns for 166 prokaryote chromosomes, providing a useful reference dataset and source for data-mining. Conclusions Up to now, the analysis of skewed oligonucleotide distributions within DNA sequences is not a commonly used tool within metagenomics. With the TETRA web-service and stand

  11. Is there an improvement of antibiotic use in China? Evidence from the usage analysis of combination antibiotic therapy for type I incisions in 244 hospitals.

    Science.gov (United States)

    Zhou, Wen-Juan; Luo, Zhen-Ni; Tang, Chang-Min; Zou, Xiao-Xu; Zhao, Lu; Fang, Peng-Qian

    2016-10-01

    The improvement of antibiotic rational use in China was studied by usage analysis of combination antibiotic therapy for type I incisions in 244 hospitals. Five kinds of hospitals, including general hospital, maternity hospital, children's hospital, stomatological hospital and cancer hospital, from 30 provinces were surveyed. A systematic random sampling strategy was employed to select outpatient prescriptions and inpatient cases in 2011 and 2012. A total of 29 280 outpatient prescriptions and 73 200 inpatient cases from 244 hospitals in each year were analyzed. Data were collected with regards to the implementation of the national antibiotic stewardship program (NASP), the overall usage and the prophylactic use of antibiotic for type I incisions. Univariate analysis was used for microbiological diagnosis rate before antimicrobial therapy, prophylactic use of antibiotics for type I incision operation, and so on. For multivariate analysis, the use of antibiotics was dichotomized according to the guidelines, and entered as binary values into logistic regression analysis. The results were compared with the corresponding criteria given by the guidelines of this campaign. The antibiotic stewardship in China was effective in that more than 80% of each kind of hospitals achieved the criteria of recommended antibiotics varieties. Hospital type appeared to be a factor statistically associated with stewardship outcome. The prophylactic use of antibiotics on type I incision operations decreased by 16.22% (Pantibiotic therapy for type I incisions was also decreased. Region and bed size were the main determinants on surgical prophylaxis for type I incision. This national analysis of hospitals on antibiotic use and stewardship allows relevant comparisons for bench marking. More efforts addressing the root cause of antibiotics abuse would continue to improve the rational use of antibiotics in China.

  12. Usage of NASA's Near Real-Time Solar and Meteorological Data for Monitoring Building Energy Systems Using RETScreen International's Performance Analysis Module

    Science.gov (United States)

    Stackhouse, Paul W., Jr.; Charles, Robert W.; Chandler, William S.; Hoell, James M.; Westberg, David; Zhang, Taiping; Ziegler, Urban; Leng, Gregory J.; Meloche, Nathalie; Bourque, Kevin

    2012-01-01

    This paper describes building energy system production and usage monitoring using examples from the new RETScreen Performance Analysis Module, called RETScreen Plus. The module uses daily meteorological (i.e., temperature, humidity, wind and solar, etc.) over a period of time to derive a building system function that is used to monitor building performance. The new module can also be used to target building systems with enhanced technologies. If daily ambient meteorological and solar information are not available, these are obtained over the internet from NASA's near-term data products that provide global meteorological and solar information within 3-6 days of real-time. The accuracy of the NASA data are shown to be excellent for this purpose enabling RETScreen Plus to easily detect changes in the system function and efficiency. This is shown by several examples, one of which is a new building at the NASA Langley Research Center that uses solar panels to provide electrical energy for building energy and excess energy for other uses. The system shows steady performance within the uncertainties of the input data. The other example involves assessing the reduction in energy usage by an apartment building in Sweden before and after an energy efficiency upgrade. In this case, savings up to 16% are shown.

  13. The Usage of Social Networking Sites by Medical Students for Educational Purposes: A Meta-analysis and Systematic Review.

    Science.gov (United States)

    Guraya, Salman Y

    2016-07-01

    Online social networking sites (SNSs) (e.g., Facebook, MySpace, Flickr, Twitter and YouTube) have emerged as rapidly growing mechanisms to exchange personal and professional information among university students. This research aims to determine the medical students' extent of usage of SNSs for educational purposes. Educational Resources Information Centre (ERIC), Cumulative Index of Nursing and Allied Health Literature (CINAHL), the Cochrane library, and Excerpta Medica Data Base (EMBASE) were searched to retrieve articles from 2004 to 2014, applying predefined search terms and inclusion criteria. The extracted 10 articles were outlined in a narrative synthesis of Quality, Utility, Extent, Strength, Target and Setting of the evidence (QUESTS). Majority (75%) of the respondents admitted using SNSs, whereas 20% used these sites for sharing academic and educational information. No single study explored the impact of the SNSs on the academic performance. Understanding and knowledge of the significant use of SNSs by the medical students demand inclusion of such domains in medical curricula. This will train tomorrow's doctors in fostering their skills of digital technology for educational purposes.

  14. Analysis of commode grab bar usage for the monitoring of older adults in the smart home environment.

    Science.gov (United States)

    Arcelus, Amaya; Holtzman, Megan; Goubran, Rafik; Sveistrup, Heidi; Guitard, Paulette; Knoefel, Frank

    2009-01-01

    The occurrence of falls inside the home is a common yet potentially hazardous issue for adults as they age. Even with the installation of physical aids such as grab bars, weight transfers on and off a toilet or bathtub can become increasingly difficult as a person's level of physical mobility and sense of balance deteriorate. Detecting this deterioration becomes an important goal in fall prevention within a smart home. This paper develops an unobtrusive method of analyzing the usage of toilet grab bars using pressure sensors embedded into the arm rests of a commode. Clinical parameters are successfully extracted automatically from a series of stand-to-sit (StSi) and sit-to-stand (SiSt) transfers performed by a trial group of young and older adults. A preliminary comparison of the parameters indicates differences between the two groups, and aligns well with published characteristics obtained using accelerometers worn on the body. The unobtrusive nature of this method provides a useful tool to be incorporated into a system of continuous monitoring of older adults within the smart home environment.

  15. The usage of social networking sites by medical students for educational purposes: A meta-analysis and systematic review

    Directory of Open Access Journals (Sweden)

    Salman Y Guraya

    2016-01-01

    Full Text Available Background: Online social networking sites (SNSs (e.g., Facebook, MySpace, Flickr, Twitter and YouTube have emerged as rapidly growing mechanisms to exchange personal and professional information among university students. This research aims to determine the medical students′ extent of usage of SNSs for educational purposes. Materials and Methods: Educational Resources Information Centre (ERIC, Cumulative Index of Nursing and Allied Health Literature (CINAHL, the Cochrane library, and Excerpta Medica Data Base (EMBASE were searched to retrieve articles from 2004 to 2014, applying predefined search terms and inclusion criteria. The extracted 10 articles were outlined in a narrative synthesis of Quality, Utility, Extent, Strength, Target and Setting of the evidence (QUESTS. Results: Majority (75% of the respondents admitted using SNSs, whereas 20% used these sites for sharing academic and educational information. No single study explored the impact of the SNSs on the academic performance. Conclusion: Understanding and knowledge of the significant use of SNSs by the medical students demand inclusion of such domains in medical curricula. This will train tomorrow′s doctors in fostering their skills of digital technology for educational purposes.

  16. EBSCO's Usage Consolidation Attempts to Streamline Gathering, Storage, and Reporting of Usage Statistics

    Science.gov (United States)

    Remy, Charlie

    2012-01-01

    This paper provides an overview of EBSCO's new Usage Consolidation product designed to streamline the harvesting, storage, and analysis of usage statistics from electronic resources. Strengths and weaknesses of the product are discussed as well as an early beta partner's experience. In the current atmosphere of flat or declining budgets, libraries…

  17. EBSCO's Usage Consolidation Attempts to Streamline Gathering, Storage, and Reporting of Usage Statistics

    Science.gov (United States)

    Remy, Charlie

    2012-01-01

    This paper provides an overview of EBSCO's new Usage Consolidation product designed to streamline the harvesting, storage, and analysis of usage statistics from electronic resources. Strengths and weaknesses of the product are discussed as well as an early beta partner's experience. In the current atmosphere of flat or declining budgets, libraries…

  18. A thermodynamic theory of codon bias in viral genes.

    Science.gov (United States)

    Rowe, G W; Trainor, L E

    1983-03-21

    The relationship between degeneracy in the genetic code and the occurrence of a strong codon bias is examined, with particular reference to a group of viral genomes. The present paper shows how codon bias may have been imposed by thermodynamic considerations at the time the primitive DNA first formed in the primordial soup. Using a four-state Ising-like model with stacking interactions between successive base pairs, we show how primeval periodic DNA polymers could have arisen the remnants of which are still observed in codon biases today.

  19. Preliminary analysis of the mitochondrial genome evolutionary pattern in primates

    Institute of Scientific and Technical Information of China (English)

    Liang ZHAO; Xingtao ZHANG; Xingkui TAO; Weiwei WANG; Ming LI

    2012-01-01

    Since the birth of molecular evolutionary analysis,primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique features.Surprisingly,to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of primates.Here,we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from GenBank.The results revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons.Likewise,an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes.Within 13 protein-coding genes,the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence,while synonymous changes differed only for individual genes,indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites.Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes,and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias.Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene,consistent with near neutrality.Recombination tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate species.Thus,with the exception of rate heterogeneity among mitochondrial genes,evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.

  20. Preliminary analysis of the mitochondrial genome evolutionary pattern in primates.

    Science.gov (United States)

    Zhao, Liang; Zhang, Xingtao; Tao, Xingkui; Wang, Weiwei; Li, Ming

    2012-08-01

    Since the birth of molecular evolutionary analysis, primates have been a central focus of study and mitochondrial DNA is well suited to these endeavors because of its unique features. Surprisingly, to date no comprehensive evaluation of the nucleotide substitution patterns has been conducted on the mitochondrial genome of primates. Here, we analyzed the evolutionary patterns and evaluated selection and recombination in the mitochondrial genomes of 44 Primates species downloaded from GenBank. The results revealed that a strong rate heterogeneity occurred among sites and genes in all comparisons. Likewise, an obvious decline in primate nucleotide diversity was noted in the subunit rRNAs and tRNAs as compared to the protein-coding genes. Within 13 protein-coding genes, the pattern of nonsynonymous divergence was similar to that of overall nucleotide divergence, while synonymous changes differed only for individual genes, indicating that the rate heterogeneity may result from the rate of change at nonsynonymous sites. Codon usage analysis revealed that there was intermediate codon usage bias in primate protein-coding genes, and supported the idea that GC mutation pressure might determine codon usage and that positive selection is not the driving force for the codon usage bias. Neutrality tests using site-specific positive selection from a Bayesian framework indicated no sites were under positive selection for any gene, consistent with near neutrality. Recombination tests based on the pairwise homoplasy test statistic supported complete linkage even for much older divergent primate species. Thus, with the exception of rate heterogeneity among mitochondrial genes, evaluating the validity assumed complete linkage and selective neutrality in primates prior to phylogenetic or phylogeographic analysis seems unnecessary.

  1. UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota.

    Science.gov (United States)

    Campbell, James H; O'Donoghue, Patrick; Campbell, Alisha G; Schwientek, Patrick; Sczyrba, Alexander; Woyke, Tanja; Söll, Dieter; Podar, Mircea

    2013-04-02

    The composition of the human microbiota is recognized as an important factor in human health and disease. Many of our cohabitating microbes belong to phylum-level divisions for which there are no cultivated representatives and are only represented by small subunit rRNA sequences. For one such taxon (SR1), which includes bacteria with elevated abundance in periodontitis, we provide a single-cell genome sequence from a healthy oral sample. SR1 bacteria use a unique genetic code. In-frame TGA (opal) codons are found in most genes (85%), often at loci normally encoding conserved glycine residues. UGA appears not to function as a stop codon and is in equilibrium with the canonical GGN glycine codons, displaying strain-specific variation across the human population. SR1 encodes a divergent tRNA(Gly)UCA with an opal-decoding anticodon. SR1 glycyl-tRNA synthetase acylates tRNA(Gly)UCA with glycine in vitro with similar activity compared with normal tRNA(Gly)UCC. Coexpression of SR1 glycyl-tRNA synthetase and tRNA(Gly)UCA in Escherichia coli yields significant β-galactosidase activity in vivo from a lacZ gene containing an in-frame TGA codon. Comparative genomic analysis with Human Microbiome Project data revealed that the human body harbors a striking diversity of SR1 bacteria. This is a surprising finding because SR1 is most closely related to bacteria that live in anoxic and thermal environments. Some of these bacteria share common genetic and metabolic features with SR1, including UGA to glycine reassignment and an archaeal-type ribulose-1,5-bisphosphate carboxylase (RubisCO) involved in AMP recycling. UGA codon reassignment renders SR1 genes untranslatable by other bacteria, which impacts horizontal gene transfer within the human microbiota.

  2. Beyond usage: understanding the use of electronic journals on the basis of information activity analysis. Electronic journals, Use studies, Information activity, Scientific communication

    Directory of Open Access Journals (Sweden)

    Annaïg Mahé

    2004-01-01

    Full Text Available In this article, which reports the second part of a two-part study of the use of electronic journals by researchers in two French research institutions, we attempt to explain the integration of the use of electronic journals in the scientists' information habits, going beyond usage analysis. First, we describe how the development of electronic journals use follows a three-phase innovation process - research-development, first uses, and technical acculturation. Then, we attempt to find more significant explanatory factors, and emphasis is placed on the wider context of information activity. Three main information activity types are outlined - marginal, parallel, and integrated. Each of these types corresponds to a particular attitude towards scientific information and to different levels of electronic journal use.

  3. World Technology Usage Lags

    OpenAIRE

    Diego A. Comin; Bart Hobijn; Emilie Rovito

    2006-01-01

    We present evidence on the differences in the intensity with which ten major technologies are used in 185 countries across the world. We do so by calculating how many years ago these technologies were used in the U.S. at the same intensity as they are used in the countries in our sample. We denote these time lags as technology usage lags and compare them with lags in real GDP per capita. We find that (i) technology usage lags are large, often comparable to lags in real GDP per capita, (ii) us...

  4. French grammar and usage

    CERN Document Server

    Hawkins, Roger

    2015-01-01

    Long trusted as the most comprehensive, up-to-date and user-friendly grammar available, French Grammar and Usage is a complete guide to French as it is written and spoken today. It includes clear descriptions of all the main grammatical phenomena of French, and their use, illustrated by numerous examples taken from contemporary French, and distinguishes the most common forms of usage, both formal and informal.Key features include:Comprehensive content, covering all the major structures of contemporary French User-friendly organisation offering easy-to-find sections with cross-referencing and i

  5. The Effect of Codon Mismatch on the Protein Translation System.

    Directory of Open Access Journals (Sweden)

    Dinglin Zhang

    Full Text Available 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.

  6. Distribution of ADAT-Dependent Codons in the Human Transcriptome

    Directory of Open Access Journals (Sweden)

    Àlbert Rafels-Ybern

    2015-07-01

    Full Text Available Nucleotide modifications in the anticodons of transfer RNAs (tRNA play a central role in translation efficiency, fidelity, and regulation of translation, but, for most of these modifications, the details of their function remain unknown. The heterodimeric adenosine deaminases acting on tRNAs (ADAT2-ADAT3, or ADAT are enzymes present in eukaryotes that convert adenine (A to inosine (I in the first anticodon base (position 34 by hydrolytic deamination. To explore the influence of ADAT activity on mammalian translation, we have characterized the human transcriptome and proteome in terms of frequency and distribution of ADAT-related codons. Eight different tRNAs can be modified by ADAT and, once modified, these tRNAs will recognize NNC, NNU and NNA codons, but not NNG codons. We find that transcripts coding for proteins highly enriched in these eight amino acids (ADAT-aa are specifically enriched in NNC, NNU and NNA codons. We also show that the proteins most enriched in ADAT-aa are composed preferentially of threonine, alanine, proline, and serine (TAPS. We propose that the enrichment in ADAT-codons in these proteins is due to the similarities in the codons that correspond to TAPS.

  7. Drug usage analysis and health care resources consumption in naïve patients with rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Sangiorgi D

    2015-11-01

    Full Text Available Diego Sangiorgi,1 Maurizio Benucci,2 Carmela Nappi,3 Valentina Perrone,1 Stefano Buda,1 Luca Degli Esposti11CliCon S.r.l., Health, Economics and Outcomes Research, Ravenna, 2Unit of Rheumatology, S. Giovanni di Dio Hospital, Florence, 3Bristol Myers Squibb S.r.l., Rome, ItalyObjectives: The use of biologic agents has revolutionized the management of rheumatoid arthritis (RA in the past 2 decades. These biologic agents directly target molecules and cells involved in the pathogenesis of RA. The purpose of this study was to assess the usage of biologic agents in terms of persistence to treatment, dose escalation, and consumption of health care resources (hospitalizations, drugs, and outpatients service in the real clinical practice in naïve patients with RA.Methods: We conducted a real-world, retrospective, observational cohort study based on data obtained from administrative databases of three Local Health Units in Italy. The population included adults diagnosed with RA who had at least one prescription between January 1, 2009 and December 31, 2011, for a biologic that was approved for treatment of RA. The patients were followed for 12 months after enrollment. The clinical characteristics of the patients enrolled in this study were also investigated in the 1-year period before the index date. The main and secondary endpoints were evaluated only in biologic-naïve patients without switches. The overall health care costs for patients were evaluated.Results: A total of 594 patients met the study criteria (mean age 53.5±13.5, female:male ratio =3:1. Thirty-nine percent received etanercept, 25% adalimumab, 14% infliximab, 10% abatacept, 9% tocilizumab, and 3% golimumab. After 1 year of observation, patients showed similar use of other RA-related medication. For the naïve patients without switches, the persistence levels were: 78% for etanercept, 72% for tocilizumab, 71% for adalimumab, 69% for infliximab, and 64% for abatacept. For all agents, dose

  8. Vehicle usage verification system

    NARCIS (Netherlands)

    Scanlon, William G.; McQuiston, Jonathan; Cotton, Simon L.

    2012-01-01

    EN)A computer-implemented system for verifying vehicle usage comprising a server capable of communication with a plurality of clients across a communications network. Each client is provided in a respective vehicle and with a respective global positioning system (GPS) by which the client can determi

  9. RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies.

    Science.gov (United States)

    Tulloch, Fiona; Atkinson, Nicky J; Evans, David J; Ryan, Martin D; Simmonds, Peter

    2014-12-09

    Mutating RNA virus genomes to alter codon pair (CP) frequencies and reduce translation efficiency has been advocated as a method to generate safe, attenuated virus vaccines. However, selection for disfavoured CPs leads to unintended increases in CpG and UpA dinucleotide frequencies that also attenuate replication. We designed and phenotypically characterised mutants of the picornavirus, echovirus 7, in which these parameters were independently varied to determine which most influenced virus replication. CpG and UpA dinucleotide frequencies primarily influenced virus replication ability while no fitness differences were observed between mutants with different CP usage where dinucleotide frequencies were kept constant. Contrastingly, translation efficiency was unaffected by either CP usage or dinucleotide frequencies. This mechanistic insight is critical for future rational design of live virus vaccines and their safety evaluation; attenuation is mediated through enhanced innate immune responses to viruses with elevated CpG/UpA dinucleotide frequencies rather the viruses themselves being intrinsically defective.

  10. BIM Software Capability and Interoperability Analysis : An analytical approach toward structural usage of BIM software (S-BIM)

    OpenAIRE

    A. Taher, Ali

    2016-01-01

    This study focused on the structuralanalysis of BIM models. Different commercial software (Autodesk products and Rhinoceros)are presented through modelling and analysis of different structures with varying complexity,section properties, geometry, and material. Beside the commercial software, differentarchitectural and different tools for structural analysis are evaluated (dynamo, grasshopper,add-on tool, direct link, indirect link via IFC). BIM and Structural BIM (S-BIM)

  11. Ribosomal readthrough at a short UGA stop codon context triggers dual localization of metabolic enzymes in Fungi and animals.

    Directory of Open Access Journals (Sweden)

    Alina C Stiebler

    2014-10-01

    Full Text Available Translation of mRNA into a polypeptide chain is a highly accurate process. Many prokaryotic and eukaryotic viruses, however, use leaky termination of translation to optimize their coding capacity. Although growing evidence indicates the occurrence of ribosomal readthrough also in higher organisms, a biological function for the resulting extended proteins has been elucidated only in very few cases. Here, we report that in human cells programmed stop codon readthrough is used to generate peroxisomal isoforms of cytosolic enzymes. We could show for NAD-dependent lactate dehydrogenase B (LDHB and NAD-dependent malate dehydrogenase 1 (MDH1 that translational readthrough results in C-terminally extended protein variants containing a peroxisomal targeting signal 1 (PTS1. Efficient readthrough occurs at a short sequence motif consisting of a UGA termination codon followed by the dinucleotide CU. Leaky termination at this stop codon context was observed in fungi and mammals. Comparative genome analysis allowed us to identify further readthrough-derived peroxisomal isoforms of metabolic enzymes in diverse model organisms. Overall, our study highlights that a defined stop codon context can trigger efficient ribosomal readthrough to generate dually targeted protein isoforms. We speculate that beyond peroxisomal targeting stop codon readthrough may have also other important biological functions, which remain to be elucidated.

  12. Wie wird GMS Medizin – Bibliothek – Information genutzt? Analyse der Zugriffszahlen einer Open Access-Zeitschrift / Usage of "GMS Medizin – Bibliothek – Information": analysis of usage data from an Open Access journal

    Directory of Open Access Journals (Sweden)

    Bauer, Bruno

    2008-12-01

    Full Text Available In 2006 the journal "MEDIZIN – BIBLIOTHEK – INFORMATION" changed from the internet platform of the "Arbeitsgemeinschaft für Medizinisches Bibliothekswesen" (AGMB to the Open Access platform German Medical Science (GMS. The printed journal version ceased. Thitherto it was sent to all members of the AGMB. The editorial staff made a few arrangements in order to support acceptance and perceptibility of this journal, now issued electronic only. The published papers were included in the database of the Deutsches Bibliothekswesen (DABI and in the Directory of Open Access Journals (DOAJ Content. Furthermore current articles were introduced in MEDINFO, a weblog for medical librarians. The paper compares usage data trends from September 2005 to May 2008 for selected articles.

  13. Hepatitis B virus pre-S2 start codon mutations in Indonesian liver disease patients

    Institute of Scientific and Technical Information of China (English)

    Andi Utama; Marlinang Diarta Siburian; Ismail Fanany; Mariana Destila Bayu Intan; Rama Dhenni; Tri Shinta Kurniasih; Syafruddin AR Lelosuta

    2012-01-01

    AIM:To identify the prevalence of pre-S2 start codon mutations and to assess their association with liver disease progression.METHODS:The mutations were identified by direct sequencing from 73 asymptomatic carriers,66 chronic hepatitis (CH),66 liver cirrhosis (LC) and 63 hepatocellular carcinoma (HCC) patients.Statistical significances were determined using Fisher's exact test,x2 test,and t-test analyses whenever appropriate.Pre-S mutation as a risk factor for advanced liver disease was estimated by unconditional logistic regression model adjusted with age,sex,and hepatitis B e antigen (HBeAg).P <0.05 was considered significant.RESULTS:Mutation of the hepatitis B virus (HBV)pre-S2 start codon was found in 59 samples from 268subjects (22.0%),with higher prevalence in patients with cirrhosis 27/66 (40.9%) followed by HCC 18/63(28.6%),chronic hepatitis 12/66 (18.2%) and asymptomatic carriers 2/73 (2.7%) (P < 0.001).Logistic regression analysis showed that pre-S2 start codon mutation was an independent factor for progressive liver disease.Other mutations,at T130,Q132,and A138,were also associated with LC and HCC,although this was not statistically significant when adjusted for age,sex,and HBeAg.The prevalence of pre-S2 start codon mutation was higher in HBV/B than in HBV/C (23.0%vs 19.1%),whilst the prevalence of T130,Q132,and A138 mutation was higher in HBV/C than in HBV/B.The prevalence of pre-S2 start codon mutation was higher in LC (38.9%) and HCC (40.0%) than CH (5.6%)in HBeAg(+) group,but it was similar between CH,LC and HCC in HBeAg(-) group.CONCLUSION:Pre-S2 start codon mutation was higher in Indonesian patients compared to other Asian countries,and its prevalence was associated with advanced liver disease,particularly in HBeAg(+) patients.

  14. Codon Preference Optimization Increases Prokaryotic Cystatin C Expression

    Directory of Open Access Journals (Sweden)

    Qing Wang

    2012-01-01

    Full Text Available Gene expression is closely related to optimal vector-host system pairing in many prokaryotes. Redesign of the human cystatin C (cysC gene using the preferred codons of the prokaryotic system may significantly increase cysC expression in Escherichia coli (E. coli. Specifically, cysC expression may be increased by removing unstable sequences and optimizing GC content. According to E. coli expression system codon preferences, the gene sequence was optimized while the amino acid sequence was maintained. The codon-optimized cysC (co-cysC and wild-type cysC (wt-cysC were expressed by cloning the genes into a pET-30a plasmid, thus transforming the recombinant plasmid into E. coli BL21. Before and after the optimization process, the prokaryotic expression vector and host bacteria were examined for protein expression and biological activation of CysC. The recombinant proteins in the lysate of the transformed bacteria were purified using Ni2+-NTA resin. Recombinant protein expression increased from 10% to 46% based on total protein expression after codon optimization. Recombinant CysC purity was above 95%. The significant increase in cysC expression in E. coli expression produced by codon optimization techniques may be applicable to commercial production systems.

  15. Usage of Recycled Pet

    Directory of Open Access Journals (Sweden)

    A. Ebru Tayyar

    2010-01-01

    Full Text Available The increasing industrialization, urbanization and the technological development have caused to increase depletion of the natural resources and environmental pollution's problem. Especially, for the countries which have not enough space recycling of the waste eliminating waste on regular basis or decreasing the amount and volume of waste have provided the important advantages. There are lots of studies and projects to develop both protect resources and prevent environmental pollution. PET bottles are commonly used in beverage industry and can be reused after physical and chemical recycling processes. Usage areas of recycled PET have been developed rapidly. Although recycled PET is used in plastic industry, composite industry also provides usage alternatives of recycled PET. Textile is a suitable sector for recycling of some plastics made of polymers too. In this study, the recycling technologies and applications of waste PET bottles have been investigated and scientific works in this area have been summarized.

  16. A model for codon position bias in RNA editing

    CERN Document Server

    Liu, T; Liu, Tsunglin; Bundschuh, Ralf

    2005-01-01

    RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of {\\it Physarum polycephalum}, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in {\\it Physarum}. This suggests that the codon position bias in {\\it Physarum} is mainly a consequence of selection at the protein level.

  17. Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum.

    Science.gov (United States)

    Heaphy, Stephen M; Mariotti, Marco; Gladyshev, Vadim N; Atkins, John F; Baranov, Pavel V

    2016-11-01

    mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3' end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  18. Arсhaeomineralogy of Ancient Nonferrous Metallurgy Pieces of the Perm Region: Experience of Usage of Electron Microprobe Analysis

    Directory of Open Access Journals (Sweden)

    I. I. Chaykovsky

    2016-12-01

    Full Text Available A series of archaeological features has been studied by means of the scanning electronic microscopy. It was shown that due to the oxidation process, the surface layer is enriched with some elements, which were present at unaltered metal (Ag, Pb and those included later (As, Zn, Pb. It imposes meaningful limitation for use of the X-ray fluorescence and spectral analysis, which allow obtaining only total (patina + metal composition. Sixteen minerals (oxides, carbonates, sulphates, chlorides, phosphates, sulfides and native phases are established in patina composition. Tin bronze structure contains the impurities, which may be an evidence of import to Perm Region of tin and silver possibly from Altai, tin and lead possibly from Karelia during "harinsky" and "rodanovsky" cultures respectively. Various composition of the alloys used for casting and filigree witnesses that ancient metallurgists had known about alloys handling. The presence of barium and fluorine can tell us about composition of the used furnacecharge. The obtained data may be the basis for chemical-metallurgical typification of pieces from nonferrous (and noble metals.

  19. Analysis of Eye-Tracking Data with Regards to the Complexity of Flight Deck Information Automation and Management - Inattentional Blindness, System State Awareness, and EFB Usage

    Science.gov (United States)

    Dill, Evan T.; Young, Steven D.

    2015-01-01

    In the constant drive to further the safety and efficiency of air travel, the complexity of avionics-related systems, and the procedures for interacting with these systems, appear to be on an ever-increasing trend. While this growing complexity often yields productive results with respect to system capabilities and flight efficiency, it can place a larger burden on pilots to manage increasing amounts of information and to understand intricate system designs. Evidence supporting this observation is becoming widespread, yet has been largely anecdotal or the result of subjective analysis. One way to gain more insight into this issue is through experimentation using more objective measures or indicators. This study utilizes and analyzes eye-tracking data obtained during a high-fidelity flight simulation study wherein many of the complexities of current flight decks, as well as those planned for the next generation air transportation system (NextGen), were emulated. The following paper presents the findings of this study with a focus on electronic flight bag (EFB) usage, system state awareness (SSA) and events involving suspected inattentional blindness (IB).

  20. Codon 201 Mutation of DCC Gene and Tumor Biologic Behavior in Human Colorectal Carcinoma

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective To explore the relationship between a point mutation of codon 201 in deleted in colorectal carcinoma ( DCC) gene and the biological behavior of colorectal carcinoma. Methods Tumor tissues and matched adjacent normal colon mucosa collected in 35 patients during surgical resection for colorectal carcinoma were analyzed. Forty normal colon mucosa tissues obtained by biopsy from patients who had neither colorectal tumor nor a family history of colorectal cancer during colonscop ic examination were used as control. Codon 201 mutatian was detected with allele-specific PCR and a restriction enzyme digestion method. The tumors were reviewed as clinical data, tumor location, histology,metastasis, and pathological staging (Dukes classification). Results The frequency of mutation at codon 201 in tumor tissue and corresponding adjacent normal mucosa was 71.4 % and 60 %, respectively, and either of the rates was significantly higher than that of normal control(32.5 % ). The point mutation rate in tumor tissues did not differ from that in the corresponding normal adjacent tissues. Statistic analysis showed that the mutation rate had no relationship to the sex, age of the patients, the histological pattern , differentiation, and invasion depth of the tumors. However, 93. 8 % of the mutation rate in colorectal cancer with lymph node invasion and/or distant metastasis is significantly higher than 52. 6 % of mutant rate in colorectal cancer uithout lymph nodes invasion or metastasis ( P <0. 05). Conclusion The point mutation at codon 201 of DCC gene is an early genetic event in colorectal cancer, and play some role in invasion and metastasis of colorectal carcinoma. It may serve as a useful genetic marker for identifying higher risk patients with colorectal carcinoma.

  1. Codon 201 Mutation of DCC Gene and Tumor Biologic Behavior in Human Colorectal Carcinoma

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Objective To explore the relationship between a point mutation of codon 201 in deleted in colorectal carcinoma ( DCC) gene and the biological behavior of colorectal carcinoma. Methods Tumor tissues and matched adjacent normal colon mucosa collected in 35 patients during surgical resection for colorectal carcinoma were analyzed. Forty normal colon mucosa tissues obtained by biopsy from patients who had neither colorectal tumor nor a family history of colorectal cancer during colonscop ic examination were used as control. Codon 201 mutatian was detected with allele-specific PCR and a restriction enzyme digestion method. The tumors were reviewed as clinical data, tumor location, histology,metastasis, and pathological staging (Dukes classification). Results The frequency of mutation at codon 201 in tumor tissue and corresponding adjacent normal mucosa was 71.4 % and 60 %, respectively, and either of the rates was significantly higher than that of normal control(32.5 % ). The point mutation rate in tumor tissues did not differ from that in the corresponding normal adjacent tissues. Statistic analysis showed that the mutation rate had no relationship to the sex, age of the patients, the histological pattern , differentiation, and invasion depth of the tumors. However, 93. 8 % of the mutation rate in colorectal cancer with lymph node invasion and/or distant metastasis is significantly higher than 52. 6 % of mutant rate in colorectal cancer uithout lymph nodes invasion or metastasis ( P <0. 05). Conclusion The point mutation at codon 201 of DCC gene is an early genetic event in colorectal cancer, and play some role in invasion and metastasis of colorectal carcinoma. It may serve as a useful genetic marker for identifying higher risk patients with colorectal carcinoma.

  2. TP53 Codon 72 Heterozygosity May Promote MicrosatelliteInstability in Sporadic Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    Mehdi Nikbahkt Dastjerdi

    2010-01-01

    Full Text Available Objective: The polymorphic variants at codon 72 of the p53 gene, encoding prolineor arginine at residue 72, produce marked changes in the p53 structure. From theevidence that the DNA mismatch repair system and p53 interact to maintain genomicintegrity, we hypothesized that codon 72 variations may influence the prevalence ofmicrosatellite instability (MSI, a feature of malignancies associated with mismatchrepair deficiency in sporadic colorectal cancer.Materials and Methods: We investigated the frequency of MSI in three P53 codon72 genotypes using genomic DNAs from 144 paraffin blocks of sporadic colorectaladenocarcinomas by testing the BAT-26 poly(A marker. We used PCR-SSCP analysisto detect tumor sample MSI for the nonisotopic detection of deletions in the BAT-26 poly (A mononucleotide repeat. Associations between qualitative variables wereevaluated using the χ2-test. Statistical significance level was set to p ≤ 0.05.Results: MSI analysis revealed that 24.3% of the tumors (n=35 were MSI-positiveand 75.7% (n=109 were MSI-negative. The frequency of microsatellite instability inthe arginine/arginine, arginine/proline and proline/proline genotypes were 11 (16.9%,22 (36.1% and 2 (11.1% respectively. A significant difference in distribution of MSIwas found for the arginine/proline genotype compared with the grouped arginine/arginineand proline/proline genotypes (p=0.05.Conclusion: Our findings suggested that colorectal adenocarcinomas arising in individualswith the p53 codon 72 arginine/proline heterozygosity are more prone tomicrosatellite instability than those with other p53 genotypes. In our study, MSI wasimportant in the carcinogenesis of sporadic colorectal cancer arising in pro/arg heterozygotes.

  3. Zeolites and Usage Areas

    Directory of Open Access Journals (Sweden)

    Jale Gülen

    2012-06-01

    Full Text Available Zeolites are formed via several reactions from the minerals that consist of aluminium and silica. Zeolites, which have a growing significance in recent days are one of important industrial raw materials. As well as being used as a catalyst, theirability to do ion exchange and adsorption make them even more valuable. Zeolites are used in several industries such as energy, agriculture and animal husbandry, mining and metallurgy, construction, detergent, paper, etc. In this study, the definiton, formation and usage areas of zeolites are explained.

  4. Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells.

    Directory of Open Access Journals (Sweden)

    Antoine Nougairede

    2013-02-01

    Full Text Available Large-scale codon re-encoding represents a powerful method of attenuating viruses to generate safe and cost-effective vaccines. In contrast to specific approaches of codon re-encoding which modify genome-scale properties, we evaluated the effects of random codon re-encoding on the re-emerging human pathogen Chikungunya virus (CHIKV, and assessed the stability of the resultant viruses during serial in cellulo passage. Using different combinations of three 1.4 kb randomly re-encoded regions located throughout the CHIKV genome six codon re-encoded viruses were obtained. Introducing a large number of slightly deleterious synonymous mutations reduced the replicative fitness of CHIKV in both primate and arthropod cells, demonstrating the impact of synonymous mutations on fitness. Decrease of replicative fitness correlated with the extent of re-encoding, an observation that may assist in the modulation of viral attenuation. The wild-type and two re-encoded viruses were passaged 50 times either in primate or insect cells, or in each cell line alternately. These viruses were analyzed using detailed fitness assays, complete genome sequences and the analysis of intra-population genetic diversity. The response to codon re-encoding and adaptation to culture conditions occurred simultaneously, resulting in significant replicative fitness increases for both re-encoded and wild type viruses. Importantly, however, the most re-encoded virus failed to recover its replicative fitness. Evolution of these viruses in response to codon re-encoding was largely characterized by the emergence of both synonymous and non-synonymous mutations, sometimes located in genomic regions other than those involving re-encoding, and multiple convergent and compensatory mutations. However, there was a striking absence of codon reversion (<0.4%. Finally, multiple mutations were rapidly fixed in primate cells, whereas mosquito cells acted as a brake on evolution. In conclusion, random

  5. Media usage as health segmentation variables.

    Science.gov (United States)

    Rodgers, Shelly; Chen, Qimei; Duffy, Margaret; Fleming, Kenneth

    2007-03-01

    The purpose of this research is to contrast a traditional audience segmentation model that uses demographics and health evaluations against a model that uses these same variables plus media usage variables. The goal was to determine whether media usage variables - typically not used in health segmentation studies - add predictive power in determining health behaviors and attitudes. The results of the analysis showed an increase in the ability to predict health behaviors such as aspirin use, vitamin use, diet, and exercise, and suggest that there is predictive value for including media variables as part of the segmentation process. Implications for public health education and campaign planning are discussed.

  6. NAT Usage in Residential Broadband Networks

    Science.gov (United States)

    Maier, Gregor; Schneider, Fabian; Feldmann, Anja

    Many Internet customers use network address translation (NAT) when connecting to the Internet. To understand the extend of NAT usage and its implications, we explore NAT usage in residential broadband networks based on observations from more than 20,000 DSL lines. We present a unique approach for detecting the presence of NAT and for estimating the number of hosts connected behind a NAT gateway using IP TTLs and HTTP user-agent strings. Furthermore, we study when each of the multiple hosts behind a single NAT gateway is active. This enables us to detect simultaneous use. In addition, we evaluate the accuracy of NAT analysis techniques when fewer information is available.

  7. Sporforming probiotics and their usage in children

    Directory of Open Access Journals (Sweden)

    Marushko RV

    2015-05-01

    Full Text Available The data of literature about spore-forming probiotics, as well as their usage in the pathology of the gastrointestinal tract in children were sumerised. Analysis of the data allows us to recommend the preparation «Biosporin-Biopharma» for preventive measures and treatment of gastrointestinal tract diseases at all levels of children health care, including infants.

  8. [Smartphone usage among adolescents].

    Science.gov (United States)

    Körmendi, Attila

    2015-01-01

    Among our technological gadgets smartphones play the most important role, new generation devices offer other functions beyond calling (internet availability, computer games, music player, camera functions etc.) In everydays can be experienced that youth spend more and more time with their smartphones and despite the actuality of this issue there are no studies on the excessive smartphone usage in Hungary and we can find only a few international studies. Our goal is to examine smartphone usage in primary and secondary schools in Hajdu-Bihar county, Hungary and its relationship with personality traits. Our sample consist of 263 youth from primary and secondary schools. We measured the characteristics of smartphone using and attitudes with a Mobilephone Using Questionnare. Personality traits are measured with Impulsiveness, Venturesomeness, Empathy Scale. The Child Behavior Checklist gives information about peer relationships, mental state and emotions. Average phone using time is 4,48 hours per day regarding the whole sample. This mean for boys is 3,40 hour for girls 5,39 hour. Average phone using time is higher at 16 (6,35 hour per day). The most frequent used applications are calling and visiting community sites. There is no connection between phone using and grades. The smartphone using time per day shows a significant positive relationship with Impulsivity, Anxiety and Depression, Attention deficits and Somatic problems within 17-19 ages. One of the explanation of excessive smartphone using may be the frequent visiting of community sites. Mobile phones in this case raise the availability of addictive object (community site) therefore contribute to the development of community site addiction. The connection with impulsivity, somatic problems and attention deficits refer to the anxiety reducing role of smartphones within 17-19 ages.

  9. A Factor Analytic Study of the Internet Usage Scale

    Science.gov (United States)

    Monetti, David M.; Whatley, Mark A.; Hinkle, Kerry T.; Cunningham, Kerry T.; Breneiser, Jennifer E.; Kisling, Rhea

    2011-01-01

    This study developed an Internet Usage Scale (IUS) for use with adolescent populations. The IUS is a 26-item scale that measures participants' beliefs about how their Internet usage impacts their behavior. The sample for this study consisted of 947 middle school students. An exploratory factor analysis with varimax rotation was conducted on the…

  10. Changes in Word Usage Frequency May Hamper Intergenerational Comparisons of Vocabulary Skills: An Ngram Analysis of Wordsum, WAIS, and WISC Test Items

    Science.gov (United States)

    Roivainen, Eka

    2014-01-01

    Research on secular trends in mean intelligence test scores shows smaller gains in vocabulary skills than in nonverbal reasoning. One possible explanation is that vocabulary test items become outdated faster compared to nonverbal tasks. The history of the usage frequency of the words on five popular vocabulary tests, the GSS Wordsum, Wechsler…

  11. What Is Different about E-Books? A MINES for Libraries® Analysis of Academic and Health Sciences Research Libraries' E-Book Usage

    Science.gov (United States)

    Plum, Terry; Franklin, Brinley

    2015-01-01

    Building on the theoretical proposals of Kevin Guthrie and others concerning the transition from print books to e-books in academic and health sciences libraries, this paper presents data collected using the MINES for Libraries® e-resource survey methodology. Approximately 6,000 e-book uses were analyzed from a sample of e-resource usage at…

  12. What Is Different about E-Books? A MINES for Libraries® Analysis of Academic and Health Sciences Research Libraries' E-Book Usage

    Science.gov (United States)

    Plum, Terry; Franklin, Brinley

    2015-01-01

    Building on the theoretical proposals of Kevin Guthrie and others concerning the transition from print books to e-books in academic and health sciences libraries, this paper presents data collected using the MINES for Libraries® e-resource survey methodology. Approximately 6,000 e-book uses were analyzed from a sample of e-resource usage at…

  13. Teachers' Awareness and Usage of Non-Violent Strategies for the Maintenance of Discipline in Nigerian Secondary Schools: A Situational Analysis

    Science.gov (United States)

    Uzoechina, Gladys Oby; Oguegbu, Adaeze; Akachukwu, Esther; Nwasor, Victor Chekume

    2015-01-01

    This study sought to determine teachers' level of awareness and usage of non-violent strategies/interventions for the maintenance of discipline in secondary schools in Anambra State, Nigeria. Corporal punishment has become an unwritten sine qua non for the maintenance of school discipline--often the first thought that comes to the minds of…

  14. The AGG codon is translated slowly in E. coli even at very low expression levels

    DEFF Research Database (Denmark)

    Bonekamp, Fons; Jensen, Kaj Frank

    1988-01-01

    Data are presented which indicate that AGG codons for arginine are translated significantly more slowly than the CGU codons for the same amino acid even when their expression level from the probe is very low. The two types of codons were inser ted (three in tandem) on a multicopy plasmid in an ar...

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

    Directory of Open Access Journals (Sweden)

    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.

  16. [Polymorphism in codon 72 of the p53 gene and cervico-uterine cancer risk in Mexico].

    Science.gov (United States)

    Suárez-Rincón, Angel Emillo; Morán-Moguel, María Cristina; Montoya-Fuentes, Héctor; Gallegos-Arreola, Martha Patricia; Sánchez-Corona, José

    2002-07-01

    A polymorphism at codon 72 in the p53 gen has been reported as a potential risk factor to cervical cancer (CC) because human papillomavirus (HPV) is more effective at degrading p53 Arg-72 than p53 Pro-72, making individuals homozygous for p53 Arg-72 seven times more likely to develop HPV-associated CC. As In Mexico the CC is a health public problem, we designed this study to determinate whether the p53 codon 72 polymorphism represent a risk factor to CC in our population. A case-controls study was performed. DNA was obtained from paraffin-embedded cervical fixed tissue samples. Analysis of the p53 genotype at position 72 was performed by polymerase chain reaction using specific primers and Accll digestion. Among cases with CC the proportions of the p53 genotypes at codon 72 were 0.05 to proline homozygous, 0.5 to heterozygous, and 0.45 to arginine-homozygous. In controls the proportions were 0.08, 0.62, and 0.31. X2 test showed no significant difference In the proportions. We conclude than In our population, as other worldwide countries, the homozygous for arginine at codon 72 of the p53 gene is not a risk factor to cervical cancer.

  17. Silencing of potato virus X coat protein gene in transgenic tobaccos by codon replacement that confers resistance to PVX infection

    Institute of Scientific and Technical Information of China (English)

    FENG Dejiang; LIU Xiang; MENG Kun; LIAO Lili; WEI Xiaoli; XU Honglin; ZHU Zhen

    2003-01-01

    To understand the effect of rare codon on the silencing ratio of foreign gene, some preferred codon in potato virus X (PVX) coat protein gene (cp) were substituted with synonymous rare codons. The modified PVX coat protein gene (cpm) and wild-type cp gene (cpw) were inserted into binary vector under the control of CaMV35S promoter, and these two plant expression constructs were transferred into tobacco (Nicotiana tabacum cv. Xanthi) genomes via Agrobacterium mediated method and transgenic plants were generated. Northern blot analysis of RNA isolated from these plants showed that the silencing ratio of cpm gene in transgenic tobaccos was higher than that of cpw (35% and 6.25% respectively). Run on results indicate that the silencing of cp gene happened at post-transcriptional level. The resistance of transgenic tobaccos carrying cpm genes to PVX is increased compared with that of transformants carrying cpw genes. These results suggest that the resistance of transgenic tobacco to PVX can be enhanced by codon replacement.

  18. Geospatial Estimates of Road Salt Usage Across a Gradient of Urbanizing Watersheds in Southern Ontario:Thesis for Masters in Spatial Analysis (MSA)

    Science.gov (United States)

    Giberson, G. K.; Oswald, C.

    2015-12-01

    In areas affected by snow, chloride (Cl) salts are widely used as a de-icing agent to improve road conditions. While the improvement in road safety is indisputable, there are environmental consequences to local aquatic ecosystems. In many waterways, Cl concentrations have been increasing since the early 1990s, often exceeding national water quality guidelines. To determine the quantity of Cl that is accumulating in urban and urbanizing watersheds, accurate estimates of road salt usage at the watershed-scale are needed. The complex jurisdictional control over road salt application in southern Ontario lends itself to a geospatial approach for calculating Cl inputs to improve the accuracy of watershed-scale Cl mass balance estimates. This study will develop a geospatial protocol for combining information on road salt applications and road network areas to refine watershed-scale Cl inputs, as well as assess spatiotemporal patterns in road salt application across the southern Ontario study region. The overall objective of this project is to use geospatial methods (predominantly ArcGIS) to develop high-accuracy estimates of road salt usage in urbanizing watersheds in southern Ontario. Specifically, the aims will be to map and summarize the types and areas ("lane-lengths") of roadways in each watershed that have road salt applied to them, to determine the most appropriate source(s) of road salt usage data for each watershed, taking into consideration multiple levels of jurisdiction (e.g. municipal, regional, provincial), to calculate and summarize sub-watershed and watershed-scale road salt usage estimates for multiple years, and to analyze intra-watershed spatiotemporal patterns of road salt usage, especially focusing on impervious surfaces. These analyses will recommend areas of concern exacerbated by high-levels of road salt distribution; recommendations around modifying on-the-ground operations will be the next step in helping to correct these issues.

  19. A primary cardiac leiomyosarcoma with mutation at H-ras codon 12.

    Science.gov (United States)

    Parissis, J; Arvanitis, D; Sourvinos, G; Spandidos, D

    1997-01-01

    The presence of activating ras mutations in a cardiac leiomyosarcoma which occurred in the right atrium of the heart of a female patient was examined. The tumor had the appearance of leiomyosarcoma in rutine histopathological examination and the definite diagnosis was confirmed by a positive immunohistochemical reaction to smooth muscle actin. Molecular analysis by polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) technique showed a point mutation of H-ras gene at codon 12. To the best of our knowledge, this is the first report describing ras gene mutation in a cardiac leiomyosarcoma implying a role for the ras oncogenes in the development of this tumor.

  20. Reduced Protein Expression in a Virus Attenuated by Codon Deoptimization

    Directory of Open Access Journals (Sweden)

    Benjamin R. Jack

    2017-09-01

    Full Text Available A general means of viral attenuation involves the extensive recoding of synonymous codons in the viral genome. The mechanistic underpinnings of this approach remain unclear, however. Using quantitative proteomics and RNA sequencing, we explore the molecular basis of attenuation in a strain of bacteriophage T7 whose major capsid gene was engineered to carry 182 suboptimal codons. We do not detect transcriptional effects from recoding. Proteomic observations reveal that translation is halved for the recoded major capsid gene, and a more modest reduction applies to several coexpressed downstream genes. We observe no changes in protein abundances of other coexpressed genes that are encoded upstream. Viral burst size, like capsid protein abundance, is also decreased by half. Together, these observations suggest that, in this virus, reduced translation of an essential polycistronic transcript and diminished virion assembly form the molecular basis of attenuation.

  1. The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons.

    Science.gov (United States)

    Simões, João; Bezerra, Ana R; Moura, Gabriela R; Araújo, Hugo; Gut, Ivo; Bayes, Mónica; Santos, Manuel A S

    2016-01-01

    The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.

  2. Human SNPs resulting in premature stop codons and protein truncation

    OpenAIRE

    Savas Sevtap; Tuzmen Sukru; Ozcelik Hilmi

    2006-01-01

    Abstract Single nucleotide polymorphisms (SNPs) constitute the most common type of genetic variation in humans. SNPs introducing premature termination codons (PTCs), herein called X-SNPs, can alter the stability and function of transcripts and proteins and thus are considered to be biologically important. Initial studies suggested a strong selection against such variations/mutations. In this study, we undertook a genome-wide systematic screening to identify human X-SNPs using the dbSNP databa...

  3. The fungus Candida albicans tolerates ambiguity at multiple codons

    Directory of Open Access Journals (Sweden)

    João Salvador Simões

    2016-03-01

    Full Text Available The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions 3% of leucine and 97% of serine are incorporated at CUG sites on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP and one SNP in the deneddylase (JAB1 gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans.

  4. Cognition, Corpora, and Computing: Triangulating Research in Usage-Based Language Learning

    Science.gov (United States)

    Ellis, Nick C.

    2017-01-01

    Usage-based approaches explore how we learn language from our experience of language. Related research thus involves the analysis of the usage from which learners learn and of learner usage as it develops. This program involves considerable data recording, transcription, and analysis, using a variety of corpus and computational techniques, many of…

  5. Cytosine usage modulates the correlation between CDS length and CG content in prokaryotic genomes.

    Science.gov (United States)

    Xia, Xuhua; Wang, Huaichun; Xie, Zheng; Carullo, Malisa; Huang, Huang; Hickey, Donal

    2006-07-01

    Previous studies have argued that, given the AT-rich nature of stop codons, the length and CG% of coding sequences (CDSs) should be positively correlated. This prediction is generally supported empirically by prokaryotic genomes. However, the correlation is weak for a number of species, with 4 species showing a negative correlation. Here we formulate a more general hypothesis incorporating selection against cytosine (C) usage to explain the lack of strong positive correlation between the length and GC% of CDSs. Two factors contribute to the selection against C usage in long CDSs. First, C is the least abundant nucleotide in the cell, and a long CDS should have fewer Cs to increase transcription efficiency. Second, C is prone to mutation to U/T and selection for increased reliability should reduce C usage in long CDSs. Empirical data from prokaryotic genomes lend strong support for this new hypothesis.

  6. The Descriptive Study of Knowledge Discovery from Web Usage Mining

    Directory of Open Access Journals (Sweden)

    Yogish H K

    2011-09-01

    Full Text Available The World Wide Web serves as huge, widely distributed, global information service centre for news, advertisements, consumer information, financial management, education, government, e-commerce and many other information services. The web also contains a rich and dynamic collection of hyperlink information and web page access and usage information, providing rich sources of data for data mining. The Web usage mining is the area of data mining which deals with the discovery and analysis of usage patterns from web logs, in order to improve web based applications. Web usage mining consists of three phases, preprocessing, pattern discovery, and pattern analysis. After the completion of these three phases the user can find the required usage patterns and use this information for the specific needs.

  7. Opposite nucleotide usage biases in different parts of the Corynebacterium diphtheriae spaC gene.

    Science.gov (United States)

    Khrustalev, Vladislav Victorovich; Barkovsky, Eugene Victorovich; Kolodkina, Valentina Leonidovna; Khrustaleva, Tatyana Aleksandrovna

    2015-01-01

    In this work we described a bacterial open reading frame with two different directions of nucleotide usage biases in its two parts. The level of GC-content in third codon positions (3GC) is equal to 40.17 ± 0.22% during the most of the length of Corynebacterium diphtheriae spaC gene. However, in the 3'-end of the same gene (from codon #1600 to codon #1873) 3GC level is equal to 64.61 ± 0.91%. Using original methodology ('VVTAK Sliding window' and 'VVTAK VarInvar') we approved that there is an ongoing mutational AT-pressure during the most of the length of spaC gene (up to codon #1599), and there is an ongoing mutational G-pressure in the 3′-end of spaC. Intragenic promoters predicted by three different methods may be the cause of the differences in preferable types of nucleotide mutations in spaC parts because of their autonomous transcription.

  8. Exploring the Relationship Between Online Social Network Site Usage and the Impact on Quality of Life for Older and Younger Users: An Interaction Analysis.

    Science.gov (United States)

    Quinn, Darren; Chen, Liming; Mulvenna, Maurice D; Bond, Raymond

    2016-09-29

    Analyzing content generated by users of social network sites has been shown to be beneficial across a number of disciplines. Such analysis has revealed the precise behavior of users that details their distinct patterns of engagement. An issue is evident whereby without direct engagement with end users, the reasoning for anomalies can only be the subject of conjecture. Furthermore, the impact of engaging in social network sites on quality of life is an area which has received little attention. Of particular interest is the impact of online social networking on older users, which is a demographic that is specifically vulnerable to social isolation. A review of the literature reveals a lack of knowledge concerning the impact of these technologies on such users and even less is known regarding how this impact varies across different demographics. The objective of our study was to analyze user interactions and to survey the attitudes of social network users directly, capturing data in four key areas: (1) functional usage, (2) behavioral patterns, (3) technology, and (4) quality of life. An online survey was constructed, comprising 32 questions. Each question directly related to a research question. Respondents were recruited through a variety of methods including email campaigns, Facebook advertisements, and promotion from related organizations. In total, data was collected from 919 users containing 446 younger and 473 older users. In comparison to younger users, a greater proportion of older users (289/473, 61.1% older vs 218/446, 48.9% younger) (PFacebook had either a positive or huge impact on their quality of life. Furthermore, a greater percentage of older users strongly agreed that Facebook strengthened their relationship with other people (64/473, 13.5% older vs 40/446, 9.0%younger) (P=.02). In comparison to younger users, a greater proportion of older users had more positive emotions-classified as slightly better or very good-during their engagement with

  9. A Comparative Study of Mobile Internet Usage between the U.S. and Korea

    Directory of Open Access Journals (Sweden)

    Luke Yunkeun Shin

    2014-08-01

    Full Text Available The introduction of smartphones illuminated mobile internet prevalence, highlighting nomophobia. This study explored the mobile internet usage dependency of Korean and U.S. mobile users and investigated the severity of such usage dependency and the factors involved. In the combined data set, it was found that Korean users have higher usage dependency levels than US users and that students, unemployed users, and younger generations are more susceptible to mobile internet usage dependency. When comparing the two countries as separate data sets Korean females present as having higher usage dependency levels. In the U.S., it is students and younger generation groups who present with higher usage dependency levels. Regression analysis found that frequency of access has higher associations with mobile internet usage dependency than usage length. country of origin and age are significantly associated with mobile internet usage dependency.

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

    Directory of Open Access Journals (Sweden)

    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.

  11. 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...

  12. Which Users Should Be the Focus of Mobile Personal Health Records? Analysis of User Characteristics Influencing Usage of a Tethered Mobile Personal Health Record.

    Science.gov (United States)

    Lee, Guna; Park, Joong Yeol; Shin, Soo-Yong; Hwang, Jong Su; Ryu, Hyeon Jeong; Lee, Jae Ho; Bates, David W

    2016-05-01

    This study was conducted to analyze the usage pattern of a hospital-tethered mobile personal health records (m-PHRs) application named My Chart in My Hand (MCMH) and to identify user characteristics that influence m-PHR usage. Access logs to MCMH and its menus were collected for a total of 18 months, from August 2011 to January 2013. Usage patterns between users without a patient identification number (ID) and users with a patient ID were compared. Users with a patient ID were divided into light and heavy user groups by the median number of monthly access. Multiple linear regression models were used to assess MCMH usage pattern by characteristics of MCMH user with a patient ID. The total number of MCMH logins was 105,603, and the median number of accesses was 15 times. Users (n = 7,096) mostly accessed the "My Chart" menu, but "OPD [outpatient department] Service Support" and "Health Management" menus were also frequently used. Patients with chronic diseases, experience of hospital visits including emergency room and OPD, and age group of 0-19 years were more frequently found among users with a patient ID (n = 2,186) (p user group (n = 1,123). Submenus of laboratory result, online appointment, and medication lists that were accessed mostly by users with a patient ID were associated with OPD visit and chronic diseases. This study showed that focuses on patients with chronic disease and more hospital visits and empowerment functions in a tethered m-PHR would be helpful to pursue the extensive use.

  13. Gene expression in chromosomal Ridge domains : influence on transcription, mRNA stability, codon usage, and evolution

    NARCIS (Netherlands)

    Gierman, H.J.

    2010-01-01

    Chromosomes are the long DNA molecules that carry the genetic code of our genes. Each gene encodes a protein, but also contains the information that controls the activity of that gene. In this thesis, we find that chromosomal domains with many active genes (so-called 'Ridges'), also control gene

  14. Antibiotics Clinical Usage Analysis on Inpatients%住院患者抗菌药物临床应用调查分析

    Institute of Scientific and Technical Information of China (English)

    罗彪峰; 蒋述科; 李春凤; 陈晓燕

    2012-01-01

    目的 了解桂林医学院附属医院抗菌药物的使用现状,从而提高临床使用抗菌药物的合理性.方法 对2010年11月8日0时~24时所有住院患者进行抗菌药物使用调查,由医院感染管理科、药剂科、护理部工作人员及临床科室医院感染监控医师组成10个调查小组,采用床旁调查、医护人员询问和病历调查相结合的调查方式,填写个案调查表.结果 在所调查的1066例住院患者中,抗菌药物使用率为36.87%,抗菌药物联合用药率为18.32%,联合用药中两联用药占18.07%,三联用药占0.25%,无四联用药.抗菌药物预防性用药占30.53%,存在外科Ⅰ类切口手术围术期预防用药过度及内科疾病抗菌药物预防性应用指征不明确等问题.住院患者病原体培养及药敏试验的送检率为34.8%.结论 治疗性用药病原学送检率较低,抗菌药物选用以经验用药为主,缺乏科学依据,需要加强抗菌药物合理应用的管理,提高抗菌药物应用水平.%Objective To investigate the usage of antibiotics, and to improve the rationality of clinical usage. Methods Antibiotics usage survey was made on November 8,2010 within the inpatients. Ten survey teems were composed by the staff of department of nosocomial infection management,phamacy department,nursing department and clinical physicians,using a combination of bedside investigations, inquirying and medical records surveying. Investigation forms were completed. Results Among 1066 inpatients, the rate of antibiotic usage was 36. 87% . The combined antibiotic rate was 18. 32% ,18. 07% were given double drug ,0. 25% were given triple and none were given quadruple therapy. The rate of prophylactic antibiotic usage was 30.53% . Excessive antibiotics usage existed in perioperative period of type I incision surgery and the indication for prophylactic antibiotics usage in physician was not clear. Rate of etiological examination for infectious patients was 34

  15. TP53 codon 72 polymorphism may predict early tumour progression in paediatric pilocytic astrocytoma

    Science.gov (United States)

    Mascelli, Samantha; Nozza, Paolo; Jones, David T.W.; Colin, Carole; Pistorio, Angela; Milanaccio, Claudia; Ravegnani, Marcello; Consales, Alessandro; Witt, Olaf; Morana, Giovanni; Cama, Armando; Capra, Valeria; Biassoni, Roberto; Pfister, Stefan M.; Figarella-Branger, Dominique; Garrè, Maria Luisa; Raso, Alessandro

    2016-01-01

    Pilocytic astrocytoma and ganglioglioma may occur in inaccessible or surgically difficult areas. In case of incomplete resection, the availability of biological predictors of tumour progression could be particularly important. To this end, an analysis of p53 codon 72 polymorphism and assessment of its role as prognostic marker were performed. The status of the p53 Arg72Pro polymorphism was evaluated by pyrosequencing method in a multicenter cohort of 170 paediatric patients. Genotype/phenotype associations were investigated either by means of bivariate or multivariate analyses. In the partially resected pilocytic astrocytomas, the Arg/Arg variant predicts early tumour progression (median survival time: 23.1 months) and is associated with poor event-free survival (p value = 0.0009). This finding remains true also in case of adjuvant therapies, with a 5-year event-free survival of 30.6% for cases with Arg/Arg variant vs. 78.7% for those with other genotypes. There is no association between ganglioglioma and the polymorphism. The assessment of Arg/Arg variant could improve the management of pilocytic astrocytoma. TP53 codon 72 analysis could distinguish low-risk cases, in which surgery could be conservative, from high-risk cases needing an aggressive surgery plan. PMID:27374106

  16. TP53 codon 72 polymorphism may predict early tumour progression in paediatric pilocytic astrocytoma.

    Science.gov (United States)

    Mascelli, Samantha; Nozza, Paolo; Jones, David T W; Colin, Carole; Pistorio, Angela; Milanaccio, Claudia; Ravegnani, Marcello; Consales, Alessandro; Witt, Olaf; Morana, Giovanni; Cama, Armando; Capra, Valeria; Biassoni, Roberto; Pfister, Stefan M; Figarella-Branger, Dominique; Garrè, Maria Luisa; Raso, Alessandro

    2016-07-26

    Pilocytic astrocytoma and ganglioglioma may occur in inaccessible or surgically difficult areas. In case of incomplete resection, the availability of biological predictors of tumour progression could be particularly important. To this end, an analysis of p53 codon 72 polymorphism and assessment of its role as prognostic marker were performed.The status of the p53 Arg72Pro polymorphism was evaluated by pyrosequencing method in a multicenter cohort of 170 paediatric patients. Genotype/phenotype associations were investigated either by means of bivariate or multivariate analyses.In the partially resected pilocytic astrocytomas, the Arg/Arg variant predicts early tumour progression (median survival time: 23.1 months) and is associated with poor event-free survival (p value = 0.0009). This finding remains true also in case of adjuvant therapies, with a 5-year event-free survival of 30.6% for cases with Arg/Arg variant vs. 78.7% for those with other genotypes. There is no association between ganglioglioma and the polymorphism.The assessment of Arg/Arg variant could improve the management of pilocytic astrocytoma. TP53 codon 72 analysis could distinguish low-risk cases, in which surgery could be conservative, from high-risk cases needing an aggressive surgery plan.

  17. What should we measure? Conceptualizing usage in health information exchange.

    Science.gov (United States)

    Vest, Joshua R; Jasperson, Jon

    2010-01-01

    Under the provisions of the Health Information Technology for Economic & Clinical Health act providers need to demonstrate their 'meaningful use' of electronic health record systems' health information exchange (HIE) capability. HIE usage is not a simple construct, but the choice of its measurement must attend to the users, context, and objectives of the system being examined. This review examined how usage is reported in the existing literature and also what conceptualizations of usage might best reflect the nature and objectives of HIE. While existing literature on HIE usage included a diverse set of measures, most were theoretically weak, did not attend to the interplay of measure, level of analysis and architectural strategy, and did not reflect how HIE usage affected the actual process of care. Attention to these issues will provide greater insight into the effects of previously inaccessible information on medical decision-making and the process of care.

  18. Altmetrics, PIRUS and Usage Factor

    Directory of Open Access Journals (Sweden)

    Peter Shepherd

    2013-11-01

    Full Text Available Scholars have moved their publications onto the web, and the ongoing conversation around the outputs of research increasingly takes place there. Beyond the research community itself, scholarly information has an impact on other professionals, as well as on the general public. Traditional measures do not reflect these wider impacts. The mission of COUNTER is to set and monitor global standards for the measurement of online usage of content. Usage is an important measure of the impact and value of publications, and as such has a role in altmetrics. Usage can be reported at the individual item and individual researcher level and aggregated to the journal or institution level. PIRUS and Usage Factor are two COUNTER-lead initiatives that are based on this approach, with the potential to provide useful altmetrics.

  19. Network mapping and usage determination

    CSIR Research Space (South Africa)

    Senekal, FP

    2007-07-01

    Full Text Available A large computer network such as the Internet contains millions of computers, services and users, interconnected in a complicated and ever changing web. This article provides an introduction to network mapping and usage determination – the study...

  20. 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.

  1. Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

    Directory of Open Access Journals (Sweden)

    Yu Xiu-Juan

    2007-10-01

    Full Text Available Abstract Background The nucleotide compositional asymmetry between the leading and lagging strands in bacterial genomes has been the subject of intensive study in the past few years. It is interesting to mention that almost all bacterial genomes exhibit the same kind of base asymmetry. This work aims to investigate the strand biases in Chlamydia muridarum genome and show the potential of the Z curve method for quantitatively differentiating genes on the leading and lagging strands. Results The occurrence frequencies of bases of protein-coding genes in C. muridarum genome were analyzed by the Z curve method. It was found that genes located on the two strands of replication have distinct base usages in C. muridarum genome. According to their positions in the 9-D space spanned by the variables u1 – u9 of the Z curve method, K-means clustering algorithm can assign about 94% of genes to the correct strands, which is a few percent higher than those correctly classified by K-means based on the RSCU. The base usage and codon usage analyses show that genes on the leading strand have more G than C and more T than A, particularly at the third codon position. For genes on the lagging strand the biases is reverse. The y component of the Z curves for the complete chromosome sequences show that the excess of G over C and T over A are more remarkable in C. muridarum genome than in other bacterial genomes without separating base and/or codon usages. Furthermore, for the genomes of Borrelia burgdorferi, Treponema pallidum, Chlamydia muridarum and Chlamydia trachomatis, in which distinct base and/or codon usages have been observed, closer phylogenetic distance is found compared with other bacterial genomes. Conclusion The nature of the strand biases of base composition in C. muridarum is similar to that in most other bacterial genomes. However, the base composition asymmetry between the leading and lagging strands in C. muridarum is more significant than that in

  2. Clinical analysis of vancomycin usage in intensive care unit%我院ICU万古霉素使用情况临床分析

    Institute of Scientific and Technical Information of China (English)

    段丽芳; 张卫星

    2010-01-01

    目的 为了了解我院ICU万古霉素临床使用情况,以指导今后规范和合理使用万古霉素.方法 回顾性分析我院ICU万古霉素的消耗、利用情况和耐甲氧西林金黄色葡萄球菌(MRSA)的检出情况以及对2008年1月至2009年6月使用万古霉素患者进行临床用药分析.结果 2007年万古霉素消耗量最大为728.0 g,MRSA检出率最高,ICU为52株(70.00%),全院为115株(49.00%).MRSA平均检出率为62.8%.74例使用万古霉素患者中最常用的初始方案1g/12 h.结论 我院ICU万古霉素使用基本合理,今后需加强血药浓度监测,利用药效学和药动学理论,实施个体化给药方案.%Objectives To investigate vancomycin usage in ICU and to rationalize the use of vancomycin.Methods Vancomycin consumption, usage and methicillin-resistant staphylococcus aureus case detection rate of vancomycin in our hospital were retrospectively analyzed. From January 2008 to June 2009, the clinical usage of vancomycin was analyzed. Results The consummation of vancomycin in 2007 was more than other years and so was the incidence rate of MRSA. The average incidence rate of MRSA was 62. 8% in ICU. The regimen of 1 g q12h was used most frequently in the 74 study cases. Conclusions The usage of vancomycin in ICU of our hospital was basi-cally reasonable. Blood concentration monitoring should be strengthened in the future. Personalized administration plan should be implemented by pharmacodynamic and pharmacokinetic theory.

  3. Sequence Analysis of In Vivo-Expressed HIV-1 Spliced RNAs Reveals the Usage of New and Unusual Splice Sites by Viruses of Different Subtypes

    Science.gov (United States)

    Vega, Yolanda; Delgado, Elena; de la Barrera, Jorge; Carrera, Cristina; Zaballos, Ángel; Cuesta, Isabel; Mariño, Ana; Ocampo, Antonio; Miralles, Celia; Pérez-Castro, Sonia; Álvarez, Hortensia; López-Miragaya, Isabel; García-Bodas, Elena; Díez-Fuertes, Francisco; Thomson, Michael M.

    2016-01-01

    HIV-1 RNAs are generated through a complex splicing mechanism, resulting in a great diversity of transcripts, which are classified in three major categories: unspliced, singly spliced (SS), and doubly spliced (DS). Knowledge on HIV-1 RNA splicing in vivo and by non-subtype B viruses is scarce. Here we analyze HIV-1 RNA splice site usage in CD4+CD25+ lymphocytes from HIV-1-infected individuals through pyrosequencing. HIV-1 DS and SS RNAs were amplified by RT-PCR in 19 and 12 samples, respectively. 13,108 sequences from HIV-1 spliced RNAs, derived from viruses of five subtypes (A, B, C, F, G), were identified. In four samples, three of non-B subtypes, five 3’ splice sites (3’ss) mapping to unreported positions in the HIV-1 genome were identified. Two, designated A4i and A4j, were used in 22% and 25% of rev RNAs in two viruses of subtypes B and A, respectively. Given their close proximity (one or two nucleotides) to A4c and A4d, respectively, they could be viewed as variants of these sites. Three 3’ss, designated A7g, A7h, and A7i, located 20, 32, and 18 nucleotides downstream of A7, respectively, were identified in a subtype C (A7g, A7h) and a subtype G (A7i) viruses, each in around 2% of nef RNAs. The new splice sites or variants of splice sites were associated with the usual sequence features of 3’ss. Usage of unusual 3’ss A4d, A4e, A5a, A7a, and A7b was also detected. A4f, previously identified in two subtype C viruses, was preferentially used by rev RNAs of a subtype C virus. These results highlight the great diversity of in vivo splice site usage by HIV-1 RNAs. The fact that four of five newly identified splice sites or variants of splice sites were detected in non-subtype B viruses allows anticipating an even greater diversity of HIV-1 splice site usage than currently known. PMID:27355361

  4. Sequence Analysis of In Vivo-Expressed HIV-1 Spliced RNAs Reveals the Usage of New and Unusual Splice Sites by Viruses of Different Subtypes.

    Directory of Open Access Journals (Sweden)

    Yolanda Vega

    Full Text Available HIV-1 RNAs are generated through a complex splicing mechanism, resulting in a great diversity of transcripts, which are classified in three major categories: unspliced, singly spliced (SS, and doubly spliced (DS. Knowledge on HIV-1 RNA splicing in vivo and by non-subtype B viruses is scarce. Here we analyze HIV-1 RNA splice site usage in CD4+CD25+ lymphocytes from HIV-1-infected individuals through pyrosequencing. HIV-1 DS and SS RNAs were amplified by RT-PCR in 19 and 12 samples, respectively. 13,108 sequences from HIV-1 spliced RNAs, derived from viruses of five subtypes (A, B, C, F, G, were identified. In four samples, three of non-B subtypes, five 3' splice sites (3'ss mapping to unreported positions in the HIV-1 genome were identified. Two, designated A4i and A4j, were used in 22% and 25% of rev RNAs in two viruses of subtypes B and A, respectively. Given their close proximity (one or two nucleotides to A4c and A4d, respectively, they could be viewed as variants of these sites. Three 3'ss, designated A7g, A7h, and A7i, located 20, 32, and 18 nucleotides downstream of A7, respectively, were identified in a subtype C (A7g, A7h and a subtype G (A7i viruses, each in around 2% of nef RNAs. The new splice sites or variants of splice sites were associated with the usual sequence features of 3'ss. Usage of unusual 3'ss A4d, A4e, A5a, A7a, and A7b was also detected. A4f, previously identified in two subtype C viruses, was preferentially used by rev RNAs of a subtype C virus. These results highlight the great diversity of in vivo splice site usage by HIV-1 RNAs. The fact that four of five newly identified splice sites or variants of splice sites were detected in non-subtype B viruses allows anticipating an even greater diversity of HIV-1 splice site usage than currently known.

  5. TGF-beta 1 codon 10 polymorphism is associated with cerebral SVD.

    Science.gov (United States)

    Tao, Hong-miao; Chen, Guo-zhong; Lu, Xiao-dong; Hu, Xiao-gang; Chen, Gan-ping; Shao, Bei

    2011-11-01

    To clarify the role of inflammation in the pathogenesis of cerebral small vessel disease (SVD), we investigated whether the gene encoding transforming growth factor-beta 1(TGF-beta 1) is a risk factor for cerebral SVD as a whole, and for two different SVD subtypes. TGF-beta 1 codon10 (T+29C) genotype was determined in 441 Chinese patients (313 male and 128 female) with cerebral SVD and 450 control subjects (326 male and 124 female). Cerebral SVD patients were retrospectively classified into two groups based on neuroimaging findings: lacunar infarction group with 112 patients and ischaemic leukoaraiosis group with 329 patients. Subjects carrying TT homozygote were susceptible to cerebral SVD [adjusted odds ratio (OR) =1.44, 95% confidence interval (CI), 1.05-1.98; P=0.026]. Further analysis of SVD subtypes revealed a moderate association with the ischaemic leukoaraiosis group [OR= 1.60, 95% CI, 1.14-2.25; P=0.007]. Codon 10 of TGF-beta 1 might be a risk factor for SVD, specifically in ischaemic leukoaraiosis phenotype.

  6. Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms.

    Science.gov (United States)

    Seward, Emily A; Kelly, Steven

    2016-11-15

    Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism's environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood. Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes. Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.

  7. HIV-1 co-receptor usage based on V3 loop sequence analysis: preferential suppression of CXCR4 virus post HAART?

    Science.gov (United States)

    Jiao, Yanmei; Wang, Pengfei; Zhang, Hongwei; Zhang, Tong; Zhang, Yonghong; Zhu, Huanzhang; Wu, Hao

    2011-01-01

    Disease progression during human immunodeficiency virus type 1 (HIV-1) infection has been associated with a switch of viral coreceptor usage from CCR5 to CXCR4. The current study investigates the effect of anti retroviral therapy (ART) on the viral tropism in a group of patients based on the V3 loop sequence, in ART naïve patients prior to and 24 weeks after ART. Genomic DNA was extracted from the PBMCs of these patients, and the C2-V5 region of the HIV-1 env genes were cloned and sequenced. The coreceptor usage was predicated based on V3 loop amino acid sequences using Geno2pheno and PSSM programs. Our results indicate that following ART, the plasma viral loads of both CXCR4 and CCR5 viruses were significantly decreased. We observed a relatively higher ratio of R5 than X4 virus after 24 weeks of ART and both the positive charges and the net charges of the V3 regions were decreased significantly (p suppression of X4 virus. These data will help improve prognostic outcomes and help clinicians determine the course of treatment in patients who exhibit virologic failure while taking a CCR5 antagonist.

  8. The Preliminary Study on Relationship between HPV-associated Cervical Cancer and p53 Codon 72 Polymorphism in Sichuan Province

    Institute of Scientific and Technical Information of China (English)

    XIMingrong; HEYuedong; YANGXiaoyun; HOUMinmin; CAOZeyi

    2003-01-01

    Objective: To study the relationship between HPV-associated cervical cancer and p53 codon 72 polymorphism in Sichuan Province. Methods: Three groups of women were studied: 30 women for normal control; 30 women with ovarian cancer; 50 women with cervical cancer. DNA from peripheral blood samples and from pathologic tissue sections was examined by PCR with allele-specific primers. Results:The proportions of individuals homozygons for the arginine allele, homozygous for the proline allele and heterozygous for the two alleles were 33.3%, 6.7% and 60% respectively among normal women; 40%, 6.7% and 53.3% in women with ovarian cancer respectively; 80%, 6% and 14% in women with cervical cancer respectively. X2 analysis showed significant differences in the proportions. Conclusion: In this population,individuals homozygons for the arginine variant of codon 72 of the p53 gene were at increased risk of cervical cancer.

  9. 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.

  10. Analysis of Influencing Factors of Condom Usage among FEWs in Changning District, Shanghai%长宁区娱乐场所女性服务人员安全套使用影响因素分析

    Institute of Scientific and Technical Information of China (English)

    倪莹青; 王震宇; 尹宁; 朱晓华; 郑敏; 刘娟; RobertS.Remis; 庄鸣华

    2011-01-01

    [ Objective ] To know the condom usage among female entertainment workers (FEWs) in Changning District of Shanghai when they have sex with different types of aexual partners, and to explore the possible factors which may affect their condom usage in last month. [ Methods ] According to the general proportion of FEWs from large scale and small scale venues of 3 : 7, a total of 125 FEWs were randomly selected and given one-to-one questionnaire survey. The questionnaire involved general demographic information, sexual behavior traits with different sexual partners, condom usage and so on. [ Results ] Only 48.8% FEWs used condom every time last month when they had sex- The unsafe sexual behaviors were common when they had sexual with regular sexual partners. Logistic regression analysis showed that the usage rate was higher in high education group, and married FEWs had higher condom usage rate than single FEWs. [ Conclusion ] Type of sexual partners, educational level and marital status are related to FEWs'condom usage. Providing intervention programs which are targeted on this group of people are the key to preventing HIV transmission through sex. It is necessary to give healdi education on safe sexual behaviors according to the traits of different places and people in order to reach the goal of 100% condom usage rate.%[目的]了解上海长宁区娱乐场所女性服务人员( female entertainment workers,FEWs)与不同性伴安全套使用情况,探讨影响FEW最近一个月每次使用安全套的可能因素.[方法]按照大:小场所比例为3:7的原则在长宁区随机选择125名FEWs.采用一对一现场问卷调查,问卷内容包括一般人口统计学变量、与不同性伴性行为特征和安全套使用情况等. [结果]只有48.8%的FEWs最近一个月每次性行为都使用安全套,与固定性伴不安全性行为普遍存在.多因素非条件logistic回归分析结果显示,文化程度越高,安全套使用率越高.已婚女

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

    Directory of Open Access Journals (Sweden)

    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.

  12. Correct usage, ease of use, and preference of two dry powder inhalers in patients with COPD: analysis of five phase III, randomized trials

    Directory of Open Access Journals (Sweden)

    Riley JH

    2016-08-01

    Full Text Available John H Riley,1 Maggie Tabberer,2 Nathalie Richard,3 Alison Donald,3 Alison Church,3 Stephanie S Harris3 1MDC Global Clinical Development – UK, GlaxoSmithKline, 2Value Evidence and Outcomes, GlaxoSmithKline, Uxbridge, Middlesex, UK; 3Respiratory Medicines Development Center, GlaxoSmithKline, Durham, NC, USA Background: Handheld inhalers are used to deliver treatment for COPD. Incorrect usage leads to suboptimal disease control. Complex treatment regimens and use of multiple inhalers may reduce patient compliance. The Anoro Ellipta™ dry powder inhaler (DPI simultaneously delivers umeclidinium bromide (UMEC and vilanterol (VI without coformulation being required.Aim: To assess the correct usage and ease of use of the Ellipta™ DPI administering UMEC/VI and to compare patient preference for Ellipta™ with the HandiHaler® through exploratory analyses of patient and observer questionnaires in five Phase III studies.Methods: Two Phase III, 3-month double-blind, placebo-controlled studies assessed the correct usage of the Ellipta™ DPI at Day 1 and after 6 weeks, and ease of use of the Ellipta™ DPI using a nonvalidated patient questionnaire after 6 weeks or early withdrawal. In three 6-month, blinded double-dummy, active comparator studies (two Phase IIIa and one Phase IIIb, patients completed a COPD device preference questionnaire between the Ellipta™ DPI and the HandiHaler® at Day 168 (Week 24 or early withdrawal.Results: In the 3-month placebo-controlled studies, ≥98% of patients used the Ellipta™ DPI correctly and 99% of patients found the inhaler easy/very easy-to-use and the dose counter easy/very easy to read. Across the two Phase IIIa active comparator studies, patients consistently stated a preference for the Ellipta™ DPI over HandiHaler® regarding the number of steps to use (59% vs 17%, time taken to use (62% vs 14%, and ease of use (63% vs 15% regardless of which inhaler contained active drug. Results were consistent

  13. Measurement and analysis of air-conditioning-usage behavior in apartments%住宅空调行为状况的实测分析

    Institute of Scientific and Technical Information of China (English)

    简毅文; 李清瑞; 刘建

    2013-01-01

    以北京市区6户住宅为研究对象,基于对夏季室内温湿度参数的连续测试及相关问卷调查,从空调开启、关闭及运行时间三个方面对住宅空调行为进行了分析,并比较了不同作息状态下的空调行为.研究表明,由于室内环境及人的生理和心理因素的共同作用,住宅空调的开启、关闭行为与室内环境尤其室温之间或许并不存在严格的单一控制关系,并不是室温超过29℃就一定开启空调,或一定要将室温降低到26℃才关闭空调;住宅空调的开启或关闭行为及上述行为持续的时间取决于人体的热感觉及其对室内热湿环境的期望状况.%Taking six apartments in Beijing as examples, based on the continuous measurement of indoor air temperature and humidity and the relevant questionnaires investigation, discusses air-conditioning-usage behavior from the three aspects of open, close and running time, and compares air-conditioning-usage behavior in different activity and rest conditions. The results show that there may not exist a strict single control relation between the open or close behavior of air conditioners and the indoor environment conditions especially indoor temperature, and that occupants may not necessarily turn on air conditioners even when indoor air temperature rises over 29 ℃ and turn off air conditioners when room temperatures drops under 26 ℃ due to the coaction of indoor environment and physical and psychological components,- air-conditioning-usage behavior will depend on occupants' thermal sensation and the expectation for the indoor thermal and humid environment.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  15. usage of electronic health records

    Directory of Open Access Journals (Sweden)

    Songul Cinaroglu

    2015-06-01

    Full Text Available Health care is an organizational field that information and technology improves quickly. With ensuring health professionals adaptation to this new information and technology environment, it is possible to achieve quality and productivity improvement goal in health care. It is known that different clinical expertises brings differences in presentation of health services. It this study it was aimed to compare nurses assessments about electronic health records usage. At the end of the study it was found that nurses assessment about electronic health records usage according to different clinical expertises has a meaningful difference (t=2,40, p<0,05. Results of this study shows that surgical nurses who are forefront with and ldquo;technical abilities and rdquo; have more positive assessments about usage of electronic medical records when they compared with medical nurses who are forefront with and ldquo;patient centered and rdquo; abilities. [TAF Prev Med Bull 2015; 14(3.000: 257-264

  16. Longitudinal Analysis of CCR5 and CXCR4 Usage in a Cohort of Antiretroviral Therapy-Naive Subjects with Progressive HIV-1 Subtype C Infection.

    Directory of Open Access Journals (Sweden)

    Martin R Jakobsen

    Full Text Available HIV-1 subtype C (C-HIV is responsible for most HIV-1 cases worldwide. Although the pathogenesis of C-HIV is thought to predominantly involve CCR5-restricted (R5 strains, we do not have a firm understanding of how frequently CXCR4-using (X4 and R5X4 variants emerge in subjects with progressive C-HIV infection. Nor do we completely understand the molecular determinants of coreceptor switching by C-HIV variants. Here, we characterized a panel of HIV-1 envelope glycoproteins (Envs (n = 300 cloned sequentially from plasma of 21 antiretroviral therapy (ART-naïve subjects who experienced progression from chronic to advanced stages of C-HIV infection, and show that CXCR4-using C-HIV variants emerged in only one individual. Mutagenesis studies and structural models suggest that the evolution of R5 to X4 variants in this subject principally involved acquisition of an "Ile-Gly" insertion in the gp120 V3 loop and replacement of the V3 "Gly-Pro-Gly" crown with a "Gly-Arg-Gly" motif, but that the accumulation of additional gp120 "scaffold" mutations was required for these V3 loop changes to confer functional effects. In this context, either of the V3 loop changes could confer possible transitional R5X4 phenotypes, but when present together they completely abolished CCR5 usage and conferred the X4 phenotype. Our results show that the emergence of CXCR4-using strains is rare in this cohort of untreated individuals with advanced C-HIV infection. In the subject where X4 variants did emerge, alterations in the gp120 V3 loop were necessary but not sufficient to confer CXCR4 usage.

  17. Comparative study of IgA VH 3 gene usage in healthy TST(-) and TST(+) population exposed to tuberculosis: deep sequencing analysis.

    Science.gov (United States)

    Chin, Siang Tean; Ignatius, Joshua; Suraiya, Siti; Tye, Gee Jun; Sarmiento, Maria E; Acosta, Armando; Norazmi, Mohd Nor; Lim, Theam Soon

    2015-02-01

    The acquired immune response against tuberculosis is commonly associated with T-cell responses with little known about the role of B cells or antibodies. There have been suggestions that B cells and humoral immunity can modulate the immune response to Mycobacterium tuberculosis. However, the mechanisms involving B-cell responses in M. tuberculosis are not fully understood, in particular the antibody gene preferences. We hypothesized that a preferential use of V genes can be seen associated with resistance to infection mainly in the IgA isotype, which is of prominent importance for infection by pathogens via the mucosal route. We studied healthy individuals with long-term exposure to tuberculosis, infected (TST(+) ) and uninfected TST(-) ) with M. tuberculosis. From a total of 22 V genes analysed, the TST(-) population preferred the VH 3-23 and Vκ1 genes. The VH 3-23 genes were subsequently subjected to 454 amplicon sequencing. The TST(-) population showed a higher frequency of the D3-10 segment compared with the D3-22 segment for the TST(+) population. The J segment usage pattern was similar for both populations with J4 segment being used the most. A preferential pairing of J4 segments to D3-3 was seen for the TST(-) population. The antibodyome difference between both populations suggests a preference for antibodies with VH 3-23, D3-3, JH 4 gene usage by the TST(-) population that could be associated with resistance to infection with M. tuberculosis.

  18. Analysis of the T-cell receptor V beta usage in monozygotic and dizygotic twins living in a Plasmodium falciparum endemic area in west Africa.

    Science.gov (United States)

    Troye-Blomberg, M; Fogdell, A; el-Ghazali, G; Larsson, A; King, M H; Sisay-Joof, F; Olerup, O; Grunewald, J; Jepson, A

    1997-05-01

    To investigate the influence of genetic and/or environmental factors in the development and shaping of the human peripheral T cell repertoire the authors studied the T-cell receptor (TCR) V beta usage in 10 adult monozygous (Mz) and nine dizygous (Dz) twin pairs living in a Plasmodium falciparum endemic area in West Africa. The TCR repertoire was determined using a small panel of anti-V beta specific monoclonal antibodies (MoAbs) using conventional immunofluorescence assays. The results revealed that the V beta repertoire was similar to that recently described for a Caucasian population using a similar panel of antibodies. The frequencies of particular V beta genes tested were influenced neither by anti-malarial antibody titres nor by parasite densities, indicating that the P. falciparum parasite is not a dominating factor in determining the peripheral T cell repertoire. All donors were human leucocyte antigen (HLA) class I and II typed; no association was found between the expression of any V beta genes and MHC haplotype. The V beta usage was more concordant within the Mz than within the Dz pairs. For a group comprising four HLA class II identical individuals, the average within-pair difference was significantly greater than for the whole Mz group, but similar to that seen for the total Dz group. Thus, the data suggest that genetic, rather than environmental, factors have a profound effect on the shaping of the human circulating T cell repertoire and that the major genetic factors are encoded by non-HLA class II genes.

  19. Using a web-based orthopaedic clinic in the curricular teaching of a German university hospital: analysis of learning effect, student usage and reception.

    Science.gov (United States)

    Wünschel, Markus; Leichtle, Ulf; Wülker, Nikolaus; Kluba, Torsten

    2010-10-01

    Modern teaching concepts for undergraduate medical students in Germany include problem based learning as a major component of the new licensing regulations for physicians. Here we describe the usage of a web-based virtual outpatient clinic in the teaching curriculum of undergraduate medical students, its effect on learning success, and student reception. Fifth year medial students were requested to examine 7 virtual orthopaedic patients which had been created by the authors using the Inmedea-Simulator. They also had to take a multiple-choice examination on two different occasions and their utilisation of the simulator was analysed subjectively and objectively. One hundred and sixty students took part in the study. The average age was 24.9 years, 60% were female. Most of the participants studied on their own using their private computer with a fast internet-connection at home. The average usage time was 263 min, most of the students worked with the system in the afternoon, although a considerable number used it late in the night. Regarding learning success, we found that the examination results were significantly better after using the system (7.66 versus 8.37, pgraphic design and the expert comments available, as well as the good applicability to real cases. Eighty-seven percent of the students graded the virtual orthopaedic clinic as appropriate to teach orthopaedic content. Using the Inmedea-Simulator is an effective method to enhance students' learning efficacy. The way the system was used by the students emphasises the advantages of the internet-like free time management and the implementation of multimedia-based content. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  20. BEHAVIORAL ASPECT OF ACCOUNTING TEACHERS’ INFORMATION TECHNOLOGY USAGE

    OpenAIRE

    Yilmaz, Emine; Özer, Gökhan

    2015-01-01

    This study aims to examine behavioral process of accounting teachers’ information technology (IT) acceptance. To this end, we collected data from accounting teachers working in trade high schools. Research model and hypotheses were developed in the light of Theory of Reasoned Action. Accordingly, relationships among attitudes, subjective norms, intentions towards information technology usage and IT usage behaviors were investigated. Explanatory factor analysis and structural equation modeling...

  1. 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...

  2. RET codon 609 mutations: a contribution for better clinical managing

    Directory of Open Access Journals (Sweden)

    Caterina Mian

    2012-01-01

    Full Text Available Medullary thyroid carcinoma currently accounts for 5-8% of all thyroid cancers. The clinical course of this disease varies from extremely indolent tumors that can go unchanged for years to an extremely aggressive variant that is associated with a high mortality rate. As many as 75% of all medullary thyroid carcinomas are sporadic, with an average age at presentation reported as 60 years, and the remaining 25% are hereditary with an earlier age of presentation, ranging from 20 to 40 years. Germline RET proto-oncogene mutations are the genetic causes of multiple endocrine neoplasia type 2 and a strong genotype-phenotype correlation exists, particularly between a specific RET codon mutation and the (a age-related onset and (b thyroid tumor progression, from C-cell hyperplasia to medullary thyroid carcinoma and, ultimately, to nodal metastases. RET mutations predispose an individual to the development of medullary thyroid carcinomas and can also influence the individual response to RET protein receptor-targeted therapies. RET codon 609point mutations are rare genetic events belonging to the intermediate risk category for the onset of medullary thyroid carcinoma. A large genealogy resulting in a less aggressive form of medullary thyroid carcinoma is associated with the high penetrance of pheochromocytoma and has been reported in the literature. In this short review article, we comment on our previous report of a large multiple endocrine neoplasia type 2A kindred with the same Cys609Ser germline RET mutation in which, conversely, the syndrome was characterized by a slightly aggressive, highly penetrant form of medullary thyroid carcinoma that was associated with low penetrance of pheochromocytoma and primary hyperparathyroidism.

  3. Analyses of clinicopathological, molecular, and prognostic associations of KRAS codon 61 and codon 146 mutations in colorectal cancer: cohort study and literature review

    Science.gov (United States)

    2014-01-01

    Background KRAS mutations in codons 12 and 13 are established predictive biomarkers for anti-EGFR therapy in colorectal cancer. Previous studies suggest that KRAS codon 61 and 146 mutations may also predict resistance to anti-EGFR therapy in colorectal cancer. However, clinicopathological, molecular, and prognostic features of colorectal carcinoma with KRAS codon 61 or 146 mutation remain unclear. Methods We utilized a molecular pathological epidemiology database of 1267 colon and rectal cancers in the Nurse’s Health Study and the Health Professionals Follow-up Study. We examined KRAS mutations in codons 12, 13, 61 and 146 (assessed by pyrosequencing), in relation to clinicopathological features, and tumor molecular markers, including BRAF and PIK3CA mutations, CpG island methylator phenotype (CIMP), LINE-1 methylation, and microsatellite instability (MSI). Survival analyses were performed in 1067 BRAF-wild-type cancers to avoid confounding by BRAF mutation. Cox proportional hazards models were used to compute mortality hazard ratio, adjusting for potential confounders, including disease stage, PIK3CA mutation, CIMP, LINE-1 hypomethylation, and MSI. Results KRAS codon 61 mutations were detected in 19 cases (1.5%), and codon 146 mutations in 40 cases (3.2%). Overall KRAS mutation prevalence in colorectal cancers was 40% (=505/1267). Of interest, compared to KRAS-wild-type, overall, KRAS-mutated cancers more frequently exhibited cecal location (24% vs. 12% in KRAS-wild-type; P colorectal cancer-specific mortality hazard ratio (HR) = 0.81, 95% confidence interval (CI) = 0.29-2.26 for codon 61 mutation; colorectal cancer-specific mortality HR = 0.86, 95% CI = 0.42-1.78 for codon 146 mutation]. Conclusions Tumors with KRAS mutations in codons 61 and 146 account for an appreciable proportion (approximately 5%) of colorectal cancers, and their clinicopathological and molecular features appear generally similar to KRAS codon 12 or 13 mutated cancers. To

  4. A Practical Ontology for the Large-Scale Modeling of Scholarly Artifacts and their Usage

    CERN Document Server

    Rodriguez, Marko A; Van de Sompel, Herbert

    2007-01-01

    The large-scale analysis of scholarly artifact usage is constrained primarily by current practices in usage data archiving, privacy issues concerned with the dissemination of usage data, and the lack of a practical ontology for modeling the usage domain. As a remedy to the third constraint, this article presents a scholarly ontology that was engineered to represent those classes for which large-scale bibliographic and usage data exists, supports usage research, and whose instantiation is scalable to the order of 50 million articles along with their associated artifacts (e.g. authors and journals) and an accompanying 1 billion usage events. The real world instantiation of the presented abstract ontology is a semantic network model of the scholarly community which lends the scholarly process to statistical analysis and computational support. We present the ontology, discuss its instantiation, and provide some example inference rules for calculating various scholarly artifact metrics.

  5. A PRACTICAL ONTOLOGY FOR THE LARGE-SCALE MODELING OF SCHOLARLY ARTIFACTS AND THEIR USAGE

    Energy Technology Data Exchange (ETDEWEB)

    RODRIGUEZ, MARKO A. [Los Alamos National Laboratory; BOLLEN, JOHAN [Los Alamos National Laboratory; VAN DE SOMPEL, HERBERT [Los Alamos National Laboratory

    2007-01-30

    The large-scale analysis of scholarly artifact usage is constrained primarily by current practices in usage data archiving, privacy issues concerned with the dissemination of usage data, and the lack of a practical ontology for modeling the usage domain. As a remedy to the third constraint, this article presents a scholarly ontology that was engineered to represent those classes for which large-scale bibliographic and usage data exists, supports usage research, and whose instantiation is scalable to the order of 50 million articles along with their associated artifacts (e.g. authors and journals) and an accompanying 1 billion usage events. The real world instantiation of the presented abstract ontology is a semantic network model of the scholarly community which lends the scholarly process to statistical analysis and computational support. They present the ontology, discuss its instantiation, and provide some example inference rules for calculating various scholarly artifact metrics.

  6. The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr.

    Science.gov (United States)

    Carlini, D B; Chen, Y; Stephan, W

    2001-01-01

    To gain insights into the relationship between codon bias, mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in degree of codon bias and level of gene expression. Individual structural elements (helices) were inferred using the comparative method. For each gene, four types of randomization simulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon position nucleotide composition (N3). In the weakly expressed, weakly biased gene Adhr, the potential for secondary structure formation was found to be much stronger than in the highly expressed, highly biased gene Adh. This is consistent with the observation of approximately equal G and C percentages in Adhr ( approximately 31% across species), whereas in Adh the N3 distribution is shifted toward C (42% across species). Perturbing the N3 distribution to approximately equal amounts of A, G, C, and T increases the potential for secondary structure formation in Adh, but decreases it in Adhr. On the other hand, simulations that reduce codon bias without changing N3 content indicate that codon bias per se has only a weak effect on the formation of secondary structures. These results suggest that, for these two drosophilid genes, secondary structure is a relatively independent, negative regulator of gene expression. Whereas the degree of codon bias is positively correlated with level of gene expression, strong individual secondary structural elements may be selected for to retard mRNA translation and to decrease gene expression. PMID:11606539

  7. Investigation and analysis for community healthcare service usage in Taiyuan City and its influential factors%太原市社区卫生服务利用情况及其影响因素的研究

    Institute of Scientific and Technical Information of China (English)

    刘建美; 刘越泽

    2009-01-01

    Objective To find out the usage of community healthcare service by citizens in Taiyuan and its influential factors,for the purpose of offering references for sustainable development of community healthcare services.Methods By means of multiphase sampling,in-home surveys were made to 800 residents in Taiyuan,recovering 768 valid questionnaires.The single factorx2 test and unconditional logistic regression analysis using SPSS13.0 software.Results The two-week visit rate is 13.28%,and two- week non-visit rate is 45.16%.Ratio of community healthcare service usage by residents surveyed was 36.72%.Factors affecting utilization of such service for residents are education level,monthly average income,and knowledge of community healthcare services.Conclusion Usage of community healthcare service is low in Taiyuan.It is recommended to improve the system of community healthcare services in Taiyuan in view of the influential factors,in order to maximize efficient usage of the service.%目的 分析太原市居民对社区卫生服务的利用情况及其影响因素,以期为社区卫生服务的可持续发展提供参考依据.方法 采用多阶段抽样,对太原市800名居民进行入户调查,收回有效问卷768份.采用SPSS13.0软件进行单因素的卡方检验和多因素的非条件Logistic分析方法进行分析.结果 被调查居民的两周就诊率为13.28%,两周患者未就诊率为45.16%.被调查居民对社区卫生服务利用率为36.72%.社区卫生服务利用的影响因素有文化程度、月平均收入、对社区卫生服务的了解程度等.结论 太原市社区卫生服务利用率偏低.针对影响因素,健全太原市社区卫生服务体系,以实现最大程度的社区卫生服务的有效利用.

  8. E-book usage on a global scale: patterns, trends and opportunities

    Directory of Open Access Journals (Sweden)

    Michael Levine-Clark

    2015-07-01

    Full Text Available This study examines worldwide usage of over 600,000 e-books from EBL and ebrary. Using multiple modes of analysis, the study shows that there are variations in usage by geographic region as well as by subject. The study examines usage in relation to availability of titles, different types of usage per session, usage of the top ten percent of titles, and intensive and extensive use. These patterns can be used for benchmarking and as a model for local e-book studies.

  9. Understanding Mobile Social Media Usage

    DEFF Research Database (Denmark)

    Gan, Chunmei; Tan, Chee-Wee

    2017-01-01

    Despite the increasing popularity and growing trend of mobile social media in China, factors affecting users’ continued usage behavior remains unclear and deserves further scholarly attention. Synthesizing theories of expectation confirmation as well as uses and gratification, we advance a uses a...

  10. Users, Use, and Usage Statistics

    Science.gov (United States)

    Grogg, Jill E.

    2010-01-01

    For the August/September 2010 issue of "Library Technology Reports" (LTR) published by the American Library Association Techsource division, the author and her colleague, Rachel A. Fleming-May, focused on use and usage, both of electronic resources and use of libraries in general. In this article, the author discusses a few of the findings from an…

  11. Modeling Educational Usage of Facebook

    Science.gov (United States)

    Mazman, Sacide Guzin; Usluel, Yasemin Kocak

    2010-01-01

    The purpose of this study is to design a structural model explaining how users could utilize Facebook for educational purposes. In order to shed light on the educational usage of Facebook, in constructing the model, the relationship between users' Facebook adoption processes and their educational use of Facebook were included indirectly while the…

  12. Modeling Educational Usage of Facebook

    Science.gov (United States)

    Mazman, Sacide Guzin; Usluel, Yasemin Kocak

    2010-01-01

    The purpose of this study is to design a structural model explaining how users could utilize Facebook for educational purposes. In order to shed light on the educational usage of Facebook, in constructing the model, the relationship between users' Facebook adoption processes and their educational use of Facebook were included indirectly while the…

  13. Multiple start codons and phosphorylation result in discrete Rad52 protein species

    DEFF Research Database (Denmark)

    de Mayolo, A.A.; Lisby, M.; Erdeniz, N.

    2006-01-01

    protein species are due to promiscuous choice of start codons as well as post-translational modification. Specifically, Rad52 is phosphorylated both in a cell cycle-independent and in a cell cycle-dependent manner. Furthermore, phosphorylation is dependent on the presence of the Rad52 C terminus......The sequence of the Saccharomyces cerevisiae RAD52 gene contains five potential translation start sites and protein-blot analysis typically detects multiple Rad52 species with different electrophoretic mobilities. Here we define the gene products encoded by RAD52. We show that the multiple Rad52......, but not dependent on its interaction with Rad51. We also show that the Rad52 protein can be translated from the last three start sites and expression from any one of them is sufficient for spontaneous recombination and the repair of gamma-ray-induced double-strand breaks....

  14. Relationship between Impulsivity, Social Media Usage and Loneliness

    Directory of Open Access Journals (Sweden)

    Mustafa Savci

    2016-03-01

    Full Text Available The purpose of this study is to examine the relationships between impulsivity, social media usage, and loneliness and to test the structural hypothetical model developed based on the literature. The study was conducted on 307 (164 female, 143 male university students. Data collection instruments of the study were the Barratt Impulsivity Scale Short Form (BIS-11-SF, Social Media Usage Scale (SMUS, and UCLA Loneliness Scale Short Form (ULS-8. The measurement models of the latent variables were tested initially and it was observed that the scales of the latent variables were efficient enough to be included in the structural equation model. In addition, the suggested hypothetical model was tested. According to the analysis, it was observed that impulsivity directly, positively and significantly predicts social media usage, that social media usage directly, positively and significantly predicts loneliness, and that impulsivity indirectly, positively and significantly predicts loneliness.

  15. 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

    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...

  16. 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.

  17. Molecular evolutionary analysis of the Alfin-like protein family in Arabidopsis lyrata, Arabidopsis thaliana, and Thellungiella halophila.

    Science.gov (United States)

    Song, Yu; Gao, Jie; Yang, Fengxi; Kua, Chai-Shian; Liu, Jingxin; Cannon, Charles H

    2013-01-01

    In previous studies, the Alfin1 gene, a transcription factor, enhanced salt tolerance in alfalfa, primarily through altering gene expression levels in the root. Here, we examined the molecular evolution of the Alfin-like (AL) proteins in two Arabidopsis species (A. lyrata and A. thaliana) and a salt-tolerant close relative Thellungiella halophila. These AL-like proteins could be divided into four groups and the two known DUF3594 and PHD-finger domains had co-evolved within each group of genes, irrespective of species, due to gene duplication events in the common ancestor of all three species while gene loss was observed only in T. halophila. To detect whether natural selection acted in the evolution of AL genes, we calculated synonymous substitution ratios (dn/ds) and codon usage statistics, finding positive selection operated on four branches and significant differences in biased codon usage in the AL family between T. halophila and A. lyrata or A. thaliana. Distinctively, only the AL7 branch was under positive selection on the PHD-finger domain and the three members on the branch showed the smallest difference when codon bias was evaluated among the seven clusters. Functional analysis based on transgenic overexpression lines and T-DNA insertion mutants indicated that salt-stress-induced AtAL7 could play a negative role in salt tolerance of A. thaliana, suggesting that adaptive evolution occurred in the members of AL gene family.

  18. Molecular evolutionary analysis of the Alfin-like protein family in Arabidopsis lyrata, Arabidopsis thaliana, and Thellungiella halophila.

    Directory of Open Access Journals (Sweden)

    Yu Song

    Full Text Available In previous studies, the Alfin1 gene, a transcription factor, enhanced salt tolerance in alfalfa, primarily through altering gene expression levels in the root. Here, we examined the molecular evolution of the Alfin-like (AL proteins in two Arabidopsis species (A. lyrata and A. thaliana and a salt-tolerant close relative Thellungiella halophila. These AL-like proteins could be divided into four groups and the two known DUF3594 and PHD-finger domains had co-evolved within each group of genes, irrespective of species, due to gene duplication events in the common ancestor of all three species while gene loss was observed only in T. halophila. To detect whether natural selection acted in the evolution of AL genes, we calculated synonymous substitution ratios (dn/ds and codon usage statistics, finding positive selection operated on four branches and significant differences in biased codon usage in the AL family between T. halophila and A. lyrata or A. thaliana. Distinctively, only the AL7 branch was under positive selection on the PHD-finger domain and the three members on the branch showed the smallest difference when codon bias was evaluated among the seven clusters. Functional analysis based on transgenic overexpression lines and T-DNA insertion mutants indicated that salt-stress-induced AtAL7 could play a negative role in salt tolerance of A. thaliana, suggesting that adaptive evolution occurred in the members of AL gene family.

  19. NSTL全国开通数据库资源建设与使用情况分析%NSTL National License Database Resources Construction and Usage Analysis

    Institute of Scientific and Technical Information of China (English)

    潘晓蓉

    2014-01-01

    NSTL全国开通数据库资源经过多年的建设,已经具有一定规模,通过对已开通资源使用情况进行分析和用户调研,分析NSTL已购资源满足国内科研、教育机构的文献需求程度及在国家科技文献资源战略保障中发挥的作用,了解用户需求,进一步研究“国家许可”模式的运作和发展。%After years of construction, NSTL national open database resources have been implemented in a certain scale. By researching the usage, we can analyze that E-resources meet the demand of domestic scientific research, in order to understand the role of E-resources in National science and technology literature resource strategic security. We can also learn the user's need and study on operation and development of"national license"mode.

  20. Quantitative Analysis of the Usage of a Pedagogical Tool Combining Questions Listed as Learning Objectives and Answers Provided as Online Videos

    Directory of Open Access Journals (Sweden)

    Odette Laneuville

    2015-05-01

    Full Text Available To improve the learning of basic concepts in molecular biology of an undergraduate science class, a pedagogical tool was developed, consisting of learning objectives listed at the end of each lecture and answers to those objectives made available as videos online. The aim of this study was to determine if the pedagogical tool was used by students as instructed, and to explore students’ perception of its usefulness. A combination of quantitative survey data and measures of online viewing was used to evaluate the usage of the pedagogical practice. A total of 77 short videos linked to 11 lectures were made available to 71 students, and 64 completed the survey. Using online tracking tools, a total of 7046 views were recorded. Survey data indicated that most students (73.4% accessed all videos, and the majority (98.4% found the videos to be useful in assisting their learning. Interestingly, approximately half of the students (53.1% always or most of the time used the pedagogical tool as recommended, and consistently answered the learning objectives before watching the videos. While the proposed pedagogical tool was used by the majority of students outside the classroom, only half used it as recommended limiting the impact on students’ involvement in the learning of the material presented in class.

  1. Differences in codon bias cannot explain differences in translational power among microbes

    Directory of Open Access Journals (Sweden)

    Dethlefsen Les

    2005-01-01

    Full Text Available Abstract Background Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. One factor known to affect translational power is biased use of synonymous codons. The correlation within an organism between expression level and degree of codon bias among genes of Escherichia coli and other bacteria capable of rapid growth is commonly attributed to selection for high translational power. Conversely, the absence of such a correlation in some slowly growing microbes has been interpreted as the absence of selection for translational power. Because codon bias caused by translational selection varies between rapidly growing and slowly growing microbes, we investigated whether observed differences in translational power among microbes could be explained entirely by differences in the degree of codon bias. Although the data are not available to estimate the effect of codon bias in other species, we developed an empirically-based mathematical model to compare the translation rate of E. coli to the translation rate of a hypothetical strain which differs from E. coli only by lacking codon bias. Results Our reanalysis of data from the scientific literature suggests that translational power can differ by a factor of 5 or more between E. coli and slowly growing microbial species. Using empirical codon-specific in vivo translation rates for 29 codons, and several scenarios for extrapolating from these data to estimates over all codons, we find that codon bias cannot account for more than a doubling of the translation rate in E. coli, even with unrealistic simplifying assumptions that exaggerate the effect of codon bias. With more realistic assumptions, our best estimate is that codon bias accelerates translation in E. coli by no more than

  2. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis.

    Science.gov (United States)

    Kille, Sabrina; Acevedo-Rocha, Carlos G; Parra, Loreto P; Zhang, Zhi-Gang; Opperman, Diederik J; Reetz, Manfred T; Acevedo, Juan Pablo

    2013-02-15

    Saturation mutagenesis probes define sections of the vast protein sequence space. However, even if randomization is limited this way, the combinatorial numbers problem is severe. Because diversity is created at the codon level, codon redundancy is a crucial factor determining the necessary effort for library screening. Additionally, due to the probabilistic nature of the sampling process, oversampling is required to ensure library completeness as well as a high probability to encounter all unique variants. Our trick employs a special mixture of three primers, creating a degeneracy of 22 unique codons coding for the 20 canonical amino acids. Therefore, codon redundancy and subsequent screening effort is significantly reduced, and a balanced distribution of codon per amino acid is achieved, as demonstrated exemplarily for a library of cyclohexanone monooxygenase. We show that this strategy is suitable for any saturation mutagenesis methodology to generate less-redundant libraries.

  3. Usage of burnable poison on research reactors

    Energy Technology Data Exchange (ETDEWEB)

    Villarino, Eduardo Anibal [INVAP S.E., San Carlos de Bariloche (Argentina)

    2002-07-01

    The fuel assemblies with burnable poison are widely used on power reactors, but there are not commonly used on research reactors. This paper shows a neutronic analysis of the advantages and disadvantages of the burnable poison usage on research reactors. This paper analyses both burnable poison design used on research reactors: Boron on the lateral wall and Cadmium wires. Both designs include a parametric study on the design parameters like the amount and geometry of the burnable poison. This paper presents the design flexibility using burnable poisons, it does not find an optimal or final design, which it will strongly depend on the core characteristics and fuel management strategy. (author)

  4. A Comparative Analysis of Energy Usage and Energy Efficiency Behavior in Low- and High-Income Households: The Case of Kitwe, Zambia

    Directory of Open Access Journals (Sweden)

    Albert Malama

    2015-11-01

    Full Text Available Energy efficiency has been an important topic since the latter part of the last century. This is because adoption of energy efficiency measures has been acknowledged as one of the key methods of addressing the negative impact of climate change. In Zambia, however, the need to adopt energy efficiency measures has not just been driven by the imperative to mitigate the negative effects of climate change but also by a critical shortage of energy. This research looks at households’ energy consumption behavior in low- and high-income areas of Kitwe. Recent studies on the relationship between household energy consumption and behavioral lifestyle have been descriptive, with limited emphasis on the relationships between various variables. In this study, descriptive and inferential statistics have been used to investigate relationships between the two income groups and various energy consumption-related variables such as knowledge about energy reduction measures, energy saving strategies, barriers to the use of energy saving strategies, and the motives for using energy reduction strategies. Methodologically, the study was largely quantitative in nature, with questionnaires administered to a combined total of 56 households. However, key interviews were also conducted that helped us to get a clearer understanding of some of the issues covered in the research. Key findings are that whereas the descriptive statistics show that there are behavioral differences between the two income groups, the inferential statistics show that there is no relationship between income level and the energy efficiency variables. This has been found to be consistent with results from studies done elsewhere. The key lesson is that there is low usage of energy efficiency measures in both low- and high-income areas and that the authorities need to change the way information is disseminated to consumers from the current method of advertising to social diffusion.

  5. Student Empowerment Through Internet Usage

    DEFF Research Database (Denmark)

    Purushothaman, Aparna

    2011-01-01

    in a University in Southern India to empower the female students through Internet usage. The study was done to find out the problems the woman students faced in gaining access and using Internet and how they can be empowered through Internet usage. Future workshop was conducted to find out the problems...... Technologies that brought massive change in the ways people communicate and how information is exchanged across the globe. Educational sector has been strongly influenced by the emergence of Internet Technologies. Digital literacy is a prerequisite for students of this generation. Studies say that woman always...... and a research design was formulated in consultation with the participants. Action research model for reflective Internet searching developed by Edwards and Bruce (2002) was deployed in the study where students did the Internet searching based on the action research cycle of planning, acting, recording...

  6. Seatbelt usage: is there an association with obesity?

    Science.gov (United States)

    Behzad, B; King, D M; Jacobson, S H

    2014-09-01

    Wearing a seatbelt can prevent motor vehicle crash deaths. While primary seatbelt laws are designed to encourage vehicle passengers to wear seatbelts by allowing law enforcement officers to issue tickets when passengers do not wear seatbelts, discomfort may discourage obese individuals from wearing a seatbelt. The objective of this study is to assess the association between state-level obesity and seatbelt usage rates in the US, and to examine the possible role played by seatbelt laws in these associations. The strength of the association between obesity rates, seatbelt usage, and primary seatbelt laws at the state level is investigated using data from 2006 to 2011. Linear regression analysis is employed. This model estimates that increasing the obesity rate by 1% in a state where a primary seatbelt law (by which law enforcement officers can issue a ticket when seatbelts are not worn) is in effect is associated with a 0.06% decrease in seatbelt usage. However the same percentage of increase in the obesity rate in a state where no primary seatbelt law is in effect is associated with a 0.55% decrease in seatbelt usage. The magnitude of the statistical association between state obesity rates and state-level seatbelt usage is related to the existence of a primary seatbelt law, such that obesity has less impact on seatbelt usage in states where primary seatbelt laws are in effect.

  7. Opportunistic Resource Usage in CMS

    Energy Technology Data Exchange (ETDEWEB)

    Kreuzer, Peter [RWTH Aachen U.; Hufnagel, Dirk [Fermilab; Dykstra, D. [Fermilab; Gutsche, O. [Fermilab; Tadel, M. [UC, San Diego; Sfiligoi, I. [UC, San Diego; Letts, J. [UC, San Diego; Wuerthwein, F. [UC, San Diego; McCrea, A. [UC, San Diego; Bockelman, B. [Nebraska U.; Fajardo, E. [Andes U., Merida; Linares, L. [Andes U., Merida; Wagner, R. [TI, San Diego; Konstantinov, P. [Sofiya, Inst. Nucl. Res.; Blumenfeld, B. [Johns Hopkins U.; Bradley, D. [Wisconsin U., Madison

    2014-01-01

    CMS is using a tiered setup of dedicated computing resources provided by sites distributed over the world and organized in WLCG. These sites pledge resources to CMS and are preparing them especially for CMS to run the experiment's applications. But there are more resources available opportunistically both on the GRID and in local university and research clusters which can be used for CMS applications. We will present CMS' strategy to use opportunistic resources and prepare them dynamically to run CMS applications. CMS is able to run its applications on resources that can be reached through the GRID, through EC2 compliant cloud interfaces. Even resources that can be used through ssh login nodes can be harnessed. All of these usage modes are integrated transparently into the GlideIn WMS submission infrastructure, which is the basis of CMS' opportunistic resource usage strategy. Technologies like Parrot to mount the software distribution via CVMFS and xrootd for access to data and simulation samples via the WAN are used and will be described. We will summarize the experience with opportunistic resource usage and give an outlook for the restart of LHC data taking in 2015.

  8. Codon optimization of xylA gene for recombinant glucose isomerase production in Pichia pastoris and fed-batch feeding strategies to fine-tune bioreactor performance.

    Science.gov (United States)

    Ata, Özge; Boy, Erdem; Güneş, Hande; Çalık, Pınar

    2015-05-01

    The objectives of this work are the optimization of the codons of xylA gene from Thermus thermophilus to enhance the production of recombinant glucose isomerase (rGI) in P. pastoris and to investigate the effects of feeding strategies on rGI production. Codons of xylA gene from T. thermophilus were optimized, ca. 30 % of the codons were replaced with those with higher frequencies according to the codon usage bias of P. pastoris, codon optimization resulted in a 2.4-fold higher rGI activity. To fine-tune bioreactor performance, fed-batch bioreactor feeding strategies were designed as continuous exponential methanol feeding with pre-calculated feeding rate based on the pre-determined specific growth rate, and fed-batch methanol-stat feeding. Six feeding strategies were designed, as follows: (S1) continuous exponential methanol- and pulse- sorbitol feeding; (S2) continuous exponential methanol- and peptone- feeding; (S3) continuous exponential methanol- and pulse- mannitol feeding; (S4) continuous exponential methanol- and peptone- feeding and pulse-mannitol feeding; (S5) methanol-stat feeding by keeping methanol concentration at 5 g L(-1); and, (S6) methanol-stat feeding by keeping methanol concentration at 5 g L(-1) and pulse-mannitol feeding. The highest cell and rGI activity was attained as 117 g L(-1) at t = 66 h and 32530 U L(-1) at t = 53 h, in strategy-S5. The use of the co-substrate mannitol does not increase the rGI activity in methanol-stat feeding, where 4.1-fold lower rGI activity was obtained in strategy-S6. The overall cell yield on total substrate was determined at t = 53 h as 0.21 g g(-1) in S5 strategy.

  9. Energy efficiency trade-offs drive nucleotide usage in transcribed regions.

    Science.gov (United States)

    Chen, Wei-Hua; Lu, Guanting; Bork, Peer; Hu, Songnian; Lercher, Martin J

    2016-04-21

    Efficient nutrient usage is a trait under universal selection. A substantial part of cellular resources is spent on making nucleotides. We thus expect preferential use of cheaper nucleotides especially in transcribed sequences, which are often amplified thousand-fold compared with genomic sequences. To test this hypothesis, we derive a mutation-selection-drift equilibrium model for nucleotide skews (strand-specific usage of 'A' versus 'T' and 'G' versus 'C'), which explains nucleotide skews across 1,550 prokaryotic genomes as a consequence of selection on efficient resource usage. Transcription-related selection generally favours the cheaper nucleotides 'U' and 'C' at synonymous sites. However, the information encoded in mRNA is further amplified through translation. Due to unexpected trade-offs in the codon table, cheaper nucleotides encode on average energetically more expensive amino acids. These trade-offs apply to both strand-specific nucleotide usage and GC content, causing a universal bias towards the more expensive nucleotides 'A' and 'G' at non-synonymous coding sites.

  10. A Comprehensive Software Suite for the Analysis of cDNAs

    Institute of Scientific and Technical Information of China (English)

    Kazuharu Arakawa; Haruo Suzuki; Kosuke Fujishima; Kenji Fujimoto; Sho Ueda; Motomu Matsui; Masaru Tomita

    2005-01-01

    We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction.The software package is freely available under the GNU General Public License at http://www.g-language.org/data/cdna/.

  11. Identification of compounds that decrease the fidelity of start codon recognition by the eukaryotic translational machinery.

    Science.gov (United States)

    Takacs, Julie E; Neary, Timothy B; Ingolia, Nicholas T; Saini, Adesh K; Martin-Marcos, Pilar; Pelletier, Jerry; Hinnebusch, Alan G; Lorsch, Jon R

    2011-03-01

    Translation initiation in eukaryotes involves more than a dozen protein factors. Alterations in six factors have been found to reduce the fidelity of start codon recognition by the ribosomal preinitiation complex in yeast, a phenotype referred to as Sui(-). No small molecules are known that affect the fidelity of start codon recognition. Such compounds would be useful tools for probing the molecular mechanics of translation initiation and its regulation. To find compounds with this effect, we set up a high-throughput screen using a dual luciferase assay in S. cerevisiae. Screening of over 55,000 compounds revealed two structurally related molecules that decrease the fidelity of start codon selection by approximately twofold in the dual luciferase assay. This effect was confirmed using additional in vivo assays that monitor translation from non-AUG start codons. Both compounds increase translation of a natural upstream open reading frame previously shown to initiate translation at a UUG. The compounds were also found to exacerbate increased use of UUG as a start codon (Sui(-) phenotype) conferred by haploinsufficiency of wild-type eukaryotic initiation factor (eIF) 1, or by mutation in eIF1. Furthermore, the effects of the compounds are suppressed by overexpressing eIF1, which is known to restore the fidelity of start codon selection in strains harboring Sui(-) mutations in various other initiation factors. Together, these data strongly suggest that the compounds affect the translational machinery itself to reduce the accuracy of selecting AUG as the start codon.

  12. The M129V polymorphism of codon 129 in the prion gene (PRNP) in the Danish population

    DEFF Research Database (Denmark)

    Dyrbye, Henrik; Broholm, Helle; Dziegiel, Morten Hanefeld

    2008-01-01

    the distribution of the codon 129 polymorphism. The occurrence of three other relevant polymorphisms were investigated: An alanine (Ala) silent mutation on codon 117, an aspargine-serine (Asn-Ser) mutation on codon 171 and deletions or insertions in the moeity known as the octapeptide region of PRNP. DNA...

  13. Codon 64 of K-ras gene mutation pattern in hepatocellular carcinomas induced by bleomycin and 1-nitropyrene in A/J mice.

    Science.gov (United States)

    Bai, Feng; Nakanishi, Yoichi; Takayama, Koichi; Pei, Xin-Hai; Inoue, Koji; Harada, Taishi; Izumi, Miiru; Hara, Nobuyuki

    2003-01-01

    Bleomycin is a radiomimetic antitumor agent with unique genotoxic properties. 1-nitropyrene is an environmental mutagen and carcinogen that undergoes both oxidative and reductive metabolism. In the present study, hepatocellular carcinomas were induced in male A/J mice by the intraperitoneal injection of bleomycin (120 mg/kg) followed by the intraperitoneal administration of 1-nitropyrene (total dose: 1,575 mg/kg). In order to understand the mechanism by which these two compounds induce hepatocellular carcinomas, the incidence and spectrum of mutations in the K-ras proto-oncogene in these hepatocellular carcinomas were analyzed. The hepatocellular carcinomas were induced by the administration of bleomycin and 1-nitropyrene were evaluated for point mutations in exon 1 and exon 2 of the K-ras gene by the polymerase chain reaction and a sequencing analysis. No mutation was found in the hotspots regions of the K-ras gene codon 12, 13, or 61. However, the codon 64 of the K-ras gene mutation was identified in 10 of 10 (100%) hepatocellular carcinomas. All mutations showed the same pattern, which was TAC-CAC transition. Codon 64 of the K-ras gene mutation may thus play an important role in the induction of hepatocellular carcinomas by bleomycin in the existence of 1-nitropyrene. As far as we know, this is the first report of a codon 64 mutation in the K-ras gene in a chemically induced tumor.

  14. 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.

  15. P53 codon 11, 72, and 248 gene polymorphisms in endometriosis

    Directory of Open Access Journals (Sweden)

    Yao-Yuan Hsieh , Chich-Sheng Lin

    2006-01-01

    Full Text Available Objective: Mutated p53 gene is related to the instability of cell growth and cell cycle progression. We aimed to evaluate the association between endometriosis and p53 codon 11, 72 and 248 gene polymorphisms. Patients and methods: Women were divided into two groups: (1 moderate/severe endometriosis (n=148, and (2 non-endometriosis groups (n=150. P53 gene polymorphisms include codon11 Glu/Gln or Lys (GAG->CAG or AAG, codon 72 Arg/Pro (CGC->CCC, and codon 248 Arg/Thr (CGG->TCG. These gene polymorphisms were amplified by polymerase chain reaction and detected by electrophoresis after restriction enzyme (Taq I, BstU I, Hap II digestions. Associations between the endometriosis and p53 polymorphisms were evaluated. Results: The distributions of p53 codon 72 polymorphisms in both groups were significantly different. The proportions of Arg homozygotes/heterozygotes/Pro homozygotes in both groups were 9.5/66.2/24.3% and 30.7/50/19.3%. The proportions of Arg/Pro alleles were 42.6/57.4% and 56/44%. The distributions of p53 codon 11 and 248 polymorphisms in both groups were non-significantly different. All individuals appeared the wild genotypes (Glu11 and Arg248 homozygotes. Conclusion: Association between endometriosis and p53 codon 72 polymorphism exists. P53 codon 72*Pro-related genotype and allele are related with higher susceptibility of endometriosis. P53 codon 11 and 248 polymorphisms are not related with endometriosis susceptibility.

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

    Science.gov (United States)

    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.

  17. Towards Reassignment of the Methionine Codon AUG to Two Different Noncanonical Amino Acids in Bacterial Translation

    Directory of Open Access Journals (Sweden)

    Alessandro De Simone

    2016-06-01

    Full Text Available Genetic encoding of noncanonical amino acids (ncAAs through sense codon reassignment is an efficient tool for expanding the chemical functionality of proteins. Incorporation of multiple ncAAs, however, is particularly challenging. This work describes the first attempts to reassign the sense methionine (Met codon AUG to two different ncAAs in bacterial protein translation. Escherichia coli methionyl-tRNA synthetase (MetRS charges two tRNAs with Met: tRNAfMet initiates protein synthesis (starting AUG codon, whereas elongator tRNAMet participates in protein elongation (internal AUG codon(s. Preliminary in vitro experiments show that these tRNAs can be charged with the Met analogues azidohomoalanine (Aha and ethionine (Eth by exploiting the different substrate specificities of EcMetRS and the heterologous MetRS / tRNAMet pair from the archaeon Sulfolobus acidocaldarius, respectively. Here, we explored whether this configuration would allow a differential decoding during in vivo protein initiation and elongation. First, we eliminated the elongator tRNAMet from a methionine auxotrophic E. coli strain, which was then equipped with a rescue plasmid harboring the heterologous pair. Although the imported pair was not fully orthogonal, it was possible to incorporate preferentially Eth at internal AUG codons in a model protein, suggesting that in vivo AUG codon reassignment is possible. To achieve full orthogonality during elongation, we imported the known orthogonal pair of Methanosarcina mazei pyrrolysyl-tRNA synthetase (PylRS / tRNAPyl and devised a genetic selection system based on the suppression of an amber stop codon in an important glycolytic gene, pfkA, which restores enzyme functionality and normal cellular growth. Using an evolved PylRS able to accept Met analogues, it should be possible to reassign the AUG codon to two different ncAAs by using directed evolution. This work is licensed under a Creative Commons Attribution 4.0 International

  18. Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts.

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    Francisco P Lobo

    Full Text Available Virus-host biological interaction is a continuous coevolutionary process involving both host immune system and viral escape mechanisms. Flaviviridae family is composed of fast evolving RNA viruses that infects vertebrate (mammals and birds and/or invertebrate (ticks and mosquitoes organisms. These host groups are very distinct life forms separated by a long evolutionary time, so lineage-specific anti-viral mechanisms are likely to have evolved. Flaviviridae viruses which infect a single host lineage would be subjected to specific host-induced pressures and, therefore, selected by them. In this work we compare the genomic evolutionary patterns of Flaviviridae viruses and their hosts in an attempt to uncover coevolutionary processes inducing common features in such disparate groups. Especially, we have analyzed dinucleotide and codon usage patterns in the coding regions of vertebrate and invertebrate organisms as well as in Flaviviridae viruses which specifically infect one or both host types. The two host groups posses very distinctive dinucleotide and codon usage patterns. A pronounced CpG under-representation was found in the vertebrate group, possibly induced by the methylation-deamination process, as well as a prominent TpA decrease. The invertebrate group displayed only a TpA frequency reduction bias. Flaviviridae viruses mimicked host nucleotide motif usage in a host-specific manner. Vertebrate-infecting viruses possessed under-representation of CpG and TpA, and insect-only viruses displayed only a TpA under-representation bias. Single-host Flaviviridae members which persistently infect mammals or insect hosts (Hepacivirus and insect-only Flavivirus, respectively were found to posses a codon usage profile more similar to that of their hosts than to related Flaviviridae. We demonstrated that vertebrates and mosquitoes genomes are under very distinct lineage-specific constraints, and Flaviviridae viruses which specifically infect these

  19. Problem analysis of preventive usage of antibiotics in 2730 cases of cesarean sections in perioperative period%2730例剖宫产围手术期抗菌药物预防使用存在问题分析

    Institute of Scientific and Technical Information of China (English)

    张景旺; 王燕鸽; 张小周

    2015-01-01

    Objective To explore the problems of prophylaxis usage of antibiotics in cesarean sections to improve rational use of antibiotics and reduce the rate of surgical sites infection. Methods Retrospective analysis of antibiotics usage for 2730 cases of cesarean sections in perioperative period in our hospital from January 2013 to September 2014 was made. Results The rate of using antibiotics to prevent infections after cesarean sections among 2730 cases was 100%. There were 1723 cases which were used single type of antibiotics (63.11%), 1007 cases which were used two types of antibiotics (36.89%) and no cases which were using three or more types of antibiotics. The usage of antibiotics last 2 to 7 days, and most of them used for 5 days. The most frequently used preventive antibiotics was Amoxicillin and Clavulanate Potassium, and the most frequently two combined used preventive antibiotics were cefuroxime for injection and ornidazole injection. In the evaluation on rational usage of antibiotics, 648 cases were prevented rationally in the cesarean sections (23.74%), and 2082 cases were irrationally prevented (76.26%). Conclusion There exists numerous irrational preventive usage of antibiotics in cesarean sections, including irrational choice of antibiotics, non-conformance between administration dosage and interval and package insert, wrong choice or overlarge volume of solvent, postoperative infusion of prophylaxis antibiotics, too long prophylaxis usage course, irrational combined application of antibiotics and irrational administration in numerous medical records. It is suggested that prophylaxis usage of antibiotics in cesarean sections should be interfered with guiding principles of clinical use of antibiotics and guide of perioperative preventive application of antimicrobial agents.%目的:通过探讨我院剖宫产手术抗菌药物的应用存在的问题,提高医院合理应用抗菌药物水平,降低手术部位的感染率。方法采用

  20. 我院2009~2011年麻醉药品用药分析%The Analysis of Narcotic Drugs usage of Our Hospital from 2009 to 2011

    Institute of Scientific and Technical Information of China (English)

    潘建华

    2012-01-01

      目的:了解我院麻醉药品的应用情况。方法:收集我院2009~2011年麻醉药品的品种、用量,运用药物频度分析法(DDDs)和排序对麻醉药品应用情况进行统计分析和评价。结果:我院麻醉药品的使用量,吗啡制剂用量最大,盐酸哌替啶注射液使用频度有所下降,注射用盐酸瑞芬太尼的用量逐年递增。结论:我院麻醉药品使用基本合理,符合WHO推荐的癌痛治疗原则。%  To know of the application of the Narcotic drugs in our hospital. Methods: We collect all the information of anesthetic drug in our hospital from 2009 to 2011 such as varieties , dosage ,DDDs and sorting and then analysis and valuate it with statistic.Results:The dosage of morphine is the largest one in our hospital. The amount of usage of Pethidine hydrochloride injection is less than before. The usage of Remifentanil hydrochloride for injection is increased yearly. Conclusions:The application of Narcotic drugs in our hospital is rational and it conforms to the principals of cancer pain of WHO.

  1. On the evolution of word usage of classical Chinese poetry

    CERN Document Server

    Liu, Liang

    2015-01-01

    The hierarchy of classical Chinese poetry has been broadly acknowledged by a number of studies in Chinese literature. However, quantitative investigations about the evolution of classical Chinese poetry are limited. The primary goal of this study is to provide quantitative evidence of the evolutionary linkages, with emphasis on word usage, among different period genres for classical Chinese poetry. Specifically, various statistical analyses were performed to find and compare the patterns of word usage in the poems of nine period genres, including shi jing, chu ci, Han shi , Jin shi, Tang shi, Song shi, Yuan shi, Ming shi, and Qing shi. The result of analysis indicates that each of nine period genres has unique patterns of word usage, with some Chinese characters being preferably used by the poems of a particular period genre. The analysis on the general pattern of word preference implies a decreasing trend in the use of ancient Chinese characters along the timeline of dynastic types of classical Chinese poetr...

  2. Enhancing functional expression of codon-optimized heterologous enzymes in Escherichia coli BL21(DE3) by selective introduction of synonymous rare codons.

    Science.gov (United States)

    Zhong, Chao; Wei, Ping; Zhang, Yi-Heng Percival

    2017-05-01

    Rare codon in a heterologous gene may cause premature termination of protein synthesis, misincorporation of amino acids, and/or slow translation of mRNA, decreasing the heterologous protein expression. However, its hypothetical function pertaining to functional protein folding has been barely reported. Here, we investigated the effects of selective introduction of synonymous rare codons (SRCs) to two codon-optimized (i.e., rare codon-free) genes sucrose phosphorylase (SP) gene from Thermoanaerobacterium thermosaccharolyticum and amidohydrolase gene from Streptomyces caatingaensis on their expression levels in Escherichia coli BL21(DE3). We investigated the introduction of a single SRC to the coding regions of alpha-helix, beta-strand, or linker in the first half of rare codon-free sp and ah gene. The introduction of a single SRC in the beginning of the coding regions of beta-strand greatly enhanced their soluble expression levels as compared to the other regions. Also, we applied directed evolution to test multi-SRC-containing sp gene mutants for enhanced soluble SP expression levels. To easily identify the soluble SP expression level of colonies growing on Petri dishes, mCherry fluorescent protein was used as a SP-folding reporter when it was fused to the 3' end of the sp gene mutant libraries. After three rounds of screening, the best sp gene mutant containing nine SRCs exhibited an approximately six-fold enhancement in soluble protein expression level as compared to the wild-type and rare codon-free sp control. This study suggests that the selective introduction of SRCs can attenuate translation at specific points and such discontinuous attenuation can temporally separate the translation of segments of the peptide chains and actively coordinates their co-translational folding, resulting in enhanced functional protein expression. Biotechnol. Bioeng. 2017;114: 1054-1064. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  3. USAGE OF BELARUS TRANSIT POSSIBILITIES

    Directory of Open Access Journals (Sweden)

    D. M. Antioushenya

    2009-01-01

    Full Text Available It has been determined that sustainable and safety operation of a transport system and also efficient functioning of transport infrastructure depend on introduction of modern systems and technologies of passenger and load transportation  with usage of logistic approaches. The paper cites results of marketing investigations testifying to availability of the potential for formation of a transport and logistic system in the Republic. A conclusion has been made that realization of the mentioned key ideas shall allow efficiently to integrate in the world economic system.

  4. Better Living Through Metadata: Examining Archive Usage

    Science.gov (United States)

    Becker, G.; Winkelman, S.; Rots, A.

    2013-10-01

    The primary purpose of an observatory's archive is to provide access to the data through various interfaces. User interactions with the archive are recorded in server logs, which can be used to answer basic questions like: Who has downloaded dataset X? When did she do this? Which tools did she use? The answers to questions like these fill in patterns of data access (e.g., how many times dataset X has been downloaded in the past three years). Analysis of server logs provides metrics of archive usage and provides feedback on interface use which can be used to guide future interface development. The Chandra X-ray Observatory is fortunate in that a database to track data access and downloads has been continuously recording such transactions for years; however, it is overdue for an update. We will detail changes we hope to effect and the differences the changes may make to our usage metadata picture. We plan to gather more information about the geographic location of users without compromising privacy; create improved archive statistics; and track and assess the impact of web “crawlers” and other scripted access methods on the archive. With the improvements to our download tracking we hope to gain a better understanding of the dissemination of Chandra's data; how effectively it is being done; and perhaps discover ideas for new services.

  5. In silico analysis of 5'-UTRs highlights the prevalence of Shine-Dalgarno and leaderless-dependent mechanisms of translation initiation in bacteria and archaea, respectively.

    Science.gov (United States)

    Srivastava, Ambuj; Gogoi, Prerana; Deka, Bhagyashree; Goswami, Shrayanti; Kanaujia, Shankar Prasad

    2016-08-07

    In prokaryotes, a heterogeneous set of protein translation initiation mechanisms such as Shine-Dalgarno (SD) sequence-dependent, SD sequence-independent or ribosomal protein S1 mediated and leaderless transcript-dependent exists. To estimate the distribution of coding sequences employing a particular translation initiation mechanism, a total of 107 prokaryotic genomes were analysed using in silico approaches. Analysis of 5'-untranslated regions (UTRs) of genes reveals the existence of three types of mRNAs described as transcripts with and without SD motif and leaderless transcripts. Our results indicate that although all the three types of translation initiation mechanisms are widespread among prokaryotes, the number of SD-dependent genes in bacteria is higher than that of archaea. In contrast, archaea contain a significantly higher number of leaderless genes than SD-led genes. The correlation analysis between genome size and SD-led & leaderless genes suggests that the SD-led genes are decreasing (increasing) with genome size in bacteria (archaea). However, the leaderless genes are increasing (decreasing) in bacteria (archaea) with genome size. Moreover, an analysis of the start-codon biasness confirms that among ATG, GTG and TTG codons, ATG is indeed the most preferred codon at the translation initiation site in most of the coding sequences. In leaderless genes, however, the codons GTG and TTG are also observed at the translation initiation site in some species contradicting earlier studies which suggested the usage of only ATG codon. Henceforth, the conventional mechanism of translation initiation cannot be generalized as an exclusive way of initiating the process of protein biosynthesis in prokaryotes.

  6. Excision repair cross-complementation group 1 codon 118 polymorphism, micro ribonucleic acid and protein expression, clinical outcome of the advanced gastric cancer response to first-line FOLFOX-4 in Qinghai-Tibetan plateau population

    Directory of Open Access Journals (Sweden)

    Yu-Juan Qi

    2013-01-01

    Full Text Available Context: The excision repair cross-complementation group 1 (ERCC1 codon 118 C/T polymorphism has been associated with clinical outcome in cancer patients treated with platinum chemotherapy. Ethnic differences in the frequency of this polymorphism have been observed in Caucasian and African populations. Aim: The aim of this study was to evaluate the frequency and survival benefit of the ERCC1 codon 118 C/T polymorphism in a high-altitude population with advanced gastric cancer. Materials and Methods: Polymerase chain reaction-restriction fragment length polymorphism was used to determine the frequency of ERCC1 118 codon C/T polymorphism in 206 advanced gastric cancer patients residing in the high-altitude Qinghai-Tibetan plateau. The influence of the ERCC1 codon 118 C/T polymorphism on its micro ribonucleic acid (mRNA and protein expression, clinicopathological features; response to the platinum-based combination chemotherapy, and the outcome was evaluated. Statistical Analysis: The Kaplan-Meier method was used for survival analysis. The correlation of ERCC1 codon 118 polymorphism with ERCC1 mRNA and protein expression, clinicopathological characteristics, and first-line oxaliplatin, 5-fluorouracil, and leucovorin (FOLFOX-4 response was determined by χ2 -test. Results and Conclusions: ERCC1 codon 118 C/T polymorphism was not associated with ERCC1 mRNA and protein expression, FOLFOX-4 response, and progression-free survival (PFS or overall survival (OS. High ERCC1 mRNA and protein expression levels were associated with significantly lower FOLFOX-4 responses, PFS, and OS. ERCC1 codon 118 C/T polymorphism is not an important prognostic marker for advanced gastric cancer. Determination of ERCC1 mRNA and protein levels may be beneficial in predicting the response and outcome of FOLFOX-4 therapy in gastric cancer.

  7. Lack of correlation between p53 codon 72 polymorphism and anal cancer risk

    Institute of Scientific and Technical Information of China (English)

    Simone S Contu; Grasiela Agnes; Andrea P Damin; Paulo C Contu; Mário A Rosito; Claudio O Alexandre; Daniel C Damin

    2009-01-01

    AIM: To investigate the potential role of p53 codon 72 polymorphism as a risk factor for development of anal cancer.METHODS: Thirty-two patients with invasive anal carcinoma and 103 healthy blood donors were included in the study. p53 codon 72 polymorphism was analyzed in blood samples through polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing.RESULTS: The relative frequency of each allele was 0.60 for Arg and 0.40 for Pro in patients with anal cancer,and 0.61 for Arg and 0.39 for Pro in normal controls.No significant differences in distribution of the codon 72 genotypes between patients and controls were found.CONCLUSION: These results do not support a role for the p53 codon 72 polymorphism in anal carcinogenesis.

  8. Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement

    Science.gov (United States)

    Isaacs, Farren J.; Carr, Peter A.; Wang, Harris H.; Lajoie, Marc J.; Sterling, Bram; Kraal, Laurens; Tolonen, Andrew C.; Gianoulis, Tara A.; Goodman, Daniel B.; Reppas, Nikos B.; Emig, Christopher J.; Bang, Duhee; Hwang, Samuel J.; Jewett, Michael C.; Jacobson, Joseph M.; Church, George M.

    2016-01-01

    We present genome engineering technologies that are capable of fundamentally reengineering genomes from the nucleotide to the megabase scale. We used multiplex automated genome engineering (MAGE) to site-specifically replace all 314 TAG stop codons with synonymous TAA codons in parallel across 32 Escherichia coli strains. This approach allowed us to measure individual recombination frequencies, confirm viability for each modification, and identify associated phenotypes. We developed hierarchical conjugative assembly genome engineering (CAGE) to merge these sets of codon modifications into genomes with 80 precise changes, which demonstrate that these synonymous codon substitutions can be combined into higher-order strains without synthetic lethal effects. Our methods treat the chromosome as both an editable and an evolvable template, permitting the exploration of vast genetic landscapes. PMID:21764749

  9. Understanding the influence of codon translation rates on cotranslational protein folding.

    Science.gov (United States)

    O'Brien, Edward P; Ciryam, Prajwal; Vendruscolo, Michele; Dobson, Christopher M

    2014-05-20

    Protein domains can fold into stable tertiary structures while they are synthesized by the ribosome in a process known as cotranslational folding. If a protein does not fold cotranslationally, however, it has the opportunity to do so post-translationally, that is, after the nascent chain has been fully synthesized and released from the ribosome. The rate at which a ribosome adds an amino acid encoded by a particular codon to the elongating nascent chain can vary significantly and is called the codon translation rate. Recent experiments have illustrated the profound impact that codon translation rates can have on the cotranslational folding process and the acquisition of function by nascent proteins. Synonymous codon mutations in an mRNA molecule change the chemical identity of a codon and its translation rate without changing the sequence of the synthesized protein. This change in codon translation rate can, however, cause a nascent protein to malfunction as a result of cotranslational misfolding. In some situations, such dysfunction can have profound implications; for example, it can alter the substrate specificity of an ABC transporter protein, resulting in patients who are nonresponsive to chemotherapy treatment. Thus, codon translation rates are crucial in coordinating protein folding in a cellular environment and can affect downstream cellular processes that depend on the proper functioning of newly synthesized proteins. As the importance of codon translation rates makes clear, a necessary aspect of fully understanding cotranslational folding lies in considering the kinetics of the process in addition to its thermodynamics. In this Account, we examine the contributions that have been made to elucidating the mechanisms of cotranslational folding by using the theoretical and computational tools of chemical kinetics, molecular simulations, and systems biology. These efforts have extended our ability to understand, model, and predict the influence of codon

  10. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

    Science.gov (United States)

    Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

    2012-01-15

    Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes.

  11. Codon 972 polymorphism in the insulin receptor substrate-1 gene, obesity, and risk of noninsulin-dependent diabetes mellitus

    Energy Technology Data Exchange (ETDEWEB)

    Sigal, R.J.; Doria, A.; Warram, J.H.; Krolewski, A.S. [Joslin Diabetes Center, Boston, MA (United States)

    1996-04-01

    Because of the role of insulin receptor substrate-1 in insulin action, the insulin receptor substrate-1 gene is a candidate gene for noninsulin-dependent diabetes mellitus (NIDDM). Modest associations between NIDDM and a GGG-AGG single base substitution (corresponding to a glycine-arginine amino acid substitution) in codon 972 of the gene have been found, but none reached statistical significance. To examine further how large a proportion of NIDDM cases could be caused by the mutation, we performed a stratified analysis combining the results from the 6 earlier studies and those from our panel of 192 unrelated NIDDM subjects and 104 healthy controls. In addition, we looked for a possibility that the codon 972 mutation plays a role only in the presence of certain conditions. Genomic DNA samples obtained from NIDDM cases and healthy controls were genotyped using a PCR-restriction fragment length polymorphism protocol modified for genomic DNA. The GGG{r_arrow}AGG substitution was found in 5.7% of the diabetic subjects (11 of 192) and 6.9% of the controls (7 of 104). The difference between groups was not statistically significant, and it was not different from the results of other studies. The Mantel-Haenszel summary odds ratio across all studies was 1.49 (P < 0.05; 95% confidence intervals, 1.01-2.2). This summary odds ratio is consistent with a small proportion of NIDDM cases ({approximately}3%) being caused by the mutation. Exploratory subgroup analyses on our panel suggested a clustering of NIDDM, the codon 972 mutation, and overweight, raising the hypothesis that the mutation may predispose to NIDDM only in the presence of excess body weight. 9 refs., 2 tabs.

  12. Codon sextets with leading role of serine create "ideal" symmetry classification scheme of the genetic code.

    Science.gov (United States)

    Rosandić, Marija; Paar, Vladimir

    2014-06-10

    The standard classification scheme of the genetic code is organized for alphabetic ordering of nucleotides. Here we introduce the new, "ideal" classification scheme in compact form, for the first time generated by codon sextets encoding Ser, Arg and Leu amino acids. The new scheme creates the known purine/pyrimidine, codon-anticodon, and amino/keto type symmetries and a novel A+U rich/C+G rich symmetry. This scheme is built from "leading" and "nonleading" groups of 32 codons each. In the ensuing 4 × 16 scheme, based on trinucleotide quadruplets, Ser has a central role as initial generator. Six codons encoding Ser and six encoding Arg extend continuously along a linear array in the "leading" group, and together with four of six Leu codons uniquely define construction of the "leading" group. The remaining two Leu codons enable construction of the "nonleading" group. The "ideal" genetic code suggests the evolution of genetic code with serine as an initiator. Copyright © 2014 Elsevier B.V. All rights reserved.

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

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    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.

  14. tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence

    Science.gov (United States)

    Chionh, Yok Hian; McBee, Megan; Babu, I. Ramesh; Hia, Fabian; Lin, Wenwei; Zhao, Wei; Cao, Jianshu; Dziergowska, Agnieszka; Malkiewicz, Andrzej; Begley, Thomas J.; Alonso, Sylvie; Dedon, Peter C.

    2016-11-01

    Microbial pathogens adapt to the stress of infection by regulating transcription, translation and protein modification. We report that changes in gene expression in hypoxia-induced non-replicating persistence in mycobacteria--which models tuberculous granulomas--are partly determined by a mechanism of tRNA reprogramming and codon-biased translation. Mycobacterium bovis BCG responded to each stage of hypoxia and aerobic resuscitation by uniquely reprogramming 40 modified ribonucleosides in tRNA, which correlate with selective translation of mRNAs from families of codon-biased persistence genes. For example, early hypoxia increases wobble cmo5U in tRNAThr(UGU), which parallels translation of transcripts enriched in its cognate codon, ACG, including the DosR master regulator of hypoxic bacteriostasis. Codon re-engineering of dosR exaggerates hypoxia-induced changes in codon-biased DosR translation, with altered dosR expression revealing unanticipated effects on bacterial survival during hypoxia. These results reveal a coordinated system of tRNA modifications and translation of codon-biased transcripts that enhance expression of stress response proteins in mycobacteria.

  15. USAGE OF ACB-MININD SOFTWARE IN THE CBA ANALYSIS FOR FINANCING INVESTMENT PROJECTS THROUGH EUROPEAN FUNDING IN CORRELATION WITH THE FINANCING FROM THE BANKING SYSTEM

    Directory of Open Access Journals (Sweden)

    Droj Gabriela

    2012-12-01

    Full Text Available The extension of the European Union with the first “wave” of new members in 2004 and later with the second “wave” of members in 2007 brought new opportunities for the countries in Eastern Europe, being obvious that “effective utilisation of EU support can foster the success of their economic performance”. Financing investment projects proposed by the SMEs can be realized through several financial sources internal and external, from which two of the most common external sources constitute from subsidies-grants and through banking system. One of the most important financing programme present in Romania, available for SMEs is SOP IEC, which awards grants for investments proposed by production companies. This financing program encourages its beneficiaries to combine the European grant with private funds mostly provided through the banking system. The paper analyzed the methodology used in Cost Benefit Analysis and also The ACB-MININD software which is compulsory to be used for the CBA analysis of these investment projects links for the first time elements of analysis used by the European Commission with elements of analysis used by the banking system. In this context the present article tries to analyze how the ACB-MININD software links the main elements of Cost-Benefit analysis such as NPV or IRR with elements of the bankability software which are mainly used by the banking system such as: cash-flow analysis, loan/interest payment and financial sustainability. Also are presented the links between the banking sector and the external financing sector in the field on investment projects. As final conclusions of this paper we will demonstrate the theoretical and practical role of cost-benefit analysis - financial component to select the best applications that will be proposed for funding under the European grant programs and to link them to the banking system in order to ensure a proper co-financing for these

  16. The Terms in the Special Language: Norms, Usage, and Tendency

    Directory of Open Access Journals (Sweden)

    Virginija Stankevičienė

    2016-06-01

    Full Text Available One of the most important issues of terminology remains term variance (or synonymy. In order to find out the trends of terms usage in the language for specific purposes, the comprehensive analysis of dictionaries, coursebooks, students’ survey was carried out. It allowed to determine prevalent types in the terminology of economics and chemistry, to analyze the prevalence of Lithuanian and international terms synonymy, term usage tendencies in students’ language and academic texts. Summarizing the investigation results it can be stated that in the special language of economics and chemistry, term variants were both presented in dictionaries and used by teachers.

  17. Web Miner: A Tool for Discovery of Usage Patterns From Web Data

    Directory of Open Access Journals (Sweden)

    Roop Ranjan

    2013-05-01

    Full Text Available As there is a huge amount of data available online, the World Wide Web is a fertile area for data mining research. In recent years a various surveys have been performed on static data of web sites toperform web usage mining. This paper deals with the Web usage mining of a website which is hosted on IIS web server. Web usage mining is the area of data mining which deals with the discovery and analysisof usage patterns from Web data, specifically web logs, in order to perform improvements in web based applications. Web usage mining consists of three phases, pre-processing, pattern discovery, and pattern analysis. After the completion of these three phases the user can find the required usage patterns and use this information for the specific needs. The research is being performed on a log file using Log Parser.

  18. THE SECURITY, ENVIRONMENT AND HEALTH POLICY DEFINED FROM AN INITIAL CRITICAL ANALYSIS AND UNFOLDED INTO OBJECTIVES, GOALS AND PROGRAMS: PRACTICAL USAGE AT ONE GAS COMPANY

    OpenAIRE

    Silva, Lily Maciene Diniz; MBA em Perícia, Auditoria e Gestão Ambiental; Cavalcanti, Yara Teixeira; MBA em Perícia, Auditoria e Gestão Ambiental; Lins, Gustavo Aveiro; CEDERJ/SEE-RJ/CEDAE; Cunha, Roberto Ricardo Rachid Saab Barbosa; UERJ; Rodrigues, Manoel Gonçalves; UERJ; de Almeida, Josimar Ribeiro; UERJ

    2013-01-01

    The establishment of a Security, Environment and Health (SMS) Policy as intent letter of the organization, expressing its global objectives and the commitment to improve the SMS performance based on an initial critical analysis allows knowing in which situation the organization is relating to SMS issues, besides to be the first phase for a management system implementation. For this work, a survey based on the five basic principles of the management system in charge of the continuous enhance, ...

  19. A DISCUSSION ON THE METHODOLOGICAL USAGE OF FACTOR ANALYSIS IN SERVQUAL STUDIES: SOME IMPLICATIONS OF AN EMPIRICAL STUDY OF EXPORT CREDIT AGENCY IN TURKEY

    OpenAIRE

    2012-01-01

    This paper aims to discuss the different results of factor analysis used to test construct validity and reliability in SERVQUAL studies, considering the fact that our study measuring service quality of Turk Eximbank, export credit agency in Turkey, resulted in more different -but not unusual- findings than those proposed by the designers of the model. These controversial results observed in both our study and various service quality investigations directed us to look more closely into this is...

  20. Context of Usage and Aesthetics of Selected Proverbs from ...

    African Journals Online (AJOL)

    OSAKUE S. OMOERA

    Deploying Dell Hymes' 'SPEAKING' model of speech analysis, ... method of expressing life which is aesthetically flavoured. Drawing on the ... context of usage of proverbs is of paramount interest to this discourse. In Nigeria ..... few, use proverbs to enliven their speeches, make critical comments on burning issues of the.

  1. USAGE OF MULTIMEDIA TECHNOLOGIES IN TRAINING OF HIGHER EDUCATIONAL STUDENT

    Directory of Open Access Journals (Sweden)

    Svitlana S. Ryzhenko

    2010-08-01

    Full Text Available The article deals with the sensibility of multimedia means of education usage in different types of classes (lectures, practical, seminars and laboratory work. Recommendations as for the giving lectures on the basis of multimedia means of education are given. The article also presents the analysis of the students’ level comprehension of the material presented in a multimedia format.

  2. Study on online community user motif using web usage mining

    Science.gov (United States)

    Alphy, Meera; Sharma, Ajay

    2016-04-01

    The Web usage mining is the application of data mining, which is used to extract useful information from the online community. The World Wide Web contains at least 4.73 billion pages according to Indexed Web and it contains at least 228.52 million pages according Dutch Indexed web on 6th august 2015, Thursday. It’s difficult to get needed data from these billions of web pages in World Wide Web. Here is the importance of web usage mining. Personalizing the search engine helps the web user to identify the most used data in an easy way. It reduces the time consumption; automatic site search and automatic restore the useful sites. This study represents the old techniques to latest techniques used in pattern discovery and analysis in web usage mining from 1996 to 2015. Analyzing user motif helps in the improvement of business, e-commerce, personalisation and improvement of websites.

  3. Identification of codon-specific serine to asparagine mistranslation in recombinant monoclonal antibodies by high-resolution mass spectrometry.

    Science.gov (United States)

    Yu, X Christopher; Borisov, Oleg V; Alvarez, Melissa; Michels, David A; Wang, Yajun Jennifer; Ling, Victor

    2009-11-15

    Translation errors in protein biosynthesis may result in low level amino acid misincorporation and contribute to product heterogeneity of recombinant protein therapeutics. We report the use of peptide map analysis by reversed-phase high-performance liquid chromatography and high-resolution mass spectrometry to detect and identify mistranslation events in recombinant monoclonal antibodies expressed in mammalian cell lines including Chinese hamster ovary (CHO) cells. Misincorporation of an asparagine residue at multiple serine positions was detected as earlier-eluting peptides with masses 27.01 Da higher than expected. The exact positions at which misincorporation occurred were identified by tandem mass spectrometry of the asparagine-containing variant peptides. The identified asparagine misincorporation sites correlated with the use of codon AGC but with none of the other five serine codons. The relative levels of misincorporation ranged from 0.01%-0.2% among multiple serine positions detected across three different antibodies by targeted analysis of expected and variant peptides. The low levels of misincorporation are consistent with published predictions for in vivo translation error rates. Our results demonstrate that state-of-the-art mass spectrometry with a combination of high sensitivity, accuracy, and dynamic range provides a new ability to discover and characterize low level protein variants that arise from mistranslation events.

  4. Development of K562 cell clones expressing beta-globin mRNA carrying the beta039 thalassaemia mutation for the screening of correctors of stop-codon mutations.

    Science.gov (United States)

    Salvatori, Francesca; Cantale, Vera; Breveglieri, Giulia; Zuccato, Cristina; Finotti, Alessia; Bianchi, Nicoletta; Borgatti, Monica; Feriotto, Giordana; Destro, Federica; Canella, Alessandro; Breda, Laura; Rivella, Stefano; Gambari, Roberto

    2009-07-09

    Nonsense mutations, giving rise to UAA, UGA and UAG stop codons within the coding region of mRNAs, promote premature translational termination and are the leading cause of approx. 30% of inherited diseases, including cystic fibrosis, Duchenne muscular dystrophy and thalassaemia. For instance, in beta(0)39-thalassaemia the CAG (glutamine) codon is mutated to the UAG stop codon, leading to premature translation termination and to mRNA destabilization through the well-described NMD (nonsense-mediated mRNA decay). In order to develop an approach facilitating translation and, therefore, protection from NMD, aminoglycoside antibiotics have been tested on mRNAs carrying premature stop codons. These drugs decrease the accuracy in the codon-anticodon base-pairing, inducing a ribosomal read-through of the premature termination codons. Interestingly, recent papers have described drugs designed and produced for suppressing premature translational termination, inducing a ribosomal read-through of premature but not normal termination codons. These findings have introduced new hopes for the development of a pharmacological approach to the therapy of beta(0)39-thalassaemia. In this context, we started the development of a cellular model of the beta(0)39-thalassaemia mutation that could be used for the screening of a high number of aminoglycosides and analogous molecules. To this aim, we produced a lentiviral construct containing the beta(0)39-thalassaemia globin gene under a minimal LCR (locus control region) control and used this construct for the transduction of K562 cells, subsequently subcloned, with the purpose to obtain several K562 clones with different integration copies of the construct. These clones were then treated with Geneticin (also known as G418) and other aminoglycosides and the production of beta-globin was analysed by FACS analysis. The results obtained suggest that this experimental system is suitable for the characterization of correction of the beta(0

  5. 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...

  6. Usage of K-cluster and factor analysis for grouping and evaluation the quality of olive oil in accordance with physico-chemical parameters

    Science.gov (United States)

    Milev, M.; Nikolova, Kr.; Ivanova, Ir.; Dobreva, M.

    2015-11-01

    25 olive oils were studied- different in origin and ways of extraction, in accordance with 17 physico-chemical parameters as follows: color parameters - a and b, light, fluorescence peaks, pigments - chlorophyll and β-carotene, fatty-acid content. The goals of the current study were: Conducting correlation analysis to find the inner relation between the studied indices; By applying factor analysis with the help of the method of Principal Components (PCA), to reduce the great number of variables into a few factors, which are of main importance for distinguishing the different types of olive oil;Using K-means cluster to compare and group the tested types olive oils based on their similarity. The inner relation between the studied indices was found by applying correlation analysis. A factor analysis using PCA was applied on the basis of the found correlation matrix. Thus the number of the studied indices was reduced to 4 factors, which explained 79.3% from the entire variation. The first one unified the color parameters, β-carotene and the related with oxidative products fluorescence peak - about 520 nm. The second one was determined mainly by the chlorophyll content and related to it fluorescence peak - about 670 nm. The third and the fourth factors were determined by the fatty-acid content of the samples. The third one unified the fatty-acids, which give us the opportunity to distinguish olive oil from the other plant oils - oleic, linoleic and stearin acids. The fourth factor included fatty-acids with relatively much lower content in the studied samples. It is enquired the number of clusters to be determined preliminary in order to apply the K-Cluster analysis. The variant K = 3 was worked out because the types of the olive oil were three. The first cluster unified all salad and pomace olive oils, the second unified the samples of extra virgin oilstaken as controls from producers, which were bought from the trade network. The third cluster unified samples from

  7. Cloning and Expression of Codon-Optimized P1 Protein Gene of Mycoplasma pneumoniae in Escherichia coli%密码子优化的肺炎支原体P1蛋白在大肠杆菌中的克隆表达

    Institute of Scientific and Technical Information of China (English)

    张奇舒; 修冰水; 宋晓国; 张贺秋; 谢宝贵

    2012-01-01

    目的:获得密码子优化的肺炎支原体P1黏附蛋白优势表位抗原基因,并在大肠杆菌中表达,为临床诊断试剂和疫苗研制打下基础.方法:采用生物信息学分析肺炎支原体P1蛋白的抗原表位,筛选特异性P1蛋白优势表位区;采用大肠杆菌优势密码子,设计上述P1蛋白优势表位基因序列;采用退火PCR技术合成上述基因,并利用载体pGEX-4T-2实现P1优势表位抗原在大肠杆菌中的表达;采用ELISA法对纯化的P1抗原活性进行测定.结果:肺炎支原体P1蛋白特异性抗原表位主要位于1154-1521 aa,获得的P1优化密码子基因平行突变37个稀有密码子和2个终止密码子;在大肠杆菌中表达的GST-P1融合蛋白的相对分子质量为65.9×103,纯化后重组抗原能与肺炎支原体感染者血清发生特异性的免疫反应.结论:采用密码子优化基因合成技术实现了肺炎支原体P1优势表位抗原在大肠杆菌中的高效表达,为肺炎支原体感染的诊断试剂研究提供了重要参考.%Objective: To obtain codon-optimized P1 adhesion protein of predominant epitope gene of Mycoplasma pneumonia (Mp), to achieve the expression of the above gene in Escherichia coli for the study of clinical diagnostic reagents and vaccines. Methods: The predominant epitopes of P1 protein were selected by bioinformatic analysis and the DNA sequences was designed according to of high-usage codons of E.coli. Above gene was expressed in E.coli by vector pGEX-4T-2, and its immunoreactivity was measured by ELISA. Results: Specific epitopes of P1 protein of Mp were mainly located at 1154-1521 aa. 37 rare codons and 2 stop codons were mutated in the acquirement of the P1 optimized DNA sequence. The molecular weight of GST-PI fusion protein expressed in E.coli was 65.9 kD. Purified recombinant antigen displayed specific immune response with sera of patients infected with Mp. Conclusion: In this study, the P1 predominant epitopes of Mp was

  8. Do anticodons of misacylated tRNAs preferentially mismatch codons coding for the misloaded amino acid?

    Directory of Open Access Journals (Sweden)

    Seligmann Hervé

    2010-05-01

    Full Text Available Abstract Background Accurate amino acid insertion during peptide elongation requires tRNAs loaded by cognate amino acids and that anticodons match codons. However, tRNA misloading does not necessarily cause misinsertions: misinsertion is avoided when anticodons mismatch codons coding for misloaded amino acids. Presentation of the hypothesis Occasional compensation of misacylation by codon-anticodon mismatch necessarily occurs. Putatively, occasional error compensation may be enhanced beyond the random combination of independent errors in tRNA loading and codon-anticodon interactions: tRNA misacylation might alter potentials for codon-anticodon mismatches, perhaps specifically increasing potentials for mismatching those codons coding for the misacylated non-cognate amino acid. This hypothetical phenomenon is called 'error coordination', in distinction from 'error compensation' that assumes independence between misacylation and mismatch. Testing the hypothesis Eventually, the hypothesis should be tested for each combination of amino acid misacylation and codon-anticodon mismatch, by comparing stabilities or frequencies of mismatched codon-anticodon duplexes formed by tRNAs loaded by their cognate amino acid with stabilities formed by that tRNA when misloaded with the amino acid coded by the mismatched codon. Competitive mismatching experiments between misloaded and correctly loaded tRNAs could also be useful, yet more sophisticated experiments. Implications of the hypothesis Detecting error coordination implies estimating error compensation, which also promotes protein synthesis accuracy. Hence even in the absence of evidence for error coordination, experiments would yield very useful insights into misacylation and mismatch processes. In case experiments consider post-transcriptional RNA modifications (especially at wobble positions, results on codon-anticodon mismatches would enable significant improvements and sophistications of secondary

  9. Analysis of the Usage of Magnetic Force-directed Approach and Visual Techniques for Interactive Context-based Drawing of Multi-attributed Graphs

    Directory of Open Access Journals (Sweden)

    Zabiniako Vitaly

    2014-12-01

    Full Text Available In this article, the authors perform an analysis in order to assess adaptation of magnetic force-directed algorithms for context-based information extraction from multi-attributed graphs during visualization sessions. Theoretic standings behind magnetic force-directed approach are stated together with review on how particular features of respective algorithms in combination with appropriate visual techniques are especially suitable for improved processing and presenting of knowledge that is captured in form of graphs. The complexity of retrieving multi-attributed information within the proposed approach is handled with dedicated tools, such as selective attraction of nodes to MFE (Magnetic Force Emitter based on search criteria, localization of POI (Point of Interest regions, graph node anchoring, etc. Implicit compatibility of aforementioned tools with interactive nature of data exploration is distinguished. Description of case study, based on bibliometric network analysis is given, which is followed by the review of existing related works in this field. Conclusions are made and further studies in the field of visualization of multi-attributed graphs are defined.

  10. Waste heat usage in commercial refrigeration systems - Energy analysis of two retail outlets; Abwaermenutzung in der gewerblichen Kaelte. Energetische Analyse von zwei Verkaufsstellen - Schlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Erb, M.; Gutzwiller, S.

    2009-09-15

    This final report for the Swiss Federal Office of Energy (SFOE) presents the results of an analysis made on the use of waste heat produced by the refrigeration systems in two retail stores. The results of field measurements made in two installations in Migros and Coop supermarkets are presented. The efficiencies of heat recovery determined for the refrigeration systems are presented and discussed. The electro-thermal amplification factors (ETV) of the systems determined for the two installations are discussed. Basically, the authors are of the opinion that the ETV noted are very good. In both installations, heat recovery is energetically and ecologically very efficient. The factors leading to a high ETV are discussed and recommendations for the planning of such heat-recovery systems are made. An appendix includes schematics of the refrigeration systems in the two stores.

  11. Genotypic identification of some lactic acid bacteria by amplified fragment length polymorphism analysis and investigation of their potential usage as starter culture combinations in Beyaz cheese manufacture.

    Science.gov (United States)

    Karahan, A G; Başyiğit Kiliç, G; Kart, A; Sanlidere Aloğlu, H; Oner, Z; Aydemir, S; Erkuş, O; Harsa, S

    2010-01-01

    In this study, 2 different starter culture combinations were prepared for cheesemaking. Starter culture combinations were formed from 8 strains of lactic acid bacteria. They were identified as Lactococcus lactis ssp. lactis (2 strains), Lactobacillus plantarum (5 strains), and Lactobacillus paraplantarum (1 strain) by amplified fragment length polymorphism analysis. The effects of these combinations on the physicochemical and microbiological properties of Beyaz cheeses were investigated. These cheeses were compared with Beyaz cheeses that were produced with a commercial starter culture containing Lc. lactis ssp. lactis and Lc. lactis ssp. cremoris as control. All cheeses were ripened in brine at 4 degrees C for 90 d. Dry matter, fat in dry matter, titratable acidity, pH, salt in dry matter, total N, water-soluble N, and ripening index were determined. Sodium dodecyl sulfate-PAGE patterns of cheeses showed that alpha(S)-casein and beta-casein degraded slightly during the ripening period. Lactic acid bacteria, total mesophilic aerobic bacteria, yeast, molds, and coliforms were also counted. All analyses were repeated twice during d 7, 30, 60, and 90. The starter culture combinations were found to be significantly different from the control group in pH, salt content, and lactobacilli, lactococci, and total mesophilic aerobic bacteria counts, whereas the cheeses were similar in fat, dry matter content, and coliform, yeast, and mold counts. The sensory analysis of cheeses indicated that textural properties of control cheeses presented somewhat lower scores than those of the test groups. The panelists preferred the tastes of treatment cheeses, whereas cheeses with starter culture combinations and control cheeses had similar scores for appearance and flavor. These results indicated that both starter culture combinations are suitable for Beyaz cheese production.

  12. The Impact of New Student Housing on Library Usage: A Case Study

    Science.gov (United States)

    Ritterbush, Jon

    2009-01-01

    A quantitative analysis of campus housing figures and library usage statistics suggests a stronger correlation than library usage compared to other enrollment figures. New residents on a university campus were surveyed on their frequency and reasons for utilizing the library's physical and online resources, before and after moving in. (Contains 1…

  13. Function Allocation in Complex Socio-Technical Systems: Procedure usage in nuclear power and the Context Analysis Method for Identifying Design Solutions (CAMIDS) Model

    Science.gov (United States)

    Schmitt, Kara Anne

    This research aims to prove that strict adherence to procedures and rigid compliance to process in the US Nuclear Industry may not prevent incidents or increase safety. According to the Institute of Nuclear Power Operations, the nuclear power industry has seen a recent rise in events, and this research claims that a contributing factor to this rise is organizational, cultural, and based on peoples overreliance on procedures and policy. Understanding the proper balance of function allocation, automation and human decision-making is imperative to creating a nuclear power plant that is safe, efficient, and reliable. This research claims that new generations of operators are less engaged and thinking because they have been instructed to follow procedures to a fault. According to operators, they were once to know the plant and its interrelations, but organizationally more importance is now put on following procedure and policy. Literature reviews were performed, experts were questioned, and a model for context analysis was developed. The Context Analysis Method for Identifying Design Solutions (CAMIDS) Model was created, verified and validated through both peer review and application in real world scenarios in active nuclear power plant simulators. These experiments supported the claim that strict adherence and rigid compliance to procedures may not increase safety by studying the industry's propensity for following incorrect procedures, and when it directly affects the outcome of safety or security of the plant. The findings of this research indicate that the younger generations of operators rely highly on procedures, and the organizational pressures of required compliance to procedures may lead to incidents within the plant because operators feel pressured into following the rules and policy above performing the correct actions in a timely manner. The findings support computer based procedures, efficient alarm systems, and skill of the craft matrices. The solution to

  14. The strategic importance of internet usage as new media tool in the studies of sports marketing: “Analysis of sports clubs’ websites in Turkey and England”

    Directory of Open Access Journals (Sweden)

    Bora Çavuşoğlu

    2011-03-01

    Full Text Available Sports being of great interest around the world has been an important factor in the marketing field thanks to both favorite sportsmen and its reaching a large target audience. The competition existed in its any field makes it necessary to be carried out a strategic marketing plan so as to raise awareness of each sport club. It attracts attention that the sport clubs in the process of branding in accordance with their marketing targets consider the developments in new media and try to be dominant in marketing activities by taking the advantage of internet. Within this context, the great interest and adherence towards sports; how sports clubs having the most championships in the last ten years both in Turkey and England use internet in the marketing field; similarities and differences between them are presented in this study through the method of content analysis of each sport clubs’ website. It has been found that English sports clubs among the other clubs analyzed in this study are more successful in both being corporate, sports marketing and using social media.

  15. Usage of XT-4000i Intelligent Blood Analysis System%XT-4000i智能型血液分析系统应用体会

    Institute of Scientific and Technical Information of China (English)

    戴启宇; 于芳芳

    2012-01-01

    The principle, characteristics, parameters and precautions of XT-4000i intelligent blood analysis system are introduced, which can be used for the detection of blood and body fluid, and thus can meet the requirements of clinical laboratory and research. The reference also is provided for the selection of clinical blood analyzer.%分析探讨了XT-4000i智能型全自动血液分析系统的检测原理、特色技术、分析参数及应用注意事项等,指出了该仪器是一种全新理念的集血液、体液检测为一体的高端智能化分析系统,能满足临床血液常规检验和临床研究工作的需求,并可为临床血液分析仪器选型提供参考.

  16. The strategic importance of internet usage as new media tool in the studies of sports marketing: “Analysis of sports clubs’ websites in Turkey and England”

    Directory of Open Access Journals (Sweden)

    Bora Çavuşoğlu

    2011-03-01

    Full Text Available Sports being of great interest around the world has been an important factor in the marketing field thanks to both favorite sportsmen and its reaching a large target audience. The competition existed in its any field makes it necessary to be carried out a strategic marketing plan so as to raise awareness of each sport club. It attracts attention that the sport clubs in the process of branding in accordance with their marketing targets consider the developments in new media and try to be dominant in marketing activities by taking the advantage of internet. Within this context, the great interest and adherence towards sports; how sports clubs having the most championships in the last ten years both in Turkey and England use internet in the marketing field; similarities and differences between them are presented in this study through the method of content analysis of each sport clubs’ website. It has been found that English sports clubs among the other clubs analyzed in this study are more successful in both being corporate, sports marketing and using social media. 

  17. [Analysis of knee joint injuries of competitive volleyball players in selected sports clubs of Poznan city--biomechanical context. Synthesis--proposal for the usage of physiotherapy methods in the prevention of the discussed injuries].

    Science.gov (United States)

    Dworak, Lechosław B; Rzepnicka, Agata; Wilkosz, Piotr; Szczesny, Łukasz

    2010-01-01

    Volleyball is a source of direct injuries and chronic overloads of the joints, which indirectly results in traumas and permanent dysfunctions. This applies particularly to: knee joints, ankle joints, shoulder joints and small joints of the hand, as well as the joints of the lower spine regions. Each league team should employ a physiotherapist who would be responsible for the implementation of an injury prevention program as well as for choosing the right training loads. The purpose of this study is to analyze the frequency and the type of knee joint injuries occurring in people practicing Volleyball at competitive level as well as to propose the usage of elements of modern physiotherapy in order to prevent these injuries. The tests were performed over a group of 19 volleyball players from Poznan. In order to propose measures that would prevent injuries, the authors carried out a review of modern physiotherapy methods and suggested the implementation of certain therapeutic techniques for the region of the knee joint. RESULT ANALYSIS AND DISCUSSION: As much as 79% of the subjects reported having chronic pain and knee joint injuries in the past. All of them, due to their conditions, declared having used various forms of physiotherapy treatment. It seems that in a professional sports club not only the presence of a massage therapist but first of all a qualified physiotherapist is indispensable.

  18. The usage of activated carbon from teak sawdust (tectona grandis l.f.) and zeolite for the adsorption of Cr(VI) and its analysis using solid-phase spectrophotometry (sps)

    Science.gov (United States)

    Saputro, S.; Masykuri, M.; Mahardiani, L.; Mulyani, B.; Qorina, I.; Yoshimura, K.; Takehara, K.; Matsuoka, S.

    2017-02-01

    This study aims to evaluate the usage of teak sawdust and zeolite as an adsorbent of Cr(VI) ion; optimal composition ratio of the composite adsorbent; and the sensitivity of solid-phase spectrophotometry (SPS) as a method to determine the levels of Cr(VI) ion as an adsorption results of adsorbents. The adsorbent used were teak sawdust activated carbon and zeolite as a single and composite adsorbents. The teak sawdust carbonization using muffle furnace and then activated with H3PO4 10% while the zeolite with H2SO4 10%. The contacting process of the adsorbents with Cr(VI) was done by varying the compositions. Analysis of Cr(VI) level was done using SPS method. Characterization of adsorbent before and after being activated is done using a FTIR. The results showed that teak sawdust and zeolite can be used as adsorbents to adsorb Cr(VI) in the simulated liquid waste with the adsorption capacity 1.19 µg/g the optimum composition ratio of teak sawdust activated carbon and zeolite was 75%:25% with the percentage of adsorption was 62.72%. Solid-phase spectrophotometry is a sensitive method to analyze the decreased levels of Cr(VI) as an adsorption results in µg/L level with the limit of detection (LOD) was 0.03 µg/L.

  19. 2015年上海市同济医院门诊抗抑郁药物的使用情况分析%Analysis on usage of antidepressants in outpatient of Shanghai Tongji Hospital in 2015

    Institute of Scientific and Technical Information of China (English)

    方昱; 祝德秋; 沈筱云

    2016-01-01

    Objective To analyze the usage and trend of antidepressants in outpatient of Shanghai Tongji Hospital, so as to provide references for clinical rational drug use.Methods The usage of antidepressants in outpatient of Shanghai Tongji Hospital was calculated by HS system, and the World Health Organization recommended daily dose was defined as index method of analysis. Antidepressants, consumption sum, defined daily dose system (DDDs), and defined daily costs (DDC) were calculated and analyzed. Results Consumption sums of escitalopram, paroxetine, and venlafaxine ranked top 3. DDDs of paroxetine, venlafaxine, escitalopram, and escitalopram ranked the top 4. Consumption sum ranks/DDDs ranks of antidepressants except escitalopram and paroxetine were between 0.80 and 1.50. DDC of antidepressants ranking the top 3 were duloxetine, escitalopram, and citalopram. Conclusion The usage of antidepressants in outpatient of Shanghai Tongji Hospital is reasonable, and selective serotonin reuptake inhibitors (SSRIs) become the first-line antidepressants, the new antidepressant escitalopram develops rapidly, but its application is questionable for higher cost.%目的:分析上海市同济医院门诊抗抑郁药使用情况和趋势,为临床合理用药提供参考。方法通过HIS系统查询上海市同济医院2015年门诊抗抑郁药的使用情况,采用世界卫生组织推荐的限定日剂量为指标的分析方法,对上海市同济医院2015年门诊抗抑郁药的品种、销售金额、用药频度(DDDs)和限定日费用(DDC)进行统计分析。结果销售金额排序前3位的分别是艾司西酞普兰、帕罗西汀、文拉法辛。DDDs排名前4位的分别为帕罗西汀、文拉法辛、艾司西酞普兰和西酞普兰,金额排序/DDDs排序除艾司西酞普兰、帕罗西汀外均在0.80~1.50。DDC排序前3位的分别是度洛西汀、艾司西酞普兰、西酞普兰。结论上海市同济医院2015年门诊抗抑郁药使用

  20. A newly identified missense mutation in RET codon 666 is associated with the development of medullary thyroid carcinoma.

    Science.gov (United States)

    Yamazaki, Masanori; Hanamura, Toru; Ito, Ken-ichi; Uchino, Shinya; Sakurai, Akihiro; Komatsu, Mitsuhisa

    2014-01-01

    A 38-year-old woman with a thyroid nodule measuring approximately 2 cm was suspected to have medullary thyroid carcinoma (MTC) because of markedly elevated serum calcitonin and carcinoembryonic antigen levels. There were no signs of pheochromocytoma, whereas primary hyperparathyroidism was suspected based on the findings of inappropriate hypersecretion of parathyroid hormone although no parathyroid tumor was detected with imaging studies. RET mutation analysis revealed a novel germline missense mutation in codon 666, c.1997A>G (p.K666R). She underwent total thyroidectomy with lymphadenectomy and simultaneous total parathyroidectomy with autotransplantation of parathyroid tissue. She was given calcium lactate and alfacalcidol to prevent postoperative hypocalcemia. Pathological findings of the thyroid tumor were compatible with MTC, but the resected parathyroid glands were intact. To our knowledge, c.1997A>G (p.K666R) is a new RET mutation. This is a minor variant, but it is significant because of the possible pathogenicity in tumor formation. It is often difficult to determine whether MTC is generated as part of MEN2-related disease or familial MTC when it is a unique manifestation. In addition, it is still unclear whether all missense mutations in this codon reported previously will lead to the same clinical course and prognosis. Further careful observations of clinical presentation are required to determine the clinical features associated with this variant.

  1. Codon optimization, promoter and expression system selection that achieved high-level production of Yarrowia lipolytica lipase in Pichia pastoris.

    Science.gov (United States)

    Zhou, Wen-Jing; Yang, Jiang-Ke; Mao, Lin; Miao, Li-Hong

    2015-04-01

    Lipase (EC 3.1.1.3) stands amongst the most important and promising biocatalysts for industrial applications. In this study, in order to realize a high-level expression of the Yarrowia lipolytica lipase gene in Pichia pastoris, we optimized the codon of LIP2 by de novo gene design and synthesis, which significantly improved the lipase expression when compared to the native lip2 gene. We also comparatively analyzed the effects of the promoter types (PAOX1 and PFLD1) and the Pichia expression systems, including the newly developed PichiaPink system, on lipase production and obtained the optimal recombinants. Bench-top scale fermentation studies indicated that the recombinant carrying the codon-optimized lipase gene syn-lip under the control of promoter PAOX1 has a significantly higher lipase production capacity in the fermenter than other types of recombinants. After undergoing methanol inducible expression for 96h, the wet cell weight of Pichia, the lipase activity and the protein content in the fermentation broth reached their highest values of 262g/L, 38,500U/mL and 2.82g/L, respectively. This study has not only greatly facilitated the bioapplication of lipase in industrial fields but the strategies utilized, such as de novo gene design and synthesis, the comparative analysis among promoters and different generations of Pichia expression systems will also be useful as references for future work in this field.

  2. An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine

    Science.gov (United States)

    Su, Dan; Lieberman, Allyson; Lang, B. Franz; Simonović, Miljan; Söll, Dieter; Ling, Jiqiang

    2011-01-01

    The standard genetic code is used by most living organisms, yet deviations have been observed in many genomes, suggesting that the genetic code has been evolving. In certain yeast mitochondria, CUN codons are reassigned from leucine to threonine, which requires an unusual tRNAThr with an enlarged 8-nt anticodon loop (). To trace its evolutionary origin we performed a comprehensive phylogenetic analysis which revealed that evolved from yeast mitochondrial tRNAHis. To understand this tRNA identity change, we performed mutational and biochemical experiments. We show that Saccharomyces cerevisiae mitochondrial threonyl-tRNA synthetase (MST1) could attach threonine to both and the regular , but not to the wild-type tRNAHis. A loss of the first nucleotide (G−1) in tRNAHis converts it to a substrate for MST1 with a Km value (0.7 μM) comparable to that of (0.3 μM), and addition of G−1 to allows efficient histidylation by histidyl-tRNA synthetase. We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with . Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment. PMID:21321019

  3. Prognostic value of codon 918 (ATG-->ACG) RET proto-oncogene mutations in sporadic medullary thyroid carcinoma.

    Science.gov (United States)

    Schilling, T; Bürck, J; Sinn, H P; Clemens, A; Otto, H F; Höppner, W; Herfarth, C; Ziegler, R; Schwab, M; Raue, F

    2001-01-20

    We have determined the frequency of 918 RET proto-oncogene mutations (ATG-->ACG) in primary MTC tumors and metastases and correlated the presence or absence of this mutation with the clinical outcome of patients suffering from sporadic medullary thyroid carcinoma (MTC). A total of 197 samples, consisting of both primary tumors and lymph node metastases from 34 patients with sporadic MTC, were collected for PCR analysis of the RET 918 mutation. In 75 of the samples (38%), codon 918 (ATG-->ACG) mutations could be detected. The mutations showed a heterogeneous distribution: 21/34 patients (62%) had mutations in at least 1 tumor sample, and in 13 patients (38%) the mutation was present in all examined samples. P