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1

Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity  

Microsoft Academic Search

BACKGROUND: There are a number of methods (also called: measures) currently in use that quantify codon usage in genes. These measures are often influenced by other sequence properties, such as length. This can introduce strong methodological bias into measurements; therefore we attempted to develop a method free from such dependencies. One of the common applications of codon usage analyses is

Fran Supek; Kristian Vlahovicek

2005-01-01

2

Synonymous codon usage in Thermosynechococcus elongatus (cyanobacteria) identifies the factors shaping codon usage variation  

PubMed Central

Analysis of synonymous codon usage pattern in the genome of a thermophilic cyanobacterium, Thermosynechococcus elongatus BP-1 using multivariate statistical analysis revealed a single major explanatory axis accounting for codon usage variation in the organism. This axis is correlated with the GC content at third base of synonymous codons (GC3s) in correspondence analysis taking T. elongatus genes. A negative correlation was observed between effective number of codons i.e. Nc and GC3s. Results suggested a mutational bias as the major factor in shaping codon usage in this cyanobacterium. In comparison to the lowly expressed genes, highly expressed genes of this organism possess significantly higher proportion of pyrimidine-ending codons suggesting that besides, mutational bias, translational selection also influenced codon usage variation in T. elongatus. Correspondence analysis of relative synonymous codon usage (RSCU) with A, T, G, C at third positions (A3s, T3s, G3s, C3s, respectively) also supported this fact and expression levels of genes and gene length also influenced codon usage. A role of translational accuracy was identified in dictating the codon usage variation of this genome. Results indicated that although mutational bias is the major factor in shaping codon usage in T. elongatus, factors like translational selection, translational accuracy and gene expression level also influenced codon usage variation.

Prabha, Ratna; Singh, Dhananjaya P; Gupta, Shailendra K; Farooqi, Samir; Rai, Anil

2012-01-01

3

Codon usage in Giardia lamblia.  

PubMed

A codon usage table for the intestinal parasite Giardia lamblia was generated by analysis of the nucleotide sequences of eight genes comprising 3,135 codons. Codon usage revealed a biased use of synonymous codons with a preference for NNC codons (42.1%). The codon usage of G. lamblia more closely resembles that of the prokaryote Halobacterium halobium (correlation coefficient r = 0.73) rather than that of other eukaryotic protozoans, i.e. Trypanosoma brucei (r = 0.434) and Plasmodium falciparum (r = -0.31). These observations are consistent with the view that G. lamblia represents the first line of descent from the ancestral cells that first took on eukaryotic features. PMID:1522548

Char, S; Farthing, M J

1992-01-01

4

Divergence in codon usage of Lactobacillus species.  

PubMed Central

We have analyzed codon usage patterns of 70 sequenced genes from different Lactobacillus species. Codon usage in lactobacilli is highly biased. Both inter-species and intra-species heterogeneity of codon usage bias was observed. Codon usage in L. acidophilus is similar to that in L. helveticus, but dissimilar to that in L. bulgaricus, L. casei, L. pentosus and L. plantarum. Codon usage in the latter three organisms is not significantly different, but is different from that in L. bulgaricus. Inter-species differences in codon usage can, at least in part, be explained by differences in mutational drift. L. bulgaricus shows GC drift, whereas all other species show AT drift. L. acidophilus and L. helveticus rarely use NNG in family-box (a set of synonymous) codons, in contrast to all other species. This result may be explained by assuming that L. acidophilus and L. helveticus, but not other species examined, use a single tRNA species for translation of family-box codons. Differences in expression level of genes are positively correlated with codon usage bias. Highly expressed genes show highly biased codon usage, whereas weakly expressed genes show much less biased codon usage. Codon usage patterns at the 5'-end of Lactobacillus genes is not significantly different from that of entire genes. The GC content of codons 2-6 is significantly reduced compared with that of the remainder of the gene. The possible implications of a reduced GC content for the control of translation efficiency are discussed.

Pouwels, P H; Leunissen, J A

1994-01-01

5

Comparative Analysis of Codon Usage Bias and Codon Context Patterns between Dipteran and Hymenopteran Sequenced Genomes  

PubMed Central

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.

Behura, Susanta K.; Severson, David W.

2012-01-01

6

Synonymous codon usage pattern analysis of Hepatitis D virus.  

PubMed

Hepatitis D virus (HDV) is the smallest animal infecting RNA virus with unique features distinguishing it from other Hepatitis viruses. Codon usage variation is considered as an indicator of the forces shaping genome evolution. RSCU (relative synonymous codon usage) values, nucleotide contents, ENC (effective number of codons) values, aromaticity and hydrophobicity of 28 HDV sequences were calculated and compared. RSCU values revealed that most of the codons ended with G or C. A comparative analysis of codon usage between HDV and human cells indicated that the synonymous codon usage pattern of HDV is a mixture of coincidence and antagonism to that of host cell. Finally the characteristics of the synonymous codon usage patterns, ENC plot and the correlation analysis revealed that the most important determinant of the codon usage pattern for HDV is mutational pressure and positive selection force might have some influence in sequence diversity. Comparison of ENC values and GC frequencies at 3rd codon position (GC3s) between HDV and other Hepatitis viruses indicated that HDV comprise a distinct entity. PMID:23352880

Bishal, Arghya Kamal; Mukherjee, Rashmi; Chakraborty, Chandan

2013-05-01

7

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency  

PubMed Central

Cellular efficiency in protein translation is an important fitness determinant in rapidly growing organisms. It is widely believed that synonymous codons are translated with unequal speeds and that translational efficiency is maximized by the exclusive use of rapidly translated codons. Here we estimate the in vivo translational speeds of all sense codons from the budding yeast Saccharomyces cerevisiae. Surprisingly, preferentially used codons are not translated faster than unpreferred ones. We hypothesize that this phenomenon is a result of codon usage in proportion to cognate tRNA concentrations, the optimal strategy in enhancing translational efficiency under tRNA shortage. Our predicted codon–tRNA balance is indeed observed from all model eukaryotes examined, and its impact on translational efficiency is further validated experimentally. Our study reveals a previously unsuspected mechanism by which unequal codon usage increases translational efficiency, demonstrates widespread natural selection for translational efficiency, and offers new strategies to improve synthetic biology.

Qian, Wenfeng; Yang, Jian-Rong; Pearson, Nathaniel M.; Maclean, Calum; Zhang, Jianzhi

2012-01-01

8

Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias  

PubMed Central

It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic Trypanosomatid species. This quantitative attempt is of direct help in the comparison of qualitative features like mutational and translational selection. Pathogens of the Leishmania and Trypanosoma genus cause debilitating disease and suffering in human beings and animals. Of these, whole genome sequences are available for only five species. The complete coding sequences (CDS), highly expressed, essential and low expressed genes have all been studied for their CUB signature. The codon usage bias of essential genes and highly expressed genes show distribution similar to codon usage bias of all CDSs in Trypanosomatids. Translational selection is the dominant force selecting the preferred codon, and selection due to mutation is negligible. In contrast to an earlier study done on these pathogens, it is found in this work that CUB and CAI may be used to distinguish the Trypanosomatid genomes at the sub-genus level. Further, CUB may effectively be used as a signature of the species differentiation by using Principal Component Analysis (PCA). Abbreviations CUB - Codon Usage Bias, CAI - Codon Adaptative Index, CDS - Coding sequences, t-RNA - Transfer RNA, PCA - Principal Component Analysis.

Rashmi, Mayank; Swati, D

2013-01-01

9

Quantifying Position-Dependent Codon Usage Bias  

PubMed Central

Although the mapping of codon to amino acid is conserved across nearly all species, the frequency at which synonymous codons are used varies both between organisms and between genes from the same organism. This variation affects diverse cellular processes including protein expression, regulation, and folding. Here, we mathematically model an additional layer of complexity and show that individual codon usage biases follow a position-dependent exponential decay model with unique parameter fits for each codon. We use this methodology to perform an in-depth analysis on codon usage bias in the model organism Escherichia coli. Our methodology shows that lowly and highly expressed genes are more similar in their codon usage patterns in the 5?-gene regions, but that these preferences diverge at distal sites resulting in greater positional dependency (pD, which we mathematically define later) for highly expressed genes. We show that position-dependent codon usage bias is partially explained by the structural requirements of mRNAs that results in increased usage of A/T rich codons shortly after the gene start. However, we also show that the pD of 4- and 6-fold degenerate codons is partially related to the gene copy number of cognate-tRNAs supporting existing hypotheses that posit benefits to a region of slow translation in the beginning of coding sequences. Lastly, we demonstrate that viewing codon usage bias through a position-dependent framework has practical utility by improving accuracy of gene expression prediction when incorporating positional dependencies into the Codon Adaptation Index model.

Hockenberry, Adam J.; Sirer, M. Irmak; Amaral, Luis A. Nunes; Jewett, Michael C.

2014-01-01

10

CodonO: codon usage bias analysis within and across genomes  

Microsoft Academic Search

Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation fre- quency and patterns, and GC compositions. Quantification of codon usage bias helps under- stand evolution of living organisms. A codon usage bias pipeline is demanding for codon usage bias

Michael C. Angellotti; Shafquat B. Bhuiyan; Guorong Chen; Xiu-feng Wan

2007-01-01

11

Codon Usage and Selection on Proteins  

Microsoft Academic Search

Selection pressures on proteins are usually measured by comparing homologous nucleotide sequences (Zuckerkandl and Pauling 1965). Recently we introduced a novel method, termed volatility, to estimate selection pressures on proteins on the basis of their synonymous codon usage (Plotkin and Dushoff 2003; Plotkin et al. 2004). Here we provide a theoretical foundation for this approach. Under the Fisher-Wright model, we

Joshua B. Plotkin; Jonathan Dushoff; Michael M. Desai; Hunter B. Fraser

2006-01-01

12

Molecular evolution of synonymous codon usage in Populus  

Microsoft Academic Search

BACKGROUND: Evolution of synonymous codon usage is thought to be determined by a balance between mutation, genetic drift and natural selection on translational efficiency. However, natural selection on codon usage is considered to be a weak evolutionary force and selection on codon usage is expected to be strongest in species with large effective population sizes. RESULTS: I examined the evolution

Pär K Ingvarsson; Umeå Plant

2008-01-01

13

Single-stranded genomic architecture constrains optimal codon usage  

PubMed Central

Viral codon usage is shaped by the conflicting forces of mutational pressure and selection to match host patterns for optimal expression. We examined whether genomic architecture (single- or double-stranded DNA) influences the degree to which bacteriophage codon usage differ from their primary bacterial hosts and each other. While both correlated equally with their hosts’ genomic nucleotide content, the coat genes of ssDNA phages were less well adapted than those of dsDNA phages to their hosts’ codon usage profiles due to their preference for codons ending in thymine. No specific biases were detected in dsDNA phage genomes. In all nine of ten cases of codon redundancy in which a specific codon was overrepresented, ssDNA phages favored the NNT codon. A cytosine to thymine biased mutational pressure working in conjunction with strong selection against non-synonymous mutations appears be shaping codon usage bias in ssDNA viral genomes.

Cardinale, Daniel J.; Duffy, Siobain

2011-01-01

14

Characterization of Codon usage bias in the newly identified DEV UL18 gene  

NASA Astrophysics Data System (ADS)

In this study, Codon usage bias (CUB) of DEV UL18 gene was analyzed, the results showed that codon usage bias in the DEV UL18 gene was strong bias towards the synonymous codons with A and T at the third codon position. Phylogenetic tree based on the amino acid sequences of the DEV UL18 gene and the 27 other herpesviruses revealed that UL18 gene of the DEV CHv strain and some fowl herpesviruses such as MeHV-1, GaHV-2 and GaHV-3 were clustered within a monophyletic clade and grouped within alphaherpesvirinae. The ENC-GC3S plot indicated that codon usage bias has strong species-specificity between DEV and 27 reference herpesviruses, and suggests that factors other than gene composition, such as translational selection leading to the codon usage variation among genes in different organisms, contribute to the codon usage among the different herpesviruses. Comparison of codon preferences of DEV UL18 gene with those of E. coli , yeast and humans showed that there were 20 codons showing distinct usage differences between DEV UL18 and yeast, 22 between DEV UL18 and humans, 23 between DEV UL18 and E.coli, which indicated the codon usage bias pattern in the DEV UL18 gene was similar to that of yeast. It is infered that the yeast expression system may be more suitable for the DEV UL18 expression.

Chen, Xiwen; Cheng, Anchun; Wang, Mingshu; Xiang, Jun

2011-10-01

15

First analysis of synonymous codon usage in porcine circovirus.  

PubMed

Porcine circovirus (PCV) is grouped into two types: PCV1 and PCV2. PCV1 is isolated from cultured cells and usually causes no clinical diseases in pigs. PCV2 is a pathogen of severe pig disease and a great threat to swine health and production. In our study, to investigate the codon usage bias of PCV, the genomic sequences of PCV1 and PCV2 were analyzed. The results showed that the codon usage bias of PCV was very low. An effective number of codons (ENC) plot analysis indicated that mutational pressure influences the codon usage bias of PCV. Neutrality plot analysis showed that mutation bias dominated over natural selection in shaping the codon usage bias of PCV1, but mutation bias and natural selection contributed equally to the codon usage bias of PCV2. Principal component analysis showed that different ORFs and dinucleotide patterns were also factors influencing the codon usage bias of PCV. Our study is helpful in understanding the codon usage pattern of PCV and the evolution of PCV. PMID:24557524

Chen, Ye; Sun, Jingchen; Tong, Xiong; Xu, Jian; Deng, Hongjuan; Jiang, Zhiguo; Jiang, Chengfeng; Duan, Junli; Li, Jingcong; Zhou, Pei; Wang, Chong

2014-08-01

16

Evidence that Natural Selection on Codon Usage in Drosophila pseudoobscura Varies Across Codons  

PubMed Central

Like other species of Drosophila, Drosophila pseudoobscura has a distinct bias toward the usage of C- and G-ending codons. Previous studies have indicated that this bias is due, at least in part, to natural selection. Codon bias clearly differs among amino acids (and other codon classes) in Drosophila, which may reflect differences in the intensity of selection on codon usage. Ongoing natural selection on synonymous codon usage should be reflected in the shapes of the site frequency spectra of derived states at polymorphic positions. Specifically, regardless of other demographic effects on the spectrum, it should be shifted toward higher values for changes from less-preferred to more-preferred codons, and toward lower values for the converse. If the intensity of natural selection is increased, shifts in the site frequency spectra should be more pronounced. A total of 33,729 synonymous polymorphic sites on Chromosome 2 in D. pseudoobscura were analyzed. Shifts in the site frequency spectra are consistent with differential intensity of natural selection on codon usage, with stronger shifts associated with higher codon bias. The shifts, in general, are greater for polymorphic synonymous sites than for polymorphic intron sites, also consistent with natural selection. However, unlike observations in D. melanogaster, codon bias is not reduced in areas of low recombination in D. pseudoobscura; the site frequency spectrum signal for selection on codon usage remains strong in these regions. However, diversity is reduced, as expected. It is possible that estimates of low recombination reflect a recent change in recombination rate.

Kliman, Richard M.

2014-01-01

17

A cross talk between codon usage bias in human oncogenes  

PubMed Central

Background: Oncogenes are the genes that have the potential to induce cancer. The extent and origin of codon usage bias is an important indicator of the forces shaping genome evolution in living organisms. Results: We observed moderate correlations between gene expression as measured by CAI and GC content at any codon site. The findings of our results showed that there is a significant positive correlation (Spearman's r= 0.45, P<0.01) between GC content at first and second codon position with that of third codon position. Further, striking negative correlation (r = -0.771, P < 0.01) between ENC with the GC3s values of each gene and positive correlation (r=0.644, P<0.01) in between CAI and ENC was also observed. Conclusions: The mutation pressure is the major determining factor in shaping the codon usage pattern of oncogenes rather than natural selection since its effects are present at all codon positions. The results revealed that codon usage bias determines the level of oncogene expression in human. Highly expressed oncogenes had rich GC contents with high degree of codon usage bias.

Mazumder, Tarikul Huda; Chakraborty, Supriyo; Paul, Prosenjit

2014-01-01

18

Codon usage bias in human cytomegalovirus and its biological implication.  

PubMed

Human cytomegalovirus (HCMV) infection, a worldwide contagion, causes a serious disorder in infected individuals. Analysis of codon usage can reveal much molecular information about this virus. The effective number of codon (ENC) values, relative synonymous codon usage (RSCU) values, codon adaptation index (CAI), and nucleotide contents was investigated in approximately 160 coding sequences (CDS) among 17 human cytomegalovirus genomes using the software CodonW. Linear regression analysis and logistic regression were performed to explore the preliminary data. The results showed that, overall, HCMV genomes had low codon usage bias (mean ENC=47.619). However, the ENC of individual CDS varied widely and was distributed unevenly between host-related genes and viral-self-function genes (P=0.002, odds ratio (OR)=3.194), as did the GC content (P=0.016, OR=2.178). The ENC values correlated with CAI, GC content, and the nucleotide composing at the 3rd codon position (GC3s) (P<0.001). There was a significant variation in the codon preference that depended on the RSCU data. The predicted ENC curve suggested that mutational pressure, rather than natural selection, was one of the main factors that determined the codon usage bias in HCMV. Among 123 genes with known function, the genes related to viral self-replication and viral-host interaction showed different ENC and CAI values, and GC and GC3s contents. In conclusion, the detailed codon usage bias theoretically revealed information concerning HCMV evolution and could be a valuable additional parameter for HCMV gene function research. PMID:24814188

Hu, Changyuan; Chen, Jing; Ye, Lulu; Chen, Renpin; Zhang, Lifang; Xue, Xiangyang

2014-07-15

19

Analysis of codon usage and nucleotide composition bias in polioviruses  

Microsoft Academic Search

Background  Poliovirus, the causative agent of poliomyelitis, is a human enterovirus and a member of the family of Picornaviridae and\\u000a among the most rapidly evolving viruses known. Analysis of codon usage can reveal much about the molecular evolution of the\\u000a viruses. However, little information about synonymous codon usage pattern of polioviruses genome has been acquired to date.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  The relative synonymous codon

Jie Zhang; Meng Wang; Wen-qian Liu; Jian-hua Zhou; Hao-tai Chen; Li-na Ma; Yao-zhong Ding; Yuan-xing Gu; Yong-sheng Liu

2011-01-01

20

Codon usage in bacteria: correlation with gene expressivity.  

PubMed Central

The nucleic acid sequence bank now contains over 600 protein coding genes of which 107 are from prokaryotic organisms. Codon frequencies in each new prokaryotic gene are given. Analysis of genetic code usage in the 83 sequenced genes of the Escherichia coli genome (chromosome, transposons and plasmids) is presented, taking into account new data on gene expressivity and regulation as well as iso-tRNA specificity and cellular concentration. The codon composition of each gene is summarized using two indexes: one is based on the differential usage of iso-tRNA species during gene translation, the other on choice between Cytosine and Uracil for third base. A strong relationship between codon composition and mRNA expressivity is confirmed, even for genes transcribed in the same operon. The influence of codon use of peptide elongation rate and protein yield is discussed. Finally, the evolutionary aspect of codon selection in mRNA sequences is studied.

Gouy, M; Gautier, C

1982-01-01

21

Evidence that Natural Selection on Codon Usage in Drosophila pseudoobscura Varies Across Codons.  

PubMed

Like other species of Drosophila, Drosophila pseudoobscura has a distinct bias toward the usage of C- and G-ending codons. Previous studies have indicated that this bias is due, at least in part, to natural selection. Codon bias clearly differs among amino acids (and other codon classes) in Drosophila, which may reflect differences in the intensity of selection on codon usage. Ongoing natural selection on synonymous codon usage should be reflected in the shapes of the site frequency spectra of derived states at polymorphic positions. Specifically, regardless of other demographic effects on the spectrum, it should be shifted toward higher values for changes from less-preferred to more-preferred codons, and toward lower values for the converse. If the intensity of natural selection is increased, shifts in the site frequency spectra should be more pronounced. A total of 33,729 synonymous polymorphic sites on Chromosome 2 in D. pseudoobscura were analyzed. Shifts in the site frequency spectra are consistent with differential intensity of natural selection on codon usage, with stronger shifts associated with higher codon bias. The shifts, in general, are greater for polymorphic synonymous sites than for polymorphic intron sites, also consistent with natural selection. However, unlike observations in D. melanogaster, codon bias is not reduced in areas of low recombination in D. pseudoobscura; the site frequency spectrum signal for selection on codon usage remains strong in these regions. However, diversity is reduced, as expected. It is possible that estimates of low recombination reflect a recent change in recombination rate. PMID:24531731

Kliman, Richard M

2014-01-01

22

CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition  

PubMed Central

The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer’s combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses.

Zaneveld, Jesse; Hamady, Micah; Sueoka, Noboru; Knight, Rob

2010-01-01

23

Efficient translation initiation dictates codon usage at gene start.  

PubMed

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

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

2013-01-01

24

Comparison of Synonymous Codon Distribution Patterns of Bacteriophage and Host Genomes  

Microsoft Academic Search

Synonymous codon usage patterns of bacteriophage and host genomes were compared. Two indexes, G + C base composition of a gene (fgc) and fraction of translationally optimal codons of the gene (fop), were used in the comparison. Synonymous codon usage data of all the coding sequences on a genome are represented as a cloud of points in the plane of

Takashi KUNISAWA; Shigehiko KANAYA; Elizabeth KUTTER

1998-01-01

25

Codon usage bias of the phosphoprotein gene of spring viraemia of carp virus and high codon adaptation to the host.  

PubMed

In this study, we calculated the relative synonymous codon usage (RSCU) value and the effective number of codons (ENC) value to carry out principal component analysis (PCA) and correlation analysis of the codon usage pattern of the phosphoprotein gene (P gene) of spring viraemia of carp virus (SVCV). The synonymous codon usage pattern in P genes is geography-specific, based on PCA analysis. The high correlation between (G + C)1,2 % and (G + C)3 % suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage and base components in P genes. At least 40 out of 59 synonymous codons are similarly selected in all functional genes within five complete SVCV genomes, and the hosts based on the RSCU data. These results not only provide insight into variations in the codon usage pattern of SVCV but also may help in understanding the processes governing the evolution of SVCV. PMID:24519460

Ma, Yan-Ping; Zhou, Zhi-Wei; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Feng, Guo-Qing; Liang, Zhi-Ling; Ke, Hao

2014-07-01

26

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

PubMed

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. PMID:22305983

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

2012-04-10

27

Estimating Selection on Synonymous Codon Usage from Noisy Experimental Data  

PubMed Central

A key goal in molecular evolution is to extract mechanistic insights from signatures of selection. A case study is codon usage, where despite many recent advances and hypotheses, two longstanding problems remain: the relative contribution of selection and mutation in determining codon frequencies and the relative contribution of translational speed and accuracy to selection. The relevant targets of selection—the rate of translation and of mistranslation of a codon per unit time in the cell—can only be related to mechanistic properties of the translational apparatus if the number of transcripts per cell is known, requiring use of gene expression measurements. Perhaps surprisingly, different gene-expression data sets yield markedly different estimates of selection. We show that this is largely due to measurement noise, notably due to differences between studies rather than instrument error or biological variability. We develop an analytical framework that explicitly models noise in expression in the context of the population-genetic model. Estimates of mutation and selection strength in budding yeast produced by this method are robust to the expression data set used and are substantially higher than estimates using a noise-blind approach. We introduce per-gene selection estimates that correlate well with previous scoring systems, such as the codon adaptation index, while now carrying an evolutionary interpretation. On average, selection for codon usage in budding yeast is weak, yet our estimates show that genes range from virtually unselected to average per-codon selection coefficients above the inverse population size. Our analytical framework may be generally useful for distinguishing biological signals from measurement noise in other applications that depend upon measurements of gene expression.

Wallace, Edward W.J.; Airoldi, Edoardo M.

2013-01-01

28

Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species  

Microsoft Academic Search

Background  Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand\\u000a codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode\\u000a species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed

Makedonka Mitreva; Michael C Wendl; John Martin; Todd Wylie; Yong Yin; Allan Larson; John Parkinson; Robert H Waterston; James P McCarter

2006-01-01

29

Genome-wide analysis of codon usage and influencing factors in chikungunya viruses.  

PubMed

Chikungunya virus (CHIKV) is an arthropod-borne virus of the family Togaviridae that is transmitted to humans by Aedes spp. mosquitoes. Its genome comprises a 12 kb single-strand positive-sense RNA. In the present study, we report the patterns of synonymous codon usage in 141 CHIKV genomes by calculating several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C and A-ended. A comparative analysis of RSCU between CHIKV and its hosts showed that codon usage patterns of CHIKV are a mixture of coincidence and antagonism. Similarity index analysis showed that the overall codon usage patterns of CHIKV have been strongly influenced by Pan troglodytes and Aedes albopictus during evolution. The overall codon usage bias was low in CHIKV genomes, as inferred from the analysis of effective number of codons (ENC) and codon adaptation index (CAI). Our data suggested that although mutation pressure dominates codon usage in CHIKV, patterns of codon usage in CHIKV are also under the influence of natural selection from its hosts and geography. To the best of our knowledge, this is first report describing codon usage analysis in CHIKV genomes. The findings from this study are expected to increase our understanding of factors involved in viral evolution, and fitness towards hosts and the environment. PMID:24595095

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

2014-01-01

30

Codon Usage and tRNA Genes in Eukaryotes: Correlation of Codon Usage Diversity with Translation Efficiency and with CG-Dinucleotide Usage as Assessed by Multivariate Analysis  

Microsoft Academic Search

.   The species-specific diversity of codon usage in five eukaryotes (Schizosaccharomyces pombe, Caenorhabditis elegans, Drosophila melanogaster, Xenopus laevis, and Homo sapiens) was investigated with principal component analysis. Optimal codons for translation were predicted on the basis of tRNA-gene\\u000a copy numbers. Highly expressed genes, such as those encoding ribosomal proteins and histones in S. pombe, C. elegans, and D. melanogaster, have

Shigehiko Kanaya; Yuko Yamada; Makoto Kinouchi; Yoshihiro Kudo; Toshimichi Ikemura

2001-01-01

31

AT2AT3profiling: A new look at synonymous codon usage  

Microsoft Academic Search

The teleology of synonymous codon usage (SCU) still awaits a unifying concept. Here the 2nd codon letter of human mRNA-codons was graphically, aided by a computer program, put in relation to the 3rd codon letter, the carrier of SCU: AT2, the density of A+T in 2nd codon position, behaves to AT3, the analogous density of the 3rd codon position, mostly

Wolfgang Pluhar

2006-01-01

32

Unusual codon usage bias in low expression genes of Vibrio cholerae  

PubMed Central

Positive correlation between gene expression and synonymous codon usage bias is well documented in the literature. However, in the present study of Vibrio cholerae genome, we have identified a group of genes having unusually high codon usage bias despite being low potential expressivity. Our results suggest that codon usage in lowly expressed genes might also be selected on to preferably use non-optimal codons to maintain a low cellular concentration of the proteins that they encode. This would predict that lowly expressed genes are also biased in codon usage, but in a way that is opposite to the bias of highly expressed genes.

Basak, Surajit; Mukherjee, Indranuj; Choudhury, Mayukh; Das, Santasabuj

2008-01-01

33

Analysis of Synonymous Codon Usage in the Capsid Gene UL38 of Duck Enteritis Virus  

Microsoft Academic Search

In the study, we calculated the codon usage bias in the newly identified UL38 gene of Duck Enteritis Virus (DEV) and performed a correlation analysis of codon bias of DEV UL38 gene and its host animal. There was a strong bias in the DEV UL38 gene towards the synonymous codons with A and T at the third codon position. The

Jun Xiang; Anchun Cheng; Mingshu Wang; Shunchuan Zhang; Hua Chang; Dekang Zhu; Renyong Jia; Qihui Luo; Hengmin Cui; Yi Zhou; Yin Wang; Zhiwen Xu; Zhengli Chen; Xiaoyue Chen; Xiaoyu Wang

2010-01-01

34

Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development  

PubMed Central

Background Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed. Results We performed a comprehensive codon usage analysis of 310 IAV strains from the pandemic of 2009. Highly biased codon usage for Ala, Arg, Pro, Thr and Ser were found. Codon usage is strongly influenced by underlying biases in base composition. When correspondence analysis (COA) on relative synonymous codon usage (RSCU) is applied, the distribution of IAV ORFs in the plane defined by the first two major dimensional factors showed that different strains are located at different places, suggesting that IAV codon usage also reflects an evolutionary process. Conclusions A general association between codon usage bias, base composition and poor adaptation of the virus to the respective host tRNA pool, suggests that mutational pressure is the main force shaping H1N1 pdm IAV codon usage. A dynamic process is observed in the variation of codon usage of the strains enrolled in these studies. These results suggest a balance of mutational bias and natural selection, which allow the virus to explore and re-adapt its codon usage to different environments. Recoding of IAV taking into account codon bias, base composition and adaptation to host tRNA may provide important clues to develop new and appropriate vaccines.

2012-01-01

35

Selection pressures on codon usage in the complete genome of bacteriophage T7  

Microsoft Academic Search

Summary We searched the complete 39,936 base DNA sequence of bacteriophage T7 for nonrandomness that might be attributed to natural selection. Codon usage in the 50 genes of T7 is nonrandom, both over the whole code and among groups of synonymous codons. There is a great excess of purineany base-pyrimidine (RNY) codons. Codon usage varies between genes, but from the

Paul M. Sharp; Mark S. Rogers; David J. McConnell

1985-01-01

36

A PECULIAR CODON USAGE PATTERN REVEALED AFTER REMOVING THE EFFECT OF DNA METHYLATION  

Microsoft Academic Search

Summary DNA methylation and deamination increases the C?T mutation rate in CpG dinucleotides, especially in vertebrate genomes. This has profound effect on codon usage in heavily vertebrate genomes, and may obscure the effect of other factors on codon usage bias. We have classified the sense codons into three groups: those decreased by DNA methylation (i.e., CpG-containing codons), those increased by

Xuhua Xia

37

Dependency of codon usage on protein sequence patterns: a statistical study  

PubMed Central

Background Codon degeneracy and codon usage by organisms is an interesting and challenging problem. Researchers demonstrated the relation between codon usage and various functions or properties of genes and proteins, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Researchers usually represent segments of proteins responsible for specific functions or structures in a family of proteins as sequence patterns or motifs. We asked the question if organisms use the same codons in pattern segments as compared to the rest of the sequence. Methods We used the likelihood ratio test, Pearson’s chi-squared test, and mutual information to compare these two codon usages. Results We showed that codon usage, in segments of genes that code for a given pattern or motif in a group of proteins, varied from the rest of the gene. The codon usage in these segments was not random. Amino acids with larger number of codons used more specific codon ratios in these segments. We studied the number of amino acids in the pattern (pattern length). As patterns got longer, there was a slight decrease in the fraction of patterns with significant different codon usage in the pattern region as compared to codon usage in the gene region. We defined a measure of specificity of protein patterns, and studied its relation to the codon usage. The difference in the codon usage between pattern region and gene region, was less for the patterns with higher specificity. Conclusions We provided a hypothesis that there are segments on genes that affect the codon usage and thus influence protein translation speed, and these regions are the regions that code protein pattern regions.

2014-01-01

38

Codon usage patterns in Chinese bayberry (Myrica rubra) based on RNA-Seq data  

PubMed Central

Background Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species. Result RNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC3s (GC content of 3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3s, especially in 'Molecular function’ category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences. Conclusion A comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species.

2013-01-01

39

Characterization of Codon Usage Bias in the Us4 Gene of Duck Plague Virus  

Microsoft Academic Search

The analysis on codon usage bias of Us4 gene of Duck Plague Virus (DPV) may provide a basis for understanding the evolution and pathogenesis of DPV and for selecting appropriate host expression systems to improve the expression of target genes in vivo and in vitro. In this study, the synonymous codon usage in the Us4 gene of DPV and 17

Xiaoyuan Yang; Anchun Cheng; Mingshu Wang; Dekang Zhu; Xiaoyue Chen; Renyong Jia; Qihui Luo; Hengmin Cui; Yi Zhou; Yin Wang; Zhiwen Xu; Zhengli Chen; Xiaoyu Wang

2010-01-01

40

Synonymous Codon Usage in Drosophila melanogaster: Natural Selection and Translational Accuracy  

Microsoft Academic Search

I present evidence that natural selection biases synonymous codon usage to enhance the accuracy of protein synthesis in Drosophila melanogaster. Since the fitness cost of a translational misincorporation will depend on how the amino acid substitution affects protein function, selection for translational accuracy predicts an association between codon usage in DNA and functional constraint at the protein level. The frequency

Hiroshi Akashi

1994-01-01

41

Complex mutation and weak selection together determined the codon usage bias in bryophyte mitochondrial genomes.  

PubMed

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 usage patterns 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 fine-tune 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. PMID:21106008

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

2010-12-01

42

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

PubMed Central

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.

2011-01-01

43

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage  

PubMed Central

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.

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

2012-01-01

44

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

PubMed Central

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, ?-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.

Mirsafian, Hoda; Mat Ripen, Adiratna; Singh, Aarti; Teo, Phaik Hwan; Merican, Amir Feisal; Mohamad, Saharuddin Bin

2014-01-01

45

Whole genome analysis of non-optimal codon usage in secretory signal sequences of Streptomyces coelicolor  

Microsoft Academic Search

Non-optimal (rare) codons have been suggested to reduce translation rate and facilitate secretion in Escherichia coli. In this study, the complete genome analysis of non-optimal codon usage in secretory signal sequences and non-secretory sequences of Streptomyces coelicolor was performed. The result showed that there was a higher proportion of non-optimal codons in secretory signal sequences than in non-secretory sequences. The

Yu-Dong Li; Yong-Quan Li; Jian-shu Chen; Hui-jun Dong; Wen-Jun Guan; Hong Zhou

2006-01-01

46

The characteristics of synonymous codon usage in the initial and terminal translation regions of encephalomyocarditis virus.  

PubMed

The synonymous codon usage patterns in the initial and terminal translation regions (ITR, TTR) of the whole coding sequence of encephalomyocarditis virus (EMCV) were analyzed in relation to those in its natural hosts using the sequences accessible in databases. In general, some low-usage host codons were found over-represented in the ITR and TTR of the virus, while some high-usage host codons were found under-represented in the two viral regions. These relationships are thought to participate in the regulation of the speed of translation of viral proteins and in the suppression of ribosomal traffic jams, both aiming at the increase of virus yields. Keywords: encephalomyocarditis virus; initial translation region; terminal translation region; synonymous codon usage. PMID:24720745

Ma, X-X; Feng, Y-P; Liu, J-L; Zhao, Y-Q; Chen, L; Guo, P-H; Guo, J-Z; Ma, Z-R

2014-01-01

47

Characterization of codon usage bias in the gI gene of duck enteritis virus  

Microsoft Academic Search

The analysis on codon usage bias of gI gene of duck enteritis virus (DEV) may provide a basis for understanding the evolution and molecular characteristic of DEV, and for selecting appropriate host expression systems to improve the expression of target gene. A comparative analysis of the codon usage bias of the DEV gI gene and 22 other refrence herpesviruses gI-like

Lijuan Li; Anchun Cheng; Mingshu Wang; Shunchuan Zhang; Dekang Zhu; Renyong Jia; Qihui Luo; Yi Zhou; Zhengli Chen; Xiaoyue Chen

2010-01-01

48

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

PubMed

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. PMID:24454907

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

2014-01-01

49

Mutational and Selective Pressures on Codon and Amino Acid Usage in Buchnera, Endosymbiotic Bacteria of Aphids  

Microsoft Academic Search

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 of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the

Claude Rispe; Francois Delmotte; Roeland C. H. J. van Ham; Andres Moya

2003-01-01

50

Constraint on di-nucleotides by codon usage bias in bacterial genomes.  

PubMed

It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative analysis of RDF between the inter-genic and the coding sequences in seventeen bacterial genomes, whose gene expression data was available. The constraint on di-nucleotides was found to be higher in the coding sequences than that in the inter-genic regions and the constraint at the 2nd codon position was more than that in the 3rd position within a genome. Further analysis revealed that the constraint on di-nucleotides at the 2nd codon position is greater in the high expression genes (HEG) than that in the whole genomes as well as in the low expression genes (LEG). We analyzed RDF at the 2nd and the 3rd codon positions in simulated coding sequences that were computationally generated by keeping the codon usage bias (CUB) according to genome G+C composition and the sequence of amino acids unaltered. In the simulated coding sequences, the constraint observed was significantly low and no significant difference was observed between the HEG and the LEG in terms of di-nucleotide constraint. This indicated that the greater constraint on di-nucleotides in the HEG was due to the stronger selection on CUB in these genes in comparison to the LEG within a genome. Further, we did comparative analyses of the RDF in the HEG rpoB and rpoC of 199 bacteria, which revealed a common pattern of constraints on di-nucleotides at the 2nd codon position across these bacteria. To validate the role of CUB on di-nucleotide constraint, we analyzed RDF at the 2nd and the 3rd codon positions in simulated rpoB/rpoC sequences. The analysis revealed that selection on CUB is an important attribute for the constraint on di-nucleotides at these positions in bacterial genomes. We believe that this study has come with major findings of the role of CUB on di-nucleotide constraint in bacterial genomes. PMID:24333347

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

2014-02-15

51

Base composition and translational selection are insufficient to explain codon usage bias in plant viruses.  

PubMed

Viral codon usage bias may be the product of a number of synergistic or antagonistic factors, including genomic nucleotide composition, translational selection, genomic architecture, and mutational or repair biases. Most studies of viral codon bias evaluate only the relative importance of genomic base composition and translational selection, ignoring other possible factors. We analyzed the codon preferences of ssRNA (luteoviruses and potyviruses) and ssDNA (geminiviruses) plant viruses that infect translationally distinct monocot and dicot hosts. We found that neither genomic base composition nor translational selection satisfactorily explains their codon usage biases. Furthermore, we observed a strong relationship between the codon preferences of viruses in the same family or genus, regardless of host or genomic nucleotide content. Our results suggest that analyzing codon bias as either due to base composition or translational selection is a false dichotomy that obscures the role of other factors. Constraints such as genomic architecture and secondary structure can and do influence codon usage in plant viruses, and likely in viruses of other hosts. PMID:23322170

Cardinale, Daniel J; DeRosa, Kate; Duffy, Siobain

2013-01-01

52

Increased Immune Response Elicited by DNA Vaccination with a Synthetic gp120 Sequence with Optimized Codon Usage  

PubMed Central

DNA vaccination elicits humoral and cellular immune responses and has been shown to confer protection against several viral, bacterial, and parasitic pathogens. Here we report that optimized codon usage of an injected DNA sequence considerably increases both humoral and cellular immune responses. We recently generated a synthetic human immunodeficiency virus type 1 gp120 sequence in which most wild-type codons were replaced with codons from highly expressed human genes (syngp120). In vitro expression of syngp120 is considerably increased in comparison to that of the respective wild-type sequence. In BALB/c mice, DNA immunization with syngp120 resulted in significantly increased antibody titers and cytotoxic T-lymphocyte reactivity, suggesting a direct correlation between expression levels and the immune response. Moreover, syngp120 is characterized by rev-independent expression and a low risk of recombination with viral sequences. Thus, synthetic genes with optimized codon usage represent a novel strategy to increase the efficacy and safety of DNA vaccination.

Andre, Stefanie; Seed, Brian; Eberle, Josef; Schraut, Winfried; Bultmann, Andreas; Haas, Jurgen

1998-01-01

53

CAIcal: A combined set of tools to assess codon usage adaptation  

PubMed Central

Background The Codon Adaptation Index (CAI) was first developed to measure the synonymous codon usage bias for a DNA or RNA sequence. The CAI quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Results We describe here CAIcal, a web-server available at that includes a complete set of utilities related with the CAI. The server provides useful important features, such as the calculation and graphical representation of the CAI along either an individual sequence or a protein multiple sequence alignment translated to DNA. The automated calculation of CAI and its expected value is also included as one of the CAIcal tools. The software is also free to be downloaded as a standalone application for local use. Conclusion The CAIcal server provides a complete set of tools to assess codon usage adaptation and to help in genome annotation. Reviewers This article was reviewed by Purificación López-García, Dan Graur, Rob Knight and Shamil Sunyaev.

Puigbo, Pere; Bravo, Ignacio G; Garcia-Vallve, Santiago

2008-01-01

54

Could protein tertiary structure influence mammary transgene expression more than tissue specific codon usage?  

PubMed

Animal mammary glands have been successfully employed to produce therapeutic recombinant human proteins. However, considerable variation in animal mammary transgene expression efficiency has been reported. We now consider whether aspects of codon usage and/or protein tertiary structure underlie this variation in mammary transgene expression. PMID:20563642

He, Zuyong; Zhao, Yiqiang; Mei, Gui; Li, Ning; Chen, Yaosheng

2010-08-01

55

System analysis of synonymous codon usage biases in archaeal virus genomes.  

PubMed

Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes. Archaeal viruses isolated from these hot habitats usually have double-stranded DNA genomes, linear or circular, and can infect members of the Archaea domain. In this study, the synonymous codon usage bias (SCUB) and dinucleotide composition in the available complete archaeal virus genome sequences have been investigated. It was found that there is a significant variation in SCUB among different Archaeal virus species, which is mainly determined by the base composition. The outcome of correspondence analysis (COA) and Spearman?s rank correlation analysis shows that codon usage of selected archaeal virus genes depends mainly on GC richness of genome, and the gene?s function, albeit with smaller effects, also contributes to codon usage in this virus. Furthermore, this investigation reveals that aromaticity of each protein is also critical in affecting SCUB of these viral genes although it was less important than that of the mutational bias. Especially, mutational pressure may influence SCUB in SIRV1, SIRV2, ARV1, AFV1, and PhiCh1 viruses, whereas translational selection could play a leading role in HRPV1?s SCUB. These conclusions not only can offer an insight into the codon usage biases of archaeal virus and subsequently the possible relationship between archaeal viruses and their host, but also may help in understanding the evolution of archaeal viruses and their gene classification, and more helpful to explore the origin of life and the evolution of biology. PMID:24685889

Li, Sen; Yang, Jie

2014-08-21

56

OPTIMIZER: a web server for optimizing the codon usage of DNA sequences  

PubMed Central

OPTIMIZER is an on-line application that optimizes the codon usage of a gene to increase its expression level. Three methods of optimization are available: the ‘one amino acid–one codon’ method, a guided random method based on a Monte Carlo algorithm, and a new method designed to maximize the optimization with the fewest changes in the query sequence. One of the main features of OPTIMIZER is that it makes it possible to optimize a DNA sequence using pre-computed codon usage tables from a predicted group of highly expressed genes from more than 150 prokaryotic species under strong translational selection. These groups of highly expressed genes have been predicted using a new iterative algorithm. In addition, users can use, as a reference set, a pre-computed table containing the mean codon usage of ribosomal protein genes and, as a novelty, the tRNA gene-copy numbers. OPTIMIZER is accessible free of charge at http://genomes.urv.es/OPTIMIZER.

Puigbo, Pere; Guzman, Eduard; Romeu, Antoni; Garcia-Vallve, Santiago

2007-01-01

57

Adjustment of the tRNA population to the codon usage in chloroplasts.  

PubMed Central

In chloroplasts there is a correlation between the amounts of tRNAs specific for a given amino acid and the codons specifying this amino acid. Furthermore, for the amino acids coded for by more than one codon, the population of isoaccepting tRNAs is adjusted to the frequency of synonymous codons used in chloroplast protein genes. A comparison by two-dimensional gel electrophoresis of the tRNA populations extracted from chloroplasts and from chloroplast polysomes shows that all chloroplast tRNAs are involved in protein biosynthesis. Images

Pfitzinger, H; Guillemaut, P; Weil, J H; Pillay, D T

1987-01-01

58

Usage of the three termination codons in a single eukaryotic cell, the Xenopus laevis oocyte.  

PubMed Central

Oocytes from Xenopus laevis were injected with purified amber (UAG), ochre (UAA), and opal (UGA) suppressor tRNAs from yeasts. The radioactively labeled proteins translated from the endogenous mRNAs were then separated on two-dimensional gels. All three termination codons are used in a single cell, the Xenopus laevis oocyte. But a surprisingly low number of readthrough polypeptides were observed from the 600 mRNAs studied in comparison to uninjected oocytes. The experimental data are compared with the conclusions obtained from the compilation of all available termination sequences on eukaryotic and prokaryotic mRNAs. This comparison indicates that the apparent resistance of natural termination codons against readthrough, as observed by the microinjection experiments, cannot be explained by tandem or very close second stop codons. Instead it suggests that specific context sequences around the termination codons may play a role in the efficiency of translation termination. Images

Bienz, M; Kubli, E; Kohli, J; deHenau, S; Huez, G; Marbaix, G; Grosjean, H

1981-01-01

59

Evidence of codon usage in the nearest neighbor spacing distribution of bases in bacterial genomes  

NASA Astrophysics Data System (ADS)

Statistical analysis of whole genomic sequences usually assumes a homogeneous nucleotide density throughout the genome, an assumption that has been proved incorrect for several organisms since the nucleotide density is only locally homogeneous. To avoid giving a single numerical value to this variable property, we propose the use of spectral statistics, which characterizes the density of nucleotides as a function of its position in the genome. We show that the cumulative density of bases in bacterial genomes can be separated into an average (or secular) plus a fluctuating part. Bacterial genomes can be divided into two groups according to the qualitative description of their secular part: linear and piecewise linear. These two groups of genomes show different properties when their nucleotide spacing distribution is studied. In order to analyze genomes having a variable nucleotide density, statistically, the use of unfolding is necessary, i.e., to get a separation between the secular part and the fluctuations. The unfolding allows an adequate comparison with the statistical properties of other genomes. With this methodology, four genomes were analyzed Burkholderia, Bacillus, Clostridium and Corynebacterium. Interestingly, the nearest neighbor spacing distributions or detrended distance distributions are very similar for species within the same genus but they are very different for species from different genera. This difference can be attributed to the difference in the codon usage.

Higareda, M. F.; Geiger, O.; Mendoza, L.; Méndez-Sánchez, R. A.

2012-02-01

60

Analysis of synonymous codon usage bias in 09H1N1  

Microsoft Academic Search

A novel subtype of influenza A virus 09H1N1 has rapidly spread across the world. Evolutionary analyses of this virus have\\u000a revealed that 09H1N1 is a triple reassortant of segments from swine, avian and human influenza viruses. In this study, we\\u000a investigated factors shaping the codon usage bias of 09H1N1 and carried out cluster analysis of 60 strains of influenza A

Zhen-peng Li; De-quan Ying; Peng Li; Fei Li; Xiao-chen Bo; Sheng-qi Wang

2010-01-01

61

Enhanced production of ?-cyclodextrin glycosyltransferase in Escherichia coli by systematic codon usage optimization.  

PubMed

Enhancing the production of ?-cyclodextrin glycosyltransferase (?-CGTase) is a key aim in ?-CGTase industries. Here, the mature ?-cgt gene from Paenibacillus macerans JFB05-01 was redesigned with systematic codon optimization to preferentially match codon frequencies of Escherichia coli without altering the amino acid sequence. Following synthesis, codon-optimized ?-cgt (co?-cgt) and wild-type ?-cgt (wt?-cgt) genes were cloned into pET-20b(+) and expressed in E. coli BL21(DE3). The total protein yield of the synthetic gene was greater than wt?-cgt expression (1,710 mg L?¹) by 2,520 mg L?¹, with the extracellular enzyme activity being improved to 55.3 U mL?¹ in flask fermentation. ?G values at -3 to +50 of the pelB site of both genes were -19.10 kcal mol?¹. Functionally, co?-CGTase was equally as effective as wt?-CGTase in forming ?-cyclodextrin (?-CD). These findings suggest that preferred codon usage is advantageous for translational efficiency to increase protein expression. Finally, batch fermentation was applied, and the extracellular co?-CGTase enzyme activity was 326 % that of wt?-CGTase. The results suggest that codon optimization is a reasonable strategy to improve the yield of ?-CGTase for industrial application. PMID:22898983

Liu, Hua; Li, Jianghua; Du, Guocheng; Zhou, Jingwen; Chen, Jian

2012-12-01

62

Environmental shaping of codon usage and functional adaptation across microbial communities  

PubMed Central

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.

Roller, Masa; Lucic, Vedran; Nagy, Istvan; Perica, Tina; Vlahovicek, Kristian

2013-01-01

63

Predicting Gene Expression Level from Relative Codon Usage Bias: An Application to Escherichia coli Genome  

PubMed Central

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest.

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

64

Lost in translation: implications of HIV-1 codon usage for immune escape and drug resistance.  

PubMed

Synonymous nucleotide substitutions in protein-coding sequences are often regarded as evolutionarily neutral and not subject to selective pressure. However, synonymous codons can sometimes lead to different patterns of amino acid substitution by single nucleotide changes. Based on the deconstruction of the standard genetic code, we propose the term 'quasi-synonymous' to describe codons that specify the same amino acid, but lie on different mutational pathways, and we show that in at least one rapidly evolving organism, HIV-1, quasi-synonymy plays a role in its evolution. We present concrete examples that demonstrate the relevance of codon usage in the development of antiretroviral-drug resistance. In the case of the host immune response, the data indicates that viral evasion is achieved through use of codons that lie on the direct path to escape mutants, and equally, permit rapid reversion to wild-type in the absence of these selective pressures. Quasi-synonymy conditions HIV-1 and, potentially, other rapidly evolving organisms in their exploration of the mutational space. PMID:15168741

Kijak, Gustavo H; Currier, Jeffrey R; Tovanabutra, Sodsai; Cox, Josephine H; Michael, Nelson L; Wegner, Scott A; Birx, Deborah L; McCutchan, Francine E

2004-01-01

65

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host  

PubMed Central

A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values. In one example, all genes of the genome of Caenorhabditis elegans were adapted to Escherichia coli codon usage and further optimized to avoid commonly used restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene codon usage was adapted to E.coli codon usage with parallel avoidance of the same restriction sites. For both, the degree of introduced changes was documented and evaluated. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. JCat is freely accessible at .

Grote, Andreas; Hiller, Karsten; Scheer, Maurice; Munch, Richard; Nortemann, Bernd; Hempel, Dietmar C.; Jahn, Dieter

2005-01-01

66

Residential energy usage comparison: Findings  

SciTech Connect

This report presents the research methods and results from the Residential Energy Usage Comparison (REUC) project, a joint effort by Southern California Edison Company (SCE) and the Electric Power Research Institute (EPRI). The REUC project design activities began in early 1986. The REUC project is an innovative demand-site project designed to measure and compare typical energy consumption patterns of energy efficient residential electric and gas appliances. 95 figs., 33 tabs.

Smith, B.A.; Uhlaner, R.T.; Cason, T.N.; Courteau, S. (Quantum Consulting, Inc., Berkeley, CA (United States))

1991-08-01

67

AT2-AT3-profiling: a new look at synonymous codon usage.  

PubMed

The teleology of synonymous codon usage (SCU) still awaits a unifying concept. Here the 2nd codon letter of human mRNA-codons was graphically, aided by a computer program, put in relation to the 3rd codon letter, the carrier of SCU: AT2, the density of A+T in 2nd codon position, behaves to AT3, the analogous density of the 3rd codon position, mostly in an inverse fashion that can be expressed as typical figures: mRNAs with an overall AT-density below 50% have a tendency to produce bulky figures called "red dragons" (when redness is attributed to graph-areas, where AT3< AT2), while mRNAs with an AT-density above 50% produce a pattern called "harlequin" consisting of alternating red and blue (blueness, in analogy, when AT3>AT2) diamonds. With more diversion of AT3 from AT2, the harlequin patterns can assume the pattern of a "blue dragon". By analysing the mRNA of known proteins, these patterns can be correlated with certain functional regions: proteins with multiple transmembrane passages show bulky "red dragons", structural proteins with a high glycine- and proline content such as collagen result in "blue dragons". Non-coding mRNAs tend to show a balance between AT2 and AT3 and hence "harlequin patterns". Signal peptides usually code red due to a low AT3 with an AT2-density at the expectance level. With this technique DNA-sequences of as yet unknown functional meaning were scanned. When stretches of harlequin patterns appear interrupted by red or blue dragons, closer scrutiny of these stretches can reveal ORFs which deserve to be looked at more closely for their protein-informational content. At least in humans, SCU appears to follow protein-dependent AT2-density in a reciprocal fashion and does not seem to serve the purpose of influencing mRNA secondary structure which is discussed in depth. PMID:16930630

Pluhar, Wolfgang

2006-12-01

68

Degeneration in Codon Usage within the Region of Suppressed Recombination in the Mating-Type Chromosomes of Neurospora tetrasperma ? †  

PubMed Central

The origin and early evolution of sex chromosomes are currently poorly understood. The Neurospora tetrasperma mating-type (mat) chromosomes have recently emerged as a model system for the study of early sex chromosome evolution, since they contain a young (<6 million years ago [Mya]), large (>6.6-Mb) region of suppressed recombination. Here we examined preferred-codon usage in 290 genes (121,831 codon positions) in order to test for early signs of genomic degeneration in N. tetrasperma mat chromosomes. We report several key findings about codon usage in the region of recombination suppression, including the following: (i) this region has been subjected to marked and largely independent degeneration among gene alleles; (ii) the level of degeneration is magnified over longer periods of recombination suppression; and (iii) both mat a and mat A chromosomes have been subjected to deterioration. The frequency of shifts from preferred codons to nonpreferred codons is greater for shorter genes than for longer genes, suggesting that short genes play an especially significant role in early sex chromosome evolution. Furthermore, we show that these degenerative changes in codon usage are best explained by altered selection efficiency in the recombinationally suppressed region. These findings demonstrate that the fungus N. tetrasperma provides an effective system for the study of degenerative genomic changes in young regions of recombination suppression in sex-regulating chromosomes.

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

2011-01-01

69

Antagonistic relationships between intron content and codon usage bias of genes in three mosquito species: functional and evolutionary implications  

PubMed Central

Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vectorborne diseases such as malaria, dengue, West Nile, and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the covariance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other nonmosquito insects. By applying a maximum likelihood–based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny-dependent manner, but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias.

Behura, Susanta K; Singh, Brajendra K; Severson, David W

2013-01-01

70

Chloroplast genes transferred to the nuclear plant genome have adjusted to nuclear base composition and codon usage.  

PubMed Central

During plant evolution, some plastid genes have been moved to the nuclear genome. These transferred genes are now correctly expressed in the nucleus, their products being transported into the chloroplast. We compared the base compositions, the distributions of some dinucleotides and codon usages of transferred, nuclear and chloroplast genes in two dicots and two monocots plant species. Our results indicate that transferred genes have adjusted to nuclear base composition and codon usage, being now more similar to the nuclear genes than to the chloroplast ones in every species analyzed.

Oliver, J L; Marin, A; Martinez-Zapater, J M

1990-01-01

71

Production of ?-cyclodextrin glycosyltransferase in Bacillus megaterium MS941 by systematic codon usage optimization.  

PubMed

?-Cyclodextrin glycosyltransferase is a key enzyme in the cyclodextrin industry. The Gram-positive bacterium Bacillus megaterium was chosen for production of recombinant ?-CGTase for safety concerns. Successful production of heterologous ?-CGTase was achieved by adapting the original ?-cgt gene to the codon usage of B. megaterium by systematic codon optimization. This balanced the tRNA pool and reduced ribosomal traffic jams. Protein expression and secretion was ensured by using the strong inducible promoter P(xyl) and the signal peptide SP(LipA). The impact of culture medium composition and induction strategies on ?-CGTase production was systematically analyzed. Production and secretion at 32 °C for 24 h using modified culture medium was optimal for ?-CGTase yield. Batch- and simple fed-batch fermentation was applied to achieve a high yield of 48.9 U·mL(-1), which was the highest activity reported for a Bacillus species, making this production system a reasonable alternative to Escherichia coli. PMID:23013320

Zhou, Jingwen; Liu, Hua; Du, Guocheng; Li, Jianghua; Chen, Jian

2012-10-17

72

Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome  

PubMed Central

Escherichia coli has long been regarded as a model organism in the study of codon usage bias (CUB). However, most studies in this organism regarding this topic have been computational or, when experimental, restricted to small datasets; particularly poor attention has been given to genes with low CUB. In this work, correspondence analysis on codon usage is used to classify E.coli genes into three groups, and the relationship between them and expression levels from microarray experiments is studied. These groups are: group 1, highly biased genes; group 2, moderately biased genes; and group 3, AT-rich genes with low CUB. It is shown that, surprisingly, there is a negative correlation between codon bias and expression levels for group 3 genes, i.e. genes with extremely low codon adaptation index (CAI) values are highly expressed, while group 2 show the lowest average expression levels and group 1 show the usual expected positive correlation between CAI and expression. This trend is maintained over all functional gene groups, seeming to contradict the E.coli–yeast paradigm on CUB. It is argued that these findings are still compatible with the mutation–selection balance hypothesis of codon usage and that E.coli genes form a dynamic system shaped by these factors.

dos Reis, Mario; Wernisch, Lorenz; Savva, Renos

2003-01-01

73

Determinants of DNA sequence divergence between Escherichia coli and Salmonella typhimurium : Codon usage, map position, and concerted evolution  

Microsoft Academic Search

Summary The nature and extent of DNA sequence divergence between homologous proteincoding genes fromEscherichia coli andSalmonella typhimurium have been examined. The degree of divergence varies greatly among genes at both synonymous (silent) and nonsynonymous sites. Much of the variation in silent substitution rates can be explained by natural selection on synonymous codon usage, varying in intensity with gene expression level.

Paul M. Sharp

1991-01-01

74

Lost in Translation: Implications of HIV1 Codon Usage for Immune Escape and Drug Resistance  

Microsoft Academic Search

Synonymous nucleotide substitutions in protein-coding sequences are often regarded as evolution- arily neutral and not subject to selective pressure. However, synonymous codons can sometimes lead to different patterns of amino acid substitution by single nucleotide changes. Based on the deconstruction of the standard genetic code, we propose the term 'quasi-synonymous' to describe codons that specify the same amino acid, but

Gustavo H. Kijak; Jeffrey R. Currier; Sodsai Tovanabutra; Josephine H. Cox; Nelson L. Michael; Scott A. Wegner; Deborah L. Birx; Francine E. McCutchan

2004-01-01

75

Codon Volatility As an Indicator of Positive Selection: Data from Eukaryotic Genome Comparisons  

Microsoft Academic Search

It has been suggested that codon volatility (the proportion of the point-mutation neighbors of a codon that encode different amino acids) can be used as an index of past positive selection. We compared codon volatility with patterns of synonymous and nonsynonymous nucleotide substitution in genome-wide comparisons of orthologous genes between three pairs of related genomes: (1) the protists Plasmodium falciparum

Robert Friedman; Austin L. Hughes

2004-01-01

76

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.  

PubMed

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 ? and ?', 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. PMID:23053196

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

2012-08-01

77

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response  

PubMed Central

S-phase and DNA damage promote increased ribonucleotide reductase (RNR) activity. Translation of RNR1 has been linked to the wobble uridine modifying enzyme tRNA methyltransferase 9 (Trm9). We predicted that changes in tRNA modification would translationally regulate RNR1 after DNA damage to promote cell cycle progression. In support, we demonstrate that the Trm9-dependent tRNA modification 5-methoxycarbonylmethyluridine (mcm?U) is increased in hydroxyurea (HU)-induced S-phase cells, relative to G? and G?, and that mcm?U is one of 16 tRNA modifications whose levels oscillate during the cell cycle. Codon-reporter data matches the mcm?U increase to Trm9 and the efficient translation of AGA codons and RNR1. Further, we show that in trm9? cells reduced Rnr1 protein levels cause delayed transition into S-phase after damage. Codon re-engineering of RNR1 increased the number of trm9? cells that have transitioned into S-phase 1 h after DNA damage and that have increased Rnr1 protein levels, similar to that of wild-type cells expressing native RNR1. Our data supports a model in which codon usage and tRNA modification are regulatory components of the DNA damage response, with both playing vital roles in cell cycle progression.

Patil, Ashish; Dyavaiah, Madhu; Joseph, Fraulin; Rooney, John P.; Chan, Clement T.Y.; Dedon, Peter C.; Begley, Thomas J.

2012-01-01

78

Codon Usage Bias and Effective Population Sizes on the X Chromosome versus the Autosomes in Drosophila melanogaster  

PubMed Central

Codon usage bias (CUB) in Drosophila is higher for X-linked genes than for autosomal genes. One possible explanation is that the higher effective recombination rate for genes on the X chromosome compared with the autosomes reduces their susceptibility to Hill–Robertson effects, and thus enhances the efficacy of selection on codon usage. The genome sequence of D. melanogaster was used to test this hypothesis. Contrary to expectation, it was found that, after correcting for the effective recombination rate, CUB remained higher on the X than on the autosomes. In contrast, an analysis of polymorphism data from a Rwandan population showed that mean nucleotide site diversity at 4-fold degenerate sites for genes on the X is approximately three-quarters of the autosomal value after correcting for the effective recombination rate, compared with approximate equality before correction. In addition, these data show that selection for preferred versus unpreferred synonymous variants is stronger on the X than the autosomes, which accounts for the higher CUB of genes on the X chromosome. This difference in the strength of selection does not appear to reflect the effects of dominance of mutations affecting codon usage, differences in gene expression levels between X and autosomes, or differences in mutational bias. Its cause therefore remains unexplained. The stronger selection on CUB on the X chromosome leads to a lower rate of synonymous site divergence compared with the autosomes; this will cause a stronger upward bias for X than A in estimates of the proportion of nonsynonymous mutations fixed by positive selection, for methods based on the McDonald–Kreitman test.

Campos, Jose L.; Zeng, Kai; Parker, Darren J.; Charlesworth, Brian; Haddrill, Penelope R.

2013-01-01

79

Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation  

PubMed Central

Background Mitochondrial (mt) gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years. It remains unclear, however, whether such long-term persistence is a consequence of some constraints on the gene order. Results Based on the analysis of codon usage and tRNA gene positions, we suggest that tRNA gene order of the typical vertebrate mt-genomes may be important for their translational efficiency. The vertebrate mt-genome encodes 2 rRNA, 22 tRNA, and 13 transmembrane proteins consisting mainly of hydrophobic domains. We found that the tRNA genes specifying the hydrophobic residues were positioned close to the control region (CR), where the transcription efficiency is estimated to be relatively high. Using 47 vertebrate mt-genome sequences representing jawless fishes to mammals, we further found a correlation between codon usage and tRNA gene positions, implying that highly-used tRNA genes are located close to the CR. In addition, an analysis considering the asymmetric nature of mtDNA replication suggested that the tRNA loci that remain in single-strand for a longer time tend to have more guanine and thymine not suffering deamination mutations in their anticodon sites. Conclusions Our analyses imply the existence of translational constraint acting on the vertebrate mt-gene arrangement. Such translational constraint, together with the deamination-related constraint, may have contributed to long-term maintenance of gene order.

2010-01-01

80

The implication of life style on codon usage patterns and predicted highly expressed genes for three Frankia genomes.  

PubMed

Frankia are nitrogen-fixing actinomycetes that form a symbiotic association with over 200 species of woody dicotyledonous plants. Recently, three Frankia genomes were completely sequenced. In this study, the synonymous codon usage patterns of three Frankia genomes (strains CcI3, ACN14a, and EAN1pec) were determined and compared to each other and to other actinobacteria. As expected for a high G+C organism, codon usage by Frankia was highly biased, but differences were observed among the three strains. Using the codon adaptation index (CAI) as a numerical estimator of gene expression level, highly expressed genes in Frankia were predicted with ribosomal protein genes as a reference. The analysis of the predicted highly expressed genes showed that Frankia strain CcI3 had a different profile from the other two strains. Strain CcI3 had fewer predicted highly expressed genes in several COG categories including lipid transport and metabolism, secondary metabolites biosynthesis, inorganic ion transport and metabolism, and general function prediction only than Frankia strains EAN1pec and ACN14a. Interestingly, Frankia EAN1pec had more predicted highly expressed genes in transcription and signal transduction mechanisms than the other two strains. These differences were not just a reflection in total gene numbers, but also based on percentage of genes within a category. These results support the hypothesis that strain CcI3 is becoming a symbiotic specialist and the other two facultative symbiotic strains are maintaining their capacity to exist as free-living soil dwellers. PMID:18293096

Sen, Arnab; Sur, Saubashya; Bothra, Asim K; Benson, David R; Normand, Philippe; Tisa, Louis S

2008-05-01

81

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

PubMed Central

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 acid composition. Most probably, the observed picture is best explained by a hitherto unknown (neutral or adaptive) mechanism that increased the guanine + cytosine content in P. tetraurelia mtDNA on the one hand, and strong purifying selection on the ancestral amino acid composition on the other hand. These contradicting forces are counterbalanced by a considerably altered codon usage pattern.

2011-01-01

82

Multiple Effects of Codon Usage Optimization on Expression and Immunogenicity of DNA Candidate Vaccines Encoding the Human Immunodeficiency Virus Type 1 Gag Protein  

Microsoft Academic Search

We have analyzed the influence of codon usage modifications on the expression levels and immunogenicity of DNA vaccines, encoding the human immunodeficiency virus type 1 (HIV-1) group-specific antigen (Gag). In the presence of Rev, an expression vector containing the wild-type (wt) gag gene flanked by essential cis-acting sites such as the 5-untranslated region and 3-Rev response element supported substantial Gag

LUDWIG DEML; ALEXANDRA BOJAK; STEPHANIE STECK; MARCUS GRAF; JENS WILD; REINHOLD SCHIRMBECK; HANS WOLF; RALF WAGNER

2001-01-01

83

Analysis of codon usage patterns and predicted highly expressed genes for six phytopathogenic Xanthomonas genomes shows a high degree of conservation.  

PubMed

Members of the genus Xanthomonas are significant phytopathogens, which cause diseases in several economically important crops including rice, canola, tomato, citrus, etc. We have analyzed the genomes of six recently sequenced Xanthomonas strains for their synonymous codon usage patterns for all of protein coding genes and specific genes associated with pathogenesis, and determined the predicted highly expressed (PHX) genes by the use of the codon adaptation index (CAI). Our results show considerable heterogeneity among the genes of these moderately G+C rich genomes. Most of the genes were moderate to highly biased in their codon usage. However, unlike ribosomal protein genes, which were governed by translational selection, those genes associated with pathogenesis (GAP) were affected by mutational pressure and were predicted to have moderate to low expression levels. Only two out of 339 GAP genes were in the PHX category. PHX genes present in clusters of orthologous groups of proteins (COGs) were identified. Genes in the plasmids present in two strains showed moderate to low expression level and only a couple of genes featured in the PHX list. Common genes present in the top-20 PHX gene-list were identified and their possible functions are discussed. Correspondence analysis showed that genes are highly confined to a core in the plot. PMID:18391244

Sen, Gargi; Sur, Saubashya; Bose, Debadin; Mondal, Uttam; Furnholm, Teal; Bothra, Asim; Tisa, Louis; Sen, Arnab

2007-01-01

84

International Comparisons of Cars and Car Usage.  

National Technical Information Service (NTIS)

Statistics relating to cars and their usage have been assembled for 19 countries for the years 1958 to 1980. These are then analysed in relation to population, national income, petrol prices and other relevant factors. Aspects considered are car ownership...

J.C. Tanner

1983-01-01

85

Codon optimizer: a freeware tool for codon optimization  

Microsoft Academic Search

Selection plays a major role in the determination of codon usage in all organisms studied so far. In highly expressed genes, a narrow set of codons is used and these codons correspond to the more abundant tRNA species. This minimizes the risk of tRNA depletion during translation. In fact, the codons in a gene may be true bottlenecks, especially in

Anders Fuglsang

2003-01-01

86

Codon optimization for high-level expression of human erythropoietin (EPO) in mammalian cells  

Microsoft Academic Search

Codon bias has been observed in many species. The usage of selective codons in a given gene is positively correlated with its expression efficiency. As an experimental approach to study codon-usage effects on heterologous gene expression in mammalian cells, we designed two human erythropoietin (EPO) genes, one in which native codons were systematically substituted with codons frequently found in highly

Chang H Kim; Younghoon Oh; Tae H Lee

1997-01-01

87

The Comparison of Usage and Availability Measurements for Evaluating Resource Preference  

Microsoft Academic Search

Abstract. Modern ecological research often involves the comparison of the usage of habitat types or food items to the availability of those resources to the animal. Widely used methods of determining preference from measurements of usage and availability depend critically on the array of components

Douglas H. Johnson

1980-01-01

88

Secret Codon  

NSDL National Science Digital Library

In this activity, "write" a secret message in genetic code as beads on a string. Learners use an amino acid codon table to determine the DNA sequences that correspond to the one-letter amino acid abbreviations that make up their secret word(s). Learners also use start and stop codons in their sequences and follow a color key for the bases. Learners can trade strands with a friend to see if they can decode their secret message.

Yu, Julie

2008-01-01

89

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

PubMed Central

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.

2012-01-01

90

Cellular immunity survey against urinary tract infection using pVAX/fimH cassette with mammalian and wild type codon usage as a DNA vaccine  

PubMed Central

Purpose FimH (the adhesion fragment of type 1 fimbriae) is implicated in uropathogenic Escherichia coli (UPEC) attachment to epithelial cells through interaction with mannose. Recently, some studies have found that UPEC can thrive intracellularly causing recurrent urinary tract infection (UTI). Almost all vaccines have been designed to induce antibodies against UPEC. Yet, the humoral immune response is not potent enough to overcome neither the primary UTI nor recurrent infections. However, DNA vaccines offer the possibility of inducing cell mediated immune responses and may be a promising preventive tool. Materials and Methods In this study, we employed two different open reading frames within mammalian (mam) and wild type (wt) codons of fimH gene. Optimized fragments were cloned in pVAX-1. Expression of the protein in COS-7 was confirmed by western blot analysis after assessing pVAX/fimH(mam) and pVAX/fimH(wt). The constructs were injected to BALB/c mice at plantar surface of feet followed by electroporation. Results The mice immunized with both constructs following booster injection with recombinant FimH showed increased interferon-? and interleukin-12 responses significantly higher than non-immunized ones (p<0.05). The immunized mice were challenged with UPEC and then the number of bacteria recovered from the immunized mice was compared with the non-immunized ones. Decreased colony count in immunized mice along with cytokine responses confirmed the promising immune response by the DNA vaccines developed in this study. Conclusion In conclusion, DNA vaccines of UPEC proteins may confer some levels of protection which can be improved by multiple constructs or boosters.

Bagherpour, Ghasem; Khoramabadi, Nima; Fallah Mehrabadi, Jalil; Mahdavi, Mehdi; Halabian, Raheleh; Amin, Mohsen; Izadi Mobarakeh, Jalal; Einollahi, Behzad

2014-01-01

91

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  

SciTech Connect

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.

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

1994-09-01

92

Effect of Codon Message on Xylanase Thermal Activity*  

PubMed Central

Because the genetic codon is known for degeneracy, its effect on enzyme thermal property is seldom investigated. A dataset was constructed for GH10 xylanase coding sequences and optimal temperatures for activity (Topt). Codon contents and relative synonymous codon usages were calculated and respectively correlated with the enzyme Topt values, which were used to describe the xylanase thermophilic tendencies without dividing them into two thermophilic and mesophilic groups. After analyses of codon content and relative synonymous codon usages were checked by the Bonferroni correction, we found five codons, with three (AUA, AGA, and AGG) correlating positively and two (CGU and AGC) correlating negatively with the Topt value. The three positive codons are purine-rich codons, and the two negative codons have A-ends. The two negative codons are pyridine-rich codons, and one has a C-end. Comparable with the codon C- and A-ending features, C- and A-content within mRNA correlated negatively and positively with the Topt value, respectively. Thereby, codons have effects on enzyme thermal property. When the issue is analyzed at the residual level, the effect of codon message is lost. The codons relating to enzyme thermal property are selected by thermophilic force at nucleotide level.

Liu, Liangwei; Wang, Linmin; Zhang, Zhang; Wang, Suya; Chen, Hongge

2012-01-01

93

ICT Usage of Pre-service Teachers: Cultural Comparison for Turkey and Bosnia and Herzegovina  

ERIC Educational Resources Information Center

The importance of ICTs has become the undisputed in the present century. Studies have been conducted to investigate the use of ICTs with the goal of increase in quality of teacher education for a long time. This study is a cross-cultural comparison in terms of pre-service teachers' level of ICT usage, ICT knowledge and attitudes. The study…

Demirli, Cihad

2013-01-01

94

Site-specific codon bias in bacteria  

SciTech Connect

Sequences of the gapA and ompA genes from 10 genera of enterobacteria have been analyzed. There is strong bias in codon usage, but different synonymous codons are preferred at different sites in the same gene. Site-specific preference for unfavored codons is not confined to the first 100 codons and is usually manifest between two codons utilizing the same tRNA. Statistical analyses, based on conclusions reached in an accompanying paper, show that the use of an unfavored codon at a given site in different genera is not due to common descent and must therefore be caused either by sequence-specific mutation or sequence-specific selection. Reasons are given for thinking that sequence-specific mutation cannot be responsible. We are unable to explain the preference between synonymous codons ending in C or T, but synonymous choice between A and G at third sites is largely explained by avoidance of AG-G (where the hyphen indicates the boundary between codons). We also observed that the preferred codon for proline in Enterobacter cloacea has changed from CCG to CCA. 27 refs., 7 tabs.

Smith, J.M.; Smith, N.H. [Univ. of Sussex, Brighton (United Kingdom)

1996-03-01

95

On Ribosome Load, Codon Bias and Protein Abundance  

PubMed Central

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.

Klumpp, Stefan; Dong, Jiajia; Hwa, Terence

2012-01-01

96

Selection on codon bias in yeast: a transcriptional hypothesis.  

PubMed

Codons that code for the same amino acid are often used with unequal frequencies. This phenomenon is termed codon bias. Here, we report a computational analysis of codon bias in yeast using experimental and theoretical genome-wide data. We show that the most used codons in highly expressed genes can be predicted by mRNA structural data and that the codon choice at each synonymous site within an mRNA is not random with respect to the local secondary structure. Because we also found that the folding stability of intron sequences is strongly correlated with codon bias and mRNA level, our results suggest that codon bias is linked to mRNA folding structure through a mechanism that, at least partially, operates before pre-mRNA splicing. Consistent with this, we report evidence supporting the adaptation of the tRNA pool to the codon profile of the most expressed genes rather than vice versa. We show that the correlation of codon usage with the gene expression level also includes the stop codons that are normally not decoded by aminoacyl-tRNAs. The results reported here are consistent with a role for transcriptional forces in driving codon usage bias via a mechanism that improves gene expression by optimizing mRNA folding structures. PMID:23945943

Trotta, Edoardo

2013-11-01

97

Codons Support the Maintenance of Intrinsic DNA Polymer Flexibility over Evolutionary Timescales  

PubMed Central

Despite our long familiarity with how the genetic code specifies the amino acid sequence, we still know little about why it is organized in the way that it is. Contrary to the view that the organization of the genetic code is a “frozen accident” of evolution, recent studies have demonstrated that it is highly nonrandom, with implications for both codon assignment and usage. We hypothesize that this inherent nonrandomness may facilitate the coexistence of both sequence and structural information in DNA. Here, we take advantage of a simple metric of intrinsic DNA flexibility to analyze mutational effects on the four phosphate linkages present in any given codon. Application of a simple evolutionary neutral model of substitution to random sequences, translated with alternative genetic codes, reveals that the standard code is highly optimized to favor synonymous substitutions that maximize DNA polymer flexibility, potentially counteracting neutral evolutionary drift toward stiffer DNA caused by spontaneous deamination. Comparison to existing mutational patterns in yeast also demonstrates evidence of strong selective constraint on DNA flexibility, especially at so-called “silent” sites. We also report a fundamental relationship between DNA flexibility, codon usage bias, and several important evolutionary descriptors of comparative genomics (e.g., base composition, transition/transversion ratio, and nonsynonymous vs. synonymous substitution rate). Recent advances in structural genomics have emphasized the role of the DNA polymer's flexibility in both gene function and whole genome folding, thereby implicating possible reasons for codons to facilitate the multiplexing of both genetic and structural information within the same molecular context.

Babbitt, G. A.; Schulze, K. V.

2012-01-01

98

GC constituents and relative codon expressed amino acid composition in cyanobacterial phycobiliproteins.  

PubMed

The genomic as well as structural relationship of phycobiliproteins (PBPs) in different cyanobacterial species are determined by nucleotides as well as amino acid composition. The genomic GC constituents influence the amino acid variability and codon usage of particular subunit of PBPs. We have analyzed 11 cyanobacterial species to explore the variation of amino acids and causal relationship between GC constituents and codon usage. The study at the first, second and third levels of GC content showed relatively more amino acid variability on the levels of G3+C3 position in comparison to the first and second positions. The amino acid encoded GC rich level including G rich and C rich or both correlate the codon variability and amino acid availability. The fluctuation in amino acids such as Arg, Ala, His, Asp, Gly, Leu and Glu in ? and ? subunits was observed at G1C1 position; however, fluctuation in other amino acids such as Ser, Thr, Cys and Trp was observed at G2C2 position. The coding selection pressure of amino acids such as Ala, Thr, Tyr, Asp, Gly, Ile, Leu, Asn, and Ser in ? and ? subunits of PBPs was more elaborated at G3C3 position. In this study, we observed that each subunit of PBPs is codon specific for particular amino acid. These results suggest that genomic constraint linked with GC constituents selects the codon for particular amino acids and furthermore, the codon level study may be a novel approach to explore many problems associated with genomics and proteomics of cyanobacteria. PMID:24933001

Kannaujiya, Vinod K; Rastogi, Rajesh P; Sinha, Rajeshwar P

2014-08-10

99

Differential Codon Adaptation between dsDNA and ssDNA Phages in Escherichia coli.  

PubMed

Because phages use their host translation machinery, their codon usage should evolve toward that of highly expressed host genes. We used two indices to measure codon adaptation of phages to their host, rRSCU (the correlation in relative synonymous codon usage [RSCU] between phages and their host) and Codon Adaptation Index (CAI) computed with highly expressed host genes as the reference set (because phage translation depends on host translation machinery). These indices used for this purpose are appropriate only when hosts exhibit little mutation bias, so only phages parasitizing Escherichia coli were included in the analysis. For double-stranded DNA (dsDNA) phages, both rRSCU and CAI decrease with increasing number of transfer RNA genes encoded by the phage genome. rRSCU is greater for dsDNA phages than for single-stranded DNA (ssDNA) phages, and the low rRSCU values are mainly due to poor concordance in RSCU values for Y-ending codons between ssDNA phages and the E. coli host, consistent with the predicted effect of C?T mutation bias in the ssDNA phages. Strong C?T mutation bias would improve codon adaptation in codon families (e.g., Gly) where U-ending codons are favored over C-ending codons ("U-friendly" codon families) by highly expressed host genes but decrease codon adaptation in other codon families where highly expressed host genes favor C-ending codons against U-ending codons ("U-hostile" codon families). It is remarkable that ssDNA phages with increasing C?T mutation bias also increased the usage of codons in the "U-friendly" codon families, thereby achieving CAI values almost as large as those of dsDNA phages. This represents a new type of codon adaptation. PMID:24586046

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-06-01

100

Differential Codon Adaptation between dsDNA and ssDNA Phages in Escherichia coli  

PubMed Central

Because phages use their host translation machinery, their codon usage should evolve toward that of highly expressed host genes. We used two indices to measure codon adaptation of phages to their host, rRSCU (the correlation in relative synonymous codon usage [RSCU] between phages and their host) and Codon Adaptation Index (CAI) computed with highly expressed host genes as the reference set (because phage translation depends on host translation machinery). These indices used for this purpose are appropriate only when hosts exhibit little mutation bias, so only phages parasitizing Escherichia coli were included in the analysis. For double-stranded DNA (dsDNA) phages, both rRSCU and CAI decrease with increasing number of transfer RNA genes encoded by the phage genome. rRSCU is greater for dsDNA phages than for single-stranded DNA (ssDNA) phages, and the low rRSCU values are mainly due to poor concordance in RSCU values for Y-ending codons between ssDNA phages and the E. coli host, consistent with the predicted effect of C?T mutation bias in the ssDNA phages. Strong C?T mutation bias would improve codon adaptation in codon families (e.g., Gly) where U-ending codons are favored over C-ending codons (“U-friendly” codon families) by highly expressed host genes but decrease codon adaptation in other codon families where highly expressed host genes favor C-ending codons against U-ending codons (“U-hostile” codon families). It is remarkable that ssDNA phages with increasing C?T mutation bias also increased the usage of codons in the “U-friendly” codon families, thereby achieving CAI values almost as large as those of dsDNA phages. This represents a new type of codon adaptation.

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-01-01

101

Study of codon bias perspective of fungal xylanase gene by multivariate analysis.  

PubMed

Fungal xylanases has important applications in food, baking, pulp and paper industries in addition to various other industries. Xylanases are produced extensively by both bacterial and fungal sources and has tremendous potential of being active at extremes of temperature and pH. In the present study an effort has been made to explore the codon bias perspective of this potential enzyme using bioinformatics tools. Multivariate analysis has been used as a tool to study codon bias perspectives of xylanases. It was further observed that the codon usage of xylanases genes from different fungal sources is not similar and to reveal this phenomenon the relative synonymous codon usage (RSCU) and base composition variation in fungal xylanase genes were also studied. The codon biasing data like GC content at third position (GC(3S)), effective codon number (N(C)), codon adaptive index (CAI) were further analyzed with statistical softwares like Sigma1plot 9.0 and Systat 11.0. Furthermore, study of translation selection was also performed to verify the influences of codon usage variation among the 94 xylanase genes. In the present study xylanase gene from 12 organisms were analyzed and codon usages of all xylanases from each organism were compared separately. Analysis indicates biased codon among all 12 fungi taken for study with Aspergillus nidulans, Chaetomium globosum, Aspergillus terreus and Aspergillus clavatus showing maximum biasing. N(C) plot and correspondence analysis on relative synonymous codon usage indicate that mutation bias and translation selection influences codon usage variation in fungal xylanase gene. To reveal the relative synonymous codon usage and base composition variation in xylanase, 94 genes from 12 fungi were used as model system. PMID:19759864

Shrivastava, Smriti; Poddar, Raju; Shukla, Pratyoosh; Mukhopadhyay, Kunal

2009-01-01

102

Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli  

Microsoft Academic Search

Within Escherichia coli and other species, a clear codon bias exists among the 61 amino acid codons found within the population of mRNA molecules, and the level of cognate tRNA appears directly proportional to the frequency of codon usage. Given this situation, one would predict translational problems with an abundant mRNA species containing an excess of rare low tRNA codons.

James F Kane

1995-01-01

103

Optimizing heterologous expression in dictyostelium: importance of 5' codon adaptation.  

PubMed

Expression of heterologous proteins in Dictyostelium discoideum presents unique research opportunities, such as the functional analysis of complex human glycoproteins after random mutagenesis. In one study, human chorionic gonadotropin (hCG) and human follicle stimulating hormone were expressed in Dictyostelium. During the course of these experiments, we also investigated the role of codon usage and of the DNA sequence upstream of the ATG start codon. The Dictyostelium genome has a higher AT content than the human, resulting in a different codon preference. The hCG-beta gene contains three clusters with infrequently used codons that were changed to codons that are preferred by Dictyostelium. The results reported here show that optimizing the first 5-17 codons of the hCG gene contributes to 4- to 5-fold increased expression levels, but that further optimization has no significant effect. These observations suggest that optimal codon usage contributes to ribosome stabilization, but does not play an important role during the elongation phase of translation. Furthermore, adapting the 5'-sequence of the hCG gene to the Dictyostelium 'Kozak'-like sequence increased expression levels approximately 1.5-fold. Thus, using both codon optimization and 'Kozak' adaptation, a 6- to 8-fold increase in expression levels could be obtained for hCG. PMID:10773074

Vervoort, E B; van Ravestein, A; van Peij, N N; Heikoop, J C; van Haastert, P J; Verheijden, G F; Linskens, M H

2000-05-15

104

Towards Improved Quality of GPCR Models by Usage of Multiple Templates and Profile-Profile Comparison  

PubMed Central

G-protein coupled receptors (GPCRs) are targets of nearly one third of the drugs at the current pharmaceutical market. Despite their importance in many cellular processes the crystal structures are available for less than 20 unique GPCRs of the Rhodopsin-like class. Fortunately, even though involved in different signaling cascades, this large group of membrane proteins has preserved a uniform structure comprising seven transmembrane helices that allows quite reliable comparative modeling. Nevertheless, low sequence similarity between the GPCR family members is still a serious obstacle not only in template selection but also in providing theoretical models of acceptable quality. An additional level of difficulty is the prediction of kinks and bulges in transmembrane helices. Usage of multiple templates and generation of alignments based on sequence profiles may increase the rate of success in difficult cases of comparative modeling in which the sequence similarity between GPCRs is exceptionally low. Here, we present GPCRM, a novel method for fast and accurate generation of GPCR models using averaging of multiple template structures and profile-profile comparison. In particular, GPCRM is the first GPCR structure predictor incorporating two distinct loop modeling techniques: Modeller and Rosetta together with the filtering of models based on the Z-coordinate. We tested our approach on all unique GPCR structures determined to date and report its performance in comparison with other computational methods targeting the Rhodopsin-like class. We also provide a database of precomputed GPCR models of the human receptors from that class. Availability GPCRM server and database: http://gpcrm.biomodellab.eu

Latek, Dorota; Pasznik, Pawel; Carlomagno, Teresa; Filipek, Slawomir

2013-01-01

105

High codon adaptation in citrus tristeza virus to its citrus host  

PubMed Central

Background Citrus tristeza virus (CTV), a member of the genus Closterovirus within the family Closteroviridae, is the causal agent of citrus tristeza disease. Previous studies revealed that the negative selection, RNA recombination and gene flow were the most important forces that drove CTV evolution. However, the CTV codon usage was not studied and thus its role in CTV evolution remains unknown. Results A detailed comparative analysis of CTV codon usage pattern was done in this study. Results of the study show that although in general CTV does not have a high degree of codon usage bias, the codon usage of CTV has a high level of resemblance to its host codon usage. In addition, our data indicate that the codon usage resemblance is only observed for the woody plant-infecting closteroviruses but not the closteroviruses infecting the herbaceous host plants, suggesting the existence of different virus-host interactions between the herbaceous plant-infecting and woody plant-infecting closteroviruses. Conclusion Based on the results, we suggest that in addition to RNA recombination, negative selection and gene flow, host plant codon usage selection can also affect CTV evolution.

2012-01-01

106

A prospective comparison of antibiotic usage in pediatric surgical patients: The safety, advantage, and effectiveness of the Surgical Infection Society guidelines versus a common practice  

Microsoft Academic Search

Background: The Surgical Infection Society (SIS) guidelines for antibiotic (Ab) usage minimally changed the surgical practice. The authors believed that clinical evidence of the safety, advantage, and effectiveness of SIS guidelines may improve inappropriate usage of Ab. Methods: A group of dedicated surgeons attempted to use Ab appropriately to SIS guidelines in their patients (group A). A comparison was made

Elzbieta Grochowska; Miroslaw Krysta; Piotr Wojciechowski; Anna Taczanowska; Beata Stanek

2002-01-01

107

First impression versus extended usage: a comparison of product testing methodologies for perfume.  

PubMed

Synopsis In the fine fragrance industry, unlike many other fast moving consumer goods (fmcg) industries, systematic consumer product-testing has usually been conspicuous by its absence. The reasons are varied, including perfume's own traditions rooted in fashion rather than in marketing, the reluctance of perfumers to see their creations tested, the frequently (and perhaps, surprisingly) short lead times accorded for new product development and, of course, costs. When consumer product-testing is carried out, it is often limited for these same reasons, to 'sniff-testing', which, in the perfume industry, is equivalent to 'first impression' testing. This paper suggests that such sniff-testing may not only be unreliable, but perhaps more unreliable for the perfume category than has been realized hitherto. Reference is made to two consumer research studies on perfume, a qualitative project in France, followed by a quantitative exercise in the UK. A comparison is made between in-home test and sniff-test results for the same set of perfumes, which illustrates the limitations of sniff-testing in general, and the misleading results that it may produce, in particular. A major implication is that perfume is one product category which should be tested in extended usage, and not just for 'first impressions'. Résumé Dans l'industrie de la parfumerie fine, contrairement aux autres industries de produits de grande consommation, les tests consommateurs systématiques sont rarement utilisés. Les raisons sont diverses; les traditions propres du parfum tournées vers la mode plutôt que vers le marketing, le refus des parfumeurs de voir leurs créations subir des tests, les délais étonnamment courts pour le développement d'un nouveau produit et, bien sûr, le coût. Lorsqu'un test consommateurs est effectué, il se résume généralement pour ces mêmes raisons, en un test 'sniff', ce qui, dans l'industrie du parfum équivaut à un test de 'première impression'. Cet article montre que ces tests 'sniff' sont encore moins fiables pour le parfum que l'on avait pensé jusqu'à maintenant. Il est fait référence à deux tests consommateurs sur le parfum, un projet qualitatif en France, suivi par un exercice quantitatif effectué en Grande Bretagne. La comparaison entre les tests réalisés à domicile d'une part, et en sale d'autre part, montre que, pour les mêmes parfums, les résultats obtenus peuvent être erronés. Une des conclusions principales est que le parfum est un produit qui devrait être testé sur une longue période et non pas sur une première impression. PMID:19272121

Shalofsky, I

1993-04-01

108

Stop codons in bacteria are not selectively equivalent  

PubMed Central

Background The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes. Results We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5?codon is universally associated with lower fitness, with TAA being the optimal for G-content??16% TGA has a higher fitness than TAG. Conclusions Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications. Reviewers This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers’ Comments section.

2012-01-01

109

Codon populations in single-stranded whole human genome DNA Are fractal and fine-tuned by the Golden Ratio 1.618  

Microsoft Academic Search

This new bioinformatics research bridges Genomics and Mathematics. We propose a universal “Fractal Genome Code Law”: The frequency\\u000a of each of the 64 codons across the entire human genome is controlled by the codon’s position in the Universal Genetic Code\\u000a table. We analyze the frequency of distribution of the 64 codons (codon usage) within single-stranded DNA sequences. Concatenating\\u000a 24 Human

Jean-Claude Perez

2010-01-01

110

Lecture Attendance and Web Based Lecture Technologies: A Comparison of Student Perceptions and Usage Patterns  

ERIC Educational Resources Information Center

This paper investigates the impact of web based lecture recordings on learning and attendance at lectures. Student opinions regarding the perceived value of the recordings were evaluated in the context of usage patterns and final marks, and compared with attendance data and student perceptions regarding the usefulness of lectures. The availability…

von Konsky, Brian R.; Ivins, Jim; Gribble, Susan J.

2009-01-01

111

The Effect of Mutation and Selection on Codon Adaptation in Escherichia coli Bacteriophage  

PubMed Central

Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C?T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C?T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages.

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-01-01

112

Converting nonsense codons into sense codons by targeted pseudouridylation.  

PubMed

All three translation termination codons, or nonsense codons, contain a uridine residue at the first position of the codon. Here, we demonstrate that pseudouridylation (conversion of uridine into pseudouridine (?), ref. 4) of nonsense codons suppresses translation termination both in vitro and in vivo. In vivo targeting of nonsense codons is accomplished by the expression of an H/ACA RNA capable of directing the isomerization of uridine to ? within the nonsense codon. Thus, targeted pseudouridylation represents a novel approach for promoting nonsense suppression in vivo. Remarkably, we also show that pseudouridylated nonsense codons code for amino acids with similar properties. Specifically, ?AA and ?AG code for serine and threonine, whereas ?GA codes for tyrosine and phenylalanine, thus suggesting a new mode of decoding. Our results also suggest that RNA modification, as a naturally occurring mechanism, may offer a new way to expand the genetic code. PMID:21677757

Karijolich, John; Yu, Yi-Tao

2011-06-16

113

Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages  

Microsoft Academic Search

In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study\\u000a the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas re-inhardtii, is investigated by measuring adaptation to this

Brian R. Morton

1998-01-01

114

The Levels of Speech Usage Rating Scale: Comparison of Client Self-Ratings with Speech Pathologist Ratings  

ERIC Educational Resources Information Center

Background: The term "speech usage" refers to what people want or need to do with their speech to fulfil the communication demands in their life roles. Speech-language pathologists (SLPs) need to know about clients' speech usage to plan appropriate interventions to meet their life participation goals. The Levels of Speech Usage is a categorical…

Gray, Christina; Baylor, Carolyn; Eadie, Tanya; Kendall, Diane; Yorkston, Kathryn

2012-01-01

115

Efficiency in natural resource usage: a comparison of market central planning policies  

SciTech Connect

The foreign-trade structure of Czechoslovakia is examined to explain the intensive absorption of natural resources in centrally planned economies (CPEs). A comparison with Austria using input-output pricing models indicates that imports are the main source of this foreign-trade bias. This is traced to a bias in technology and domestic preferences toward natural resource products. It is concluded that pricing in CPEs should reflect the resulting scarcities.

Drabek, Z.

1981-02-01

116

Nonneutral GC3 and Retroelement Codon Mimicry in Phytophthora  

Microsoft Academic Search

Phytophthora is a genus entirely comprised of destructive plant pathogens. It belongs to the Stramenopila, a unique branch of eukaryotes,\\u000a phylogenetically distinct from plants, animals, or fungi. Phytophthora genes show a strong preference for usage of codons ending with G or C (high GC3). The presence of high GC3 in genes can be\\u000a utilized to differentiate coding regions from noncoding

Rays H. Y. Jiang; Francine Govers

2006-01-01

117

Functional significance of an evolutionarily conserved alanine (GCA) resume codon in tmRNA in Escherichia coli.  

PubMed

Occasionally, ribosomes stall on mRNAs prior to the completion of the polypeptide chain. In Escherichia coli and other eubacteria, tmRNA-mediated trans-translation is a major mechanism that recycles the stalled ribosomes. The tmRNA possesses a tRNA-like domain and a short mRNA region encoding a short peptide (ANDENYALAA in E. coli) followed by a termination codon. The first amino acid (Ala) of this peptide encoded by the resume codon (GCN) is highly conserved in tmRNAs in different species. However, reasons for the high evolutionary conservation of the resume codon identity have remained unclear. In this study, we show that changing the E. coli tmRNA resume codon to other efficiently translatable codons retains efficient functioning of the tmRNA. However, when the resume codon was replaced with the low-usage codons, its function was adversely affected. Interestingly, expression of tRNAs decoding the low-usage codon from plasmid-borne gene copies restored efficient utilization of tmRNA. We discuss why in E. coli, the GCA (Ala) is one of the best codons and why all codons in the short mRNA of the tmRNA are decoded by the abundant tRNAs. PMID:21602351

Kapoor, Suman; Samhita, Laasya; Varshney, Umesh

2011-07-01

118

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

NASA Astrophysics Data System (ADS)

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

Mitarai, Namiko; Pedersen, Steen

2013-10-01

119

Codon Optimization of Human Parvovirus B19 Capsid Genes Greatly Increases Their Expression in Nonpermissive Cells? †  

PubMed Central

Parvovirus B19 (B19V) is pathogenic for humans and has an extreme tropism for human erythroid progenitors. We report cell type-specific expression of the B19V capsid genes (VP1 and VP2) and greatly increased B19V capsid protein production in nonpermissive cells by codon optimization. Codon usage limitation, rather than promoter type and the 3? untranslated region of the capsid genes, appears to be a key factor in capsid protein production in nonpermissive cells. Moreover, B19 virus-like particles were successfully generated in nonpermissive cells by transient transfection of a plasmid carrying both codon-optimized VP1 and VP2 genes.

Zhi, Ning; Wan, Zhihong; Liu, Xiaohong; Wong, Susan; Kim, Dong Joo; Young, Neal S.; Kajigaya, Sachiko

2010-01-01

120

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

Microsoft Academic Search

Background  Codon adaptation indices (CAIs) represent an evolutionary strategy to modulate gene expression and have widely been used to\\u000a predict potentially highly expressed genes within microbial genomes. Here, we evaluate and compare two very different methods\\u000a for estimating CAI values, one corresponding to translational codon usage bias and the second obtained mathematically by searching\\u000a for the most dominant codon bias.\\u000a \\u000a \\u000a \\u000a \\u000a Results  The

Hanni Willenbrock; Carsten Friis; Agnieszka S Juncker; David W Ussery

2007-01-01

121

Expression of codon optimized human bone morphogenetic protein 4 in Pichia pastoris.  

PubMed

Bone morphogenetic proteins (BMPs) are TGF-? family member proteins that have therapeutic potential. The amount of BMPs from natural resources is limited, and the production of biologically active BMPs in heterologous protein expression systems remains an obstacle for their clinical application. In this study, the DNA sequence of human BMP4 mature domain (hBMP4) was optimized according to the codon relative synonymous codon usage values in Pichia pastoris, and the A+T content in the sequence after optimization was within the range of 30% to 55%. In Pichia pastoris cultured in shake-flask, the expression level of hBMP4 protein from the optimized sequence (48 mg/L) increased fourfold in comparison with that from the native sequence (12 mg/L). Recombinant hBMP4 protein was purified by SP Sepharose and heparin affinity chromatography. The biological activities of recombinant hBMP4 were examined by measuring proliferation stimulation in cells and induction of ectopic cartilage formation in mouse models. Our results demonstrated that the optimized DNA sequence could significantly enhance hBMP4 protein expression in Pichia pastoris compared with the native sequence and produce biologically active recombinant hBMP4; this indicates the potential of this optimized sequence for bulk production of hBMP4 protein in future clinical applications. PMID:23941573

Huang, Yide; Zhen, Binqiong; Lin, Yao; Cai, Yanhui; Lin, Zhen; Deng, Chunmei; Zhang, Yanding

2014-01-01

122

Preferred codons and amino acid couples in hyperthermophiles  

PubMed Central

Background Most organisms grow at temperatures from 20 to 50°C but some prokaryotes, including Archaea and Bacteria, are capable of withstanding higher temperatures, from 60 to >100°C. What makes these cells so resistant to heat? Their biomolecules must be sufficiently stable, especially proteins, to work under these extreme conditions, but the bases for thermostability remains elusive. Results The preferential usage of certain couples of amino acids and codons in thermal adaptation was investigated, by comparative proteome analysis, using 28 complete genomes from 18 mesophiles, 4 thermophiles, and 6 hyperthermophiles. In the hyperthermophiles proteomes, whenever the percent of Glu (E) and Lys (K) Increased, the percent of Gln (Q) and His (H) decreased, so that the E+K/Q+H ratio was > 4,5; in the mesophiles proteomes, it was < 2,5 and in the thermophiles an intermediary value was observed. The E+K/Q+H ratios for chaperonins, potentially thermostable proteins, were higher than their proteome ratios whereas, for DNA ligases, not necessarily thermostable, they followed the proteome ones. Analysis of codon usage revealed that hyperthermophiles preferred AGR codons for Arg in detriment of CGN codons, which were preferred by mesophiles. Conclusions The results suggested that the E+K/Q+H ratio may provide a useful mark for distinguishing hyperthermophilic, thermophilic and mesophilic prokaryotes and that the high percent of the amino acid couple E+K, consistently associated to the low percent of the pair Q+H, could contribute to protein thermostability. Second, the preference for AGR codons for Arg was a signature of all hyperthermophilics so far analyzed.

2002-01-01

123

Computational codon optimization of synthetic gene for protein expression  

PubMed Central

Background The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression. Results In this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU. Conclusions The proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology.

2012-01-01

124

Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes  

PubMed Central

Background Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed genes are thought to experience stronger selection pressures on synonymous codons. This should result in codon usage bias even in species with relatively low effective population sizes, like mammals, where synonymous site selection is thought to be weak. Here we use phylogenetic codon-based likelihood models to explore patterns of codon usage bias in a dataset of 18 mammalian rhodopsin sequences, the protein mediating the first step in vision in the eye, and one of the most highly expressed genes in vertebrates. We use these patterns to infer selection pressures on key translational mechanisms including polypeptide elongation, protein folding, mRNA stability, and splicing. Results Overall, patterns of selection in mammalian rhodopsin appear to be correlated with post-transcriptional and translational processes. We found significant evidence for selection at synonymous sites using phylogenetic mutation-selection likelihood models, with C-ending codons found to have the highest relative fitness, and to be significantly more abundant at conserved sites. In general, these codons corresponded with the most abundant tRNAs in mammals. We found significant differences in codon usage bias between rhodopsin loops versus helices, though there was no significant difference in mean synonymous substitution rate between these motifs. We also found a significantly higher proportion of GC-ending codons at paired sites in rhodopsin mRNA secondary structure, and significantly lower synonymous mutation rates in putative exonic splicing enhancer (ESE) regions than in non-ESE regions. Conclusions By focusing on a single highly expressed gene we both distinguish synonymous codon selection from mutational effects and analytically explore underlying functional mechanisms. Our results suggest that codon bias in mammalian rhodopsin arises from selection to optimally balance high overall translational speed, accuracy, and proper protein folding, especially in structurally complicated regions. Selection at synonymous sites may also be contributing to mRNA stability and splicing efficiency at exonic-splicing-enhancer (ESE) regions. Our results highlight the importance of investigating highly expressed genes in a broader phylogenetic context in order to better understand the evolution of synonymous substitutions.

2014-01-01

125

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

PubMed Central

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.

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

2013-01-01

126

English Usage in Hong Kong.  

ERIC Educational Resources Information Center

Articles contained in this special issue on language usage in Hong Kong, particularly in the context of elementary and secondary education, include: "A Comparison of English Errors Made by Hong Kong Students and Those Made by Non-Native Learners of English Internationally" (David Bunton); "Errors in Guides to English Usage for Hong Kong Students"…

Bunton, David, Ed.; Green, Christopher F., Ed.

1991-01-01

127

Comparison of Turkish and US Pre-Service Teachers' Web 2.0 Tools Usage Characteristics  

ERIC Educational Resources Information Center

As the Internet and computer develop, the world is changing dramatically and fantastically. Usage of technological tools is increased day by day in daily life besides ICT. All the technological tools shape individual behavior, life style and learning style as well as individual lives. Today's child use different tools and different way to…

Kiyici, Mubin; Akyeampong, Albert; Balkan Kiyici, Fatime

2013-01-01

128

A Comparison of the Influence of Social Factors and Technological Factors on Adoption and Usage of Knowledge Management Systems  

Microsoft Academic Search

Knowledge management strives for effective capture and application of organizational knowledge, a valuable resource imperative in sustaining an organization. In an effort to better achieve knowledge management initiatives, consideration of factors influencing adoption and usage of knowledge management systems are of great interest. Implementation of technological solutions are often considered organizational innovations subject to potential problems of resistance deeming social

Andrea J. Hester

2010-01-01

129

Benchmarking usage of Third Party Logistics: a comparison of practices between firms in Malaysia and Saudi Arabia  

Microsoft Academic Search

This paper presents a comparative analysis on the outsourcing of logistics services by manufacturing organisations in the Malaysia and Saudi Arabia. The study addresses key issues relating to extent of usage of third party logistics services, implementation issues, obstacles and plans of current users of contract logistics services. Results based on a survey shows that there are some differences on

M. Sadiq Sohail

2006-01-01

130

Relationship of codon bias to mRNA concentration and protein length inSaccharomyces cerevisiae  

Microsoft Academic Search

In 1982, Ikemura reported a strikingly unequal usage of different synonymous codons, in five Saccharomyces cerevisiae nuclear genes having high protein levels. To study this trend in detail, we examined data from three independent studies that used oligonucleotide arrays or SAGE to estimate mRNA concentrations for nearly all genes in the genome. Correlation coefficients were calculated for the relationship of

Avril Coghlan; Kenneth H. Wolfe

2000-01-01

131

Stop codon recognition in ciliates: Euplotes release factor does not respond to reassigned UGA codon  

PubMed Central

In eukaryotes, the polypeptide release factor 1 (eRF1) is involved in translation termination at all three stop codons. However, the mechanism for decoding stop codons remains unknown. A direct interaction of eRF1 with the stop codons has been postulated. Recent studies focus on eRF1 from ciliates in which some stop codons are reassigned to sense codons. Using an in vitro assay based on mammalian ribosomes, we show that eRF1 from the ciliate Euplotes aediculatus responds to UAA and UAG as stop codons and lacks the capacity to decipher the UGA codon, which encodes cysteine in this organism. This result strongly suggests that in ciliates with variant genetic codes eRF1 does not recognize the reassigned codons. Recent hypotheses describing stop codon discrimination by eRF1 are not fully consistent with the set of eRF1 sequences available so far and require direct experimental testing.

Kervestin, Stephanie; Frolova, Ludmila; Kisselev, Lev; Jean-Jean, Olivier

2001-01-01

132

A theoretical analysis of codon adaptation index of the Boophilus microplus bm86 gene directed to the optimization of a DNA vaccine.  

PubMed

DNA vaccines utilize host cell molecules for gene transcription and translation to proteins, and the interspecific difference of codon usage is one of the major obstacles for effective induction of specific and strong immune response. In an attempt to improve codon usage effects of DNA vaccine on protein expression, a quantitative study was conducted to clarify the relationship of codon usage in the tick gene bm86 and its potential expression in bovine cells. The calculated relative synonymous codon usage (RSCU) and codon adaptation index (CAI) values of bm86 from Boophilus microplus and a set of 14 highly expressed genes from Bos taurus indicated that some codons utilized frequently in bm86 are rarely used in B. taurus genes and vice versa. The different translational efficiencies obtained suggested that after DNA vaccination using the wild bm86 gene, the protein Bm86 would be expressed in bovines, but it would not be the optimum sequence. However, using the codon-optimized bm86 gene to bovines, whose sequence was theoretically designed, would probably improve the level of the immune response generated against ticks. PMID:16171828

Ruiz, Lina María; Armengol, Gemma; Habeych, Edwin; Orduz, Sergio

2006-04-21

133

Experimentally Increased Codon Bias in the Drosophila Adh Gene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity  

PubMed Central

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.

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

2010-01-01

134

Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations  

PubMed Central

An ab initio model for gene prediction in prokaryotic genomes is proposed based on physicochemical characteristics of codons calculated from molecular dynamics (MD) simulations. The model requires a specification of three calculated quantities for each codon: the double-helical trinucleotide base pairing energy, the base pair stacking energy, and an index of the propensity of a codon for protein-nucleic acid interactions. The base pairing and stacking energies for each codon are obtained from recently reported MD simulations on all unique tetranucleotide steps, and the third parameter is assigned based on the conjugate rule previously proposed to account for the wobble hypothesis with respect to degeneracies in the genetic code. The third interaction propensity parameter values correlate well with ab initio MD calculated solvation energies and flexibility of codon sequences as well as codon usage in genes and amino acid composition frequencies in ?175,000 protein sequences in the Swissprot database. Assignment of these three parameters for each codon enables the calculation of the magnitude and orientation of a cumulative three-dimensional vector for a DNA sequence of any length in each of the six genomic reading frames. Analysis of 372 genomes comprising ?350,000 genes shows that the orientations of the gene and nongene vectors are well differentiated and make a clear distinction feasible between genic and nongenic sequences at a level equivalent to or better than currently available knowledge-based models trained on the basis of empirical data, presenting a strong support for the possibility of a unique and useful physicochemical characterization of DNA sequences from codons to genomes.

Singhal, Poonam; Jayaram, B.; Dixit, Surjit B.; Beveridge, David L.

2008-01-01

135

Comparison of ALAD activities of Citrobacter and Pseudomonas strains and their usage as biomarker for Pb contamination.  

PubMed

Delta-aminolevulinate dehydratase (ALAD) activity has been used in prokaryotes and eukaryotes as a biomarker for environmental lead (Pb) exposure and toxicity. Microorganisms are sensitive indicators of toxicity at the fundamental level of ecological organization, but bacterial biomarker studies are focused on the Pseudomonas strains in Group I and E coli. The objectives of the present work were to determine if Burkholderia gladioli belonging to group II, due to its 16SrRNA similarity, can be used as biomarker in metal contamination and compare its possible usage with Pseudomonas aeruginosa and Citrobacter freundii (previously known as Esherichia freundii) and Bacterium freundii which are classified in Group I. In this study, ALAD activity in an environmental strains of Burkholderia gladioli, Pseudomonas aeruginosa, Citrobacter freundii were investigated to evaluate potential inhibition by Pb and other toxic metals. When the ALAD activity of Burkholderia gladioli was tested, Co and Pb decreased activity by 27 and 71%, respectively. In addition to these findings, Zn increased the activity up to 26%. These effects were found to be statistically meaningful (p < 0.05). It was determined that the increase of lead concentration inhibites the ALAD activity at each of the three strains. There was a statistically significant dose-response relationship between ALAD activity in cells of Burkholderia gladioli and Pb (Pearson correlation coefficent = -0.665; r(2) = 0.665, and p < 0.001). The strongest ALAD inhibition which was measured was 90% at Burkholderia gladioli when protein extracts were incubated with 750 muM of Pb. The relationship between Pb and ALAD activity was statistically described by [ALAD Activity] = 0.476-0.000597 x [Pb]. According to the obtained results, we suggest that the ALAD of Burkholderia gladioli can be used as a biomarker for lead contamination in the environment. PMID:17516138

Ci?erci, I Hakki; Korcan, S Elif; Konuk, Muhsin; Oztürk, Sevda

2008-04-01

136

A study of the purine/pyrimidine codon occurrence with a reduced centered variable and an evaluation compared to the frequency statistic.  

PubMed

With the three-letter alphabet [R,Y,N] (R = purine, Y = pyrimidine, N = R or Y), there are 26 codons (NNN being excluded): RNN,...,NNY (six codons at two unspecified bases N), RRN,...,NYY (12 codons at one unspecified base N), RRR,...,YYY (eight specified codons). A statistical methodology that uses the codon frequency and a reduced centered variable leads to similar results for a codon occurrence study, regardless of gene function and regardless of a particular protein coding gene taxonomic population. Therefore, this variable can be considered a new codon usage index, whose use removes certain nonsignificant results found with the frequency statistic. This methodology identifies the common and rare codons (i.e., the codons having the highest and lowest occurrence) and leads to a model of codon evolution at three successive states: RNN, then RNY, and finally RYY. Some biological relations between this model and the YRY(N)6YRY preferential occurrence are also presented. PMID:2520209

Michel, C J

1989-12-01

137

Codon choice in genes depends on flanking sequence information--implications for theoretical reverse translation  

PubMed Central

Algorithms for theoretical reverse translation have direct applications in degenerate PCR. The conventional practice is to create several degenerate primers each of which variably encode the peptide region of interest. In the current work, for each codon we have analyzed the flanking residues in proteins and determined their influence on codon choice. From this, we created a method for theoretical reverse translation that includes information from flanking residues of the protein in question. Our method, named the neighbor correlation method (NCM) and its enhancement, the consensus-NCM (c-NCM) performed significantly better than the conventional codon-usage statistic method (CSM). Using the methods NCM and c-NCM, we were able to increase the average sequence identity from 77% up to 81%. Furthermore, we revealed a significant increase in coverage, at 80% identity, from < 20% (CSM) to > 75% (c-NCM). The algorithms, their applications and implications are discussed herein.

Sivaraman, Karthikeyan; Seshasayee, AswinSaiNarain; Tarwater, Patrick M.; Cole, Alexander M.

2008-01-01

138

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models  

PubMed Central

Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with nucleotide or amino acid models. Thus, for protein-coding genes, phylogenetic inference is expected to be more accurate under codon models. So far, phylogeny reconstruction under codon models has been elusive due to computational difficulties of dealing with high dimension matrices. Here, we present a fast maximum likelihood (ML) package for phylogenetic inference, CodonPhyML offering hundreds of different codon models, the largest variety to date, for phylogeny inference by ML. CodonPhyML is tested on simulated and real data and is shown to offer excellent speed and convergence properties. In addition, CodonPhyML includes most recent fast methods for estimating phylogenetic branch supports and provides an integral framework for models selection, including amino acid and DNA models.

Gil, Manuel; Zoller, Stefan; Anisimova, Maria

2013-01-01

139

CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models.  

PubMed

Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with nucleotide or amino acid models. Thus, for protein-coding genes, phylogenetic inference is expected to be more accurate under codon models. So far, phylogeny reconstruction under codon models has been elusive due to computational difficulties of dealing with high dimension matrices. Here, we present a fast maximum likelihood (ML) package for phylogenetic inference, CodonPhyML offering hundreds of different codon models, the largest variety to date, for phylogeny inference by ML. CodonPhyML is tested on simulated and real data and is shown to offer excellent speed and convergence properties. In addition, CodonPhyML includes most recent fast methods for estimating phylogenetic branch supports and provides an integral framework for models selection, including amino acid and DNA models. PMID:23436912

Gil, Manuel; Zanetti, Marcelo Serrano; Zoller, Stefan; Anisimova, Maria

2013-06-01

140

Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags  

PubMed Central

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.

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

2013-01-01

141

Comparative study of codon substitution patterns in foot-and-mouth disease virus (serotype O)  

PubMed Central

We compared genetic variations in the VP1 gene of foot-and-mouth disease viruses (FMDVs) isolated since 2000 from various region of the world. We analyzed relative synonymous codon usage (RSCU) and phylogenetic relationship between geographical regions, and calculated the genetic substitution patterns between Korean isolate and those from other countries. We calculated the ratios of synonymously substituted codons (SSC) to all observed substitutions and developed a new analytical parameter, EMC (the ratio of exact matching codons within each synonymous substitution group) to investigate more detailed substitution patterns within each synonymous codon group. We observed that FMDVs showed distinct RSCU patterns according to phylogenetic relationships in the same serotype (serotype O). Moreover, while the SSC and EMC values of FMDVs decreased according to phylogenetic distance, G + C composition at the third codon position was strictly conserved. Although there was little variation among the SSC values of 18 amino acids, more dynamic differences were observed in EMC values. The EMC values of 4- and 6-fold degenerate amino acids showed significantly lower values while most 2-fold degenerate amino acids showed no significant difference. Our findings suggest that different EMC patterns among the 18 amino acids might be an important factor in determining the direction of evolution in FMDV.

Ahn, Insung; Bae, Se-Eun

2011-01-01

142

Codon-based encoding for DNA sequence analysis.  

PubMed

With the exponential growth of biological sequence data (DNA or Protein Sequence), DNA sequence analysis has become an essential task for biologist to understand the features, functions, structures, and evolution of species. Encoding DNA sequences is an effective method to extract the features from DNA sequences. It is commonly used for visualizing DNA sequences and analyzing similarities/dissimilarities between different species or cells. Although there have been many encoding approaches proposed for DNA sequence analysis, we require more elegant approaches for higher accuracy. In this paper, we propose a noble encoding approach for measuring the degree of similarity/dissimilarity between different species. Our approach can preserve the physiochemical properties, positional information, and the codon usage bias of nucleotides. An extensive performance study shows that our approach provides higher accuracy than existing approaches in terms of the degree of similarity. PMID:24530970

Jeong, Byeong-Soo; Golam Bari, A T M; Rokeya Reaz, Mst; Jeon, Seokhee; Lim, Chae-Gyun; Choi, Ho-Jin

2014-06-01

143

A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae  

PubMed Central

Background Heterologous gene expression is an important tool for synthetic biology that enables metabolic engineering and the production of non-natural biologics in a variety of host organisms. The translational efficiency of heterologous genes can often be improved by optimizing synonymous codon usage to better match the host organism. However, traditional approaches for optimization neglect to take into account many factors known to influence synonymous codon distributions. Results Here we define an alternative approach for codon optimization that utilizes systems level information and codon context for the condition under which heterologous genes are being expressed. Furthermore, we utilize a probabilistic algorithm to generate multiple variants of a given gene. We demonstrate improved translational efficiency using this condition-specific codon optimization approach with two heterologous genes, the fluorescent protein-encoding eGFP and the catechol 1,2-dioxygenase gene CatA, expressed in S. cerevisiae. For the latter case, optimization for stationary phase production resulted in nearly 2.9-fold improvements over commercial gene optimization algorithms. Conclusions Codon optimization is now often a standard tool for protein expression, and while a variety of tools and approaches have been developed, they do not guarantee improved performance for all hosts of applications. Here, we suggest an alternative method for condition-specific codon optimization and demonstrate its utility in Saccharomyces cerevisiae as a proof of concept. However, this technique should be applicable to any organism for which gene expression data can be generated and is thus of potential interest for a variety of applications in metabolic and cellular engineering.

2014-01-01

144

Context specific misreading of phenylalanine codons  

Microsoft Academic Search

It has previously been shown that the phenylalanine codon UUC encoding residue 8 of the Escherichia coli argI gene product, ornithine transcarbamylase, is misread as leucine at a high frequency during phenylalanine starvation. However, no misreading of the UUU encoding residue 3 was observed under these conditions. Using oligonucleotide-directed, site-specific mutagenesis, we have constructed mutants where these codons have been

James Precup; Amy K. Ulrich; Osha Roopnarine; Jack Parker

1989-01-01

145

Transfer RNA misidentification scrambles sense codon recoding.  

PubMed

Sense codon recoding is the basis for genetic code expansion with more than two different noncanonical amino acids. It requires an unused (or rarely used) codon, and an orthogonal tRNA synthetase:tRNA pair with the complementary anticodon. The Mycoplasma capricolum genome contains just six CGG arginine codons, without a dedicated tRNA(Arg). We wanted to reassign this codon to pyrrolysine by providing M. capricolum with pyrrolysyl-tRNA synthetase, a synthetic tRNA with a CCG anticodon (tRNA(Pyl)(CCG)), and the genes for pyrrolysine biosynthesis. Here we show that tRNA(Pyl)(CCG) is efficiently recognized by the endogenous arginyl-tRNA synthetase, presumably at the anticodon. Mass spectrometry revealed that in the presence of tRNA(Pyl)(CCG), CGG codons are translated as arginine. This result is not unexpected as most tRNA synthetases use the anticodon as a recognition element. The data suggest that tRNA misidentification by endogenous aminoacyl-tRNA synthetases needs to be overcome for sense codon recoding. PMID:24000185

Krishnakumar, Radha; Prat, Laure; Aerni, Hans-Rudolf; Ling, Jiqiang; Merryman, Chuck; Glass, John I; Rinehart, Jesse; Söll, Dieter

2013-10-11

146

Codon Modified Human Papillomavirus Type 16 E7 DNA Vaccine Enhances Cytotoxic T-Lymphocyte Induction and Anti-tumour Activity  

Microsoft Academic Search

Polynucleotide immunisation with the E7 gene of human papillomavirus (HPV) type 16 induces only moderate levels of immune response, which may in part be due to limitation in E7 gene expression influenced by biased HPV codon usage. Here we compare for expression and immunogenicity polynucleotide expression plasmids encoding wild-type (pWE7) or synthetic codon optimised (pHE7) HPV16 E7 DNA. Cos-1 cells

Wen Jun Liu; Fengguang Gao; Kong Nan Zhao; Weiming Zhao; Germain J. G. Fernando; Ranjeny Thomas; Ian H. Frazer

2002-01-01

147

Most Used Codons per Amino Acid and per Genome in the Code of Man Compared to Other Organisms According to the Rotating Circular Genetic Code  

PubMed Central

My previous theoretical research shows that the rotating circular genetic code is a viable tool to make easier to distinguish the rules of variation applied to the amino acid exchange; it presents a precise and positional bio-mathematical balance of codons, according to the amino acids they codify. Here, I demonstrate that when using the conventional or classic circular genetic code, a clearer pattern for the human codon usage per amino acid and per genome emerges. The most used human codons per amino acid were the ones ending with the three hydrogen bond nucleotides: C for 12 amino acids and G for the remaining 8, plus one codon for arginine ending in A that was used approximately with the same frequency than the one ending in G for this same amino acid (plus *). The most used codons in man fall almost all the time at the rightmost position, clockwise, ending either in C or in G within the circular genetic code. The human codon usage per genome is compared to other organisms such as fruit flies (Drosophila melanogaster), squid (Loligo pealei), and many others. The biosemiotic codon usage of each genomic population or ‘Theme’ is equated to a ‘molecular language’. The C/U choice or difference, and the G/A difference in the third nucleotide of the most used codons per amino acid are illustrated by comparing the most used codons per genome in humans and squids. The human distribution in the third position of most used codons is a 12-8-2, C-G-A, nucleotide ending signature, while the squid distribution in the third position of most used codons was an odd, or uneven, distribution in the third position of its most used codons: 13-6-3, U-A-G, as its nucleotide ending signature. These findings may help to design computational tools to compare human genomes, to determine the exchangeability between compatible codons and amino acids, and for the early detection of incompatible changes leading to hereditary diseases.

Castro-Chavez, Fernando

2011-01-01

148

Ancestral Inference and the Study of Codon Bias Evolution: Implications for Molecular Evolutionary Analyses of the Drosophila melanogaster Subgroup  

PubMed Central

Reliable inference of ancestral sequences can be critical to identifying both patterns and causes of molecular evolution. Robustness of ancestral inference is often assumed among closely related species, but tests of this assumption have been limited. Here, we examine the performance of inference methods for data simulated under scenarios of codon bias evolution within the Drosophila melanogaster subgroup. Genome sequence data for multiple, closely related species within this subgroup make it an important system for studying molecular evolutionary genetics. The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. Maximum parsimony inference, which has been widely employed in analyses of Drosophila codon bias evolution, was compared to an approach that attempts to account for uncertainty in ancestral inference by weighting ancestral reconstructions by their posterior probabilities. The latter approach employs maximum likelihood estimation of rate and base composition parameters. For equilibrium and most non-equilibrium scenarios that were investigated, the probabilistic method appears to generate reliable ancestral codon bias inferences for molecular evolutionary studies within the D. melanogaster subgroup. These reconstructions are more reliable than parsimony inference, especially when codon usage is strongly skewed. However, inference biases are considerable for both methods under particular departures from stationarity (i.e., when adaptive evolution is prevalent). Reliability of inference can be sensitive to branch lengths, asymmetry in substitution rates, and the locations and nature of lineage-specific processes within a gene tree. Inference reliability, even among closely related species, can be strongly affected by (potentially unknown) patterns of molecular evolution in lineages ancestral to those of interest.

Akashi, Hiroshi; Goel, Piyush; John, Anoop

2007-01-01

149

The Effects of Codon Context on In Vivo Translation Speed  

PubMed Central

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.

Chevance, Fabienne F. V.; Le Guyon, Soazig; Hughes, Kelly T.

2014-01-01

150

Selection on GGU and CGU codons in the high expression genes in bacteria.  

PubMed

The fourfold degenerate site (FDS) in coding sequences is important for studying the effect of any selection pressure on codon usage bias (CUB) because nucleotide substitution per se is not under any such pressure at the site due to the unaltered amino acid sequence in a protein. We estimated the frequency variation of nucleotides at the FDS across the eight family boxes (FBs) defined as Um(g), the unevenness measure of a gene g. The study was made in 545 species of bacteria. In many bacteria, the Um(g) correlated strongly with Nc'-a measure of the CUB. Analysis of the strongly correlated bacteria revealed that the U-ending codons (GGU, CGU) were preferred to the G-ending codons (GGG, CGG) in Gly and Arg FBs even in the genomes with G+C % higher than 65.0. Further evidence suggested that these codons can be used as a good indicator of selection pressure on CUB in genomes with higher G+C %. PMID:24271854

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

2014-01-01

151

Across Bacterial Phyla, Distantly-Related Genomes with Similar Genomic GC Content Have Similar Patterns of Amino Acid Usage  

PubMed Central

The GC content of bacterial genomes ranges from 16% to 75% and wide ranges of genomic GC content are observed within many bacterial phyla, including both Gram negative and Gram positive phyla. Thus, divergent genomic GC content has evolved repeatedly in widely separated bacterial taxa. Since genomic GC content influences codon usage, we examined codon usage patterns and predicted protein amino acid content as a function of genomic GC content within eight different phyla or classes of bacteria. We found that similar patterns of codon usage and protein amino acid content have evolved independently in all eight groups of bacteria. For example, in each group, use of amino acids encoded by GC-rich codons increased by approximately 1% for each 10% increase in genomic GC content, while the use of amino acids encoded by AT-rich codons decreased by a similar amount. This consistency within every phylum and class studied led us to conclude that GC content appears to be the primary determinant of the codon and amino acid usage patterns observed in bacterial genomes. These results also indicate that selection for translational efficiency of highly expressed genes is constrained by the genomic parameters associated with the GC content of the host genome.

Lightfield, John; Fram, Noah R.; Ely, Bert

2011-01-01

152

An Improved Implementation of Codon Adaptation Index  

PubMed Central

Codon adaptation index is a widely used index for characterizing gene expression in general and translation efficiency in particular. Current computational implementations have a number of problems leading to various systematic biases. I illustrate these problems and provide a better computer implementation to solve these problems. The improved CAI can predict protein production better than CAI from other commonly used implementations.

Xia, Xuhua

2007-01-01

153

VH4 codon signature for multiple sclerosis  

US Patent & Trademark Office Database

The present invention provides for the diagnosis and prediction of multiple sclerosis (MS) in subject utilizing a unique a codon signature in VH4 expressing B cells that has now been associated with MS and not with any other autoimmune disease.

2013-03-12

154

Key for protein coding sequences identification: computer analysis of codon strategy.  

PubMed Central

The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be detected at N-termini of the proteins, the A/U enrichment results from a biased usage of the code degeneracy. A computer analysis is presented which allows easy detection of the codon strategy. N-terminal codons carry rather systematically A or U in third position, which suggests a mechanism for translation initiation and helps to detect protein coding sequences in sequenced DNA.

Rodier, F; Gabarro-Arpa, J; Ehrlich, R; Reiss, C

1982-01-01

155

Two-codon T-box riboswitch binding two tRNAs  

PubMed Central

T-box riboswitches control transcription of downstream genes through the tRNA-binding formation of terminator or antiterminator structures. Previously reported T-boxes were described as single-specificity riboswitches that can bind specific tRNA anticodons through codon–anticodon interactions with the nucleotide triplet of their specifier loop (SL). However, the possibility that T-boxes might exhibit specificity beyond a single tRNA had been overlooked. In Clostridium acetobutylicum, the T-box that regulates the operon for the essential tRNA-dependent transamidation pathway harbors a SL with two potential overlapping codon positions for tRNAAsn and tRNAGlu. To test its specificity, we performed extensive mutagenic, biochemical, and chemical probing analyses. Surprisingly, both tRNAs can efficiently bind the SL in vitro and in vivo. The dual specificity of the T-box is allowed by a single base shift on the SL from one overlapping codon to the next. This feature allows the riboswitch to sense two tRNAs and balance the biosynthesis of two amino acids. Detailed genomic comparisons support our observations and suggest that “flexible” T-box riboswitches are widespread among bacteria, and, moreover, their specificity is dictated by the metabolic interconnection of the pathways under control. Taken together, our results support the notion of a genome-dependent codon ambiguity of the SLs. Furthermore, the existence of two overlapping codons imposes a unique example of tRNA-dependent regulation at the transcriptional level.

Saad, Nizar Y.; Stamatopoulou, Vassiliki; Braye, Melanie; Drainas, Denis; Stathopoulos, Constantinos; Becker, Hubert Dominique

2013-01-01

156

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

ERIC Educational Resources Information Center

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…

Roivainen, Eka

2014-01-01

157

The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids  

PubMed Central

Background The question of whether synonymous codon choice is affected by cellular tRNA abundance has been positively answered in many organisms. In some recent works, concerning the human genome, this relation has been studied, but no conclusive answers have been found. In the human genome, the variation in base composition and the absence of cellular tRNA count data makes the study of the question more complicated. In this work we study the relation between codon choice and tRNA abundance in the human genome by correcting relative codon usage for background base composition and using a measure based on tRNA-gene copy numbers as a rough estimate of tRNA abundance. Results We term major codons to be those codons with a relatively large tRNA-gene copy number for their corresponding amino acid. We use two measures of expression: breadth of expression (the number of tissues in which a gene was expressed) and maximum expression level among tissues (the highest value of expression of a gene among tissues). We show that for half the amino acids in the study (8 of 16) the relative major codon usage rises with breadth of expression. We show that these amino acids are significantly more frequent, are smaller and simpler, and are more ancient than the rest of the amino acids. Similar, although weaker, results were obtained for maximum expression level. Conclusion There is evidence that codon bias in the human genome is related to selection, although the selection forces acting on codon bias may not be straightforward and may be different for different amino acids. We suggest that, in the first group of amino acids, selection acts to enhance translation efficiency in highly expressed genes by preferring major codons, and acts to reduce translation rate in lowly expressed genes by preferring non-major ones. In the second group of amino acids other selection forces, such as reducing misincorporation rate of expensive amino acids, in terms of their size/complexity, may be in action. The fact that codon usage is more strongly related to breadth of expression than to maximum expression level supports the notion, presented in a recent study, that codon choice may be related to the tRNA abundance in the tissue in which a gene is expressed.

Kotlar, Daniel; Lavner, Yizhar

2006-01-01

158

Universal Pattern and Diverse Strengths of Successive Synonymous Codon Bias in Three Domains of Life, Particularly Among Prokaryotic Genomes  

PubMed Central

There has been significant progress in understanding the process of protein translation in recent years. One of the best examples is the discovery of usage bias in successive synonymous codons and its role in eukaryotic translation efficiency. We observed here a similar type of bias in the other two life domains, bacteria and archaea, although the bias strength was much smaller than in eukaryotes. Among 136 prokaryotic genomes, 98 were found to have significant bias from random use of successive synonymous codons with Z scores larger than three. Furthermore, significantly different bias strengths were found between prokaryotes grouped by various genomic or biochemical characteristics. Interestingly, the bias strength measured by a general Z score could be fitted well (R = 0.83, P < 10?15) by three genomic variables: genome size, G + C content, and tRNA gene number based on multiple linear regression. A different distribution of synonymous codon pairs between protein-coding genes and intergenic sequences suggests that bias is caused by translation selection. The present results indicate that protein translation is tuned by codon (pair) usage, and the intensity of the regulation is associated with genome size, tRNA gene number, and G + C content.

Guo, Feng-Biao; Ye, Yuan-Nong; Zhao, Hai-Long; Lin, Dan; Wei, Wen

2012-01-01

159

Stop codon reassignments in the wild.  

PubMed

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. PMID:24855270

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

160

AGRICULTURAL CHEMICAL USAGE DATA  

EPA Science Inventory

This report, which summarizes the use of agricultural chemicals is issued by the National Agricultural Statistics Service (NASS) as part of its series on Agricultural Chemical Usage. Other publications in the series present statistics for on-farm agricultural chemical usage for f...

161

Online Medical CBT Usage  

Microsoft Academic Search

The website MedicalEducation.nl enables to students to access online medical Computer Based Training material any time and any place. For three types of embedding of CBT material in a medical curriculum, the relation between embedding type and usage statistics are described. The introduction of competition is shown to enhance CBT re-usage.

A. J. M. De Man; P. M. Bloemendaal; S. Eggermont

2007-01-01

162

Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes  

PubMed Central

Introduction Genomic base composition ranges from less than 25% AT to more than 85% AT in prokaryotes. Since only a small fraction of prokaryotic genomes is not protein coding even a minor change in genomic base composition will induce profound protein changes. We examined how amino acid and codon frequencies were distributed in over 2000 microbial genomes and how these distributions were affected by base compositional changes. In addition, we wanted to know how genome-wide amino acid usage was biased in the different genomes and how changes to base composition and mutations affected this bias. To carry this out, we used a Generalized Additive Mixed-effects Model (GAMM) to explore non-linear associations and strong data dependences in closely related microbes; principal component analysis (PCA) was used to examine genomic amino acid- and codon frequencies, while the concept of relative entropy was used to analyze genomic mutation rates. Results We found that genomic amino acid frequencies carried a stronger phylogenetic signal than codon frequencies, but that this signal was weak compared to that of genomic %AT. Further, in contrast to codon usage bias (CUB), amino acid usage bias (AAUB) was differently distributed in AT- and GC-rich genomes in the sense that AT-rich genomes did not prefer specific amino acids over others to the same extent as GC-rich genomes. AAUB was also associated with relative entropy; genomes with low AAUB contained more random mutations as a consequence of relaxed purifying selection than genomes with higher AAUB. Conclusion Genomic base composition has a substantial effect on both amino acid- and codon frequencies in bacterial genomes. While phylogeny influenced amino acid usage more in GC-rich genomes, AT-content was driving amino acid usage in AT-rich genomes. We found the GAMM model to be an excellent tool to analyze the genomic data used in this study.

Bohlin, Jon; Brynildsrud, Ola; Vesth, Tammi; Skjerve, Eystein; Ussery, David W.

2013-01-01

163

UpGene: Application of a web-based DNA codon optimization algorithm.  

PubMed

Although DNA codon optimization is a standard molecular biology strategy to overcome poor gene expression, to date no public software exists to facilitate this process. Among the uses of codon optimization, human immunodeficiency virus (HIV) vaccine development represents one of the most difficult challenges. A key obstacle to an effective DNA-based vaccine is the low-level expression of HIV genes in mammalian cells, which is due primarily to the instability of HIV mRNAs resulting from AU-rich elements and rare codon usage. In this report we describe the development of a DNA optimization algorithm integrated with a PCR primer design program to redesign specific coding sequences for maximal gene expression. Using this algorithm combination, together with PCR-based gene assembly, we have successfully optimized gene sequences for simian immunodeficiency virus (SIV) strain mac239 structural antigenic proteins gag and env, resulting in high-level gene expression in eukaryotic cells. Our findings demonstrate that our user-friendly algorithm is a valuable tool for DNA-based HIV vaccine development. Moreover, it can be used to optimize any other genes of interest and is freely available online at http://www.vectorcore.pitt.edu/upgene.html. PMID:15058988

Gao, Wentao; Rzewski, Alexis; Sun, Huijie; Robbins, Paul D; Gambotto, Andrea

2004-01-01

164

The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria.  

PubMed

Protein synthesis by ribosomes takes place on a linear substrate but at non-uniform speeds. Transient pausing of ribosomes can affect a variety of co-translational processes, including protein targeting and folding. These pauses are influenced by the sequence of the messenger RNA. Thus, redundancy in the genetic code allows the same protein to be translated at different rates. However, our knowledge of both the position and the mechanism of translational pausing in vivo is highly limited. Here we present a genome-wide analysis of translational pausing in bacteria by ribosome profiling--deep sequencing of ribosome-protected mRNA fragments. This approach enables the high-resolution measurement of ribosome density profiles along most transcripts at unperturbed, endogenous expression levels. Unexpectedly, we found that codons decoded by rare transfer RNAs do not lead to slow translation under nutrient-rich conditions. Instead, Shine-Dalgarno-(SD)-like features within coding sequences cause pervasive translational pausing. Using an orthogonal ribosome possessing an altered anti-SD sequence, we show that pausing is due to hybridization between the mRNA and 16S ribosomal RNA of the translating ribosome. In protein-coding sequences, internal SD sequences are disfavoured, which leads to biased usage, avoiding codons and codon pairs that resemble canonical SD sites. Our results indicate that internal SD-like sequences are a major determinant of translation rates and a global driving force for the coding of bacterial genomes. PMID:22456704

Li, Gene-Wei; Oh, Eugene; Weissman, Jonathan S

2012-04-26

165

Codon usage suggests that translational selection has a major impact on protein expression in trypanosomatids  

Microsoft Academic Search

BACKGROUND: Different proteins are required in widely different quantities to build a living cell. In most organisms, transcription control makes a major contribution to differential expression. This is not the case in trypanosomatids where most genes are transcribed at an equivalent rate within large polycistronic clusters. Thus, trypanosomatids must use post-transcriptional control mechanisms to balance gene expression requirements. RESULTS: Here,

David Horn

2008-01-01

166

Codon usage variability determines the correlation between proteome and transcriptome fold changes  

Microsoft Academic Search

Background  The availability of high throughput experimental methods has made possible to observe the relationships between proteome and\\u000a transcirptome. The protein abundances show a positive but weak correlation with the concentrations of their cognate mRNAs.\\u000a This weak correlation implies that there are other crucial effects involved in the regulation of protein translation, different\\u000a from the sole availability of mRNA. It is

Roberto Olivares-Hernández; Sergio Bordel; Jens Nielsen

2011-01-01

167

Spectinomycin operon of Micrococcus luteus : Evolutionary implications of organization and novel codon usage  

Microsoft Academic Search

Summary  The complete DNA sequence of theMicrococcus luteus spectinomycin (spc) operon and its adjacent regions has been determined. The sequence has revealed the presence of genes\\u000a that are homologous to those of theEscherichia coli ribosomal and related proteins, L14, L24, L5, S8, L6, L18, S5, L30, L15, and secretion protein Y (secY), and the gene for\\u000a adenylate kinase (adk). The gene

Takeshi Ohama; Akira Muto; Syozo Osawa

1989-01-01

168

Codon usage limitation in the expression of HIV1 envelope glycoprotein  

Microsoft Academic Search

Background: The expression of both the env and gag gene products of human immunodeficiency virus type 1 (HIV-1) is known to be limited by cis elements in the viral RNA that impede egress from the nucleus and reduce the efficiency of translation. Identifying these elements has proven difficult, as they appear to be disseminated throughout the viral genome.Results Here, we

Jürgen Haas; Eun-Chung Park; Brian Seed

1996-01-01

169

Ruminant Nitrogen Usage.  

National Technical Information Service (NTIS)

Latest research on protein absorption by ruminants has been compiled into the report. Contains information on how to calculate optimal nutrient requirements for ruminants and considers bacterial digestion in the methodology. Ruminant Nitrogen Usage presen...

1985-01-01

170

Automotive materials usage trends  

Microsoft Academic Search

The materials composition of US passenger cars is traced from 1960 and projected into 1990's. Sales-weighted average vehicle-weight trends are analyzed in terms of shifts in the large\\/small car mix, downsizing, and downweighting. The growth in the usage of lightweight materials: -high strength steels, cast\\/wrought aluminum, plastics and composites - are examined in detail. Usage trends in a host of

Gjostein

1986-01-01

171

Novel polymorphisms at codons 146 and 151 in the prion protein gene of Cyprus goats, and their association with natural scrapie.  

PubMed

To discern whether an association exists between specific combinations of polymorphisms of the prion protein (PrP) and natural scrapie in Cyprus goats, 250 goats were examined, including 164 histologically positive cases. Previously reported amino acid polymorphisms were detected at codons 154 (R-->H), 168(P-->Q), 220(Q-->H) and 240 (S-->P) and nucleotide alterations at codons 42 (a-->g) and 138 (c-->t). Additionally, novel amino acid polymorphisms were detected at codons 146 (N-->S or D) and 151 (R-->H) and new "silent" mutations were found at codons 179 (V,g-->t), 181 (D,c-->t) and 219 (T,c-->t). The two novel polymorphisms at codon 146 were found only in the healthy control and scrapie-negative goats. By comparison, none of the scrapie-affected goats encoded these polymorphisms. PMID:16314132

Papasavva-Stylianou, Penelope; Kleanthous, Marina; Toumazos, Pavlos; Mavrikiou, Petroula; Loucaides, Phedias

2007-03-01

172

Codon-by-Codon Modulation of Translational Speed and Accuracy Via mRNA Folding  

PubMed Central

Rapid cell growth demands fast protein translational elongation to alleviate ribosome shortage. However, speedy elongation undermines translational accuracy because of a mechanistic tradeoff. Here we provide genomic evidence in budding yeast and mouse embryonic stem cells that the efficiency–accuracy conflict is alleviated by slowing down the elongation at structurally or functionally important residues to ensure their translational accuracies while sacrificing the accuracy for speed at other residues. Our computational analysis in yeast with codon resolution suggests that mRNA secondary structures serve as elongation brakes to control the speed and hence the fidelity of protein translation. The position-specific effect of mRNA folding on translational accuracy is further demonstrated experimentally by swapping synonymous codons in a yeast transgene. Our findings explain why highly expressed genes tend to have strong mRNA folding, slow translational elongation, and conserved protein sequences. The exquisite codon-by-codon translational modulation uncovered here is a testament to the power of natural selection in mitigating efficiency–accuracy conflicts, which are prevalent in biology.

Yang, Jian-Rong; Chen, Xiaoshu; Zhang, Jianzhi

2014-01-01

173

Dual Accelerometer Usage Strategy for Onboard Space Navigation  

NASA Technical Reports Server (NTRS)

This work introduces a dual accelerometer usage strategy for onboard space navigation. In the proposed algorithm the accelerometer is used to propagate the state when its value exceeds a threshold and it is used to estimate its errors otherwise. Numerical examples and comparison to other accelerometer usage schemes are presented to validate the proposed approach.

Zanetti, Renato; D'Souza, Chris

2012-01-01

174

Usage as Rhetoric.  

ERIC Educational Resources Information Center

Even though linguistics has freed us from misconceptions, we have continued to seek answers to usage problems primarily by looking to linguistics. The myth of the verbal authority of standard speakers has given way to the evaluation of statistical frequency of forms. No matter how extensive or accurate the statistics, they must still be followed…

Gorrell, Robert M.

175

Diversity in smartphone usage  

Microsoft Academic Search

Using detailed traces from 255 users, we con- duct a comprehensive study of smartphone use. We char- acterize intentional user activities - interactions with the device and the applications used - and the impact of those activities on network and energy usage. We find immense diversity among users. Along all aspects that we study, users differ by one or more

Hossein Falaki; Ratul Mahajan; Srikanth Kandula; Dimitrios Lymberopoulos; Ramesh Govindan; Deborah Estrin

2010-01-01

176

Determinants of Initiation Codon Selection during Translation in Mammalian Cells  

PubMed Central

Factors affecting translation of mRNA contribute to the complexity of eukaryotic proteomes. In some cases, translation of a particular mRNA can generate multiple proteins. However, the factors that determine whether ribosomes initiate translation from the first AUG codon in the transcript, from a downstream codon, or from multiple sites are not completely understood. Various mRNA properties, including AUG codon-accessibility and 5? leader length have been proposed as potential determinants that affect where ribosomes initiate translation. To explore this issue, we performed studies using synthetic mRNAs with two in-frame AUG codons?both in excellent context. Open reading frames initiating at AUG1 and AUG2 encode large and small isoforms of a reporter protein, respectively. Translation of such an mRNA in COS-7 cells was shown to be 5? cap-dependent and to occur efficiently from both AUG codons. AUG codon-accessibility was modified by using two different elements: an antisense locked nucleic acid oligonucleotide and an exon-junction complex. When either element was used to mask AUG1, the ratio of the proteins synthesized changed, favoring the smaller (AUG2-initiated) protein. In addition, we observed that increased leader length by itself changed the ratio of the proteins and favored initiation at AUG1. These observations demonstrate that initiation codon selection is affected by various factors, including AUG codon-accessibility and 5? leader length, and is not necessarily determined by the order of AUG codons (5??3?). The modulation of AUG codon accessibility may provide a powerful means of translation regulation in eukaryotic cells.

Matsuda, Daiki; Mauro, Vincent P.

2010-01-01

177

Two-Dimensional Turbulent Separated Flow. Comparison of Criteria for Industrial Application Decollements Turbulents Bidimensionnels. Comparaison de Criteres a Usage Industriel.  

National Technical Information Service (NTIS)

The criteria of Michel-Quemard-Cousteix, Nikuradze and Stratford are compared in regard to assistance to the profile industrial design engineer. The comparison was performed on the NACA 0012 and GA(W)-1 profiles. It is shown that the Stratford criterion i...

Y. Semezis M. Robert

1977-01-01

178

Effect of 3' terminal codon pairs with different frequency of occurrence on the expression of cat gene in Escherichia coli.  

PubMed

In a previous study, we have identified four types of 3' terminal codon pairs depending on their frequency of occurrence in the Escherichia coli genome: overrepresented, moderately represented, underrepresented, and missing. In this study, the influence of eight codon pairs belonging to these four groups on the efficiency of chloramphenicol acetyltransferase ( cat) gene expression in E. coli is examined. Our results show that the missing codon pairs CCU:UAG (Pro:Stop) and CCC:UAG (Pro:Stop) had decreasing effect, whereas another missing pair CCU:AGG (Pro:Arg) had an opposite effect on the yield of CAT protein in comparison with the wild-type cat gene. PMID:15057475

Boycheva, Svetlana S; Bachvarov, Boris I; Berzal-Heranz, Alfredo; Ivanov, Ivan G

2004-02-01

179

UAG is a sense codon in several chlorophycean mitochondria.  

PubMed

The mitochondrial genetic code of those land plants and green algae that have been examined does not deviate from the universal one. A red alga, Chondrus crispus, is the sole reported example throughout the algae that uses a deviant (non-universal) mitochondrial genetic code (UGA=Trp). We have analyzed 366-bp DNA sequences of the gene for mitochondrial cytochrome oxidase subunit I (COXI) from ten chlorophyceaen algae, and detected 3-8 in-frame UAG codons in the sequences of five species. Comparisons of these sequences with those of other algae and land plants have shown that most of the UAG sites in Hydrodictyon reticulatum, Pediastrum boryanum and Tetraedron bitridens correspond to alanine, and those of Coelastrum microporum and Scenedesmus quadricauda to leucine. The three species in which UAG probably codes for alanine are characterized by zoospore formation in asexual reproduction and form a clade in the COXI phylogenetic tree. The two species in which UAG codes for leucine are known to form daughter coenobia and pair in the tree. This is the first report on a deviant mitochondrial genetic code in green algae. Mutational change(s) in the release factor corresponding to UAG would be involved in these code changes. No genetic code deviation has been found in five other species examined. PMID:8662206

Hayashi-Ishimaru, Y; Ohama, T; Kawatsu, Y; Nakamura, K; Osawa, S

1996-06-01

180

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

PubMed Central

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

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

1994-01-01

181

Selenocysteine insertion or termination: factors affecting UGA codon fate and complementary anticodon:codon mutations.  

PubMed Central

Translation of UGA as selenocysteine instead of termination occurs in numerous proteins, and the process of recording UGA requires specific signals in the corresponding mRNAs. In eukaryotes, stem-loops in the 3' untranslated region of the mRNAs confer this function. Despite the presence of these signals, selenocysteine incorporation is inefficient. To investigate the reason for this, we examined the effects of the amount of deiodinase cDNA on UGA readthrough in transfected cells, quantitating the full-length and UGA terminated products by Western blotting. The gene for the selenocysteine-specific tRNA was also cotransfected to determine if it was limiting. We find that the concentrations of both the selenoprotein DNA and the tRNA affect the ratio of selenocysteine incorporation to termination. Selenium depletion was also found to decrease readthrough. The fact that the truncated peptide is synthesized intracellularly demonstrates unequivocally that UGA can serve as both a stop and a selenocysteine codon in a single mRNA. Mutation of UGA to UAA (stop) or UUA (leucine) in the deiodinase mRNA abolishes deiodinase activity; but activity is partially restored when selenocysteine tRNAs containing complementary mutations are contransfected. Thus, UGA is not essential for selenocysteine incorporation in mammalian cells, provided that codon:anticodon complementarity is maintained. Images

Berry, M J; Harney, J W; Ohama, T; Hatfield, D L

1994-01-01

182

The empirical codon mutation matrix as a communication channel  

PubMed Central

Background A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino acids or codons derive one protein sequence from its ancestral sequence during evolution. In this paper, we regard the Empirical Codon Mutation (ECM) Matrix as a communication channel and compute the corresponding channel capacity. Results The channel capacity of 4.1875 bit, which is needed to preserve the information determined by the amino acid distribution, is obtained with an exponential factor of 0.26 applied to the ECM matrix. Additionally, we have obtained the optimum capacity achieving codon distribution. Compared to the biological distribution, there is an obvious difference, however, the distribution among synonymous codons is preserved. More importantly, the results show that the biological codon distribution allows for a “transmission” at a rate very close to the capacity. Conclusion We computed an exponential factor for the ECM matrix that would still allow for preserving the genetic information given the redundancy that is present in the codon-to-amino acid mapping. This gives an insight how such a mutation matrix relates to the preservation of a species in an information-theoretic sense.

2014-01-01

183

Modified 'one amino acid-one codon' engineering of high GC content TaqII-coding gene from thermophilic Thermus aquaticus results in radical expression increase  

PubMed Central

Background An industrial approach to protein production demands maximization of cloned gene expression, balanced with the recombinant host’s viability. Expression of toxic genes from thermophiles poses particular difficulties due to high GC content, mRNA secondary structures, rare codon usage and impairing the host’s coding plasmid replication. TaqII belongs to a family of bifunctional enzymes, which are a fusion of the restriction endonuclease (REase) and methyltransferase (MTase) activities in a single polypeptide. The family contains thermostable REases with distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI and a few enzymes found in mesophiles. While not being isoschizomers, the enzymes exhibit amino acid (aa) sequence homologies, having molecular sizes of ~120 kDa share common modular architecture, resemble Type-I enzymes, cleave DNA 11/9 nt from the recognition sites, their activity is affected by S-adenosylmethionine (SAM). Results We describe the taqIIRM gene design, cloning and expression of the prototype TaqII. The enzyme amount in natural hosts is extremely low. To improve expression of the taqIIRM gene in Escherichia coli (E. coli), we designed and cloned a fully synthetic, low GC content, low mRNA secondary structure taqIIRM, codon-optimized gene under a bacteriophage lambda (?) P R promoter. Codon usage based on a modified ‘one amino acid–one codon’ strategy, weighted towards low GC content codons, resulted in approximately 10-fold higher expression of the synthetic gene. 718 codons of total 1105 were changed, comprising 65% of the taqIIRM gene. The reason for we choose a less effective strategy rather than a resulting in high expression yields ‘codon randomization’ strategy, was intentional, sub-optimal TaqII in vivo production, in order to decrease the high ‘toxicity’ of the REase-MTase protein. Conclusions Recombinant wt and synthetic taqIIRM gene were cloned and expressed in E. coli. The modified ‘one amino acid–one codon’ method tuned for thermophile-coded genes was applied to obtain overexpression of the ‘toxic’ taqIIRM gene. The method appears suited for industrial production of thermostable ‘toxic’ enzymes in E. coli. This novel variant of the method biased toward increasing a gene’s AT content may provide economic benefits for industrial applications.

2014-01-01

184

Notational usage modulates attention networks in binumerates  

PubMed Central

Multicultural environments require learning multiple number notations wherein some are encountered more frequently than others. This leads to differences in exposure and consequently differences in usage between notations. We find that differential notational usage imposes a significant neurocognitive load on number processing. Despite simultaneous acquisition, twenty four adult binumerates, familiar with two positional writing systems namely Hindu Nagari digits and Hindu Arabic digits, reported significantly lower preference and usage for Nagari as compared to Arabic. Twenty-four participants showed significantly increased reaction times and reduced accuracy while performing magnitude comparison tasks in Nagari with respect to Arabic. Functional magnetic resonance imaging revealed that processing Nagari elicited significantly greater activity in number processing and attention networks. A direct subtraction of networks for Nagari and Arabic notations revealed a neural circuit comprising of bilateral Intra-parietal Sulcus (IPS), Inferior and Mid Frontal Gyri, Fusiform Gyrus and the Anterior Cingulate Cortex (FDR p < 0.005). Additionally, whole brain correlation analysis showed that activity in the left inferior parietal region was modulated by task performance in Nagari. We attribute the increased activation in Nagari to increased task difficulty due to infrequent exposure and usage. Our results reiterate the role of left IPS in modulating performance in numeric tasks and highlight the role of the attention network for monitoring symbolic notation mode in binumerates.

Koul, Atesh; Tyagi, Vaibhav; Singh, Nandini C.

2014-01-01

185

Exploring Codon Optimization and Response Surface Methodology to Express Biologically Active Transmembrane RANKL in E. coli  

PubMed Central

Receptor activator of nuclear factor (NF)-?B ligand (RANKL), a master cytokine that drives osteoclast differentiation, activation and survival, exists in both transmembrane and extracellular forms. To date, studies on physiological role of RANKL have been mainly carried out with extracellular RANKL probably due to difficulties in achieving high level expression of functional transmembrane RANKL (mRANKL). In the present study, we took advantage of codon optimization and response surface methodology to optimize the soluble expression of mRANKL in E. coli. We optimized the codon usage of mRANKL sequence to a preferred set of codons for E. coli changing its codon adaptation index from 0.64 to 0.76, tending to increase its expression level in E. coli. Further, we utilized central composite design to predict the optimum combination of variables (cell density before induction, lactose concentration, post-induction temperature and post-induction time) for the expression of mRANKL. Finally, we investigated the effects of various experimental parameters using response surface methodology. The best combination of response variables was 0.6 OD600, 7.5 mM lactose, 26°C post-induction temperature and 5 h post-induction time that produced 52.4 mg/L of fusion mRANKL. Prior to functional analysis of the protein, we purified mRANKL to homogeneity and confirmed the existence of trimeric form of mRANKL by native gel electrophoresis and gel filtration chromatography. Further, the biological activity of mRANKL to induce osteoclast formation on RAW264.7 cells was confirmed by tartrate resistant acid phosphatase assay and quantitative real-time polymerase chain reaction assays. Importantly, a new finding from this study was that the biological activity of mRANKL is higher than its extracellular counterpart. To the best of our knowledge, this is the first time to report heterologous expression of mRANKL in soluble form and to perform a comparative study of functional properties of both forms of RANKL.

Bok, Jin-Duck; Kim, Jeong-In; Jiang, Tao; Cho, Chong-Su; Kang, Sang-Kee; Choi, Yun-Jaie

2014-01-01

186

An evaluation of data-driven motion estimation in comparison to the usage of external-surrogates in cardiac SPECT imaging  

NASA Astrophysics Data System (ADS)

Motion estimation methods in single photon emission computed tomography (SPECT) can be classified into methods which depend on just the emission data (data-driven), or those that use some other source of information such as an external surrogate. The surrogate-based methods estimate the motion exhibited externally which may not correlate exactly with the movement of organs inside the body. The accuracy of data-driven strategies on the other hand is affected by the type and timing of motion occurrence during acquisition, the source distribution, and various degrading factors such as attenuation, scatter, and system spatial resolution. The goal of this paper is to investigate the performance of two data-driven motion estimation schemes based on the rigid-body registration of projections of motion-transformed source distributions to the acquired projection data for cardiac SPECT studies. Comparison is also made of six intensity based registration metrics to an external surrogate-based method. In the data-driven schemes, a partially reconstructed heart is used as the initial source distribution. The partially-reconstructed heart has inaccuracies due to limited angle artifacts resulting from using only a part of the SPECT projections acquired while the patient maintained the same pose. The performance of different cost functions in quantifying consistency with the SPECT projection data in the data-driven schemes was compared for clinically realistic patient motion occurring as discrete pose changes, one or two times during acquisition. The six intensity-based metrics studied were mean-squared difference, mutual information, normalized mutual information (NMI), pattern intensity (PI), normalized cross-correlation and entropy of the difference. Quantitative and qualitative analysis of the performance is reported using Monte-Carlo simulations of a realistic heart phantom including degradation factors such as attenuation, scatter and system spatial resolution. Further the visual appearance of motion-corrected images using data-driven motion estimates was compared to that obtained using the external motion-tracking system in patient studies. Pattern intensity and normalized mutual information cost functions were observed to have the best performance in terms of lowest average position error and stability with degradation of image quality of the partial reconstruction in simulations. In all patients, the visual quality of PI-based estimation was either significantly better or comparable to NMI-based estimation. Best visual quality was obtained with PI-based estimation in one of the five patient studies, and with external-surrogate based correction in three out of five patients. In the remaining patient study there was little motion and all methods yielded similar visual image quality.

Mitra Mukherjee, Joyeeta; Hutton, Brian F.; Johnson, Karen L.; Hendrik Pretorius, P.; King, Michael A.

2013-11-01

187

Feasibility Study of a Rotorcraft Health and Usage Monitoring System (HUMS): Usage and Structural Life Monitoring Evaluation  

NASA Technical Reports Server (NTRS)

The objective of this study was to evaluate two techniques, Flight Condition Recognition (FCR) and Flight Load Synthesis (FIS), for usage monitoring and assess the potential benefits of extending the retirement intervals of life-limited components, thus reducing the operator's maintenance and replacement costs. Both techniques involve indirect determination of loads using measured flight parameters and subsequent fatigue analysis to calculate the life expended on the life-limited components. To assess the potential benefit of usage monitoring, the two usage techniques were compared to current methods of component retirement. In addition, comparisons were made with direct load measurements to assess the accuracy of the two techniques.

Dickson, B.; Cronkhite, J.; Bielefeld, S.; Killian, L.; Hayden, R.

1996-01-01

188

Specific use of start codons and cellular localization of splice variants of human phosphodiesterase 9A gene  

PubMed Central

Background Phosphodiesterases are an important protein family that catalyse the hydrolysis of cyclic nucleotide monophosphates (cAMP and cGMP), second intracellular messengers responsible for transducing a variety of extra-cellular signals. A number of different splice variants have been observed for the human phosphodiesterase 9A gene, a cGMP-specific high-affinity PDE. These mRNAs differ in the use of specific combinations of exons located at the 5' end of the gene while the 3' half, that codes for the catalytic domain of the protein, always has the same combination of exons. It was observed that to deduce the protein sequence with the catalytic domain from all the variants, at least two ATG start codons have to be used. Alternatively some variants code for shorter non-functional polypeptides. Results In the present study, we expressed different splice variants of PDE9A in HeLa and Cos-1 cells with EGFP fluorescent protein in phase with the catalytic domain sequence in order to test the different start codon usage in each splice variant. It was found that at least two ATG start codons may be used and that the open reading frame that includes the catalytic domain may be translated. In addition the proteins produced from some of the splice variants are targeted to membrane ruffles and cellular vesicles while other variants appear to be cytoplasmic. A hypothesis about the functional meaning of these results is discussed. Conclusion Our data suggest the utilization of two different start codons to produce a variety of different PDE9A proteins, allowing specific subcellular location of PDE9A splice variants.

Rentero, Carles; Puigdomenech, Pere

2006-01-01

189

Identification of stop codon readthrough genes in Saccharomyces cerevisiae.  

PubMed

We specifically sought genes within the yeast genome controlled by a non-conventional translation mechanism involving the stop codon. For this reason, we designed a computer program using the yeast database genomic regions, and seeking two adjacent open reading frames separated only by a unique stop codon (called SORFs). Among the 58 SORFs identified, eight displayed a stop codon bypass level ranging from 3 to 25%. For each of the eight sequences, we demonstrated the presence of a poly(A) mRNA. Using isogenic [PSI(+)] and [psi(-)] yeast strains, we showed that for two of the sequences the mechanism used is a bona fide readthrough. However, the six remaining sequences were not sensitive to the PSI state, indicating either a translation termination process independent of eRF3 or a new stop codon bypass mechanism. Our results demonstrate that the presence of a stop codon in a large ORF may not always correspond to a sequencing error, or a pseudogene, but can be a recoding signal in a functional gene. This emphasizes that genome annotation should take into account the fact that recoding signals could be more frequently used than previously expected. PMID:12711673

Namy, Olivier; Duchateau-Nguyen, Guillemette; Hatin, Isabelle; Hermann-Le Denmat, Sylvie; Termier, Michel; Rousset, Jean-Pierre

2003-05-01

190

Codon Preference Optimization Increases Prokaryotic Cystatin C Expression  

PubMed Central

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.

Wang, Qing; Mei, Cui; Zhen, Honghua; Zhu, Jess

2012-01-01

191

Patterns of Teenage Computer Usage.  

ERIC Educational Resources Information Center

Describes the results of a study of computer usage at school and at home by 1,747 students between 14 and 18 years old in the United Kingdom. Highlights include gender differences and issues related to the developmental sequence in usage from computer games to more complete uses of computer facilities. (Author/LRW)

Fife-Schaw, C.; And Others

1986-01-01

192

Usage Management in Cloud Computing  

Microsoft Academic Search

User concerns regarding data handling within the cloud will gain increasing importance as cloud computing becomes more pervasive. Existing service level agreement (SLA) frameworks are not designed for flexibly handling even relatively straightforward usage policies. This paper introduces the notion and importance of usage management in cloud computing. It provides an analysis of features and challenges involved in deploying a

Pramod A. Jamkhedkar; Christopher C. Lamb; Gregory L. Heileman

2011-01-01

193

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons  

NASA Astrophysics Data System (ADS)

A key feature of mitochondrial translation is the reduced number of transfer RNAs and reassignment of codons. For human mitochondria, a major unresolved problem is how the set of stop codons are decoded by the release factors mtRF1a and mtRF1. Here we present three-dimensional structural models of human mtRF1a and mtRF1 based on their homology to bacterial RF1 in the codon recognition domain, and the strong conservation between mitochondrial and bacterial ribosomal RNA in the decoding region. Sequence changes in the less homologous mtRF1 appear to be correlated with specific features of the mitochondrial rRNA. Extensive computer simulations of the complexes with the ribosomal decoding site show that both mitochondrial factors have similar specificities and that neither reads the putative vertebrate stop codons AGA and AGG. Instead, we present a structural model for a mechanism by which the ICT1 protein causes termination by sensing the presence of these codons in the A-site of stalled ribosomes.

Lind, Christoffer; Sund, Johan; Åqvist, Johan

2013-12-01

194

Compositional nonrandomness upstream of start codons in archaebacteria  

Microsoft Academic Search

Since the regions directing transcriptional and translational initiation in archaebacteria are poorly characterized, the purpose of this study was to characterize them using measurements of nonrandomness upstream of start codons on eight fully sequenced archaebacterial genomes. Two distinctly different regions with conservation were identified. The location of the first corresponded well to the classical Shine–Dalgarno region (? peak), and the

Anders Fuglsang

2004-01-01

195

Marijuana Usage and Hypnotic Susceptibility  

ERIC Educational Resources Information Center

Anonymous self-reported drug usage data and hypnotic susceptibility scores were obtained from 282 college students. Frequent marijuana users (more than 10 times) showed greater susceptibility to hypnosis than nonusers. (Author)

Franzini, Louis R.; McDonald, Roy D.

1973-01-01

196

Trends in Usage of Chromium.  

National Technical Information Service (NTIS)

Contents: Chromium supply (World resources, World production, Government stockpile specifications, Conclusions); Metallurgical applications (Stainless, alloy, and tool steels; Heat- and corrosion-resistant materials, Usage of heat- and corrosion-resistant...

1970-01-01

197

The 'polysemous' codon--a codon with multiple amino acid assignment caused by dual specificity of tRNA identity.  

PubMed Central

In some Candida species, the universal CUG leucine codon is translated as serine. However, in most cases, the serine tRNAs responsible for this non-universal decoding (tRNA(Ser)CAG) accept in vitro not only serine, but also, to some extent, leucine. Nucleotide replacement experiments indicated that m1G37 is critical for leucylation activity. This finding was supported by the fact that the tRNA(Ser)CAGs possessing the leucylation activity always have m1G37, whereas that of Candida cylindracea, which possesses no leucylation activity, has A37. Quantification of defined aminoacetylated tRNAs in cells demonstrated that 3% of the tRNA(Ser)CAGs possessing m1G37 were, in fact, charged with leucine in vivo. A genetic approach using an auxotroph mutant of C.maltosa possessing this type of tRNA(Ser)CAG also suggested that the URA3 gene inactivated due to the translation of CUG as serine was rescued by a slight incorporation of leucine into the polypeptide, which demonstrated that the tRNA charged with multiple amino acids could participate in the translation. These findings provide the first evidence that two distinct amino acids are assigned by a single codon, which occurs naturally in the translation process of certain Candida species. We term this novel type of codon a 'polysemous codon'.

Suzuki, T; Ueda, T; Watanabe, K

1997-01-01

198

The Stringency of Start Codon Selection in the Filamentous Fungus Neurospora crassa*  

PubMed Central

In eukaryotic cells initiation may occur from near-cognate codons that differ from AUG by a single nucleotide. The stringency of start codon selection impacts the efficiency of initiation at near-cognate codons and the efficiency of initiation at AUG codons in different contexts. We used a codon-optimized firefly luciferase reporter initiated with AUG or each of the nine near-cognate codons in preferred context to examine the stringency of start codon selection in the model filamentous fungus Neurospora crassa. In vivo results indicated that the hierarchy of initiation at start codons in N. crassa (AUG ? CUG > GUG > ACG > AUA ? UUG > AUU > AUC) is similar to that in human cells. Similar results were obtained by translating mRNAs in a homologous N. crassa in vitro translation system or in rabbit reticulocyte lysate. We next examined the efficiency of initiation at AUG, CUG, and UUG codons in different contexts in vitro. The preferred context was more important for efficient initiation from near-cognate codons than from AUG. These studies demonstrated that near-cognate codons are used for initiation in N. crassa. Such events could provide additional coding capacity or have regulatory functions. Analyses of the 5?-leader regions in the N. crassa transcriptome revealed examples of highly conserved near-cognate codons in preferred contexts that could extend the N termini of the predicted polypeptides.

Wei, Jiajie; Zhang, Ying; Ivanov, Ivaylo P.; Sachs, Matthew S.

2013-01-01

199

Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from Molecular Dynamics Simulations  

Microsoft Academic Search

An ab initio model for gene prediction in prokaryotic genomes is proposed based on physicochemical characteristics of codons calculated from molecular dynamics (MD) simulations. The model requires a specification of three calculated quantities for each codon: the double-helical trinucleotide base pairing energy, the base pair stacking energy, and an index of the propensity of a codon for protein-nucleic acid interactions.

Poonam Singhal; B. Jayaram; Surjit B. Dixit; David L. Beveridge

2008-01-01

200

Following translation by single ribosomes one codon at a time  

Microsoft Academic Search

We have followed individual ribosomes as they translate single messenger RNA hairpins tethered by the ends to optical tweezers. Here we reveal that translation occurs through successive translocation-and-pause cycles. The distribution of pause lengths, with a median of 2.8s, indicates that at least two rate-determining processes control each pause. Each translocation step measures three bases-one codon-and occurs in less than

Jin-Der Wen; Laura Lancaster; Courtney Hodges; Ana-Carolina Zeri; Shige H. Yoshimura; Harry F. Noller; Carlos Bustamante; Ignacio Tinoco

2008-01-01

201

Rational protein sequence diversification by multi-codon scanning mutagenesis  

PubMed Central

Summary A new method for protein sequence diversification is based on generating random codon mutations to an encoding DNA. This allows for the scanning of user-defined amino acid changes to any protein of interest, and is an alternative to traditional directed evolution strategies. This chapter describes the procedures required to apply this technology to any protein of interested. The resulting libraries can then be screened for new or improved protein function.

Liu, Jia; Cropp, T. Ashton

2014-01-01

202

Feasibility Study of a Rotorcraft Health and Usage Monitoring System ( HUMS): Usage and Structural Life Monitoring Evaluation  

NASA Technical Reports Server (NTRS)

The objective of this study was to evaluate two techniques, Flight Condition Recognition (FCR) and Flight Load Synthesis (FLS), for usage monitoring and assess the potential benefits of extending the retirement intervals of life-limited components, thus reducing the operator's maintenance and replacement costs. Both techniques involve indirect determination of loads using measured flight parameters and subsequent fatigue analysis to calculate the life expended on the life-limited components. To assess the potential benefit of usage monitoring, the two usage techniques were compared to current methods of component retirement. In addition, comparisons were made with direct load measurements to assess the accuracy of the two techniques. The data that was used for the evaluation of the usage monitoring techniques was collected under an independent HUMS Flight trial program, using a commercially available HUMS and data recording system. The usage data collect from the HUMS trial aircraft was analyzed off-line using PC-based software that included the FCR and FLS techniques. In the future, if the technique prove feasible, usage monitoring would be incorporated into the onboard HUMS.

Dickson, B.; Cronkhite, J.; Bielefeld, S.; Killian, L.; Hayden, R.

1996-01-01

203

Translational Redefinition of UGA Codons Is Regulated by Selenium Availability*  

PubMed Central

Incorporation of selenium into ?25 mammalian selenoproteins occurs by translational recoding whereby in-frame UGA codons are redefined to encode the selenium containing amino acid, selenocysteine (Sec). Here we applied ribosome profiling to examine the effect of dietary selenium levels on the translational mechanisms controlling selenoprotein synthesis in mouse liver. Dietary selenium levels were shown to control gene-specific selenoprotein expression primarily at the translation level by differential regulation of UGA redefinition and Sec incorporation efficiency, although effects on translation initiation and mRNA abundance were also observed. Direct evidence is presented that increasing dietary selenium causes a vast increase in ribosome density downstream of UGA-Sec codons for a subset of selenoprotein mRNAs and that the selenium-dependent effects on Sec incorporation efficiency are mediated in part by the degree of Sec-tRNA[Ser]Sec Um34 methylation. Furthermore, we find evidence for translation in the 5?-UTRs for a subset of selenoproteins and for ribosome pausing near the UGA-Sec codon in those mRNAs encoding the selenoproteins most affected by selenium availability. These data illustrate how dietary levels of the trace element selenium can alter the readout of the genetic code to affect the expression of an entire class of proteins.

Howard, Michael T.; Carlson, Bradley A.; Anderson, Christine B.; Hatfield, Dolph L.

2013-01-01

204

Analyses of clinicopathological, molecular, and prognostic associations of KRAS codon 61 and codon 146 mutations in colorectal cancer: cohort study and literature review  

PubMed Central

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?codon, though statistical power was limited for codon 61 mutants. Neither KRAS codon 61 nor codon 146 mutation was significantly associated with clinical outcome or prognosis in univariate or multivariate analysis [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 further assess clinical utility of KRAS codon 61 and 146 testing, large-scale trials are warranted.

2014-01-01

205

Bacillus subtilis tRNA(Pro) with the anticodon mo5UGG can recognize the codon CCC.  

PubMed

In Bacillus subtilis, four codons, CCU, CCC, CCA, and CCG, are used for proline. There exists, however, only one proline-specific tRNA having the anticodon mo(5)UGG. Here, we found that this tRNA(Pro)(mo(5)UGG) can read not only the codons CCA, CCG and CCU but also CCC, using an in vitro assay system. This means that the first nucleoside of its anticodon, 5-methoxyuridine (mo(5)U), recognizes A, G, U and C. On the other hand, it was reported that mo(5)U at the first position of the anticodon of tRNA(Val)(mo(5)UAC) can recognize A, G, and U but not C. A comparison of the structure of the anticodon stem and loop of tRNA(Pro)(mo(5)UGG) with those of other tRNAs containing mo(5)U at the first positions of the anticodons suggests that a modification of nucleoside 32 to pseudouridine (Psi) enables tRNA(Pro)(mo(5)UGG) to read the CCC codon. PMID:15833716

Yamada, Yuko; Matsugi, Jitsuhiro; Ishikura, Hisayuki; Murao, Katsutoshi

2005-05-01

206

On the Usage of "Ms".  

ERIC Educational Resources Information Center

This paper is an overview of the introduction of "Ms." into language usage as part of the process of changing sexist language. Included are: (1) history of the term, (2) a discussion of the rationale for its introduction, (3) a report on the other suggested forms of address that do or do not specify sex and marital status, (4) a discussion of the…

Blaubergs, Maija S.

207

Users, Use, and Usage Statistics  

ERIC Educational Resources Information Center

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…

Grogg, Jill E.

2010-01-01

208

Code Usage Analysis System (CUAS)  

NASA Technical Reports Server (NTRS)

A set of computer programs is offered to aid a user in evaluating performance of an application program. The system provides reports of subroutine usage, program errors, and segment loading which occurred during the execution of an application program. It is presented in support of the development and validation of the space vehicle dynamics project.

Horsley, P. H.; Oliver, J. D.

1976-01-01

209

Health Usage Monitoring System Testing.  

National Technical Information Service (NTIS)

This TOP establishes the testing that will be performed to support certification by a cognitive agency and Health Usage Monitoring System (HUMS). Any system that is intended to be permanently installed on an aircraft and that will be used to perform maint...

2011-01-01

210

Modeling educational usage of Facebook  

Microsoft Academic Search

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 relationship between users' purposes in using Facebook

Sacide Güzin Mazman; Yasemin Koçak Usluel

2010-01-01

211

Lack of influence of MGMT codon Leu84Phe and codon Ileu143Val polymorphisms on esophageal cancer risk in the Kashmir Valley.  

PubMed

The enzyme encoded by the MGMT gene is involved in the repair of alkylated lesions formed in DNA by carcinogenic nitrosamines. Since dietary items consumed by the Kashmiri population contain high concentrations of these agents, it is biologically plausible that MGMT polymorphic variants may be associated with their risk of esophageal cancer. The present study was performed to assess whether non-synonymous SNPS at codon Leu84Phe and codon Ileu143Val of the MGMT gene, close to the active site of the protein, might be linked to predisposition of Kashmiris to esophageal cancer. Genotyping was carried out by polymerase chain reaction-restriction fragment length polymorphism on 92 cases and 77 healthy controls. Codon 84 and codon 143 SNPs of the MGMT gene were not associated with any increase in risk. While the frequency of the Phe allele at codon 84 in cases was (0.16), slightly higher than controls (0.12), the difference was not statistically significant. Similarly, the frequency of Valine allele in cases at codon 143 (0.08) and controls (0.09) was nearly equal. Moreover, no significant association of MGMT genotypes with the clinicopatholgic variables of esophageal cancer patients was observed. In conclusion, MGMT variants at codon 84 and codon143 may not be involved in the susceptibility of the Kashmiri population to esophageal cancer. PMID:22994708

Shah, Mohd A; Shaff, Sheikh M; Lone, Ghulam Nabi; Jan, Syed Mudassar

2012-01-01

212

Weather dissemination and public usage  

NASA Technical Reports Server (NTRS)

The existing public usage of weather information was examined. A survey was conducted to substantiate the general public's needs for dissemination of current (0-12 hours) weather information, needs which, in a previous study, were found to be extensive and urgent. The goal of the study was to discover how the general public obtains weather information, what information they seek and why they seek it, to what use this information is put, and to further ascertain the public's attitudes and beliefs regarding weather reporting and the diffusion of weather information. Major findings from the study include: 1. The public has a real need for weather information in the 0-6 hour bracket. 2. The visual medium is preferred but due to the lack of frequent (0-6 hours) forecasts, the audio media only, i.e., telephone recordings and radio weathercasts, were more frequently used. 3. Weather information usage is sporadic.

Stacey, M. S.

1973-01-01

213

ARUM: Application Resource Usage Monitor  

Microsoft Academic Search

We present the design and initial implementation of ARUM, an Application Resource Usage Monitor for multi-core and multi-processor AMD and Intel systems running the Linux operating system. ARUM is a lightweight, easy-to-use tool that operates on unmodified binaries, requires no kernel modifications or special user privileges to support access to hardware counters, and is designed to measure both system level

Rashawn L. Knapp; Douglas M. Pase; Karen L. Karavanic

214

Efficient initiation of mammalian mRNA translation at a CUG codon.  

PubMed Central

Nucleotide substitutions were made at the initiation codon of an influenza virus NS cDNA clone in a vector carrying the bacteriophage T7 promoter. When capped mRNA transcripts of these constructs were translated in the rabbit reticulocyte lysate, a change in the initiation codon from...AUAAUGG...to...AUACUGG...reduced the in vitro translational efficiency by only 50-60%, and resulted in only a small increase in the yield of short products presumed to be initiated at downstream sites. Synthesis of the full-length product was initiated exclusively at the mutated codon, with negligible use either of in-frame upstream CUG or GUG codons, or of an in-frame downstream GUG codon. We conclude that CUG has the potential to function as an efficient initiation codon in mammalian systems, at least in certain contexts. Images

Dasso, M C; Jackson, R J

1989-01-01

215

Opportunistic Resource Usage in CMS  

NASA Astrophysics Data System (ADS)

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.

Kreuzer, Peter; Hufnagel, Dirk; Dykstra, D.; Gutsche, O.; Tadel, M.; Sfiligoi, I.; Letts, J.; Wuerthwein, F.; McCrea, A.; Bockelman, B.; Fajardo, E.; Linares, L.; Wagner, R.; Konstantinov, P.; Blumenfeld, B.; Bradley, D.; Cms Collaboration

2014-06-01

216

Premature Stop Codon in MMP20 Causing Amelogenesis Imperfecta  

PubMed Central

Proteolytic enzymes are necessary for the hardening of dental enamel during development, and mutations in the kallikrein 4 (KLK4) and enamelysin (MMP20) genes cause autosomal recessive amelogenesis imperfecta (ARAI). So far, only one KLK4 and two MMP20 mutations have been reported. We have identified an ARAI-causing point mutation (c.l02G>A, g.l02G>A, and p.W34X) in exon 1 of MMP20 in a proband with autosomal recessive hypoplastic-hypomaturation amelogenesis imperfecta. The G to A transition changes the tryptophan (W) codon (TGG) at amino acid position 34 into a translation termination (X) codon (TGA). No disease-causing sequence variations were detected in KLK4. The affected enamel is thin, with mild spacing in the anterior dentition. The enamel layer is hypomineralized, does not contrast with dentin on radiographs, and tends to chip away from the underlying dentin. An intrinsic yellowish pigmentation is evident even during eruption. The phenotype supports current ideas concerning the function of enamelysin.

Papagerakis, P.; Lin, H-K.; Lee, K. Y.; Hu, Y.; Simmer, J. P.; Bartlett, J. D.; Hu, J. C-C

2009-01-01

217

Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons  

Microsoft Academic Search

The use of several translation initiation codons in a single mRNA, by expressing several proteins from a single gene, contributes to the generation of protein diversity. A small, yet growing, number of mammalian mRNAs initiate translation from a non-AUG codon, in addition to initiating at a downstream in-frame AUG codon. Translation initiation on such mRNAs results in the synthesis of

Christian Touriol; Stéphanie Bornes; Sophie Bonnal; Sylvie Audigier; Hervé Prats; Anne-Catherine Prats; Stéphan Vagner

2003-01-01

218

On Negative Selection Against ATG Triplets Near Start Codons in Eukaryotic and Prokaryotic Genomes  

Microsoft Academic Search

.   The frequencies of ATG triplets in the genomes of various species were systematically analyzed, and the frequency of ATG\\u000a triplets was significantly low around start codons in both prokaryotic and eukaryotic genomes. In eukaryotes, however, the\\u000a frequency decrease before the start codon is much more evident than that after the start codon. In prokaryotes, on the other\\u000a hand, the

Rintaro Saito; Masaru Tomita

1999-01-01

219

Patterns of codon recognition by isoacceptor aminoacyl-tRNAs from wheat germ.  

PubMed Central

Isoacceptors of Ala-, Arg-, Glu-, Gln-, Ile-, Leu-, Lys-, Ser-, Thr- and Val-tRNAs from wheat germ have been resolved by reverse phast chromatography. Codon recognition properties have been determined on isolated fractions of each of these aa-tRNAs and codon assignments have been made to a number of isoacceptors. Evolutionary changes which have occurred in patterns of codon recognition by isoacceptor aa-tRNAs in wheat germ and other organisms are discussed.

Hatfield, D; Rice, M

1978-01-01

220

Rationalization and prediction of selective decoding of pseudouridine-modified nonsense and sense codons.  

PubMed

A stop or nonsense codon is an in-frame triplet within a messenger RNA that signals the termination of translation. One common feature shared among all three nonsense codons (UAA, UAG, and UGA) is a uridine present at the first codon position. It has been recently shown that the conversion of this uridine into pseudouridine (?) suppresses translation termination, both in vitro and in vivo. Furthermore, decoding of the pseudouridylated nonsense codons is accompanied by the incorporation of two specific amino acids in a nonsense codon-dependent fashion. ? differs from uridine by a single N¹H group at the C5 position; how ? suppresses termination and, more importantly, enables selective decoding is poorly understood. Here, we provide molecular rationales for how pseudouridylated stop codons are selectively decoded. Our analysis applies crystal structures of ribosomes in varying states of translation to consider weakened interaction of ? with release factor; thermodynamic and geometric considerations of the codon-anticodon base pairs to rank and to eliminate mRNA-tRNA pairs; the mechanism of fidelity check of the codon-anticodon pairing by the ribosome to evaluate noncanonical codon-anticodon base pairs and the role of water. We also consider certain tRNA modifications that interfere with the ?-coordinated water in the major groove of the codon-anticodon mini-helix. Our analysis of nonsense codons enables prediction of potential decoding properties for ?-modified sense codons, such as decoding ?UU potentially as Cys and Tyr. Our results provide molecular rationale for the remarkable dynamics of ribosome decoding and insights on possible reprogramming of the genetic code using mRNA modifications. PMID:22282339

Parisien, Marc; Yi, Chengqi; Pan, Tao

2012-03-01

221

Cognitive performance of patients with mesial temporal lobe epilepsy is not associated with human prion protein gene variant allele at codons 129 and 171.  

PubMed

Cognitive impairment has long been recognized in people with medically refractory epilepsies. Mesial temporal lobe epilepsy related to hippocampal sclerosis (MTLE-HS), the most common surgically remediable epileptic syndrome, has been associated with a cellular prion protein (PrPc) gene (Prnp) variant allele at codon 171. The polymorphism consisting of a methionine-for-valine substitution at codon 129 has been associated with early cognitive deterioration in elderly people and patients with Down syndrome. The same variant allele in homozygosis (V129V) has been associated to a lower long-term memory in healthy humans. PrPc mediates several processes related to neuroplasticity, and its role in cognitive processes remains unknown. In this study, we evaluated the genetic contribution of Prnp alleles to cognitive performance in patients with MTLE-HS. Cognitive performance, measured with 19 neuropsychological tests, of patients with refractory MTLE-HS with the normal Prnp genotypes was compared with that of patients with the variant alleles at codons 129 and 171. With the effects of clinical, demographic, electrophysiological, and neuroimaging variable interactions controlled by multiple linear regression analysis and adjustment for multiple test comparisons, the presence of Prnp variant alleles was found not to be significantly associated to cognitive performance of patients with MTLE-HS. The presence of variant alleles at codons 129 and 171 is not associated to cognitive performance of patients with refractory MTLE-HS. PMID:16580884

Coimbra, Erica R; Rezek, Karinne; Escorsi-Rosset, Sara; Landemberger, Michele C; Castro, Rosa M R P S; Valadão, Michelle N; Guarnieri, Ricardo; Velasco, Tonicarlo R; Terra-Bustamante, Vera C; Bianchin, Marino M; Wichert-Ana, Lauro; Alexandre, Veriano; Brentani, Ricardo R; Martins, Vilma R; Sakamoto, Américo C; Walz, Roger

2006-05-01

222

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

SciTech Connect

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.

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

1996-04-01

223

Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs  

PubMed Central

Translational stop codon readthrough provides a regulatory mechanism of gene expression that is extensively utilised by positive-sense ssRNA viruses. The misreading of termination codons is achieved by a variety of naturally occurring suppressor tRNAs whose structure and function is the subject of this survey. All of the nonsense suppressors characterised to date (with the exception of selenocysteine tRNA) are normal cellular tRNAs that are primarily needed for reading their cognate sense codons. As a consequence, recognition of stop codons by natural suppressor tRNAs necessitates unconventional base pairings in anticodon–codon interactions. A number of intrinsic features of the suppressor tRNA contributes to the ability to read non-cognate codons. Apart from anticodon–codon affinity, the extent of base modifications within or 3? of the anticodon may up- or down-regulate the efficiency of suppression. In order to out-compete the polypeptide chain release factor an absolute prerequisite for the action of natural suppressor tRNAs is a suitable nucleotide context, preferentially at the 3? side of the suppressed stop codon. Three major types of viral readthrough sites, based on similar sequences neighbouring the leaky stop codon, can be defined. It is discussed that not only RNA viruses, but also the eukaryotic host organism might gain some profit from cellular suppressor tRNAs.

Beier, Hildburg; Grimm, Michael

2001-01-01

224

Web Usage Mining: Discovery and Applications of Usage Patterns from Web Data  

Microsoft Academic Search

Web usage mining is the application of data mining techniques to discover usage patterns from Web data, in order to understand and better serve the needs of Web-based applications. Web usage mining consists of three phases, namely . This paper describes each of these phases in detail. Given its application potential, Web usage mining has seen a rapid increase in

Jaideep Srivastava; Robert Cooley; Mukund Deshpande; Pang-Ning Tan

2000-01-01

225

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

SciTech Connect

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

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

1993-10-01

226

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

PubMed Central

Fatal familial insomnia (FFI) is a disease linked to a GAC(Asp)-->AAC(Asn) mutation in codon 178 of the prion protein (PrP) gene. FFI is characterized clinically by untreatable progressive insomnia, dysautonomia, and motor dysfunctions and is characterized pathologically by selective thalamic atrophy. We confirmed the 178Asn mutation in the PrP gene of a third FFI family of French ancestry. Three family members who are under 40 years of age and who inherited the mutation showed only reduced perfusion in the basal ganglia on single photon emission computerized tomography. Some FFI features differ from the clinical and neuropathologic findings associated with 178Asn reported elsewhere. However, additional intragenic mutations accounting for the phenotypic differences were not observed in two affected individuals. In other sporadic and familial forms of Creutzfeldt-Jakob disease and Gerstmann-Sträussler syndrome, Met or Val homozygosity at polymorphic codon 129 is associated with a more severe phenotype, younger age at onset, and faster progression. In FFI, young and old individuals at disease onset had 129Met/Val. Moreover, of five 178Asn individuals who are above age-at-onset range and who are well, two have 129Met and three have 129Met/Val, suggesting that polymorphic site 129 does not modulate FFI phenotypic expression. Genetic heterogeneity and environment may play an important role in inter- and intrafamilial variability of the 178Asn mutation. Images Figure 2 Figure 3 Figure 4 Figure 5

Medori, R; Tritschler, H J

1993-01-01

227

Analysis of codon:anticodon interactions within the ribosome provides new insights into codon reading and the genetic code structure.  

PubMed Central

Although the decoding rules have been largely elucidated, the physical-chemical reasons for the "correctness" of codon:anticodon duplexes have never been clear. In this work, on the basis of the available data, we propose that the correct codon:anticodon duplexes are those whose formation and interaction with the ribosomal decoding center are not accompanied by uncompensated losses of hydrogen and ionic bonds. Other factors such as proofreading, base-base stacking and aminoacyl-tRNA concentration contribute to the efficiency and accuracy of aminoacyl-tRNA selection, and certainly these factors are important; but we suggest that analyses of hydrogen and ionic bonding alone provides a robust first-order approximation of decoding accuracy. Thus our model can simplify predictions about decoding accuracy and error. The model can be refined with data, but is already powerful enough to explain all of the available data on decoding accuracy. Here we predict which duplexes should be considered correct, which duplexes are responsible for virtually all misreading, and we suggest an evolutionary scheme that gave rise to the mixed boxes of the genetic code.

Lim, V I; Curran, J F

2001-01-01

228

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

PubMed

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. PMID:24772979

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

2013-12-01

229

Virus-Host Coevolution: Common Patterns of Nucleotide Motif Usage in Flaviviridae and Their Hosts  

PubMed Central

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 possess 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 lineages appear to be subject to the same evolutionary pressures that shaped their host coding regions, evidencing the lineage-specific coevolutionary processes between the viral and host groups.

Lobo, Francisco P.; Mota, Bruno E. F.; Pena, Sergio D. J.; Azevedo, Vasco; Macedo, Andrea M.; Tauch, Andreas; Machado, Carlos R.; Franco, Gloria R.

2009-01-01

230

Double mutations at codon 180 and codon 232 of the PRNP gene in an apparently sporadic case of Creutzfeldt-Jakob disease.  

PubMed

Several polymorphisms of the prion protein gene are associated with the occurrence of familial Creutzfeldt-Jakob disease. We described a 84-year-old Japanese man with neuropathologically verified Creutzfeldt-Jakob disease of apparently sporadic type. His clinical presentation was atypical in point of a very late age at onset and absence of periodic synchronous discharge on electroencephalography. The patient carried double hitherto undescribed mutations of the prion protein gene; at codon 180 on one allele and at codon 232 on another. The mutation at codon 180 abolishes the Tth111I cutting site, which may be misunderstood to represent codon 178 mutation on routine restriction fragment length polymorphism study. PMID:8138811

Hitoshi, S; Nagura, H; Yamanouchi, H; Kitamoto, T

1993-12-15

231

Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast  

PubMed Central

Recent analysis of genomic signatures in mammals, flies, and worms indicates that functional translational stop codon readthrough is considerably more abundant in metazoa than previously recognized, but this analysis provides only limited clues about the function or mechanism of readthrough. If an mRNA known to be read through in one species is also read through in another, perhaps these questions can be studied in a simpler setting. With this end in mind, we have investigated whether some of the readthrough genes in human, fly, and worm also exhibit readthrough when expressed in S. cerevisiae. We found that readthrough was highest in a gene with a post-stop hexamer known to trigger readthrough, while other metazoan readthrough genes exhibit borderline readthrough in S. cerevisiae.

Chan, Clara S.; Jungreis, Irwin; Kellis, Manolis

2013-01-01

232

Henipavirus Receptor Usage and Tropism  

PubMed Central

Nipah (NiV) and Hendra (HeV) viruses are the deadliest human pathogens within the Paramyxoviridae family, which include human and animal pathogens of global biomedical importance. NiV and HeV infections cause respiratory and encephalitic illness with high mortality rates in humans. Henipaviruses (HNV) are the only paramyxoviruses classified as biosafety level 4 (BSL4) pathogens due to their extreme pathogenicity, potential for bioterrorism, and lack of licensed vaccines and therapeutics. HNV use ephrin-B2 and ephrin-B3, highly conserved proteins, as viral entry receptors. This likely accounts for their unusually broad species tropism, and also provides opportunities to study how receptor usage, cellular tropism, and end-organ pathology relates to the pathobiology of HNV infections. The clinical and pathologic manifestations of Nipah and Hendra virus infections are reviewed in the chapters by Wong et. al. and Geisbert et.al. in this issue. Here, we will review the biology of the henipavirus receptors, and how receptor usage relates to henipavirus cell tropism in vitro and in vivo.

Pernet, Olivier; Lee, Benhur

2013-01-01

233

Short spacing between the Shine-Dalgarno sequence and P codon destabilizes codon-anticodon pairing in the P site to promote +1 programmed frameshifting  

PubMed Central

Summary Programmed frameshifting in the RF2 gene (prfB) involves an intragenic Shine-Dalgarno (SD) sequence. To investigate the role of SD-ASD pairing in the mechanism of frameshifting, we have analyzed the effect of spacing between the SD sequence and P codon on P-site tRNA binding and RF2-dependent termination. When the spacing between an extended SD sequence and the P codon is decreased from 4 to 1 nucleotides (nt), the dissociation rate (koff) for P-site tRNA increases by >100-fold. Toeprinting analysis shows that pretranslocation complexes cannot be formed when the spacer sequence is ? 2 nt. Instead, the tRNA added secondarily to fill the A site and its corresponding codon move spontaneously into the P site, resulting in a complex with a 3-nt longer spacer between the SD-ASD helix and the P codon. While close proximity of the SD clearly destabilizes P-site tRNA, RF2-dependent termination and EF-Tu-dependent decoding are largely unaffected in analogous complexes. These data support a model in which formation of the SD-ASD helix in ribosomes stalled at the in-frame UGA codon of prfB generates tension on the mRNA that destabilizes codon-anticodon pairing in the P site and promotes slippage of the mRNA in the 5? direction.

Devaraj, Aishwarya; Fredrick, Kurt

2010-01-01

234

A Study of the purine\\/pyrimidine codon occurrence with a reduced centered variable and an evaluation compared to the frequency statistic  

Microsoft Academic Search

With the three-letter alphabet {R,Y,N} (R = purine, Y = pyrimidine, N= R or Y), there are 26 codons (NNN being excluded): RNN, . ,NNY (six codons at two unspecified bases N), RRN,. ,NYY (12 codons at one unspecified base N), RRR ,.._, YYY (eight specified codons). A statistical methodology that uses the codon frequency and a reduced centered variable

CHRISTIAN J. MICHEL

1989-01-01

235

Downstream Secondary Structure Facilitates Recognition of Initiator Codons by Eukaryotic Ribosomes  

Microsoft Academic Search

Recognition of an AUG initiator codon in a suboptimal context improves when a modest amount of secondary structure is introduced near the beginning of the protein-coding sequence. This facilitating effect depends on the position of the downstream stem-loop (hairpin) structure. The strongest facilitation is seen when the hairpin is separated from the preceding AUG codon by 14 nucleotides. Because 14

Marilyn Kozak

1990-01-01

236

Frameshift suppression at tandem AGA and AGG codons by cloned tRNA genes: assigning a codon to argU tRNA and T4 tRNA(Arg).  

PubMed Central

Arginine is coded for by CGN (N = G, A, U, C), AGA and AGG. In Escherichia coli there is little tRNA for AGA and AGG and the use of these codons is strongly avoided in virtually all genes. Recently, we demonstrated that the presence of tandem AGA or AGG codons in mRNA causes frameshifts with high frequency. Here, we show that phaseshifts can be suppressed when cells are transformed with the gene for tRNA(T4Arg) or E. coli tRNA(argU,Arg) demonstrating that such errors are the result of tRNA depletion. Bacteriophage T4 encoded tRNA(Arg) (anticodon UCU) corrects shifts at AGA-AGA but not at AGG-AGG, suggesting that this tRNA can only read AGA. Similarly, comparison of the translational efficiencies in an argU (Ts) mutant and in its isogenic wild type parent indicates that argU tRNA (anticodon UCU) reads AGA but not AGG. An argU (Ts) mutant barely reads through AGA-AGA at 42 degrees C but translation of AGG-AGG is hardly, if at all, affected. Overexpression of argU+ relaxes the codon specificity. The thermosensitive mutant in argU, previously called dnaY because it is defective in DNA replication, can be complemented for growth by the gene for tRNA(T4Arg). This implies that the sole function of the argU gene product is to sustain protein synthesis and that its role in replication is probably indirect. Images

Spanjaard, R A; Chen, K; Walker, J R; van Duin, J

1990-01-01

237

Impact of the six nucleotides downstream of the stop codon on translation termination.  

PubMed

The efficiency of translation termination is influenced by local contexts surrounding stop codons. In Saccharomyces cerevisiae, upstream and downstream sequences act synergistically to influence the translation termination efficiency. By analysing derivatives of a leaky stop codon context, we initially demonstrated that at least six nucleotides after the stop codon are a key determinant of readthrough efficiency in S. cerevisiae. We then developed a combinatorial-based strategy to identify poor 3' termination contexts. By screening a degenerate oligonucleotide library, we identified a consensus sequence -CA(A/G)N(U/C/G)A-, which promotes >5% readthrough efficiency when located downstream of a UAG stop codon. Potential base pairing between this stimulatory motif and regions close to helix 18 and 44 of the 18S rRNA provides a model for the effect of the 3' stop codon context on translation termination. PMID:11520858

Namy, O; Hatin, I; Rousset, J P

2001-09-01

238

NASA C-17 Usage Overview  

NASA Technical Reports Server (NTRS)

The usage and integrated vehicle health management of the NASA C-17. Propulsion health management flight objectives for the aircraft include mapping of the High Pressure Compressor in order to calibrate a Pratt and Whitney engine model and the fusion of data collected from existing sensors and signals to develop models, analysis methods and information fusion algorithms. An additional health manage flight objective is to demonstrate that the Commercial Modular Aero-Propulsion Systems Simulation engine model can successfully execute in real time onboard the C-17 T-1 aircraft using engine and aircraft flight data as inputs. Future work will address aircraft durability and aging, airframe health management, and propulsion health management research in the areas of gas path and engine vibration.

Miller, Christopher R.

2008-01-01

239

Association of Vancomycin-Resistant Enterococcus Bacteremia and Ceftriaxone Usage  

PubMed Central

Objective Vancomycin-resistant Enterococci (VRE) have become a public health concern with implications for patient mortality and costs. Hospital antibiotic usage may impact VRE incidence, but the relationship is poorly understood. Animal investigations suggest ceftriaxone may be associated with VRE proliferation. We measured antimicrobial usage and VRE bloodstream infection (BSI) incidence to test our hypothesis that increased ceftriaxone use would be associated with a higher incidence of VRE-BSI. Setting The University of Alabama at Birmingham Medical Center is a 900-bed urban tertiary-care hospital Methods Retrospective analysis of antimicrobial usage and VRE-BSI from 2005 to 2008 (43 months). Antimicrobial usage quantified as days of therapy/1,000 patient-days (DOT). VRE-BSI incidence calculated as cases/1,000 patient-days. Negative binomial regression with adjustment for correlation between consecutive observations measured the association between antimicrobial usage and VRE-BSI incidence at the hospital- and care-unit levels. Results VRE-BSI incidence increased from 0.06 to 0.17 infections/1,000 patient-days. Hospital VRE-BSI incidence was associated with prior-month ceftriaxone DOT (Incidence Rate Ratio 1.38 per 10 DOT; p=0.005). After controlling for ceftriaxone, prior-month cephalosporin use (class) was not predictive of VRE-BSI (p=0.70). Similarly, prior-month use of piperacillin-tazobactam, ceftazidime, cefepime, cefazolin, or vancomycin was not predictive of VRE-BSI when considered individually (p?0.4 for all comparisons). The final model suggests that type of intensive care unit was related to VRE-BSI incidence. Conclusions Ceftriaxone use in the prior month, but not cephalosporin (class) or vancomycin use, was related to VRE-BSI incidence. These findings suggest that an antimicrobial stewardship program that limits ceftriaxone may reduce nosocomial VRE-BSI incidence.

McKinnell, James A.; Kunz, Danielle F.; Chamot, Eric; Patel, Mukesh; Shirley, Rhett M.; Moser, Stephen A.; Baddley, John W.; Pappas, Peter G.; Miller, Loren G.

2013-01-01

240

Sensitive allele-specific real-time PCR test for mutations in BRAF codon V600 in skin melanoma.  

PubMed

Mutations at BRAF codon V600 are used as predictive biomarkers for targeted therapy of skin melanoma. Here, a simple sensitive test to detect mutations of BRAF-V600 was developed using real-time PCR with allele-specific primers and TaqMan probes. Two versions of the test using sense and antisense allele-specific primers were designed and evaluated. The test detected 1% mutant allele V600E/K in 10?ng DNA standard made from wild-type human DNA spiked with BRAF-V600E or the V600K plasmid. The test was validated on clinical formalin-fixed paraffin-embedded samples of skin melanoma using pyrosequencing as a reference method. In the clinical samples, we detected the common mutation V600E, as well as the rare mutations V600K, V600E2 (codon GAA), V600E2 K601del, V600D-K601del, and V600R. In comparison with pyrosequencing, both versions of the test had 100% specificity with sensitivities of 97 and 86% for sense and antisense allele-specific primers, respectively. Using the PCR test with sense allele-specific primers, mutations in V600 were found in 33 of 51 Russian patients (64.7%) with cutaneous melanoma. This closed-tube real-time PCR test can be used as a simple and sensitive assay for mutations of BRAF-V600 in cutaneous melanoma. PMID:24922189

Pisareva, Ekaterina; Gutkina, Nadezhda; Kovalenko, Sergei; Kuehnapfel, Sarah; Hartmann, Arndt; Heinzerling, Lucie; Schneider-Stock, Regine; Lyubchenko, Lyudmila; Shamanin, Vladimir A

2014-08-01

241

GNAS codon 201 mutations are uncommon in intraductal papillary neoplasms of the bile duct  

PubMed Central

Background Activating point mutations of GNAS at codon 201 have been detected in approximately two thirds of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas. Intraductal papillary neoplasms of the bile ducts (IPNBs) morphologically resemble pancreatic IPMNs. This study sought to assess the mutational status of GNAS at codon 201 in IPNBs. Methods Thirty-four patients were included. DNA from microdissected IPNBs was subjected to a polymerase chain reaction and ligation method for the detection of GNAS mutations at codon 201 and of KRAS mutations at codon 12. Mutational status was compared with clinical and pathologic data. Results The IPNBs had a median diameter of 3.5 cm and were located intrahepatically (n= 6), extrahepatically (n= 13), both intra- and extrahepatically (n= 4) or in the gallbladder (intracystic papillary neoplasms, n= 11). Most exhibited pancreatobiliary differentiation (n= 20), high-grade dysplasia (n= 26) and an associated adenocarcinoma (n= 20). Analysis of GNAS codon 201 identified only one mutant sample in a multifocal intestinal subtype intrahepatic IPNB with high-grade dysplasia. Six lesions harboured a KRAS codon 12 mutation. Conclusions GNAS codon 201 mutations are uncommon in IPNBs, by contrast with pancreatic IPMNs. More comprehensive molecular profiling is needed to uncover the pathways involved in IPNB development.

Matthaei, Hanno; Wu, Jian; Dal Molin, Marco; Debeljak, Marija; Lingohr, Philipp; Katabi, Nora; Klimstra, David S; Adsay, N Volkan; Eshleman, James R; Schulick, Richard D; Kinzler, Kenneth W; Vogelstein, Bert; Hruban, Ralph H; Maitra, Anirban

2012-01-01

242

The unfolded protein response affects readthrough of premature termination codons.  

PubMed

One-third of monogenic inherited diseases result from premature termination codons (PTCs). Readthrough of in-frame PTCs enables synthesis of full-length functional proteins. However, extended variability in the response to readthrough treatment is found among patients, which correlates with the level of nonsense transcripts. Here, we aimed to reveal cellular pathways affecting this inter-patient variability. We show that activation of the unfolded protein response (UPR) governs the response to readthrough treatment by regulating the levels of transcripts carrying PTCs. Quantitative proteomic analyses showed substantial differences in UPR activation between patients carrying PTCs, correlating with their response. We further found a significant inverse correlation between the UPR and nonsense-mediated mRNA decay (NMD), suggesting a feedback loop between these homeostatic pathways. We uncovered and characterized the mechanism underlying this NMD-UPR feedback loop, which augments both UPR activation and NMD attenuation. Importantly, this feedback loop enhances the response to readthrough treatment, highlighting its clinical importance. Altogether, our study demonstrates the importance of the UPR and its regulatory network for genetic diseases caused by PTCs and for cell homeostasis under normal conditions. PMID:24705877

Oren, Yifat S; McClure, Michelle L; Rowe, Steven M; Sorscher, Eric J; Bester, Assaf C; Manor, Miriam; Kerem, Eitan; Rivlin, Joseph; Zahdeh, Fouad; Mann, Matthias; Geiger, Tamar; Kerem, Batsheva

2014-05-01

243

The unfolded protein response affects readthrough of premature termination codons  

PubMed Central

One-third of monogenic inherited diseases result from premature termination codons (PTCs). Readthrough of in-frame PTCs enables synthesis of full-length functional proteins. However, extended variability in the response to readthrough treatment is found among patients, which correlates with the level of nonsense transcripts. Here, we aimed to reveal cellular pathways affecting this inter-patient variability. We show that activation of the unfolded protein response (UPR) governs the response to readthrough treatment by regulating the levels of transcripts carrying PTCs. Quantitative proteomic analyses showed substantial differences in UPR activation between patients carrying PTCs, correlating with their response. We further found a significant inverse correlation between the UPR and nonsense-mediated mRNA decay (NMD), suggesting a feedback loop between these homeostatic pathways. We uncovered and characterized the mechanism underlying this NMD-UPR feedback loop, which augments both UPR activation and NMD attenuation. Importantly, this feedback loop enhances the response to readthrough treatment, highlighting its clinical importance. Altogether, our study demonstrates the importance of the UPR and its regulatory network for genetic diseases caused by PTCs and for cell homeostasis under normal conditions.

Oren, Yifat S; McClure, Michelle L; Rowe, Steven M; Sorscher, Eric J; Bester, Assaf C; Manor, Miriam; Kerem, Eitan; Rivlin, Joseph; Zahdeh, Fouad; Mann, Matthias; Geiger, Tamar; Kerem, Batsheva

2014-01-01

244

Suppression of premature termination codons as a therapeutic approach.  

PubMed

In this review, we describe our current understanding of translation termination and pharmacological agents that influence the accuracy of this process. A number of drugs have been identified that induce suppression of translation termination at in-frame premature termination codons (PTCs; also known as nonsense mutations) in mammalian cells. We discuss efforts to utilize these drugs to suppress disease-causing PTCs that result in the loss of protein expression and function. In-frame PTCs represent a genotypic subset of mutations that make up ~11% of all known mutations that cause genetic diseases, and millions of patients have diseases attributable to PTCs. Current approaches aimed at reducing the efficiency of translation termination at PTCs (referred to as PTC suppression therapy) have the goal of alleviating the phenotypic consequences of a wide range of genetic diseases. Suppression therapy is currently in clinical trials for treatment of several genetic diseases caused by PTCs, and preliminary results suggest that some patients have shown clinical improvements. While current progress is promising, we discuss various approaches that may further enhance the efficiency of this novel therapeutic approach. PMID:22672057

Keeling, Kim M; Wang, Dan; Conard, Sara E; Bedwell, David M

2012-09-01

245

NECTAR: a database of codon-centric missense variant annotations.  

PubMed

NECTAR (Non-synonymous Enriched Coding muTation ARchive; http://nectarmutation.org) is a database and web application to annotate disease-related and functionally important amino acids in human proteins. A number of tools are available to facilitate the interpretation of DNA variants identified in diagnostic or research sequencing. These typically identify previous reports of DNA variation at a given genomic location, predict its effects on transcript and protein sequence and may predict downstream functional consequences. Previous reports and functional annotations are typically linked by the genomic location of the variant observed. NECTAR collates disease-causing variants and functionally important amino acid residues from a number of sources. Importantly, rather than simply linking annotations by a shared genomic location, NECTAR annotates variants of interest with details of previously reported variation affecting the same codon. This provides a much richer data set for the interpretation of a novel DNA variant. NECTAR also identifies functionally equivalent amino acid residues in evolutionarily related proteins (paralogues) and, where appropriate, transfers annotations between them. As well as accessing these data through a web interface, users can upload batches of variants in variant call format (VCF) for annotation on-the-fly. The database is freely available to download from the ftp site: ftp://ftp.nectarmutation.org. PMID:24297257

Gong, Sungsam; Ware, James S; Walsh, Roddy; Cook, Stuart A

2014-01-01

246

Definite Article Usage across Varieties of English  

ERIC Educational Resources Information Center

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…

Wahid, Ridwan

2013-01-01

247

Active guidance towards proper cane usage  

Microsoft Academic Search

The usage of conventional assistive cane devices is critical in reducing the risk of falls, which are particularly detrimental to the elderly and disabled. Individuals that experience the greatest risks rely on cane devices for support of ambulation. Results of many studies, however, have shown that incorrect cane usage is prevalent among cane users. The original SmartCane assistive system has

Lawrence K. Au; Winston H. Wu; Maxim A. Batalin; William J. Kaiser

2008-01-01

248

Food Supplement Usage by Adolescent Males.  

ERIC Educational Resources Information Center

Adolescent males (N=568) responded to a questionnaire examining their food supplement usage, types of food supplements consumed, reasons for use and non-use, relationship of use to concern for health, and demographic and external factors influencing supplement use. Presents factors related to food supplement usage. (RC)

Fleischer, Barbara; Read, Marsha

1982-01-01

249

Arab Consumers' Behavior Towards Credit Card Usage  

Microsoft Academic Search

Credit card usage by consumers across the oil-rich Arab countries (such as Qatar, Bahrain, and Kuwait) is changing the landscape of consumer behavior, motivating Arab consumers to buy more often, and promoting impulse buying. Our study examines Arab consumers' behavior towards credit card usage from multi-cultural perspective by replicating a western model propounded by Kaynak et al. (1986) and Kaynak

Khalid Al. Sulaiti; Zafar U. Ahmed; Sri Beldona

2006-01-01

250

A Codon-Optimized Bacterial Antibiotic Gene Used as Selection Marker for Stable Nuclear Transformation in the Marine Red Alga Pyropia yezoensis.  

PubMed

Marine macroalgae play an important role in marine coastal ecosystems and are widely used as sea vegetation foodstuffs and for industrial purposes. Therefore, there have been increased demands for useful species and varieties of these macroalgae. However, genetic transformation in macroalgae has not yet been established. We have developed a dominant selection marker for stable nuclear transformation in the red macroalga Pyropia yezoensis. We engineered the coding region of the aminoglycoside phosphotransferase gene aph7? from Streptomyces hygroscopicus to adapt codon usage of the nuclear genes of P. yezoensis. We designated this codon-optimized aph7? gene as PyAph7. After bombarding P. yezoensis cells with plasmids containing PyAph7 under the control of their endogenous promoter, 1.9 thalli (or individuals) of hygromycin-resistant strains were isolated from a 10-mm square piece of the bombarded thallus. These transformants were stably maintained throughout the asexual life cycle. Stable expression of PyAph7was verified using Southern blot analysis and genomic PCR and RT-PCR analyses. PyAph7 proved to be a new versatile tool for stable nuclear transformation in P. yezoensis. PMID:24149658

Uji, Toshiki; Hirata, Ryo; Fukuda, Satoru; Mizuta, Hiroyuki; Saga, Naotsune

2014-06-01

251

Role of codon choice in the leader region of the ilvGMEDA operon of Serratia marcescens.  

PubMed Central

Leucine participates in multivalent repression of the Serratia marcescens ilvGMEDA operon by attenuation (J.-H. Hsu, E. Harms, and H.E. Umbarger, J. Bacteriol. 164:217-222, 1985), although there is only one single leucine codon that could be involved in this type of control. This leucine codon is the rarely used CUA. The contribution of this leucine codon to the control of transcription by attenuation was examined by replacing it with the commonly used leucine codon CUG and with a nonregulatory proline codon, CCG. These changes left intact the proposed secondary structure of the leader. The effects of the codon changes were assessed by placing the mutant leader regions upstream of the ilvGME structural genes or the cat gene and measuring acetohydroxy acid synthase II, transaminase B, or chloramphenicol acetyltransferase activities in cells grown under limiting and repressing conditions. The presence of the common leucine codon in place of the rare leucine codon reduced derepression by about 70%. Eliminating the leucine codon by converting it to proline abolished leucine control. Furthermore, a possible context effect of the adjacent upstream serine codon on leucine control was examined by changing it into a glycine codon.

Harms, E; Umbarger, H E

1987-01-01

252

Unusual base pairing during the decoding of a stop codon by the ribosome  

PubMed Central

During normal translation, binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (?) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires formation of two normally forbidden purine-purine base pairs1. We have determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNASer bound to the ?AG stop codon in the A site. The ?A base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which display an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding center to accommodate non-canonical base pairs.

Fernandez, Israel S.; Ng, Chyan Leong; Kelley, Ann C.; Wu, Guowei

2013-01-01

253

Understanding the influence of codon translation rates on cotranslational protein folding.  

PubMed

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 translation rates on cotranslational protein folding and misfolding. The application of such approaches to this important problem is creating a framework for making quantitative predictions of the impact of synonymous codon substitutions on cotranslational folding that has led to a novel hypothesis regarding the role of fast-translating codons in coordinating cotranslational folding. In addition, it is providing new insights into proteome-wide cotranslational folding behavior and making it possible to identify potential molecular mechanisms by which molecular chaperones can influence such behavior during protein synthesis. As we discuss in this Account, bringing together these theoretical developments with experimental approaches is increasingly helping answer fundamental questions about the nature of nascent protein folding on the ribosome. PMID:24784899

O'Brien, Edward P; Ciryam, Prajwal; Vendruscolo, Michele; Dobson, Christopher M

2014-05-20

254

Codon optimization enhances protein expression of human peptide deformylase in E. coli  

Microsoft Academic Search

Human peptide deformylase (hPDF), located in the mitochondria, has recently become a promising target for anti-cancer therapy. However, the expression of the hPDF gene in Escherichia coli is not efficient likely due to extremely high levels of GC content as well as the presence of rare codons. We performed codon optimization of the hPDF gene in order to reduce GC

Ji-Hoon Han; Yun-Seok Choi; Won-Je Kim; Young Ho Jeon; Seung Kyu Lee; Bong-Jin Lee; Kyoung-Seok Ryu

2010-01-01

255

FPGA curved track fitter with very low resource usage  

SciTech Connect

Standard least-squares curved track fitting process is tailored for FPGA implementation. The coefficients in the fitting matrices are carefully chosen so that only shift and accumulation operations are used in the process. The divisions and full multiplications are eliminated. Comparison in an application example shows that the fitting errors of the low resource usage implementation are less than 4% bigger than the fitting errors of the exact least-squares algorithm. The implementation is suitable for low-cost, low-power applications such as high energy physics detector trigger systems.

Wu, Jin-Yuan; Wang, M.; Gottschalk, E.; Shi, Z.; /Fermilab

2006-11-01

256

Translational termination efficiency in mammals is influenced by the base following the stop codon.  

PubMed Central

The base following stop codons in mammalian genes is strongly biased, suggesting that it might be important for the termination event. This proposal has been tested experimentally both in vivo by using the human type I iodothyronine deiodinase mRNA and the recoding event at the internal UGA codon and in vitro by measuring the ability of each of the 12 possible 4-base stop signals to direct the eukaryotic polypeptide release factor to release a model peptide, formylmethionine, from the ribosome. The internal UGA in the deiodinase mRNA is used as a codon for incorporation of selenocysteine into the protein. Changing the base following this UGA codon affected the ratio of termination to selenocysteine incorporation in vivo at this codon: 1:3 (C or U) and 3:1 (A or G). These UGAN sequences have the same order of efficiency of termination as was found with the in vitro termination assay (4th base: A approximately G >> C approximately U). The efficiency of in vitro termination varied in the same manner over a 70-fold range for the UAAN series and over an 8-fold range for the UGAN and UAGN series. There is a correlation between the strength of the signals and how frequently they occur at natural termination sites. Together these data suggest that the base following the stop codon influences translational termination efficiency as part of a larger termination signal in the expression of mammalian genes. Images Fig. 3

McCaughan, K K; Brown, C M; Dalphin, M E; Berry, M J; Tate, W P

1995-01-01

257

Codon sextets with leading role of serine create "ideal" symmetry classification scheme of the genetic code.  

PubMed

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. PMID:24709107

Rosandi?, Marija; Paar, Vladimir

2014-06-10

258

Clinical relevance of KRAS mutations in codon 13: Where are we?  

PubMed

Recent advances in molecular diagnosis and the trend towards personalized medicine have made colorectal cancer one of the tumors where therapies have significantly improved patient survival after metastasis development. KRAS mutations in codon 12 and 13 are recognized biomarkers that are analyzed in clinic previously for anti-EGFR therapies administration. Since originally mutations in both codons were considered as a predictor of lack of response to cetuximab or panitumumab, the European Medicines Agency and the US Food and Drug Administration suggested that patients harboring any of those mutations should be excluded from the treatment. However, subsequent retrospective analysis has shown that mutations in codon 12 and codon 13 of KRAS gene could be different in their biological characteristics and as a result could confer variable effects in patients. In addition and increasing and sometimes contradictory number of solutions have been published demonstrating that patients with mutations in codon 13 could have worse outcome but could obtain a significant clinical benefit from anti-EGFR therapies. Here, we review and update the latest data on the biological role leading to a predictive outcome and benefit from anti-EGFR antibodies in patients with specific KRAS mutations in codon 13. PMID:24051306

Er, Tze-Kiong; Chen, Chih-Chieh; Bujanda, Luis; Herreros-Villanueva, Marta

2014-02-01

259

Estimating toner usage with laser electrophotographic printers  

NASA Astrophysics Data System (ADS)

Accurate estimation of toner usage is an area of on-going importance for laser, electrophotographic (EP) printers. We propose a new two-stage approach in which we first predict on a pixel-by-pixel basis, the absorptance from printed and scanned pages. We then form a weighted sum of these pixel values to predict overall toner usage on the printed page. The weights are chosen by least-squares regression to toner usage measured with a set of printed test pages. Our twostage predictor significantly outperforms existing methods that are based on a simple pixel counting strategy in terms of both accuracy and robustness of the predictions.

Wang, Lu; Abramsohn, Dennis; Ives, Thom; Shaw, Mark; Allebach, Jan

2013-02-01

260

Evidence that UGA is read as a tryptophan codon rather than as a stop codon by Mycoplasma pneumoniae, Mycoplasma genitalium, and Mycoplasma gallisepticum.  

PubMed Central

Molecular cloning and sequencing showed that Mycoplasma gallisepticum, like Mycoplasma capricolum, contains both tRNA(UCA) and tRNA(CCA) genes, while Mycoplasma pneumoniae and Mycoplasma genitalium each appear to have only a tRNA(UCA) gene. Therefore, these mycoplasma species contain a tRNA with the anticodon UCA that can translate both UGA and UGG codons.

Inamine, J M; Ho, K C; Loechel, S; Hu, P C

1990-01-01

261

Design of ERIC Usage Studies. Volume II.  

National Technical Information Service (NTIS)

This document contains reports examining research designs for Educational Resources Information Center (ERIC) usage studies at three levels: (1) system operations; (2) subscribers to the services provided; and (3) the ultimate 'end-users' of the service. ...

1978-01-01

262

The usage of INTERKOSMOS satellite for astrodynamics  

Microsoft Academic Search

The anticipated physical parameters of the INTERCOSMOS satellite and the properties of laser corner cube reflectors are given. The possible physical parameters and the visibility conditions are estimated. A short discussion concerns some scientific usage of the satellite observations.

J. Klokocnik; P. Lala; P. Navara; M. Prokes; L. Sehnal; M. Solaric

1975-01-01

263

Understanding Road Usage Patterns in Urban Areas  

NASA Astrophysics Data System (ADS)

In this paper, we combine the most complete record of daily mobility, based on large-scale mobile phone data, with detailed Geographic Information System (GIS) data, uncovering previously hidden patterns in urban road usage. We find that the major usage of each road segment can be traced to its own - surprisingly few - driver sources. Based on this finding we propose a network of road usage by defining a bipartite network framework, demonstrating that in contrast to traditional approaches, which define road importance solely by topological measures, the role of a road segment depends on both: its betweeness and its degree in the road usage network. Moreover, our ability to pinpoint the few driver sources contributing to the major traffic flow allows us to create a strategy that achieves a significant reduction of the travel time across the entire road system, compared to a benchmark approach.

Wang, Pu; Hunter, Timothy; Bayen, Alexandre M.; Schechtner, Katja; González, Marta C.

2012-12-01

264

Understanding Road Usage Patterns in Urban Areas  

PubMed Central

In this paper, we combine the most complete record of daily mobility, based on large-scale mobile phone data, with detailed Geographic Information System (GIS) data, uncovering previously hidden patterns in urban road usage. We find that the major usage of each road segment can be traced to its own - surprisingly few - driver sources. Based on this finding we propose a network of road usage by defining a bipartite network framework, demonstrating that in contrast to traditional approaches, which define road importance solely by topological measures, the role of a road segment depends on both: its betweeness and its degree in the road usage network. Moreover, our ability to pinpoint the few driver sources contributing to the major traffic flow allows us to create a strategy that achieves a significant reduction of the travel time across the entire road system, compared to a benchmark approach.

Wang, Pu; Hunter, Timothy; Bayen, Alexandre M.; Schechtner, Katja; Gonzalez, Marta C.

2012-01-01

265

Alcohol and Adaptation to Mechanical Usage.  

National Technical Information Service (NTIS)

These studies are designed to determine whether ethanol antagonizes the ability of the skeleton to adapt to increased mechanical usage. Ethanol reversibly alters the biophysical properties of cell membranes. The overall hypothesis to be tested in adult ra...

R. T. Turner

2001-01-01

266

Vocabulary Usage and Intelligibility in Learner Language  

Microsoft Academic Search

In verbal communication, the primary purpose of which is to convey and understand messages, speakers need to make intelligible utterances. The intelligibility of an utterance depends on the sentence structure, discourse, and the vocabulary usage. In foreign-language utterances, \\

Emi Izumi; Kiyotaka Uchimoto; Hitoshi Isahara

267

NCI-Frederick TMM - Investigator Usage  

Cancer.gov

Transgenic and Knock-Out Services - Investigator Usage Principal Investigators Who Used Transgenic Mouse Model September 26, 2003 – September 25, 2004 Principal Investigator Laboratory Number of Constructs Completed Dr. S. Abrams Tumor Immunology and

268

College Student Credit Card Usage and Debt.  

ERIC Educational Resources Information Center

Provides an overview of the concerns related to credit card usage by college students. Offers information student affairs professionals can use to help college students make responsible choices. (Contains 26 references.) (GCP)

Rybka, Kathryn M.

2001-01-01

269

Personality variables as predictors of Facebook usage.  

PubMed

This study investigates the role of personality factors as predictors of Facebook usage. Data concerning Facebook usage and personality factors from 654 Facebook users were gathered using a web survey. Using path analysis, the results showed Openness was a predictor of Facebook early adoption, Conscientiousness with sparing use, Extraversion with long sessions and abundant friendships, and Neuroticism with high frequency of sessions. The possible role of Agreeableness in predicting low session frequency and friendships needs further validation. PMID:24897905

Caci, Barbara; Cardaci, Maurizio; Tabacchi, Marco E; Scrima, Fabrizio

2014-04-01

270

American Heritage Book of English Usage  

NSDL National Science Digital Library

This Web site takes visitors to the American Heritage Book of English Usage, which is a guide to current problems and debates in English language usage that will be valuable for native and non-native speakers alike. The work may be searched by keyword, or users may elect to browse through its 10 chapters. The subjects covered by the various chapters include gender, science terms, e-mail, word choice, and style.

2000-01-01

271

Identification of eRF1 residues that play critical and complementary roles in stop codon recognition.  

PubMed

The initiation and elongation stages of translation are directed by codon-anticodon interactions. In contrast, a release factor protein mediates stop codon recognition prior to polypeptide chain release. Previous studies have identified specific regions of eukaryotic release factor one (eRF1) that are important for decoding each stop codon. The cavity model for eukaryotic stop codon recognition suggests that three binding pockets/cavities located on the surface of eRF1's domain one are key elements in stop codon recognition. Thus, the model predicts that amino acid changes in or near these cavities should influence termination in a stop codon-dependent manner. Previous studies have suggested that the TASNIKS and YCF motifs within eRF1 domain one play important roles in stop codon recognition. These motifs are highly conserved in standard code organisms that use UAA, UAG, and UGA as stop codons, but are more divergent in variant code organisms that have reassigned a subset of stop codons to sense codons. In the current study, we separately introduced TASNIKS and YCF motifs from six variant code organisms into eRF1 of Saccharomyces cerevisiae to determine their effect on stop codon recognition in vivo. We also examined the consequences of additional changes at residues located between the TASNIKS and YCF motifs. Overall, our results indicate that changes near cavities two and three frequently mediated significant effects on stop codon selectivity. In particular, changes in the YCF motif, rather than the TASNIKS motif, correlated most consistently with variant code stop codon selectivity. PMID:22543865

Conard, Sara E; Buckley, Jessica; Dang, Mai; Bedwell, Gregory J; Carter, Richard L; Khass, Mohamed; Bedwell, David M

2012-06-01

272

E-Book Usage and the "Choice" Outstanding Academic Book List: Is There a Correlation?  

ERIC Educational Resources Information Center

In this study, the staff of the library at Auburn University at Montgomery analyzed circulation patterns for electronic books in the fields of Political Science, Public Administration and Law to see if favorable "Choice" reviews can be used to predict usage of electronic books. A comparison of the circulations between print and electronic books…

Carter Williams, Karen; Best, Rickey

2006-01-01

273

Print and Electronic Resources: Usage Statistics at Guru Gobind Singh Indraprastha University Library  

ERIC Educational Resources Information Center

Purpose: The purpose of this paper is to quantify the use of electronic journals in comparison with the print collections in the Guru Gobind Singh Indraprastha University Library. Design/methodology/approach: A detailed analysis was made of the use of lending services, the Xerox facility and usage of electronic journals such as Science Direct,…

Kapoor, Kanta

2010-01-01

274

Cloning of the Zymomonas mobilis structural gene encoding alcohol dehydrogenase I (adhA): Sequence comparison and expression in Escherichia coli  

SciTech Connect

Zymomonas mobilis ferments sugars to produce ethanol with two biochemically distinct isoenzymes of alcohol dehydrogenase. The adhA gene encoding alcohol dehydrogenase I has now been sequenced and compared with the adhB gene, which encodes the second isoenzyme. The deduced amino acid sequences for these gene products exhibited no apparent homology. Alcohol dehydrogenase I contained 337 amino acids, with a subunit molecular weight of 36,096. Based on comparisons of primary amino acid sequences, this enzyme belongs to the family of zinc alcohol dehydrogenases which have been described primarily in eucaryotes. Nearly all of the 22 strictly conserved amino acids in this group were also conserved in Z. mobilis alcohol dehydrogenase I. Alcohol dehydrogenase I is an abundant protein, although adhA lacked many of the features previously reported in four other highly expressed genes from Z. mobilis. Codon usage in adhA is not highly biased and includes many codons which were unused by pdc, adhB, gap, and pgk. The ribosomal binding region of adhA lacked the canonical Shine-Dalgarno sequence found in the other highly expressed genes from Z. mobilis. Although these features may facilitate the expression of high enzyme levels, they do not appear to be essential for the expression of Z. mobilis adhA.

Keshav, K.F.; Yomano, L.P.; Haejung An; Ingram, L.O. (Univ. of Florida, Gainesville (USA))

1990-05-01

275

Cloning of the Zymomonas mobilis structural gene encoding alcohol dehydrogenase I (adhA): sequence comparison and expression in Escherichia coli.  

PubMed Central

Zymomonas mobilis ferments sugars to produce ethanol with two biochemically distinct isoenzymes of alcohol dehydrogenase. The adhA gene encoding alcohol dehydrogenase I has now been sequenced and compared with the adhB gene, which encodes the second isoenzyme. The deduced amino acid sequences for these gene products exhibited no apparent homology. Alcohol dehydrogenase I contained 337 amino acids, with a subunit molecular weight of 36,096. Based on comparisons of primary amino acid sequences, this enzyme belongs to the family of zinc alcohol dehydrogenases which have been described primarily in eucaryotes. Nearly all of the 22 strictly conserved amino acids in this group were also conserved in Z. mobilis alcohol dehydrogenase I. Alcohol dehydrogenase I is an abundant protein, although adhA lacked many of the features previously reported in four other highly expressed genes from Z. mobilis. Codon usage in adhA is not highly biased and includes many codons which were unused by pdc, adhB, gap, and pgk. The ribosomal binding region of adhA lacked the canonical Shine-Dalgarno sequence found in the other highly expressed genes from Z. mobilis. Although these features may facilitate the expression of high enzyme levels, they do not appear to be essential for the expression of Z. mobilis adhA. Images

Keshav, K F; Yomano, L P; An, H J; Ingram, L O

1990-01-01

276

Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and -D Isolates, Further Supports Possible Subclassification within the MPV Genus  

PubMed Central

Four avian metapneumovirus (AMPV) subgroups (A–D) have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively) have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV) sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus “clusters” HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II.

Brown, Paul A.; Lemaitre, Evelyne; Briand, Francois-Xavier; Courtillon, Celine; Guionie, Olivier; Allee, Chantal; Toquin, Didier; Bayon-Auboyer, Marie-Helene; Jestin, Veronique; Eterradossi, Nicolas

2014-01-01

277

ProxiMAX randomization: a new technology for non-degenerate saturation mutagenesis of contiguous codons  

PubMed Central

Back in 2003, we published ‘MAX’ randomization, a process of non-degenerate saturation mutagenesis using exactly 20 codons (one for each amino acid) or else any required subset of those 20 codons. ‘MAX’ randomization saturates codons located in isolated positions within a protein, as might be required in enzyme engineering, or else on one face of an ?-helix, as in zinc-finger engineering. Since that time, we have been asked for an equivalent process that can saturate multiple contiguous codons in a non-degenerate manner. We have now developed ‘ProxiMAX’ randomization, which does just that: generating DNA cassettes for saturation mutagenesis without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, ProxiMAX randomization uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents. Thus it requires no specialized chemistry, reagents or equipment, and simply relies on a process of saturation cycling comprising ligation, amplification and digestion for each cycle. The process can encode both unbiased representation of selected amino acids or else encode them in predefined ratios. Each saturated position can be defined independently of the others. We demonstrate accurate saturation of up to 11 contiguous codons. As such, ProxiMAX randomization is particularly relevant to antibody engineering.

Ashraf, Mohammed; Frigotto, Laura; Smith, Matthew E.; Patel, Seema; Hughes, Marcus D.; Poole, Andrew J.; Hebaishi, Husam R.M.; Ullman, Christopher G.; Hine, Anna V.

2013-01-01

278

Investigating protein-coding sequence evolution with probabilistic codon substitution models.  

PubMed

This review is motivated by the true explosion in the number of recent studies both developing and ameliorating probabilistic models of codon evolution. Traditionally parametric, the first codon models focused on estimating the effects of selective pressure on the protein via an explicit parameter in the maximum likelihood framework. Likelihood ratio tests of nested codon models armed the biologists with powerful tools, which provided unambiguous evidence for positive selection in real data. This, in turn, triggered a new wave of methodological developments. The new generation of models views the codon evolution process in a more sophisticated way, relaxing several mathematical assumptions. These models make a greater use of physicochemical amino acid properties, genetic code machinery, and the large amounts of data from the public domain. The overview of the most recent advances on modeling codon evolution is presented here, and a wide range of their applications to real data is discussed. On the downside, availability of a large variety of models, each accounting for various biological factors, increases the margin for misinterpretation; the biological meaning of certain parameters may vary among models, and model selection procedures also deserve greater attention. Solid understanding of the modeling assumptions and their applicability is essential for successful statistical data analysis. PMID:18922761

Anisimova, Maria; Kosiol, Carolin

2009-02-01

279

Connection between stop codon reassignment and frequent use of shifty stop frameshifting.  

PubMed

Ciliated protozoa of the genus Euplotes have undergone genetic code reassignment, redefining the termination codon UGA to encode cysteine. In addition, Euplotes spp. genes very frequently employ shifty stop frameshifting. Both of these phenomena involve noncanonical events at a termination codon, suggesting they might have a common cause. We recently demonstrated that Euplotes octocarinatus peptide release factor eRF1 ignores UGA termination codons while continuing to recognize UAA and UAG. Here we show that both the Tetrahymena thermophila and E. octocarinatus eRF1 factors allow efficient frameshifting at all three termination codons, suggesting that UGA redefinition also impaired UAA/UAG recognition. Mutations of the Euplotes factor restoring a phylogenetically conserved motif in eRF1 (TASNIKS) reduced programmed frameshifting at all three termination codons. Mutation of another conserved residue, Cys124, strongly reduces frameshifting at UGA while actually increasing frameshifting at UAA/UAG. We will discuss these results in light of recent biochemical characterization of these mutations. PMID:19329535

Vallabhaneni, Haritha; Fan-Minogue, Hua; Bedwell, David M; Farabaugh, Philip J

2009-05-01

280

ProxiMAX randomization: a new technology for non-degenerate saturation mutagenesis of contiguous codons.  

PubMed

Back in 2003, we published 'MAX' randomization, a process of non-degenerate saturation mutagenesis using exactly 20 codons (one for each amino acid) or else any required subset of those 20 codons. 'MAX' randomization saturates codons located in isolated positions within a protein, as might be required in enzyme engineering, or else on one face of an ?-helix, as in zinc-finger engineering. Since that time, we have been asked for an equivalent process that can saturate multiple contiguous codons in a non-degenerate manner. We have now developed 'ProxiMAX' randomization, which does just that: generating DNA cassettes for saturation mutagenesis without degeneracy or bias. Offering an alternative to trinucleotide phosphoramidite chemistry, ProxiMAX randomization uses nothing more sophisticated than unmodified oligonucleotides and standard molecular biology reagents. Thus it requires no specialized chemistry, reagents or equipment, and simply relies on a process of saturation cycling comprising ligation, amplification and digestion for each cycle. The process can encode both unbiased representation of selected amino acids or else encode them in predefined ratios. Each saturated position can be defined independently of the others. We demonstrate accurate saturation of up to 11 contiguous codons. As such, ProxiMAX randomization is particularly relevant to antibody engineering. PMID:24059507

Ashraf, Mohammed; Frigotto, Laura; Smith, Matthew E; Patel, Seema; Hughes, Marcus D; Poole, Andrew J; Hebaishi, Husam R M; Ullman, Christopher G; Hine, Anna V

2013-10-01

281

Evidence of abundant stop codon readthrough in Drosophila and other metazoa  

PubMed Central

While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions in 12 species of Drosophila and showed that for 149 genes, the open reading frame following the stop codon has a protein-coding conservation signature, hinting that stop codon readthrough might be common in Drosophila. We return to this observation armed with deep RNA sequence data from the modENCODE project, an improved higher-resolution comparative genomics metric for detecting protein-coding regions, comparative sequence information from additional species, and directed experimental evidence. We report an expanded set of 283 readthrough candidates, including 16 double-readthrough candidates; these were manually curated to rule out alternatives such as A-to-I editing, alternative splicing, dicistronic translation, and selenocysteine incorporation. We report experimental evidence of translation using GFP tagging and mass spectrometry for several readthrough regions. We find that the set of readthrough candidates differs from other genes in length, composition, conservation, stop codon context, and in some cases, conserved stem–loops, providing clues about readthrough regulation and potential mechanisms. Lastly, we expand our studies beyond Drosophila and find evidence of abundant readthrough in several other insect species and one crustacean, and several readthrough candidates in nematode and human, suggesting that functionally important translational stop codon readthrough is significantly more prevalent in Metazoa than previously recognized.

Jungreis, Irwin; Lin, Michael F.; Spokony, Rebecca; Chan, Clara S.; Negre, Nicolas; Victorsen, Alec; White, Kevin P.; Kellis, Manolis

2011-01-01

282

Activating point mutation in Ki-ras codon 63 in a chemically induced rat renal tumor.  

PubMed

Renal mesenchymal tumors induced in F344 rats with methyl(methoxymethyl)nitrosamine (DMN-OMe) have previously been shown by our laboratory to contain transforming Ki-ras sequences, activated most commonly by a variety of codon 12 mutations. Further sequence analysis of the one DMN-OMe-induced tumor with transforming Ki-ras sequences detected by NIH 3T3 transfection assay but with no mutation in codon 12 detected by selective oligonucleotide hybridization has now revealed an activating point mutation in codon 63. The observed GAG----AAG transition in codon 63, which replaces glutamic acid with lysine, was the only detectable mutation in exon 1 and 2 hotspot regions of Ki-ras in this tumor. The same mutation was also detected in Ki-ras sequences derived from first- and second-cycle transformants in NIH 3T3 transfection assays. Although random mutagenesis studies of cloned Ha-ras sequences by Fasano et al. (Proc Natl Acad Sci USA 81:4008-4012, 1984) had already indicated that GAG----AAG mutations in codon 63 of ras are transforming, this is the first demonstration of the natural occurrence of this particular activating mutation in a tumor. PMID:1554412

Higinbotham, K G; Rice, J M; Perantoni, A O

1992-01-01

283

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

PubMed Central

Background Fluorescent proteins are used widely as reporter genes in many organisms. We previously codon-optimized mCherry for Mycobacterium tuberculosis and generated expression constructs with high level expression in mycobacteria with multiple uses in vitro and in vivo. However, little is known about the expression of fluorescent proteins in mycobacteria and the translational start codon for mCherry has not been experimentally determined. Results We determined the translational start site for functional (fluorescent) mCherry in mycobacteria. Several potential translational start codons were identified; introduction of downstream stop codons by mutagenesis was used to determine which start codon was utilized in the bacterial cells. Fluorescent protein was expressed from a construct which would allow translation of a protein of 226 amino acids or a protein of 235 amino acids. No fluorescence was seen when a construct which could give rise to a protein of 219 amino acids was used. Similar results were obtained in mycobacteria and in Escherichia coli. Western blotting confirmed that mCherry was expressed from the constructs encoding 235 or 226 amino acids, but not from the plasmid encoding 219 amino acids. N-terminal sequencing and mass determination confirmed that the mature protein was 226 amino acids and commenced with the amino acid sequence AIIKE. Conclusion We conclude that mCherry is expressed in M. tuberculosis as a smaller protein than expected lacking the GFP-derived N-terminal sequence designed to allow efficient fusions.

2014-01-01

284

Efficient web usage mining process for sequential patterns  

Microsoft Academic Search

The tremendous growth in volume of web usage data results in the boost of web mining research with focus on discovering potentially useful knowledge from web usage data. This paper presents a new web usage mining process for finding sequential patterns in web usage data which can be used for predicting the possible next move in browsing sessions for web

Sang T. T. Nguyen

2009-01-01

285

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

ERIC Educational Resources Information Center

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…

Remy, Charlie

2012-01-01

286

Translational readthrough of the PDE2 stop codon modulates cAMP levels in Saccharomyces cerevisiae.  

PubMed

The efficiency of translation termination in yeast can vary several 100-fold, depending on the context around the stop codon. We performed a computer analysis designed to identify yeast open reading frames (ORFs) containing a readthrough motif surrounding the termination codon. Eight ORFs were found to display inefficient stop codon recognition, one of which, PDE2, encodes the high-affinity cAMP phosphodiesterase. We demonstrate that Pde2p stability is very impaired by the readthrough-dependent extension of the protein. A 20-fold increase in readthrough of PDE2 was observed in a [PSI+] as compared with a [psi-] strain. Consistent with this observation, an important increase in cAMP concentration was observed in suppressor backgrounds. These results provide a molecular explanation for at least some of the secondary phenotypes associated with suppressor backgrounds. PMID:11929521

Namy, Olivier; Duchateau-Nguyen, Guillemette; Rousset, Jean-Pierre

2002-02-01

287

Predominance of six different hexanucleotide recoding signals 3? of read-through stop codons  

PubMed Central

Redefinition of UAG, UAA and UGA to specify a standard amino acid occurs in response to recoding signals present in a minority of mRNAs. This ‘read-through’ is in competition with termination and is utilized for gene expression. One of the recoding signals known to stimulate read-through is a hexanucleotide sequence of the form CARYYA 3? adjacent to the stop codon. The present work finds that of the 91 unique viral sequences annotated as read-through, 90% had one of six of the 64 possible codons immediately 3? of the read-through stop codon. The relative efficiency of these read-through contexts in mammalian tissue culture cells has been determined using a dual luciferase fusion reporter. The relative importance of the identity of several individual nucleotides in the different hexanucleotides is complex.

Harrell, Lance; Melcher, Ulrich; Atkins, John F.

2002-01-01

288

Suppression of UAA and UGA termination codons in mutant murine leukemia viruses.  

PubMed Central

Genomes of mammalian type C retroviruses contain a UAG termination codon between the gag and pol coding regions. The pol region is expressed in the form of a gag-pol fusion protein following readthrough suppression of the UAG codon. We have used oligonucleotide-directed mutagenesis to change the UAG in Moloney murine leukemia virus to UAA or UGA. These alternate termination codons were also suppressed, both in infected cells and in reticulocyte lysates. Thus, the signal or context inducing suppression of UAG in wild-type Moloney murine leukemia virus is also effective with UAA and UGA. Further, mammalian cells and cell extracts contain tRNAs capable of translating UAA and UGA as amino acids. To our knowledge, this is the first example of natural suppression of UAA in higher eucaryotes. Images

Feng, Y X; Levin, J G; Hatfield, D L; Schaefer, T S; Gorelick, R J; Rein, A

1989-01-01

289

NAT Usage in Residential Broadband Networks  

NASA Astrophysics Data System (ADS)

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.

Maier, Gregor; Schneider, Fabian; Feldmann, Anja

290

Motivations and usage patterns of Weibo.  

PubMed

Referred to as "Weibo," microblogging in China has witnessed an exponential growth. In addition to the Twitter-like functionality, Weibo allows rich media uploads into user feeds, provides threaded comments, and offers applications, games, and Weibo medals. This expanded functionality, as well as the observed differences in trending content, suggests potentially different user motivations to join Weibo and their usage patterns compared to Twitter. This pioneering study identifies dominant Weibo user motivations and their effects on usage patterns. We discuss the findings of an online survey of 234 Weibo users and suggest managerial implications and future research directions. PMID:22703037

Zhang, Lixuan; Pentina, Iryna

2012-06-01

291

Dependence of nucleotide physical properties on their placement in codons and determinative degree  

PubMed Central

Various physical properties such as dipole moment, heat of formation and energy of the most stable formation of nucleotides and bases were calculated by PM3 (modified neglect of diatomic overlap, parametric method number 3) and AM1 (austin model 1) methods. As distinct from previous calculations, for nucleotides the interaction with neighbours is taken into account up to gradient of convergence equaling 1. The dependencies of these variables from the place in the codon and the determinative degree were obtained. The difference of these variables for codons and anticodons is shown.

Berezhnoy, A.Y.; Duplij, S.A.

2005-01-01

292

Synonymous but not the same: the causes and consequences of codon bias  

PubMed Central

Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.

Plotkin, Joshua B.; Kudla, Grzegorz

2010-01-01

293

Fossil fuel usage and the environment  

Microsoft Academic Search

The Greenhouse Effect and global warming, ozone formation in the troposphere, ozone destruction in the stratosphere, and acid rain are important environmental issues. The relationship of fossil fuel usage to some of these issues is discussed. Data on fossil fuel consumption and the sources and sinks of carbon dioxide, carbon monoxide, methane, nitrogen and sulfur oxides, and ozone indicate that

Klass

1990-01-01

294

Measuring Computer Usage in a College Setting.  

ERIC Educational Resources Information Center

In spring 1998, a total of 452 students in 49 selected classes and 44% of faculty at Johnson County Community College returned surveys assessing respondents' computer usage and future computer needs. Results indicate a trend toward greater utilization of computers in education. (Contains nine references.) (PGS)

Coklin, Karen A.

1999-01-01

295

Women Veterans Usage of VA Hospitalization.  

National Technical Information Service (NTIS)

The use of VA hospitals by women veterans is analyzed in this report. Age distributions are assessed and usage patterns by women veterans are compared with corresponding patterns among male veterans. It was found that there has been a substantial increase...

D. Stockford W. Page

1982-01-01

296

Female Athletes and Performance-Enhancer Usage  

ERIC Educational Resources Information Center

The purpose of this study was to develop a knowledge base on factors associated with performance-enhancer usage among female athletes at the high school level in order to identify markers for a future prevention-education program. The study used a pretest-only, between-subjects Likert Scale survey to rank the importance of internal and external…

Fralinger, Barbara K.; Pinto-Zipp, Genevieve; Olson, Valerie; Simpkins, Susan

2007-01-01

297

Rhetoric and Usage in Technical Writing.  

ERIC Educational Resources Information Center

Selecting criteria for usage is done in basically the same way for both technical writing and other forms of composition. Similarly, the same rhetorical theory applies to the teaching of both, and proves especially helpful in the teaching of formal report-writing skills in required freshman composition courses. Focusing on the appropriate voice,…

Young, Art

298

Discursive Usage of Six Chinese Punctuation Marks  

Microsoft Academic Search

Both rhetorical structure and punctuation have been helpful in discourse processing. Based on a corpus annotation project, this paper reports the discursive usage of 6 Chinese punctuation marks in news commentary texts: Colon, Dash, Ellipsis, Exclamation Mark, Question Mark, and Semicolon. The rhetorical patterns of these marks are compared against patterns around cue phrases in general. Results show that these

YUE Ming

2006-01-01

299

Task and Activity Models in Hypertext Usage  

Microsoft Academic Search

In this chapter we examine hypertext usage from the point of view of the information processing tasks performed by hypertext users. Our main purpose is to provide a general framework to identify the tasks which may be effectively supported by hypertext environments. First we present different approaches to the analysis of information processing tasks, as they appear in hypertext and

Jean-François Rouet; André Tricot

300

Fume Hood Energy Usage and Incentivization  

Microsoft Academic Search

Fume hoods typically use three to four times the energy of a house, accounting for approximately $4.2 billion dollars in energy bills nationwide. At Caltech, there are over 800 fume hoods. The aim of this SURF was to perform a cost analysis of existing fume hoods and to observe behavior patterns in fume hood usage. Variable air volume fume hoods

Silas Hilliard

301

Cost Focussed Firms and Internet Usage  

Microsoft Academic Search

This paper looks at Internet usage by Australian firms that have a cost focussed competitive strategy. The data source for this analysis is the Melbourne Institute Business Survey, conducted by the Melbourne Institute of Applied Economic and Social Research. The survey was conducted in late 2001, and targeted large Australian firms. Instrumental variables estimation found that cost-focussed organizations utilised the

Joanne Loundes

2002-01-01

302

White Paper on Electronic Journal Usage Statistics.  

ERIC Educational Resources Information Center

This paper provides a snapshot of developments in the electronic journal industry. The first section identifies issues affecting librarians and publishers, including: (1) issues of common concern to both publishers and librarians, e.g., lack of comparable data, lack of context, incomplete usage data, marketing, content provided, interface…

Luther, Judy

303

Production, Usage, and Comprehension in Animal Vocalizations  

ERIC Educational Resources Information Center

In this review, we place equal emphasis on production, usage, and comprehension because these components of communication may exhibit different developmental trajectories and be affected by different neural mechanisms. In the animal kingdom generally, learned, flexible vocal production is rare, appearing in only a few orders of birds and few…

Seyfarth, Robert M.; Cheney, Dorothy L.

2010-01-01

304

An Approach to Teaching English Usage.  

ERIC Educational Resources Information Center

GRADES OR AGES: K-12. SUBJECT MATTER: English Usage. ORGANIZATION AND PHYSICAL APPEARANCE: There are four major sections: Prekindergarten-grade 3; grade 4-grade 6; grade 7-grade 9; grade 10-grade 12. Learning experiences are listed for each grade. The guide is offset printed and bound with a soft cover. OBJECTIVES AND ACTIVITIES: The program is…

Chandler, William J., Comp.; And Others

305

Experimentation with Usage-Based Reading  

Microsoft Academic Search

Software inspections are regarded as an important technique to detect faults throughout the software development process. The individual preparation phase of software inspections has enlarged its focus from only comprehension to also include fault searching. Hence, reading techniques to support the reviewers on fault detection are needed. Usage-based reading (UBR) is a reading technique, which focuses on the important parts

Thomas Thelin; Magnus Erlansson; Martin Höst; Claes Wohlin

2003-01-01

306

Style and Usage Software: Mentor, not Judge.  

ERIC Educational Resources Information Center

Computer software style and usage checkers can encourage students' recursive revision strategies. For example, HOMER is based on the revision pedagogy presented in Richard Lanham's "Revising Prose," while Grammatik II focuses on readability, passive voice, and possibly misused words or phrases. Writer's Workbench "Style" (a UNIX program) provides…

Smye, Randy

307

Collaborative Portfolio's Effect on Library Usage  

ERIC Educational Resources Information Center

Library resources are expensive and it is the library media specialist's responsibility to ensure that use of the library's resources is maximized to support the School Strategic Plan (SSP). This library usage study examined data on the scheduling of high school classes for research-based assignments, related to content area curriculum standards,…

Bryan, Valerie

2011-01-01

308

[Dental welding titanium and its clinical usage].  

PubMed

Due to its excellent biocompatibility, desirable chemical and mechanical properties, Titanium has been used for implant denture, RPD and FPD, where welding techniques were indispensable. This paper introduces 5 useful modern ways to weld Titanium and their clinical usage. They are: laser, plasma welding, TIG, infraned brazing and Hruska electrowelding. PMID:12553259

Li, H; Xiao, M; Zhao, Y

1998-09-01

309

College Student Performance and Credit Card Usage.  

ERIC Educational Resources Information Center

Examines the relationship between credit card usage, employment, and academic performance among a group of college students with credit cards. Results reveal that the students differed significantly in the level of anxiety felt from carrying debt, perceived need to work, and perceived impact of employment on academic performance. (Contains 57…

Pinto, Mary Beth; Parente, Diane H.; Palmer, Todd Starr

2001-01-01

310

Usage patterns of an online search system  

Microsoft Academic Search

This article examines the usage patterns of the ELHILL retrieval program of the National Library of Medicine's MEDLARS systeni. Based on a sample of 6759 searches, the study anaiyzes the frequency of various commands and command options, classifies messages issued by the system, and investigates searcher error rates. The ar- ticle conciudes with suggestions for improving and redesigning both the

Michael D. Cooper

1983-01-01

311

Improving the Efficiency of the Genetic Code by Varying the Codon Length—The Perfect Genetic Code  

Microsoft Academic Search

The function of DNA is to specify protein sequences. The four-base “alphabet” used in nucleic acids is translated to the 20 base alphabet of proteins (plus a stop signal) via the genetic code. The code is neither overlapping nor punctuated, but has mRNA sequences read in successive triplet codons until reaching a stop codon. The true genetic code uses three

Andrew J. Doig

1997-01-01

312

Adherence to the First-AUG Rule When a Second AUG Codon Follows Closely Upon the First  

Microsoft Academic Search

The rule that eukaryotic ribosomes initiate translation exclusively at the 5' proximal AUG codon is abrogated under rare conditions. One circumstance that has been suggested to allow dual initiation is close apposition of a second AUG codon. A possible mechanism might be that the scanning 40S ribosomal subunit flutters back and forth instead of stopping cleanly at the first AUG.

Marilyn Kozak

1995-01-01

313

Point mutations close to the AUG initiator codon affect the efficiency of translation of rat preproinsulin in vivo  

Microsoft Academic Search

To determine whether sequence context influences the ability of an AUG triplet to be recognized as an initiator codon by eukaryotic ribosomes, single nucleotide changes were introduced near the translational start site in a cloned preproinsulin gene. Maximum synthesis of preproinsulin occurred when a purine, preferably adenosine, was located three nucleotides upstream from the initiator codon. Adenosine is found most

Marilyn Kozak

1984-01-01

314

In vitro readthrough of termination codons by gentamycin in the Stüve–Wiedemann Syndrome  

Microsoft Academic Search

The Stüve–Wiedemann Syndrome (SWS) is a frequently lethal chondrodysplasia caused by null mutations in the leukemia inhibitory factor receptor gene (LIFR) responsible for an impaired activation of the JAK–STAT pathway after LIF stimulation. Most LIFR mutations are nonsense mutations, thus prompting us to investigate the impact of aminoglycosides on the readthrough of premature termination codons (PTCs). Culturing skin fibroblasts from

Samuel Bellais; Carine Le Goff; Nathalie Dagoneau; Arnold Munnich; Valérie Cormier-Daire

2010-01-01

315

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV1 Gag  

Microsoft Academic Search

HIV avoids elimination by cytotoxic T-lymphocytes (CTLs) through the evolution of escape mutations. Although there is mounting evidence that these escape pathways are broadly consistent among individuals with similar human leukocyte antigen (HLA) class I alleles, previous population-based studies have been limited by the inability to simultaneously account for HIV codon covariation, linkage disequilibrium among HLA alleles, and the confounding

Jonathan M. Carlson; Zabrina L. Brumme; Christine M. Rousseau; Chanson J. Brumme; Philippa Matthews; Carl Kadie; James I. Mullins; Bruce D. Walker; P. Richard Harrigan; Philip J. R. Goulder; David Heckerman

2008-01-01

316

Differences in codon bias cannot explain differences in translational power among microbes  

Microsoft Academic Search

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

Les Dethlefsen; Thomas M. Schmidt

2005-01-01

317

Association of TP53 gene codon 72 polymorphism with endometriosis risk in Isfahan  

PubMed Central

Background: Endometriosis is a female health disorder that occurs when cells from the lining of the uterus grow in other areas of the body. The cause of endometriosis is unknown. Objective: The purpose of this study was to investigate TP53 gene codon 72 polymorphism in women with endometriosis and compared it with healthy samples in Isfahan. Materials and Methods: We undertook a case-control study to examine the possible association of the TP53 gene codon 72 polymorphism with the risk of endometriosis in Isfahan. Ninety whole blood specimens from normal people as controls and ninety endometriosis specimens were analyzed. p53 codon 72 genotypes were identified using allele-specific polymerase chain reaction. Results: Frequency of genotype Arg/Arg (Arginine/Arginine) in the samples of endometriosis was 28.9% and in healthy samples 42.2%. Frequency of genotype Pro/Pro (Proline/Proline) in the samples of endometriosis was 15.6% and in healthy ones. Frequency of heterozygote's Arg/Pro was 55.6% in endometriosis samples and 54.45% in healthy ones 3.3%. By comparing statistical genotype Pro/Pro with two other genotypes in both groups there was a statistical meaningful difference between control group and endometriosis group. [p=0.009, CI=95%, OR=5.34 (1047-19.29)]. Conclusion: Recent research shows that genotype Pro/Pro codon72 exon4 TP53 gene may be one predisposing genetic factor for endometriosis in Isfahan.

Nikbakht Dastjerdi, Mehdi; Aboutorabi, Roshanak; Eslami Farsani, Bahram

2013-01-01

318

PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments  

Microsoft Academic Search

PAL2NAL is a web server that constructs a multiple codonalignmentfromthecorrespondingalignedpro- tein sequences. Such codon alignments can be used to evaluate the type and rate of nucleotide substitu- tions in coding DNA for a wide range of evolutionary analyses, such as the identification of levels of selective constraint acting on genes, or to perform DNA-based phylogenetic studies. The server takes a

Mikita Suyama; David Torrents; Peer Bork

2006-01-01

319

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

Microsoft Academic Search

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

Herman Tse; James J Cai; Hoi-Wah Tsoi; Esther PT Lam; Kwok-Yung Yuen

2010-01-01

320

HER2 Codon 655 Polymorphism and Risk of Breast Cancer in African Americans and Whites  

Microsoft Academic Search

Background. Several recent epidemiologic studies examined the association between breast cancer risk and an inherited, single-nucleotide polymorphism in the HER2 gene, codon 655 G to A, which leads to an amino acid substitution of Ile to Val. Results of previous studies have been mixed, with most studies showing no association but some suggesting an association in younger women or women

Robert Millikan; Allison Eaton; Kendra Worley; Lorna Biscocho; Elizabeth Hodgson; Wen-Yi Huang; Joseph Geradts; Mary Iacocca; David Cowan; Kathleen Conway; Lynn Dressler

2003-01-01

321

Unusual base pairing during the decoding of a stop codon by the ribosome.  

PubMed

During normal translation, the binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in the termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (?) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires the formation of two normally forbidden purine-purine base pairs. Here we determined the crystal structure at 3.1?Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNA(Ser) bound to the ?AG stop codon in the A site. The ?A base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which show an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding centre to accommodate non-canonical base pairs. PMID:23812587

Fernández, Israel S; Ng, Chyan Leong; Kelley, Ann C; Wu, Guowei; Yu, Yi-Tao; Ramakrishnan, V

2013-08-01

322

Codon optimization enhances protein expression of human peptide deformylase in E. coli.  

PubMed

Human peptide deformylase (hPDF), located in the mitochondria, has recently become a promising target for anti-cancer therapy. However, the expression of the hPDF gene in Escherichia coli is not efficient likely due to extremely high levels of GC content as well as the presence of rare codons. We performed codon optimization of the hPDF gene in order to reduce GC content and to eliminate rare codons. Putative stable secondary structures of the optimized gene were also reduced. Codon optimization increased the expression of hPDF protein (residues 63-243) presumably by reducing the GC content. A large amount of soluble hPDF was obtained upon its fusion with thioredoxin (Trx-hPDF), although an insoluble fraction was still dominant. We confirmed that Co(2+) is an optimal metal for increasing the activity of purified Trx-hPDF, and that actinonin acts as an efficient inhibitor. Therefore, a large amount of purified hPDF protein would provide many benefits for the screening of various drug candidates. PMID:19825416

Han, Ji-Hoon; Choi, Yun-Seok; Kim, Won-Je; Jeon, Young Ho; Lee, Seung Kyu; Lee, Bong-Jin; Ryu, Kyoung-Seok

2010-04-01

323

High-level accumulation of recombinant miraculin protein in transgenic tomatoes expressing a synthetic miraculin gene with optimized codon usage terminated by the native miraculin terminator  

Microsoft Academic Search

In our previous study, a transgenic tomato line that expressed the MIR gene under control of the cauliflower mosaic virus 35S promoter and the nopaline synthase terminator (tNOS) produced the taste-modifying protein miraculin (MIR). However, the concentration of MIR in the tomatoes was lower than that\\u000a in the MIR gene’s native miracle fruit. To increase MIR production, the native MIR

Kyoko Hiwasa-Tanase; Mpanja Nyarubona; Tadayoshi Hirai; Kazuhisa Kato; Takanari Ichikawa; Hiroshi Ezura

2011-01-01

324

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

Microsoft Academic Search

Background  Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial\\u000a genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain\\u000a some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents\\u000a are very different between

Dana Barth; Thomas U Berendonk

2011-01-01

325

Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes  

PubMed Central

Background Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. Results Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. Conclusions/Significance The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences.

Miyazawa, Sanzo

2011-01-01

326

Analysis of serine codon conservation reveals diverse phenotypic constraints on hepatitis C virus glycoprotein evolution.  

PubMed

Serine is encoded by two divergent codon types, UCN and AGY, which are not interchangeable by a single nucleotide substitution. Switching between codon types therefore occurs via intermediates (threonine or cysteine) or via simultaneous tandem substitutions. Hepatitis C virus (HCV) chronically infects 2 to 3% of the global population. The highly variable glycoproteins E1 and E2 decorate the surface of the viral envelope, facilitate cellular entry, and are targets for host immunity. Comparative sequence analysis of globally sampled E1E2 genes, coupled with phylogenetic analysis, reveals the signatures of multiple archaic codon-switching events at seven highly conserved serine residues. Limited detection of intermediate phenotypes indicates that associated fitness costs restrict their fixation in divergent HCV lineages. Mutational pathways underlying codon switching were probed via reverse genetics, assessing glycoprotein functionality using multiple in vitro systems. These data demonstrate selection against intermediate phenotypes can act at the structural/functional level, with some intermediates displaying impaired virion assembly and/or decreased capacity for target cell entry. These effects act in residue/isolate-specific manner. Selection against intermediates is also provided by humoral targeting, with some intermediates exhibiting increased epitope exposure and enhanced neutralization sensitivity, despite maintaining a capacity for target cell entry. Thus, purifying selection against intermediates limits their frequencies in globally sampled strains, with divergent functional constraints at the protein level restricting the fixation of deleterious mutations. Overall our study provides an experimental framework for identification of barriers limiting viral substitutional evolution and indicates that serine codon-switching represents a genomic "fossil record" of historical purifying selection against E1E2 intermediate phenotypes. PMID:24173227

Brown, Richard J P; Koutsoudakis, George; Urbanowicz, Richard A; Mirza, Deeman; Ginkel, Corinne; Riebesehl, Nina; Calland, Noémie; Albecka, Anna; Price, Louisa; Hudson, Natalia; Descamps, Véronique; Backx, Matthijs; McClure, C Patrick; Duverlie, Gilles; Pecheur, Eve-Isabelle; Dubuisson, Jean; Perez-del-Pulgar, Sofia; Forns, Xavier; Steinmann, Eike; Tarr, Alexander W; Pietschmann, Thomas; Ball, Jonathan K

2014-01-01

327

Comparing internet and mobile phone usage: digital divides of usage, adoption, and dropouts  

Microsoft Academic Search

Results from a national representative telephone survey of Americans in 2000 show that Internet and mobile phone usage was very similar, and that several digital divides exist with respect to both Internet and mobile phone usage. The study identifies and analyzes three kinds of digital divides for both the Internet and mobile phones—users\\/nonuser, veteran\\/recent, and continuing\\/dropout—and similarities and differences among

Ronald E. Rice; James E. Katz

2003-01-01

328

CRPV genomes with synonymous codon optimizations in the CRPV E7 gene show phenotypic differences in growth and altered immunity upon E7 vaccination.  

PubMed

Papillomaviruses use rare codons relative to their hosts. Recent studies have demonstrated that synonymous codon changes in viral genes can lead to increased protein production when the codons are matched to those of cells in which the protein is being expressed. We theorized that the immunogenicity of the virus would be enhanced by matching codons of selected viral genes to those of the host. We report here that synonymous codon changes in the E7 oncogene are tolerated in the context of the cottontail rabbit papillomavirus (CRPV) genome. Papilloma growth rates differ depending upon the changes made indicating that synonymous codons are not necessarily neutral. Immunization with wild type E7 DNA yielded significant protection from subsequent challenge by both wild type and codon-modified genomes. The reduction in growth was most dramatic with the genome containing the greatest number of synonymous codon changes. PMID:18698362

Cladel, Nancy M; Hu, Jiafen; Balogh, Karla K; Christensen, Neil D

2008-01-01

329

alpha-L-iduronidase premature stop codons and potential read-through in mucopolysaccharidosis type I patients.  

PubMed

alpha-L-Iduronidase is a glycosyl hydrolase involved in the sequential degradation of the glycosaminoglycans heparan sulphate and dermatan sulphate. A deficiency in alpha-L-iduronidase results in the lysosomal accumulation and urinary secretion of partially degraded glycosaminoglycans and is the cause of the lysosomal storage disorder mucopolysaccharidosis type I (MPS I; Hurler and Scheie syndromes; McKusick 25280). The premature stop codons Q70X and W402X are two of the most common alpha-l-iduronidase gene (IDUA) mutations accounting for up to 70% of MPS I disease alleles in some populations. Here, we have reported a new mutation, making a total of 15 different mutations that can cause premature IDUA stop codons and have investigated the biochemistry of these mutations. Natural stop codon read-through was dependent on the fidelity of the codon when evaluated at Q70X and W402X in CHO-K1 cells, but the three possible stop codons TAA, TAG and TGA, had different effects on mRNA stability and this effect was context dependent. In CHO-K1 cells expressing the Q70X and W402X mutations, the level of gentamicin-enhanced stop codon read-through was slightly less than the increment in activity caused by a lower fidelity stop codon. In this system, gentamicin had more effect on read-through for the TAA and TGA stop codons when compared to the TAG stop codon. In an MPS I patient study, premature TGA stop codons were associated with a slightly attenuated clinical phenotype, when compared to classical Hurler syndrome (e.g. W402X/W402X and Q70X/Q70X genotypes with TAG stop codons). Natural read-through of premature stop codons is a potential explanation for variable clinical phenotype in MPS I patients. Enhanced stop codon read-through is a potential treatment strategy for a large sub-group of MPS I patients. PMID:15081804

Hein, Leanne K; Bawden, Michael; Muller, Vivienne J; Sillence, David; Hopwood, John J; Brooks, Doug A

2004-04-30

330

Monitoring Object Library Usage and Changes  

NASA Technical Reports Server (NTRS)

The NASA Ames Numerical Aerodynamic Simulation program Aeronautics Consolidated Supercomputing Facility (NAS/ACSF) supercomputing center services over 1600 users, and has numerous analysts with root access. Several tools have been developed to monitor object library usage and changes. Some of the tools do "noninvasive" monitoring and other tools implement run-time logging even for object-only libraries. The run-time logging identifies who, when, and what is being used. The benefits are that real usage can be measured, unused libraries can be discontinued, training and optimization efforts can be focused at those numerical methods that are actually used. An overview of the tools will be given and the results will be discussed.

Owen, R. K.; Craw, James M. (Technical Monitor)

1995-01-01

331

Energy usage for UGVs executing coverage tasks  

NASA Astrophysics Data System (ADS)

Proper management of the available on-board battery power is critical for reliable UGV operations. In this paper, we will focus on the task of area coverage - in which a UGV is required to move through an area and travel within a certain distance of each point - with limited available energy. We compare coverage paths generated by existing methods and generate optimal trajectories by using a novel cost function. Using an iRobot Packbot, we present results showing dierences in energy usage while following these trajectories. We also compare the energy usage of the Packbot while traveling at a dierent velocities. Our results show that it is more ecient, when traveling at a constant velocity, to travel at a faster velocity by computing the ratio of the energy used to distance traveled.

Broderick, John; Tilbury, Dawn; Atkins, Ella

2012-05-01

332

Detection of Fraudulent Usage in Wireless Networks  

Microsoft Academic Search

The complexity of cellular mobile systems renders prevention-based techniques not adequate to guard against all potential attacks. An intrusion detection system has become an indispensable component to provide defense-in-depth security mechanisms for wireless networks. In this paper, by exploiting regularities demonstrated in users' behaviors, we present a suite of detection techniques to identify fraudulent usage of mobile telecommunication services. Specifically,

Bo Sun; Yang Xiao; Ruhai Wang

2007-01-01

333

Context-Aware Usage Control for Android  

Microsoft Academic Search

\\u000a The security of smart phones is increasingly important due to their rapid popularity. Mobile computing on smart phones introduces\\u000a many new characteristics such as personalization, mobility, pay-for-service and limited resources. These features require\\u000a additional privacy protection and resource usage constraints in addition to the security and privacy concerns on traditional\\u000a computers. As one of the leading open source mobile platform,

Guangdong Bai; Liang Gu; Tao Feng; Yao Guo; Xiangqun Chen

2010-01-01

334

Usage-Centered Engineering for Web Applications  

Microsoft Academic Search

This paper presents a lightweight form of usage-centered design that has proved particularly effective in designing highly usable Web- based applications. Fully compatible with both traditional object-oriented software engineering methods and newer agile techniques such as Extreme Programming, this approach employs rapid, card-based techniques to develop simplified models of user roles, tasks, and user interface contents. The process attempts to

Larry L. Constantine; Lucy A. D. Lockwood

2002-01-01

335

[Depersonalization after withdrawal from cannabis usage].  

PubMed

The phenomenon of depersonalization during cannabis usage (intoxication) is commonly known. However, its appearance after drug stoppage is relatively unknown. This article reviews the literature on depersonalization after cannabis withdrawal and discusses three representing cases demonstrating the severity of the problem. Clinical features are described as well as effects on functioning and the long-term nature of this disorder. The treatment approach in each case is also presented. PMID:15889607

Shufman, E; Lerner, A; Witztum, E

2005-04-01

336

Flexible diaphragm-extreme temperature usage  

NASA Technical Reports Server (NTRS)

A diaphragm suitable for extreme temperature usage, such as encountered in critical aerospace applications, is fabricated by a unique method, and of a unique combination of materials. The materials include multilayered lay-ups of diaphragm materials sandwiched between layers of bleeder fabrics. After being formed in the desired shape on a mold, they are vacuum sealed and then cured under pressure, in a heated autoclave. A bond capable of withstanding extreme temperatures are produced.

Lerma, Guillermo (inventor)

1991-01-01

337

Space Shuttle Usage of z/OS  

NASA Technical Reports Server (NTRS)

This viewgraph presentation gives a detailed description of the avionics associated with the Space Shuttle's data processing system and its usage of z/OS. The contents include: 1) Mission, Products, and Customers; 2) Facility Overview; 3) Shuttle Data Processing System; 4) Languages and Compilers; 5) Application Tools; 6) Shuttle Flight Software Simulator; 7) Software Development and Build Tools; and 8) Fun Facts and Acronyms.

Green, Jan

2009-01-01

338

Usage-style centered research for creative product design  

Microsoft Academic Search

The purpose of this paper is to present systemic creative product design methods based on usage-style. According to the basic meanings of usage-style, the logical hierarchical structure of usage-style was outlined and established. Combining with product design principle, this work focused on the product values system and product structure system, established the design frameworks of `value forming from usage-style' and

Wu Zhi-jun; Li Liang-zhi; Na Cheng-ai; Xing Jiang-hao

2009-01-01

339

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

PubMed Central

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, ?2 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 268 subjects (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.

Utama, Andi; Siburian, Marlinang Diarta; Fanany, Ismail; Intan, Mariana Destila Bayu; Dhenni, Rama; Kurniasih, Tri Shinta; Lelosutan, Syafruddin AR; Achwan, Wenny Astuti; Zubir, Nasrul; Arnelis; Lukito, Benyamin; Yusuf, Irawan; Lesmana, Laurentius Adrianus; Sulaiman, Ali

2012-01-01

340

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

Microsoft Academic Search

BACKGROUND: Models of codon evolution have proven useful for investigating the strength and direction of natural selection. In some cases, a priori biological knowledge has been used successfully to model heterogeneous evolutionary dynamics among codon sites. These are called fixed-effect models, and they require that all codon sites are assigned to one of several partitions which are permitted to have

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

2007-01-01

341

A Structural Equation Model for ICT Usage in Higher Education  

ERIC Educational Resources Information Center

This study focuses on Information and Communication Technologies (ICT) usage, which is the indicator of diffusion. A model composed of the variables which can explain ICT usage in Turkish higher education is established and tested within the study. The two dimensions of ICT usage are considered: instructional and managerial. The data collected…

Usluel, Yasemin Kocak; Askar, Petek; Bas, Turgay

2008-01-01

342

Preparation of an ochre suppressor tRNA recognizing exclusively UAA codon by using the molecular surgery technique.  

PubMed

In order to create an ochre suppressor tRNA which exclusively recognizes UAA codon, we replaced the G34 at the first position of yeast tRNA(Tyr)[GPsiA] anticodon with pseudouridine34 (Psi34) by using the molecular surgery technique. This tRNA(Tyr)[PsiPsiA] recognized only the UAA codon as expectedly, but tRNA(Tyr)[UPsiA] made as a control also behaved similarly. This result may suggest that U34 must be somehow modified to facilitate the wobble-pairing to G at the third position of codon. PMID:19749377

Yokogawa, Takashi; Hassan, Hanim Munirah Binti Che; Yokota, Yukiko; Ohno, Satoshi; Nishikawa, Kazuya

2009-01-01

343

Amino termini of many yeast proteins map to downstream start codons.  

PubMed

Comprehensive knowledge of proteome complexity is crucial to understanding cell function. Amino termini of yeast proteins were identified through peptide mass spectrometry on glutaraldehyde-treated cell lysates as well as a parallel assessment of publicly deposited spectra. An unexpectedly large fraction of detected amino-terminal peptides (35%) mapped to translation initiation at AUG codons downstream of the annotated start codon. Many of the implicated genes have suboptimal sequence contexts for translation initiation near their annotated AUG, and their ribosome profiles show elevated tag densities consistent with translation initiation at downstream AUGs as well as their annotated AUGs. These data suggest that a significant fraction of the yeast proteome derives from initiation at downstream AUGs, increasing significantly the repertoire of encoded proteins and their potential functions and cellular localizations. PMID:23140384

Fournier, Claire T; Cherny, Justin J; Truncali, Kris; Robbins-Pianka, Adam; Lin, Miin S; Krizanc, Danny; Weir, Michael P

2012-12-01

344

In vitro readthrough of termination codons by gentamycin in the Stüve-Wiedemann Syndrome.  

PubMed

The Stüve-Wiedemann Syndrome (SWS) is a frequently lethal chondrodysplasia caused by null mutations in the leukemia inhibitory factor receptor gene (LIFR) responsible for an impaired activation of the JAK-STAT pathway after LIF stimulation. Most LIFR mutations are nonsense mutations, thus prompting us to investigate the impact of aminoglycosides on the readthrough of premature termination codons (PTCs). Culturing skin fibroblasts from three SWS patients and controls for 48 h in the presence of gentamycin (200-500 microg/ml) partially restored the JAK-STAT3 pathway when stimulated by LIF. Consistently, quantitative RT-PCR analysis showed that gentamycin stabilized LIFR mRNAs carrying UGA premature termination codons. We conclude that high gentamycin concentrations can partially restore functional LIFR protein synthesis in vitro, prompting us to investigate PTC readthrough using less toxic and more efficient drugs in this presently untreatable lethal condition. PMID:19603067

Bellais, Samuel; Le Goff, Carine; Dagoneau, Nathalie; Munnich, Arnold; Cormier-Daire, Valérie

2010-01-01

345

Efficient suppression of the amber codon in E. coli in vitro translation system.  

PubMed

An mRNA encoding the esterase from Alicyclobacillus acidocaldarius with catalytically essential serine codon (ACG) replaced by an amber (UAG) codon was used to study the suppression in in vitro translation system. Suppression of UAG by tRNA(Ser(CUA)) was monitored by determination of the full-length and active esterase. It was shown that commonly used increase of suppressor tRNA concentration inhibits protein production and therefore limits suppression. In situ deactivation of release factor by specific antibodies leads to efficient suppression already at low suppressor tRNA concentration and allows an in vitro synthesis of fully active enzyme in high yield undistinguishable from wild-type protein. PMID:15811334

Agafonov, Dmitry E; Huang, Yiwei; Grote, Michael; Sprinzl, Mathias

2005-04-11

346

Amino Termini of Many Yeast Proteins Map to Downstream Start Codons  

PubMed Central

Comprehensive knowledge of proteome complexity is crucial to understanding cell function. Amino termini of yeast proteins were identified through peptide mass spectrometry on glutaraldehyde-treated cell lysates as well as a parallel assessment of publicly-deposited spectra. An unexpectedly large fraction of detected amino-terminal peptides (35%) mapped to translation initiation at AUG codons downstream of the annotated start codon. Many of the implicated genes have suboptimal sequence contexts for translation initiation near their annotated AUG, and their ribosome profiles show elevated tag densities consistent with translation initiation at downstream AUGs as well as their annotated AUGs. These data suggest that a significant fraction of the yeast proteome derives from initiation at downstream AUGs, increasing significantly the repertoire of encoded proteins and their potential functions and cellular localizations.

Fournier, Claire T.; Cherny, Justin J.; Truncali, Kris; Robbins-Pianka, Adam; Lin, Miin S.; Krizanc, Danny; Weir, Michael P.

2012-01-01

347

HIV-2 genomic RNA contains a novel type of IRES located downstream of its initiation codon.  

PubMed

Eukaryotic translation initiation begins with assembly of a 48S ribosomal complex at the 5' cap structure or at an internal ribosomal entry segment (IRES). In both cases, ribosomal positioning at the AUG codon requires a 5' untranslated region upstream from the initiation site. Here, we report that translation of the genomic RNA of human immunodeficiency virus type 2 takes place by attachment of the 48S ribosomal preinitiation complex to the coding region, with no need for an upstream 5' untranslated RNA sequence. This unusual mechanism is mediated by an RNA sequence that has features of an IRES with the unique ability to recruit ribosomes upstream from its core domain. A combination of translation assays and structural studies reveal that sequences located 50 nucleotides downstream of the AUG codon are crucial for IRES activity. PMID:16244661

Herbreteau, Cécile H; Weill, Laure; Décimo, Didier; Prévôt, Déborah; Darlix, Jean-Luc; Sargueil, Bruno; Ohlmann, Théophile

2005-11-01

348

Rabbit liver tRNA1Val:I. Primary structure and unusual codon recognition.  

PubMed Central

The major valine acceptor tRNA1Val from rabbit liver was purified and its nucleotide sequence determined by in vitro [32P] - labeling with T4 phage induced polynucleotide kinase and finger-printing techniques. Its primary structure was found to be identical with the major valine tRNA from mouse myeloma cells. According to the wobble hypothesis this tRNA, which exclusively has an IAC anticodon, should decode the valine codons GUU, GUC and GUA only. However, this tRNA recognizes all four valine codons with a surprising preference for GUG. It is unknown whether this is due to the lack of A37 modification next to the 3' end of the anticodon IAC. The nature of the inosine-guanosine interaction remains to be clarified.

Jank, P; Shindo-Okada, N; Nishimura, S; Gross, H J

1977-01-01

349

Translation of CGA codon repeats in yeast involves quality control components and ribosomal protein L1.  

PubMed

Translation of CGA codon repeats in the yeast Saccharomyces cerevisiae is inefficient, resulting in dose-dependent reduction in expression and in production of an mRNA cleavage product, indicative of a stalled ribosome. Here, we use genetics and translation inhibitors to understand how ribosomes respond to CGA repeats. We find that CGA codon repeats result in a truncated polypeptide that is targeted for degradation by Ltn1, an E3 ubiquitin ligase involved in nonstop decay, although deletion of LTN1 does not improve expression downstream from CGA repeats. Expression downstream from CGA codons at residue 318, but not at residue 4, is improved by deletion of either ASC1 or HEL2, previously implicated in inhibition of translation by polybasic sequences. Thus, translation of CGA repeats likely causes ribosomes to stall and exploits known quality control systems. Expression downstream from CGA repeats at amino acid 4 is improved by paromomycin, an aminoglycoside that relaxes decoding specificity. Paromomycin has no effect if native tRNA(Arg(ICG)) is highly expressed, consistent with the idea that failure to efficiently decode CGA codons might occur in part due to rejection of the cognate tRNA(Arg(ICG)). Furthermore, expression downstream from CGA repeats is improved by inactivation of RPL1B, one of two genes encoding the universally conserved ribosomal protein L1. The effects of rpl1b-? and of either paromomycin or tRNA(Arg(ICG)) on CGA decoding are additive, suggesting that the rpl1b-? mutant suppresses CGA inhibition by means other than increased acceptance of tRNA(Arg(ICG)). Thus, inefficient decoding of CGA likely involves at least two independent defects in translation. PMID:23825054

Letzring, Daniel P; Wolf, Andrew S; Brule, Christina E; Grayhack, Elizabeth J

2013-09-01

350

Codons of Consciousness: Neurological Characteristics of Ordinary and Pathological States of Consciousness  

Microsoft Academic Search

\\u000a It may eventually be possible to identify completely the temporal sequences of electrical microstates that underlie consciousness.\\u000a From these “codons of consciousness” a DNA-like mathematical model of normal sequencing of the “atoms of thought” could be\\u000a constructed and matched to subjective experience and behaviour. This would allow the prediction of thought and behaviour from\\u000a the building blocks of consciousness. Having

Gerard A. Kennedy

351

Examination of the function of two kelch proteins generated by stop codon suppression  

Microsoft Academic Search

The Drosophila kelch gene produces a single transcript with a UGA stop codon separating two open reading frames (ORF1 and ORF2). From the transcript, 76 kDa ORF1 and 160 kDa full-length (ORF1 + ORF2) proteins are made. The expression of these two proteins is regulated in a tissue- specific manner causing the ratio of full-length to ORF1 protein to vary

Douglas N. Robinson; Lynn Cooley

352

Codon optimization significantly improves the expression level of a keratinase gene in Pichia pastoris.  

PubMed

The main keratinase (kerA) gene from the Bacillus licheniformis S90 was optimized by two codon optimization strategies and expressed in Pichia pastoris in order to improve the enzyme production compared to the preparations with the native kerA gene. The results showed that the corresponding mutations (synonymous codons) according to the codon bias in Pichia pastoris were successfully introduced into keratinase gene. The highest keratinase activity produced by P. pastoris pPICZ?A-kerAwt, pPICZ?A-kerAopti1 and pPICZ?A-kerAopti2 was 195 U/ml, 324 U/ml and 293 U/ml respectively. In addition, there was no significant difference in biomass concentration, target gene copy numbers and relative mRNA expression levels of every positive strain. The molecular weight of keratinase secreted by recombinant P. pastori was approx. 39 kDa. It was optimally active at pH 7.5 and 50°C. The recombinant keratinase could efficiently degrade both ?-keratin (keratin azure) and ?-keratin (chicken feather meal). These properties make the P. pastoris pPICZ?A-kerAopti1 a suitable candidate for industrial production of keratinases. PMID:23472192

Hu, Hong; Gao, Jie; He, Jun; Yu, Bing; Zheng, Ping; Huang, Zhiqing; Mao, Xiangbing; Yu, Jie; Han, Guoquan; Chen, Daiwen

2013-01-01

353

Enhanced activity of meso-secondary alcohol dehydrogenase from Klebsiella species by codon optimization.  

PubMed

Meso-secondary alcohol dehydrogenases (meso-SADH) from Klebsiella oxytoca KCTC1686 and Klebsiella pneumoniae KCTC2242 were codon optimized and expressed in Escherichia coli W3110. The published gene data of K. pneumoniae NTUH-K2044 (NCBI accession number AP006725), K. pneumoniae 342 (NCBI accession number CP000964), and K. pneumoniae MGH 78578 (NCBI accession number CP000647), were compared with the meso-SADH sequences of each strain, respectively. Codon-optimized meso-SADH enzymes of K. oxytoca and K. pneumoniae showed approximately twofold to fivefold increased enzyme activities for acetoin reduction over native enzymes. The highest activities for each strain were obtained at 30-37 °C and pH 6-7 (yielding 203.1 U/mg of protein and 156.5 U/mg of protein, respectively). The increased enzyme activity of the codon-optimized enzymes indicated that these modified enzymes could convert acetoin into 2,3-butanediol with a high yield. PMID:23053416

Lee, Soojin; Kim, Borim; Oh, Minkyu; Kim, Youngrok; Lee, Jinwon

2013-07-01

354

Relationship between p53 gene codon-72 polymorphisms and hypertrophic scar formation following caesarean section  

PubMed Central

The aim of the present study was to determine the relationship between p53 gene codon-72 polymorphisms and hypertrophic scar formation following caesarean section (CS). Blood samples from 260 female patients were collected one week following a CS for the detection of p53 gene polymorphisms using a molecular beacon-coupled quantitative polymerase chain reaction technique. Patients had follow-ups for 12–18 months to observe the scar formation. From these observations, the relationship between the p53 codon-72 polymorphisms and hypertrophic scar formation occurrence was investigated. Among the patients with the CCC/CCC genotype, nine patients had hypertrophic scars and 46 patients showed normal healing, which is a ratio of 0.19. However, the follow-up investigations indicated that the presence of a homozygous or heterozygous C-to-G alteration at the codon-72 site in gene p53 resulted in 13 patients with hypertrophic scars and 192 patients with normal healing, which is a ratio of 0.07. Therefore, these results indicate that patients with the CCC/CCC genotype had a higher risk of developing hypertrophic scars compared with that for patients with the CCC/CGC or CGC/CGC genotypes.

GAO, JIANHUA; CHEN, YING; LIAO, NONG; ZHAO, WEI; ZENG, WEISEN; LI, YINGTAO; WANG, SHAOJING; LU, FENG

2014-01-01

355

Widespread polymorphism in the positions of stop codons in Drosophila melanogaster.  

PubMed

The mechanisms underlying evolutionary changes in protein length are poorly understood. Protein domains are lost and gained between species and must have arisen first as within-species polymorphisms. Here, we use Drosophila melanogaster population genomic data combined with between species divergence information to understand the evolutionary forces that generate and maintain polymorphisms causing changes in protein length in D. melanogaster. Specifically, we looked for protein length variations resulting from premature termination codons (PTCs) and stop codon losses (SCLs). We discovered that 438 genes contained polymorphisms resulting in truncation of the translated region (PTCs) and 119 genes contained polymorphisms predicted to lengthen the translated region (SCLs). Stop codon polymorphisms (SCPs) (especially PTCs) appear to be more deleterious than other polymorphisms, including protein amino acid changes. Genes harboring SCPs are in general less selectively constrained, more narrowly expressed, and enriched for dispensable biological functions. However, we also observed exceptional cases such as genes that have multiple independent SCPs, alleles that are shared between D. melanogaster and Drosophila simulans, and high-frequency alleles that cause extreme changes in gene length. SCPs likely have an important role in the evolution of these genes. PMID:22051795

Lee, Yuh Chwen G; Reinhardt, Josephine A

2012-01-01

356

A codon-optimized luciferase from Gaussia princeps facilitates the in vivo monitoring of gene expression in the model alga Chlamydomonas reinhardtii  

PubMed Central

The unicellular green alga Chlamydomonas reinhardtii has emerged as a superb model species in plant biology. Although the alga is easily transformable, the low efficiency of transgene expression from the Chlamydomonas nuclear genome has severely hampered functional genomics research. For example, poor transgene expression is held responsible for the lack of sensitive reporter genes to monitor gene expression in vivo, analyze subcellular protein localization or study protein–protein interactions. Here, we have tested the luciferase from the marine copepod Gaussia princeps (G-Luc) for its suitability as a sensitive bioluminescent reporter of gene expression in Chlamydomonas. We show that a Gaussia luciferase gene variant, engineered to match the codon usage in the Chlamydomonas nuclear genome, serves as a highly sensitive reporter of gene expression from both constitutive and inducible algal promoters. Its bioluminescence signal intensity greatly surpasses previously developed reporters for Chlamydomonas nuclear gene expression and reaches values high enough for utilizing the reporter as a tool to monitor responses to environmental stresses in vivo and to conduct high-throughput screenings for signaling mutants in Chlamydomonas.

Shao, Ning

2008-01-01

357

Does the clinical phenotype of fatal familial insomnia depend on PRNP codon 129 methionine-valine polymorphism?  

PubMed

Fatal familial insomnia (FFI) is a rare, hereditary prion-protein disease. Methionine-valine polymorphism at codon 129 of the prion-protein gene (PRNP) determines the phenotype in other hereditary prion-protein diseases, but association with the clinical phenotype in FFI remains uncertain. Early clinical findings in FFI comprise disturbances of the sleep-wake cycle and mild neuropsychiatric changes which typically emerge during middle to late adulthood. Here we describe an unusually early onset and rapid progression of FFI associated with dorsal midbrain involvement in a female patient with PRNP mutation at codon 178 and homozygote methionine polymorphism at codon 129. Early dorsal midbrain involvement became apparent by total loss of REM sleep and isolated bilateral trochlear nerve palsy. Early onset and rapid progression disease type associated with dorsal midbrain involvement may indicate a different spatiotemporal distribution of the neurodegenerative process in FFI patients with PRNP mutation and codon 129 methionine homozygosity compared to methioninevaline heterozygosity. PMID:24340298

Rupprecht, Sven; Grimm, Alexander; Schultze, Torsten; Zinke, Jan; Karvouniari, Panagiota; Axer, Hubertus; Witte, Otto W; Schwab, Matthias

2013-01-01

358

Correlation between the development of extracolonic manifestations in FAP patients and mutations beyond codon 1403 in the APC gene.  

PubMed Central

The APC gene was investigated in 31 unrelated polyposis coli families by SSCP analysis and the protein truncation test. Twenty-three germline mutations were identified which gave rise to a variety of different phenotypes. Some of these mutations have already been described; however we report six previously unpublished mutations. Typical disease symptoms were observed in families who harboured mutations between exon 4 (codon 169) and codon 1393 of exon 15. Mutations beyond codon 1403 were associated with more varied phenotype with respect to the development of extracolonic symptoms. In this report we provide support for the notion that there appears to be a correlation between the location of an APC mutation (beyond codon 1403) and extracolonic manifestations of familial adenomatous polyposis. Images

Dobbie, Z; Spycher, M; Mary, J L; Haner, M; Guldenschuh, I; Hurliman, R; Amman, R; Roth, J; Muller, H; Scott, R J

1996-01-01

359

Near-cognate suppression of amber, opal and quadruplet codons competes with aminoacyl-tRNAPyl for genetic code expansion  

PubMed Central

Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to ‘statistical protein’ that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNAPyl orthogonal pair cannot completely outcompete contamination by natural amino acids.

O'Donoghue, Patrick; Prat, Laure; Heinemann, Ilka U.; Ling, Jiqiang; Odoi, Keturah; Liu, Wenshe R.; Soll, Dieter

2012-01-01

360

Self-catalytic DNA Depurination Underlies Human ?-Globin Gene Mutations at Codon 6 That Cause Anemias and Thalassemias*  

PubMed Central

The human ?-globin gene contains an 18-nucleotide coding strand sequence centered at codon 6 and capable of forming a stem-loop structure that can self-catalyze depurination of the 5?G residue of that codon. The resultant apurinic lesion is subject to error-prone repair, consistent with the occurrence about this codon of mutations responsible for 6 anemias and ?-thalassemias and additional substitutions without clinical consequences. The 4-residue loop of this stem-loop-forming sequence shows the highest incidence of mutation across the gene. The loop and first stem base pair-forming residues appeared early in the mammalian clade. The other stem-forming segments evolved more recently among primates, thereby conferring self-depurination capacity at codon 6. These observations indicate a conserved molecular mechanism leading to ?-globin variants underlying phenotypic diversity and disease.

Alvarez-Dominguez, Juan R.; Amosova, Olga; Fresco, Jacques R.

2013-01-01

361

Allelic frequency and genotypes of prion protein at codon 136 and 171 in Iranian Ghezel sheep breeds.  

PubMed

PrP genotypes at codons 136 and 171 in one hundred twenty Iranian Ghezel sheep breeds were studied using allele-specific PCR amplification and compared with the well-known sheep breeds in North America, the United States, and Europe. The frequency of V allele and VV genotype at codon 136 of Ghezel sheep breed was significantly lower than AA and AV. At codon 171, the frequency of allele H was significantly lower than Q and R. Despite the similarities of PrP genotypes at codons 136 and 171 between Iranian Ghezel sheep breeds and some of the studied breeds, significant differences were found with others. Planning of effective breeding control and successful eradication of susceptible genotypes in Iranian Ghezel sheep breeds will not be possible unless the susceptibility of various genotypes in Ghezel sheep breeds to natural or experimental scrapie has been elucidated. PMID:21778818

Salami, Siamak; Zadeh, Reza Ashrafi; Omrani, Mir Davood; Ramezani, Fatemeh; Amniattalab, Amir

2011-01-01

362

Allelic frequency and genotypes of prion protein at codon 136 and 171 in Iranian Ghezel sheep breeds  

PubMed Central

PrP genotypes at codons 136 and 171 in 120 Iranian Ghezel sheep breeds were studied using allele-specific PCR amplification and compared with the well-known sheep breeds in North America, the United States and Europe. The frequency of V allele and VV genotype at codon 136 of Ghezel sheep breed was significantly lower than AA and AV. At codon 171, the frequency of allele H was significantly lower than Q and R. Despite the similarities of PrP genotypes at codons 136 and 171 between Iranian Ghezel sheep breeds and some of the studied breeds, significant differences were found with others. Planning of effective breeding control and successful eradication of susceptible genotypes in Iranian Ghezel sheep breeds will not be possible unless the susceptibility of various genotypes in Ghezel sheep breeds to natural or experimental scrapie has been elucidated.

Zadeh, Reza Ashrafi; Omrani, Mir Davood; Ramezani, Fatemeh; Amniattalab, Amir

2011-01-01

363

XPD codon 312 and 751 polymorphisms, and AFB1 exposure, and hepatocellular carcinoma risk  

PubMed Central

Background Genetic polymorphisms in DNA repair genes may influence individual variation in DNA repair capacity, which may be associated with risk of hepatocellular carcinoma (HCC) related to the exposure of aflatoxin B1 (AFB1). In this study, we have focused on the polymorphisms of xeroderma pigmentosum complementation group D (XPD) codon 312 and 751 (namely Asp312Asn and Lys751Gln), involved in nucleotide excision repair. Methods We conducted a case-control study including 618 HCC cases and 712 controls to evaluate the associations between these two polymorphisms and HCC risk for Guangxi population by means of TaqMan-PCR and PCR-RFLP analysis. Results We found that individuals featuring the XPD genotypes with codon 751 Gln alleles (namely XPD-LG or XPD-GG) were related to an elevated risk of HCC compared to those with the homozygote of XPD codon 751 Lys alleles [namely XPD-LL, adjusted odds ratios (ORs) were 1.75 and 2.47; 95% confidence interval (CIs) were 1.30-2.37 and 1.62-3.76, respectively]. A gender-specific role was evident that showed an higher risk for women (adjusted OR was 8.58 for XPD-GG) than for men (adjusted OR = 2.90 for XPD-GG). Interestingly, the interactive effects of this polymorphism and AFB1-exposure information showed the codon 751 Gln alleles increase the risk of HCC for individuals facing longer exposure years (Pinteraction = 0.011, OR = 0.85). For example, long-exposure-years (> 48 years) individuals who carried XDP-GG had an adjusted OR of 470.25, whereas long-exposure-years people with XDP-LL were at lower risk (adjusted OR = 149.12). However, we did not find that XPD codon 312 polymorphism was significantly associated with HCC risk. Conclusion These findings suggest that XPD Lys751Gln polymorphism is an important modulator of AFB1 related-HCC development in Guangxi population.

2009-01-01

364

Contrast in Usage of FCAT-Approved Anatomical Terminology Between Members of Two Anatomy Associations in North America  

NSDL National Science Digital Library

This article describes the outcomes of a AAA survey comparing the frequency of FCAT term usage among HAPS instructors. The survey had already been conducted among AAA members and comparisons between societies were made. An initial reporting of the differences and similarities among societies and anatomy teaching backgrounds are discussed.

Bradford Martin (Loma Linda University Physical Therapy)

2009-11-04

365

Usage analysis of user files in UNIX  

NASA Technical Reports Server (NTRS)

Presented is a user-oriented analysis of short term file usage in a 4.2 BSD UNIX environment. The key aspect of this analysis is a characterization of users and files, which is a departure from the traditional approach of analyzing file references. Two characterization measures are employed: accesses-per-byte (combining fraction of a file referenced and number of references) and file size. This new approach is shown to distinguish differences in files as well as users, which cam be used in efficient file system design, and in creating realistic test workloads for simulations. A multi-stage gamma distribution is shown to closely model the file usage measures. Even though overall file sharing is small, some files belonging to a bulletin board system are accessed by many users, simultaneously and otherwise. Over 50% of users referenced files owned by other users, and over 80% of all files were involved in such references. Based on the differences in files and users, suggestions to improve the system performance were also made.

Devarakonda, Murthy V.; Iyer, Ravishankar K.

1987-01-01

366

Convergence and constraint in eukaryotic release factor 1 (eRF1) domain 1: the evolution of stop codon specificity  

PubMed Central

Class 1 release factor in eukaryotes (eRF1) recognizes stop codons and promotes peptide release from the ribosome. The ‘molecular mimicry’ hypothesis suggests that domain 1 of eRF1 is analogous to the tRNA anticodon stem–loop. Recent studies strongly support this hypothesis and several models for specific interactions between stop codons and residues in domain 1 have been proposed. In this study we have sequenced and identified novel eRF1 sequences across a wide diversity of eukaryotes and re-evaluated the codon-binding site by bioinformatic analyses of a large eRF1 dataset. Analyses of the eRF1 structure combined with estimates of evolutionary rates at amino acid sites allow us to define the residues that are under structural (i.e. those involved in intramolecular interactions) versus non-structural selective constraints. Furthermore, we have re-assessed convergent substitutions in the ciliate variant code eRF1s using maximum likelihood-based phylogenetic approaches. Our results favor the model proposed by Bertram et al. that stop codons bind to three ‘cavities’ on the protein surface, although we suggest that the stop codon may bind in the opposite orientation to the original model. We assess the feasibility of this alternative binding orientation with a triplet stop codon and the eRF1 domain 1 structures using molecular modeling techniques.

Inagaki, Yuji; Blouin, Christian; Doolittle, W. Ford; Roger, Andrew J.

2002-01-01

367

Association between mismatch repair gene MSH3 codons 1036 and 222 polymorphisms and sporadic prostate cancer in the Iranian population.  

PubMed

The mismatch repair system (MMR) is a post-replicative DNA repair mechanism whose defects can lead to cancer. The MSH3 protein is an essential component of the system. We postulated that MSH3 gene polymorphisms might therefore be associated with prostate cancer (PC). We studied MSH3 codon 222 and MSH3 codon 1036 polymorphisms in a group of Iranian sporadic PC patients. A total of 60 controls and 18 patients were assessed using the polymerase chain reaction and single strand conformational polymorphism. For comparing the genotype frequencies of patients and controls the chi-square test was applied. The obtained result indicated that there was significantly association between G/A genotype of MSH3 codon 222 and G/G genotype of MSH3 codon 1036 with an increased PC risk (P=0.012 and P=0.02 respectively). Our results demonstrated that MSH3 codon 222 and MSH3 codon 1036 polymorphisms may be risk factors for sporadic prostate cancer in the Iranian population. PMID:23464402

Jafary, Fariba; Salehi, Mansoor; Sedghi, Maryam; Nouri, Nayereh; Jafary, Farzaneh; Sadeghi, Farzaneh; Motamedi, Shima; Talebi, Maede

2012-01-01

368

A third mutation at the CpG dinucleotide of codon 504 and a silent mutation at codon 506 of the HEX A gene.  

PubMed Central

Two CpG mutations at codon 504 of the gene encoding the alpha-subunit of beta-hexosaminidase (the HEX A gene) have been identified previously: (1) a C deletion resulting in premature termination of the alpha-subunit and (2) a G----A transition resulting in 504Arg----His substitution, in patients with infantile Tay-Sachs disease and juvenile GM2 gangliosidosis, respectively. This prompted a search for a C----T transition in the same dinucleotide, as would be expected from the mechanism of CpG mutagenesis. Such a mutation, which results in a substitution of cysteine for arginine, was found in a patient with chronic GM2 gangliosidosis, in compound heterozygosity with the known 269Gly----Ser allele. The biochemical phenotype of the 504Arg----Cys mutation was examined by site-directed mutagenesis of the alpha-subunit cDNA and transfection of Cos-1 cells. The expression of the mutagenized cDNA with the cysteine substitution gave rise to an alpha-subunit with the same defects as those resulting from expression of mutagenized cDNA with the histidine substitution--i.e., secretion primarily as the alpha-monomer rather than as the alpha alpha dimer, along with absence of enzymatic activity. The 504Arg----Cys/269Gly----Ser genotype of the chronic GM2 gangliosidosis patient is shared by her sibling, who has mild adult-onset GM2 gangliosidosis, implying that the clinical differences between them must be attributed to other factors. The family is unique in yet another respect--namely, that the normal allele of the mother and of a 504Arg----Cys heterozygous sibling has a silent mutation, a G----A transition in the wobble position of the glutamic acid codon at position 506.(ABSTRACT TRUNCATED AT 250 WORDS) Images Figure 1 Figure 2 Figure 3

Paw, B H; Wood, L C; Neufeld, E F

1991-01-01

369

Individuals' Decision to Co-Donate or Donate Alone: An Archival Study of Married Whole Body Donors in Hawaii  

PubMed Central

Background Human cadavers are crucial to numerous aspects of health care, including initial and continuing training of medical doctors and advancement of medical research. Concerns have periodically been raised about the limited number of whole body donations. Little is known, however, about a unique form of donation, namely co-donations or instances when married individuals decide to register at the same time as their spouse as whole body donors. Our study aims to determine the extent of whole body co-donation and individual factors that might influence co-donation. Methods and Findings We reviewed all records of registrants to the University of Hawaii Medical School’s whole body donation program from 1967 through 2006 to identify married registrants. We then examined the 806 married individuals’ characteristics to understand their decision to register alone or with their spouse. We found that married individuals who registered at the same time as their spouse accounted for 38.2 percent of married registrants. Sex differences provided an initial lens to understand co-donation. Wives were more likely to co-donate than to register alone (p?=?0.002). Moreover, registrants’ main occupational background had a significant effect on co-donations (p?=?0.001). Married registrants (regardless of sex) in female-gendered occupations were more likely to co-donate than to donate alone (p?=?0.014). Female-gendered occupations were defined as ones in which women represented more than 55 percent of the workforce (e.g., preschool teachers). Thus, variations in donors’ occupational backgrounds explained co-donation above and beyond sex differences. Conclusions Efforts to secure whole body donations have historically focused on individual donations regardless of donors’ marital status. More attention needs to be paid, however, to co-donations since they represent a non-trivial number of total donations. Also, targeted outreach efforts to male and female members of female-gendered occupations might prove a successful way to increase donations through co-donations.

Anteby, Michel; Garip, Filiz; Martorana, Paul V.; Lozanoff, Scott

2012-01-01

370

Identification of TTA codon containing genes in Frankia and exploration of the role of tRNA in regulating these genes.  

PubMed

The TTA codon, one of the six available codons for the amino acid leucine, is the rarest codon among the high GC genomes of Actinobacteria including Frankia. This codon has been implicated in various regulatory mechanisms involving secondary metabolism and morphological development. TTA-mediated gene regulation is well documented in Streptomyces coelicolor, but that role has not been investigated in other Actinobacteria including Frankia. Among the various Actinomycetes with a GC content of more than 70%, Frankia genomes had the highest percentages of TTA-containing genes ranging from 5.2 to 10.68% of the genome. In contrast, TTA-bearing genes comprised 1.7, 3.4 and 4.1% of the Streptomyces coelicolor, S. avermitilis and Nocardia farcinia genomes, respectively. We analyzed their functional role, evolutionary significance, horizontal acquisition and the codon-anticodon interaction. The TTA-bearing genes were found to be well represented in metabolic genes involved in amino acid transport and secondary metabolism. A reciprocal Blast search reveal that many of the TTA-bearing genes have orthologs in the other Frankia genomes, and some of these orthologous genes also have a TTA codon in them. The gene expression level of TTA-containing genes was estimated by the use of the codon adaption index (CAI), and the CAI values were found to have a positive correlation with the GC3 (GC content at the 3rd codon position). A full-atomic 3D model of the leucine tRNA recognizing the TTA (UUA) codon was generated and utilized for in silico docking to determine binding affinity in codon-anticodon interaction. We found a proficient codon-anticodon interaction for this codon which is perhaps why so many genes hold on to this rare codon without compromising their translational efficiency. PMID:21773800

Sen, Arnab; Thakur, Subarna; Bothra, Asim K; Sur, Saubashya; Tisa, Louis S

2012-01-01

371

Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine  

PubMed Central

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes.

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

372

Configuration of wobble base pairs having pyrimidines as anticodon wobble bases: significance for codon degeneracy.  

PubMed

Degeneracy of the genetic code was attributed by Crick to imprecise hydrogen-bonded base-pairing at the wobble position during codon-anticodon pairing. The Crick wobble rules define but do not explain the RNA base pair combinations allowed at this position. We select six pyrimidine bases functioning as anticodon wobble bases (AWBs) to study their H-bonded pairing properties with the four major RNA bases using density functional theory at the B3LYP/6-31G(d,p) level. This is done to assess the extent to which the configuration of a solitary RNA wobble base pair may in itself determine specificity and degeneracy of the genetic code by allowing or disallowing the given base pair during codon-anticodon pairing. Calculated values of select configuration markers for the base pairs screen well between allowed and disallowed base pairs for most cases examined here, where the base pair width emerges as an important factor. A few allowed wobble pairs invoke the involvement of RNA nucleoside conformation, as well as involvement of the exocyclic substituent in H-bonding. This study, however, cannot explain the disallowed status of the Ura?Gua wobble pair on the basis of configuration alone. Explanation of the allowed status of the V?Ura pair requires further study on the mediatory role of water molecules. Apart from these two cases, these computational results are sufficient, on the basis of base pair configuration alone, to account for the specificity and degeneracy of the genetic code for all known cases of codon-anticodon pairing which involve the pyrimidine AWBs studied here. PMID:23968386

Das, Gunajyoti; Duncan Lyngdoh, R H

2014-09-01

373

Expression studies of mutant factor VIII alleles with premature termination codons with regard to inhibitor formation.  

PubMed

About 10% of mutations in haemophilia A cases generate a premature termination codon in the factor VIII gene (F8). Upon therapeutic FVIII substitution, it was noted that the risk of developing inhibitors is higher when the nonsense mutation is located in the light chain (LC) of the factor VIII (FVIII) protein than in the heavy chain (HC). We analysed the impact of six different nonsense mutations distributed over the six FVIII domains on recombinant FVIII expression to elucidate the process of inhibitor formation in haemophilic patients. Full-length F8 mRNA was transcribed from all constructs despite the presence of nonsense mutations. Polyclonal antigen assays revealed high antigen levels in transfection experiments with constructs truncated in LC whereas low antigen was detected from constructs truncated in HC. Those results were supported by FVIII localization experiments. These findings suggest that F8 transcription occurs in a usual way despite nonsense mutations, whereas translation appears to be interrupted by the premature stop codon. We hypothesize that the inclusion of the B domain enables proteins truncated in LC to accumulate in the ER. Proteins truncated in HC are mainly degraded or may pass through the ER and be secreted into the blood circulation, thus presumably preventing inhibitor formation after therapeutic FVIII substitution. The LC is known to have higher immunogenicity than the HC. Moreover, translation of the F8B gene comprising F8 exons 23-26 may be dependent on the position of the premature stop codon and thus contributes to the immune response of truncated FVIII proteins. PMID:24602271

Zimmermann, M A; Oldenburg, J; Müller, C R; Rost, S

2014-05-01

374

Different modes of stop codon restriction by the Stylonychia and Paramecium eRF1 translation termination factors  

PubMed Central

In universal-code eukaryotes, a single-translation termination factor, eukaryote class-1 polypeptide release factor (eRF1), decodes the three stop codons: UAA, UAG, and UGA. In some ciliates, like Stylonychia and Paramecium, eRF1s exhibit UGA-only decoding specificity, whereas UAG and UAA are reassigned as sense codons. Because variant-code ciliates may have evolved from universal-code ancestor(s), structural features should exist in ciliate eRF1s that restrict their stop codon recognition. In omnipotent eRF1s, stop codon recognition is associated with the N-terminal domain of the protein. Using both in vitro and in vivo assays, we show here that chimeric molecules composed of the N-terminal domain of Stylonychia eRF1 fused to the core domain (MC domain) of human eRF1 retained specificity toward UGA; this unambiguously associates eRF1 stop codon specificity to the nature of its N-terminal domain. Functional analysis of eRF1 chimeras constructed by swapping ciliate N-terminal domain sequences with the matching ones from the human protein highlighted the crucial role of the tripeptide QFM in restricting Stylonychia eRF1 specificity toward UGA. Using the site-directed mutagenesis, we show that Paramecium eRF1 specificity toward UGA resides within the NIKS (amino acids 61–64) and YxCxxxF (amino acids 124–131) motifs. Thus, we establish that eRF1 from two different ciliates relies on different molecular mechanisms to achieve specificity toward the UGA stop codon. This finding suggests that eRF1 restriction of specificity to only UGA might have been an early event occurring in independent instances in ciliate evolutionary history, possibly facilitating the reassignment of UAG and UAA to sense codons.

Lekomtsev, Sergey; Kolosov, Petr; Bidou, Laure; Frolova, Ludmila; Rousset, Jean-Pierre; Kisselev, Lev

2007-01-01

375

Clinical atovaquone-proguanil resistance of Plasmodium falciparum associated with cytochrome b codon 268 mutations.  

PubMed

Plasmodium falciparum resistance to atovaquone-proguanil has so far been associated with Y268S or Y268N mutations in cytochrome b, although these changes were identified in only seven of the 11 treatment failures. Here, we describe 10 new cases of atovaquone-proguanil treatment failures among which the parasite resistance was confirmed in six cases, either by identifying correct plasma drug concentrations or by observing in vitro atovaquone resistance. Resistance was consistently associated with codon 268 mutations (Y268S or a previously unidentified mutation, Y268C). Notably, mutations were not detected before the treatment but only after the drug exposure. PMID:16962361

Musset, Lise; Bouchaud, Olivier; Matheron, Sophie; Massias, Laurent; Le Bras, Jacques

2006-09-01

376

Constitutive high-level expression of a codon-optimized ?-fructosidase gene from the hyperthermophile Thermotoga maritima in Pichia pastoris.  

PubMed

Enzymes for use in the sugar industry are preferred to be thermotolerant. In this study, a synthetic codon-optimized gene encoding a highly thermostable ?-fructosidase (BfrA, EC 3.2.1.26) from the bacterium Thermotoga maritima was expressed in the yeast Pichia pastoris. The gradual increase of the transgene dosage from one to four copies under the control of the constitutive glyceraldehyde 3-phosphate dehydrogenase promoter had an additive effect on BfrA yield without causing cell toxicity. Maximal values of cell biomass (115 g/l, dry weight) and overall invertase activity (241 U/ml) were reached at 72 h in fed-batch fermentations using cane sugar as the main carbon source for growth. Secretion driven by the Saccharomyces cerevisiae ?-factor signal peptide resulted in periplasmic retention (44 %) and extracellular release (56 %) of BfrA. The presence of N-linked oligosaccharides did not influence the optimal activity, thermal stability, kinetic properties, substrate specificity, and exo-type action mode of the yeast-secreted BfrA in comparison to the native unglycosylated enzyme. Complete inversion of cane sugar at initial concentration of 60 % (w/v) was achieved by periplasmic BfrA in undisrupted cells reacting at pH 5.5 and 70 °C, with average productivity of 4.4 g of substrate hydrolyzed per grams of biomass (wet weight) per hour. The high yield of fully active glycosylated BfrA here attained by recombinant P. pastoris in a low-cost fermentation process appears to be attractive for the large-scale production of this thermostable enzyme useful for the manufacture of inverted sugar syrup. PMID:22821437

Menéndez, Carmen; Martínez, Duniesky; Trujillo, Luis E; Mazola, Yuliet; González, Ernesto; Pérez, Enrique R; Hernández, Lázaro

2013-02-01

377

Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 3' nucleotide to the codon has a context effect.  

PubMed Central

Codon context can affect translational efficiency by several molecular mechanisms. The base stacking interactions between a codon-anticodon complex and the neighboring nucleotide immediately 3' can facilitate translation by amber suppressors and the tRNA structure is also known to modulate the sensitivity to context. In this study the relative rates of aminoacyl-tRNA selection were measured at four sense codons (UGG, CUC, UUC and UCA), in all four 3' nucleotide contexts, through direct competition with a programmed frameshift at a site derived from the release factor 2 gene. Two codons (UGG and UUC) are read by tRNAs with small variable regions and their rates of aminoacyl-tRNA selection correlated with the potential base stacking strength of the 3' neighboring nucleotide. The other two codons (CUC and UCA) are read by tRNAs with large variable regions and the rate of selection of the aminoacyl-tRNAs in these cases varied little among the four contexts. Re-examination of published data on amber suppression also revealed an inverse correlation between context sensitivity and the size of the variable region. Collectively the data suggest that a large variable loop in a tRNA decreases the influence of the 3' context on tRNA selection, probably by strengthening tRNA-ribosomal interactions.

Curran, J F; Poole, E S; Tate, W P; Gross, B L

1995-01-01

378

File Usage Analysis and Resource Usage Prediction: a Measurement-Based Study. Ph.D. Thesis  

NASA Technical Reports Server (NTRS)

A probabilistic scheme was developed to predict process resource usage in UNIX. Given the identity of the program being run, the scheme predicts CPU time, file I/O, and memory requirements of a process at the beginning of its life. The scheme uses a state-transition model of the program's resource usage in its past executions for prediction. The states of the model are the resource regions obtained from an off-line cluster analysis of processes run on the system. The proposed method is shown to work on data collected from a VAX 11/780 running 4.3 BSD UNIX. The results show that the predicted values correlate well with the actual. The coefficient of correlation between the predicted and actual values of CPU time is 0.84. Errors in prediction are mostly small. Some 82% of errors in CPU time prediction are less than 0.5 standard deviations of process CPU time.

Devarakonda, Murthy V.-S.

1987-01-01

379

Does the Clinical Phenotype of Fatal Familial Insomnia Depend on PRNP codon 129 Methionine-Valine Polymorphism?  

PubMed Central

Fatal familial insomnia (FFI) is a rare, hereditary prion-protein disease. Methionine-valine polymorphism at codon 129 of the prion-protein gene (PRNP) determines the phenotype in other hereditary prion-protein diseases, but association with the clinical phenotype in FFI remains uncertain. Early clinical findings in FFI comprise disturbances of the sleep-wake cycle and mild neuropsychiatric changes which typically emerge during middle to late adulthood. Here we describe an unusually early onset and rapid progression of FFI associated with dorsal midbrain involvement in a female patient with PRNP mutation at codon 178 and homozygote methionine polymorphism at codon 129. Early dorsal midbrain involvement became apparent by total loss of REM sleep and isolated bilateral trochlear nerve palsy. Early onset and rapid progression disease type associated with dorsal midbrain involvement may indicate a different spatiotemporal distribution of the neurodegenerative process in FFI patients with PRNP mutation and codon 129 methionine homozygosity compared to methioninevaline heterozygosity. Citation: Rupprecht S; Grimm A; Schultze T; Zinke J; Karvouniari P; Axer H; Witte OW; Schwab M. Does the clinical phenotype of fatal familial insomnia depend on PRNP codon 129 methionine-valine polymorphism? J Clin Sleep Med 2013;9(12):1343-1345.

Rupprecht, Sven; Grimm, Alexander; Schultze, Torsten; Zinke, Jan; Karvouniari, Panagiota; Axer, Hubertus; Witte, Otto W.; Schwab, Matthias

2013-01-01

380

Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon  

SciTech Connect

The primary structure of human apolipoprotein (apo) B-48 has been deduced and shown by a combination of DNA excess hybridization, sequencing of tryptic peptides, cloned complementary DNAs, and intestinal messenger RNAs (mRNAs) to be the product of an intestinal mRNA with an in-frame UAA stop codon resulting from a C to U change in the codon CAA encoding Gln/sup 2153/ in apoB-100 mRNA. The carboxyl-terminal Ile/sup 2152/ of apoB-48 purified from chylous ascites fluid has apparently been cleaved from the initial translation product, leaving Met/sup 2151/ as the new carboxyl-terminus. These data indicate that approx.85% of the intestinal mRNAs terminate within approx. 0.1 to 1.0 kilobase downstream from the stop codon. The other approx. 15% have lengths similar to hepatic apoB-100 mRNA even though they have the same in-frame stop codon. The organ-specific introduction of a stop codon to a mRNA appears unprecedented and might have implications for cryptic polyadenylation signal recognition and RNA processing.

Chen, S.H.; Habib, G.; Yang, C.Y.; Gu, Z.W.; Lee, B.R.; Weng, S.A.; Silberman, S.R.; Cai, S.J.; Deslypere, J.P.; Rosseneu, M.; Gotton, A.M. Jr.

1987-10-16

381

Experience with the use of the Codonics Safe Label System(™) to improve labelling compliance of anaesthesia drugs.  

PubMed

The Codonics Safe Labeling System(™) (http://www.codonics.com/Products/SLS/flash/) is a piece of equipment that is able to barcode scan medications, read aloud the medication and the concentration and print a label of the appropriate concentration in the appropriate colour code. We decided to test this system in our facility to identify risks, benefits and usability. Our project comprised a baseline survey (25 anaesthesia cases during which 212 syringes were prepared from 223 drugs), an observational study (47 cases with 330 syringes prepared) and a user acceptability survey. The baseline compliance with all labelling requirements was 58%. In the observational study the compliance using the Codonics system was 98.6% versus 63.8% with conventional labelling. In the user acceptability survey the majority agreed the Codonics machine was easy to use, more legible and adhered with better security than the conventional preprinted label. However, most were neutral when asked about the likelihood of flexibility and customisation and were dissatisfied with the increased workload. Our findings suggest that the Codonics labelling machine is user-friendly and it improved syringe labelling compliance in our study. However, staff need to be willing to follow proper labelling workflow rather than batch label during preparation. Future syringe labelling equipment developers need to concentrate on user interface issues to reduce human factor and workflow problems. Support logistics are also an important consideration prior to implementation of any new labelling system. PMID:24967766

Ang, Sbl; Hing, Wc; Tung, Sy; Park, T

2014-07-01

382

Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria  

PubMed Central

The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic biology. Here we report a novel reassignment event in the mitochondria of Ashbya (Eremothecium) gossypii, a filamentous-growing plant pathogen related to yeast (Saccharomycetaceae). Bioinformatics studies of conserved positions in mitochondrial DNA-encoded proteins suggest that CUU and CUA codons correspond to alanine in A. gossypii, instead of leucine in the standard code or threonine in yeast mitochondria. Reassignment of CUA to Ala was confirmed at the protein level by mass spectrometry. We further demonstrate that a predicted is transcribed and accurately processed in vivo, and is responsible for Ala reassignment. Enzymatic studies reveal that is efficiently recognized by A. gossypii mitochondrial alanyl-tRNA synthetase (AgAlaRS). AlaRS typically recognizes the G3:U70 base pair of tRNAAla; a G3A change in Ashbya abolishes its recognition by AgAlaRS. Conversely, an A3G mutation in Saccharomyces cerevisiae confers tRNA recognition by AgAlaRS. Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched.

Ling, Jiqiang; Daoud, Rachid; Lajoie, Marc J.; Church, George M.; Soll, Dieter; Lang, B. Franz

2014-01-01

383

Codon optimization for high level expression of human bone morphogenetic protein-2 in Escherichia coli.  

PubMed

Codons in the open reading frame (ORF) encoding for human bone morphogenetic protein-2 (hBMP-2) were optimized to reach high level expression in Escherichia coli. The optimization was done by the computer programs DNA works and DNA Star according to Thermodynamically Balanced Inside Out (TBIO) approach. The ORF consisting of 342 base pairs (bp) was assembled using two-steps Polymerase Chain Reaction, cloned into a pGEM-T vector with a mutation rate of 6.38 bp per kb and transformed into E. coli JM109. After a DNA sequence confirmation, mutation-free ORF was subcloned into pET32b and transformed into E. coli BL21(DE3). The rhBMP-2 was produced as a thioredoxin-his-tag fusion protein at relatively high level, approximately 60% of total intracellular proteins as inclusion bodies (IB), with a yield of 1.39 g per liter culture. Solubilization of IB gave soluble monomer rhBMP-2 with a recovery of 13.6% and refolding of soluble rhBMP-2 produced dimeric forms with a yield of 8.7%. The size and identity of the purified rhBMP-2 was confirmed by nano-LC-MS/MS2 analysis. Our work demonstrates for the first time that by using TBIO approach, a codon-optimized ORF encoding for rhBMP-2 protein can be expressed at high level in E. coli expression system. PMID:22691543

Retnoningrum, Debbie S; Pramesti, H T; Santika, P Y; Valerius, O; Asjarie, S; Suciati, T

2012-08-01

384

Start/stop codon like trinucleotides extensions in primate alpha satellites.  

PubMed

The centromeres remain "the final frontier" in unexplored segments of genome landscape in primate genomes, characterized by 2-5 Mb arrays of evolutionary rapidly evolving alpha satellite (AS) higher order repeats (HORs). Alpha satellites as specific noncoding sequences may be also significant in light of regulatory role of noncoding sequences. Using the Global Repeat Map (GRM) algorithm we identify in NCBI assemblies of chromosome 5 the species-specific alpha satellite HORs: 13mer in human, 5mer in chimpanzee, 14mer in orangutan and 3mers in macaque. The suprachromosomal family (SF) classification of alpha satellite HORs and surrounding monomeric alpha satellites is performed and specific segmental structure was found for major alpha satellite arrays in chromosome 5 of primates. In the framework of our novel concept of start/stop Codon Like Trinucleotides (CLTs) as a "new DNA language in noncoding sequences", we find characteristics and differences of these species in CLT extensions, in particular the extensions of stop-TGA CLT. We hypothesize that these are regulators in noncoding sequences, acting at a distance, and that they can amplify or weaken the activity of start/stop codons in coding sequences in protein genesis, increasing the richness of regulatory phenomena. PMID:23026763

Rosandi?, Marija; Glun?i?, Matko; Paar, Vladimir

2013-01-21

385

Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy.  

PubMed

Weak protein-protein interactions are critical in numerous biological processes. Unfortunately, they are difficult to characterize due to the high concentrations required for the production and detection of the complex population. The inherent sensitivity of NMR spectroscopy to the chemical environment makes it an excellent tool to tackle this problem. NMR permits the exploration of interactions over a range of affinities, yielding essential insights into dynamic biological processes. The conversion of messanger RNA to protein is one such process that requires the coordinated association of many low-affinity proteins. During start codon recognition, eukaryotic initiation factors assemble into high-order complexes that bind messanger RNA and bring it to the ribosome for decoding. Many of the structures of the eukaryotic initiation factors have been determined; however, little is known regarding the weak binary complexes formed and their structure-function mechanisms. Herein, we use start codon recognition as a model system to review the relevant NMR methods for the characterization of weak interactions and the development of small molecule inhibitors. PMID:24393460

Luna, Rafael E; Akabayov, Sabine R; Ziarek, Joshua J; Wagner, Gerhard

2014-04-01

386

Codon optimisation improves the expression of Trichoderma viride sp. endochitinase in Pichia pastoris.  

PubMed

The mature cDNA of endochitinase from Trichoderma viride sp. was optimised based on the codon bias of Pichia pastoris GS115 and synthesised by successive PCR; the sequence was then transformed into P. pastoris GS115 via electroporation. The transformant with the fastest growth rate on YPD plates containing 4?mg/mL G418 was screened and identified. This transformant produced 23.09?U/mL of the recombinant endochitinase, a 35% increase compared to the original strain bearing the wild-type endochitinase cDNA. The recombinant endochitinase was sequentially purified by ammonia sulphate precipitation, DE-52 anion-exchange chromatography and Sephadex G-100 size-exclusion chromatography. Thin-layer chromatography indicated that the purified endochitinase could hydrolyse chito-oligomers or colloidal chitin to generate diacetyl-chitobiose (GlcNAc)? as the main product. This study demonstrates (1) a means for high expression of Trichoderma viride sp. endochitinase in P. pastoris using codon optimisation and (2) the preparation of chito-oligomers using endochitinase. PMID:24154717

Yu, Ping; Yan, Yuan; Gu, Qing; Wang, Xiangyang

2013-01-01

387

In VitroCodon-Reading Specificities of Unmodified tRNA Molecules with Different Anticodons on the Sequence Background of Escherichia colitRNA Ser 1  

Microsoft Academic Search

The codon-reading properties of wobble-position variants of the unmodified form ofEscherichia colitRNASer1(the UGA anticodon) were measured in a cell-free translation system. Two variants, with the AGA and CGA anticodons, each exclusively read a single codon, UCU and UCG, respectively. The only case of efficient wobbling occurred with the variant with the GGA anticodon, which reads the UCU codon in addition

Kazuyuki Takai; Hiroshi Takaku; Shigeyuki Yokoyama

1999-01-01

388

40 CFR 52.254 - Organic solvent usage.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false Organic solvent usage. 52.254 Section 52...IMPLEMENTATION PLANS California § 52.254 Organic solvent usage. (a) This section...the atmosphere more than 15 pounds of organic materials in any 1 day or more than...

2013-07-01

389

Mobile Phone Usage Behavior of University Students in Oman  

Microsoft Academic Search

The purpose of this paper is to study the mobile phone usage behavior of university students in Oman. A survey was conducted in Muscat and Sohar cities of Oman where 200 students were contacted using questionnaires and interview methods. Students in higher educational institutions were covered and hypotheses about mobile services usage among students were formulated and tested on different

Rakesh Belwal; Shweta Belwal

2009-01-01

390

The Relationship between Teacher's Technology Integration Ability and Usage  

ERIC Educational Resources Information Center

Despite a steady supply of equipment and continuous training, teachers' use of computers for instruction seems to be limited. Whether the problem is due to teachers' ability or usage of computers for instruction is not well understood. In order to better understand the role of ability and usage in technology integration, teachers' proficiency of…

Hsu, Shihkuan

2010-01-01

391

Effects of Different Metaphor Usage on Hypertext Learning  

ERIC Educational Resources Information Center

There are many studies that offer different opinions on the effects of hypertext usage as an educational tool. Given the differences of opinion, it is useful to research the effects of metaphor usage in hypertext education and the use of hypertext as an educational tool. In this study, the effects of metaphors' uses in constructing the…

Merdivan, Ece; Ozdener, Nesrin

2011-01-01

392

Women Veterans: Usage of VA (Veterans Administration) Hospitalization.  

National Technical Information Service (NTIS)

This is a revision of a report relating to the usage of veterans' hospitalization benefits by women (Women Veterans Usage of VA Hospitalization, Aug. 1982, VA/82-7009). This revision updates VA hospital data through 1983, and also incorporates the latest ...

W. F. Page D. Stockford

1984-01-01

393

Reviewing and Critiquing Computer Learning and Usage among Older Adults  

ERIC Educational Resources Information Center

By searching the keywords of "older adult" and "computer" in ERIC, Academic Search Premier, and PsycINFO, this study reviewed 70 studies published after 1990 that address older adults' computer learning and usage. This study revealed 5 prominent themes among reviewed literature: (a) motivations and barriers of older adults' usage of computers, (b)…

Kim, Young Sek

2008-01-01

394

Reduced usage phase impact using demand side management  

Microsoft Academic Search

Determining whether an appliance should be reused or recycled is an important environmental issue. Reducing the life cycle impact of appliance is paramount. The argument for recycling focuses on the usage phase of appliances accounting for more than 80% of the life cycle impact. In order to deduce what the actual environmental effects of the usage phase, cumulative energy demand

P. Finn; M. O'Connell; C. Fitzpatrick

2011-01-01

395

(Not) Hearing Optional Subjects: The Effects of Pragmatic Usage Preferences  

ERIC Educational Resources Information Center

Previous research has shown that usage preferences (non-categorical constraints on the distribution of syntactic structures) shape many grammatical alternations. In the present study, we show that usage preferences also influence which alternate listeners report hearing when presented with acoustically degraded input. We investigated the English…

Mack, Jennifer E.; Clifton, Charles, Jr.; Frazier, Lyn; Taylor, Patrick V.

2012-01-01

396

Emotions as determinants of electric car usage intention  

Microsoft Academic Search

In a sample of 1202 Belgians, the determining factors of the usage intention of an electric car and the differences between early and late usage intention segments are investigated. The Theory of Planned Behaviour (TPB) framework is extended with emotional reactions towards the electric car and car driving in general. Emotions and the attitude towards the electric car are the

Ingrid Moons; Patrick De Pelsmacker

2012-01-01

397

Benchmarking Usage Statistics in Collection Management Decisions for Serials  

ERIC Educational Resources Information Center

Usage statistics are an important metric for making decisions on serials. Although the University of Nevada, Las Vegas (UNLV) Libraries have been collecting usage statistics, the statistics had not frequently been used to make decisions and had not been included in collection development policy. After undergoing a collection assessment, the…

Tucker, Cory

2009-01-01

398

Premarital Contraceptives Usage among Male and Female Adolescents.  

ERIC Educational Resources Information Center

Variables important in predicting female contraception usage were found to be those which involved dyadic commitment, conditions of love, self-esteem, and father's occupation (social class). The best predictors of male contraception usage involved experience in dating and internalization of role models via mother's and father's permissiveness.…

Hornick, Joesph P.; And Others

1979-01-01

399

Characterizing data usage patterns in a large cellular network  

Microsoft Academic Search

Using heterogeneous data sources collected from one of the largest 3G cellular networks in the US over three months, in this paper we investigate the usage patterns of mobile data users. We observe that data usage across mobile users are highly uneven. Most of the users access data services occasionally, while a small number of heavy users contribute to a

Yu Jin; Nick Duffield; Alexandre Gerber; Patrick Haffner; Wen-Ling Hsu; Guy Jacobson; Subhabrata Sen; Shobha Venkataraman; Zhi-Li Zhang

2012-01-01

400

New Trends in Web Usage Patterns and Web Traffic.  

ERIC Educational Resources Information Center

As the Web is expanding, the Web traffic is changing, and so are the users. To get an adequate understanding of the Web as a medium, it is of paramount importance to know the users and the dominant usage patterns. The purpose of this paper is to map important aspects of Web usage patterns, Web traffic and Web search behavior. Issues dealt with…

Jensen, Jens F.

401

Reviewing prescription spending and accessory usage.  

PubMed

This article aims to explore the role of the stoma nurse specialist in the community and how recent initiatives within the NHS have impacted on the roles in stoma care to react to the rising prescription costs in the specialty. The article will explore how the stoma care nurse conducted her prescription reviews within her own clinical commissioning group (CCG). The findings of the reviews will be highlighted by a small case history and a mini audit that reveals that some stoma patients may be using their stoma care accessories inappropriately, which may contribute to the rise in stoma prescription spending. To prevent the incorrect use of stoma appliances it may necessitate an annual review of ostomates (individuals who have a stoma), as the author's reviews revealed that inappropriate usage was particularly commonplace when a patient may have not been reviewed by a stoma care specialist for some considerable amount of time. Initial education of the ostomate and ongoing education of how stoma products work is essential to prevent the misuse of stoma appliances, particularly accessories, as the reviews revealed that often patients were not always aware of how their products worked in practice. PMID:24642774

Oxenham, Julie

402

[Optimizing the expression of Mx gene in Escherichia coli based on rare codon and mRNA structure].  

PubMed

Rare codon and mRNA secondary structure of translation initiation region were analyzed. Four bioengineered bacterium BL21(DE3)/pET-Mx, Rosseta (DE3)/pET-Mx, BL21(DE3)/pGEX-Mx, and Rosseta (DE3)/pGEX-Mx were obtained. Through optimizing the rare codon and mRNA secondary structure of translation initiation region, Mx protein was expressed in Rosseta (DE3)/pET-Mx, and Rosseta (DE3)/pGEX-Mx. The specified product of 75 kDa was detected by means of Western blotting analysis. The result showed that Rosetta (DE3) strain expressing some rare codon used in our experiment can obtain Mx protein expression, and the lower energy of mRNA structure can improve the expression level of Mx protein. This is the first report on the expression of the full open reading frame of Mx gene. PMID:19138905

Yin, Chun-Guang; DU, Li-Xin; Zhao, Gui-Ping; Li, Hong-Bin

2009-01-01

403

No association of the p53 codon 72 polymorphism with malaria in Ghanaian primiparae and Rwandan children.  

PubMed

The p53 protein is a key cell-signaling mediator integrating host responses to various types of stress. A common polymorphism of the encoding TP53 gene (codon 72, Pro > Arg, rs1042522) is associated with susceptibility to virus-related and other cancers. The p53 has also been shown to be central for successful Plasmodium liver stage infection. We examined whether the polymorphism is associated with P. falciparum infection in Ghanaian primiparae and Rwandan children. The allele frequency of TP53 codon 72 Arg was 0.30 among 314 Ghanaian primiparae and 0.31 among 545 Rwandan children, respectively, and it was not associated with infection prevalence or parasite density. This does not exclude p53 to be of pathophysiological relevance in malaria but argues against a major respective role of the TP53 codon 72 polymorphism. PMID:24710610

Gai, Prabhanjan P; Meese, Stefanie; Bedu-Addo, George; Gahutu, Jean Bosco; Mockenhaupt, Frank P

2014-06-01

404

Transcripts of a heterologous gene encoding mite allergen Der f 7 are stabilized by codon optimization in Aspergillus oryzae.  

PubMed

We have previously demonstrated that transcripts of an AT-biased heterologous gene encoding mite allergen Der f 7 from Dermatophagoides farinae were polyadenylated prematurely within the coding region when native cDNA was expressed in Aspergillus oryzae, and that this premature polyadenylation was prevented by the codon optimization of the Der f 7 gene, resulting in increased steady-state mRNA levels. In this study, we tested the stability of transcription products derived from expression constructs of the native and codon-optimized Der f 7 gene in A. oryzae using 1,10-phenanthroline as a transcription inhibitor. Transcription products of native Der f 7 cDNA fused to the A. oryzae glucoamylase gene (glaA) were rapidly degraded; the half-life of the mRNA was approximately 13 min. However, the half-life of codon-optimized Der f 7 mRNA fused to glaA was approximately 43 min, which was highly similar to that of endogenous glaA mRNA. These results indicate that Der f 7 mRNA is significantly stabilized by codon optimization. In addition, Der f 7 mRNA was stabilized by the codon optimization of only the 3'-half region, where premature polyadenylation sites were exclusively situated; the half-life of the chimeric Der f 7 mRNA was approximately 39 min. This suggested that destabilization of native Der f 7 mRNA is mainly triggered by premature polyadenylation within the coding region. To the best of our knowledge, this is the first report to provide experimental evidence that heterologous mRNA is significantly stabilized by codon optimization in eukaryotic cells. PMID:22644529

Tanaka, Mizuki; Tokuoka, Masafumi; Shintani, Takahiro; Gomi, Katsuya

2012-12-01

405

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

PubMed Central

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

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

2012-01-01

406

Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells  

PubMed Central

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 codon re-encoding provides important information on the evolution and genetic stability of CHIKV viruses and could be exploited to develop a safe, live attenuated CHIKV vaccine.

Nougairede, Antoine; De Fabritus, Lauriane; Aubry, Fabien; Gould, Ernest A.; Holmes, Edward C.; de Lamballerie, Xavier

2013-01-01

407

Angiosperm divergence times: the effect of genes, codon positions, and time constraints.  

PubMed

An understanding of the evolution of modern terrestrial ecosystems requires an understanding of the dynamics associated with angiosperm evolution, including the timing of their origin and diversification into their extraordinary present-day diversity. Molecular estimates of angiosperm age have varied widely, and many substantially predate the Early Cretaceous fossil appearance of the group. In this study, the effect of different genes, codon positions, and chronological constraints on node ages are examined on divergence time estimates across seed plants, with a special focus on angiosperms. Penalized likelihood was used to estimate divergence times on a phylogenetic hypothesis for seed plants derived from Bayesian analysis, with branch lengths estimated with maximum likelihood. The plastid genes atpB, psaA, psbB, and rbcL were used individually and in combination, using first and second, third, and the three codon positions, including and excluding age constraints on 20 nodes derived from a critical examination of the land-plant fossil record. The optimal level of rate smoothing according to each unconstrained and constrained dataset was obtained with penalized likelihood. Tests for a molecular clock revealed significantly unclocklike rates in all datasets. Addition of fossil constraints resulted in even greater departures from constancy. Consistently with significant deviations from a clock, estimated optimal smoothing values were low, but a strict correlation between rate heterogeneity and optimal smoothing value was not found. Age estimates for nodes across the phylogeny varied, sometimes substantially, with gene and codon position. Nevertheless, estimates based on the four concatenated genes are very similar to the mean of the four individual gene estimates. For any given node, unconstrained age estimates are more variable than constrained estimates and are frequently younger than well-substantiated fossil members of the clade. Constrained estimates of ages of clades are older than unconstrained estimates and oldest fossil representatives, sometimes substantially so. Angiosperm age estimates decreased as rate smoothing increased. Whereas the range of unconstrained angiosperm age estimates spans the fossil age of the clade, the range of constrained estimates is narrower (and older) than the earliest angiosperm fossils. Results unambiguously indicate the relevance of constraints in reducing the variability of ages derived from different partitions of the data and diminishing the effect of the smoothing parameter. Constrained optimizations of divergence times and substitution rates across the phylogeny suggest appreciably different evolutionary dynamics for angiosperms and for gymnosperms. Whereas the gymnosperm crown group originated shortly after the origin of seed plants, a long time elapsed before the origin of crown group angiosperms. Although absolute age estimates of angiosperms and angiosperm clades are older than their earliest fossils, the estimated pace of phylogenetic diversification largely agrees with the rapid appearance of angiosperm lineages in stratigraphic sequences. PMID:16329238

Magallón, Susana A; Sanderson, Michael J

2005-08-01

408

Application Examples for Handle System Usage  

NASA Astrophysics Data System (ADS)

Besides the well-known DOI (Digital Object Identifiers) as a special form of Handles that resolve to scientific publications there are various other applications in use. Others perhaps are just not yet. We present some examples for the existing ones and some ideas for the future. The national German project C3-Grid provides a framework to implement a first solution for provenance tracing and explore unforeseen implications. Though project-specific, the high-level architecture is generic and represents well a common notion of data derivation. Users select one or many input datasets and a workflow software module (an agent in this context) to execute on the data. The output data is deposited in a repository to be delivered to the user. All data is accompanied by an XML metadata document. All input and output data, metadata and the workflow module receive Handles and are linked together to establish a directed acyclic graph of derived data objects and involved agents. Data that has been modified by a workflow module is linked to its predecessor data and the workflow module involved. Version control systems such as svn or git provide Internet access to software repositories using URLs. To refer to a specific state of the source code of for instance a C3 workflow module, it is sufficient to reference the URL to the svn revision or git hash. In consequence, individual revisions and the repository as a whole receive PIDs. Moreover, the revision specific PIDs are linked to their respective predecessors and become part of the provenance graph. Another example for usage of PIDs in a current major project is given in EUDAT (European Data Infrastructure) which will link scientific data of several research communities together. In many fields it is necessary to provide data objects at multiple locations for a variety of applications. To ensure consistency, not only the master of a data object but also its copies shall be provided with a PID. To verify transaction safety and to keep all copies consistent requires that the chain from master to copy and vice versa has to be resolvable, preferably through PIDs directly. As part of EUDAT necessary services are created on the basis of iRODS. These form the core structure of the data infrastructure developed within EUDAT. Though many implementations of PID systems already exist, many valuable web accessible data sources come with unresolvable identifiers like UUIDs, with instable recognition patterns like URLs, or even with proprietary implementations. However, other data collections would like to link to them in the data descriptions of their metadata. In addition, by usage of PIDs one can decouple the responsibilities for data and MD in projects where necessary. For some metadata entities like persons or even institutes it makes sense to give them single PIDs that point to contact and/or location information. ORCID (Open Researcher & Contributor ID), e.g., keeps track of persons working in scholarly fields, independent of name changes and linguistic variances. The ISO 27729 based International Standard Name Identifier (ISNI) also identifies legal entities and fictional characters besides natural persons. Other systems exist that, e.g., reference geographic localities. IDs of this kind may resolve to a URL where detailed information is given.

Toussaint, F.; Weigel, T.; Thiemann, H.; Höck, H.; Stockhause, M.; Lautenschlager, M.

2012-12-01

409

Energy Usage Optimisation in South African Mines  

NASA Astrophysics Data System (ADS)

In recent years, South Africa has encountered a critical electricity supply which necessitated the implementation of demand-side management (DSM) projects. Load shifting and energy (EE) efficiency projects were introduced in mining sector to reduce the electricity usage during day peak time. As the compressed air networks and the water pumping systems are using large amounts of the mines' electricity, possible ways were investigated and implemented to improve and optimise the energy consumption and to reduce the costs. Implementing DSM and EE in four different mines resulted in achieving the desired energy savings and load-shifting. W ostatnich latach w Po?udniowej Afryce zanotowano pewne trudno?ci z dostawami energii elektrycznej, co wymusi?o wdro?enie dzia?a? maj?cych na celu skuteczne zarz?dzanie zagadnieniami energetycznymi. Wprowadzono dzia?ania maj?ce na celu zmian? systemu obci??e? roboczych i bardziej efektywne wykorzystanie energii tak, by obni?y? zapotrzebowanie na energi? w trakcie szczytowych godzin w ci?gu dnia. Sieci dostarczaj?ce spr??one powietrze oraz stacje pomp zu?ywaj? znaczne ilo?ci energii w kopalni, przeanalizowano wi?c mo?liwe sposoby redukcji i optymalizacji zapotrzebowania na energi? i tym samym obni?enia kosztów produkcji. Wdro?enie odpowiednich projektów nakierowanych na oszcz?dno?ci i optymalizacj? w czterech kopalniach doprowadzi?o do oczekiwanych oszcz?dno?ci energii i umo?liwi?o zmian? systemu obci??e? roboczych w trakcie procesu produkcji.

Hasan, Ali; Twala, Bhekisipho; Ouahada, Khmaies; Marwala, Tshilidzi

2014-03-01

410

Intranet usage and potential in acute care hospitals in the United States: survey-2000.  

PubMed

This paper provides the results of the Survey-2000 measuring Intranet and its potential in health care. The survey measured the levels of Internet and Intranet existence and usage in acute care hospitals. Business-to-business electronic commerce and electronic commerce for customers were measured. Since the Intranet was not studied in survey-1997, no comparisons could be made. Therefore the results were presented and discussed. The Intranet data were compared with the Internet data and statistically significant differences were presented and analyzed. This information will assist hospitals to plan Internet and Intranet technology. This is the third of three articles based upon the results of the Survey-2000. Readers are referred to prior articles by the author, which discusses the survey design and provides a tutorial on technology transfer in acute care hospitals.(1) The first article based upon the survey results discusses technology transfer, system design approaches, user involvement, and decision-making purposes. (2) The second article based upon the survey results discusses distribution of Internet usage and rating of Internet usage applied to specific applications. Homepages, advertising, and electronic commerce are discussed from an Internet perspective. PMID:11708394

Hatcher, M

2001-12-01

411

Primitive molecular machine scenario for the origin of the three base codon composition.  

PubMed

We set up a scenario for the operation of primordial synthesis machines operating in outer space quasi one dimensional channels, where polymers interact with fixed particles. The scheme allows for polymerization, translocation and translation. We will show that under very general conditions the particle/polymer interaction potential has spatial regularities with an average distance of three between neighboring minima. We present a model that exhibits how primitive molecular machines may convert the structural properties of the potential into locomotion regularities. On average, polymer movement takes place by shifts with long time intervals every three displacements. We argue that this feature is generic and lies at the origin of the three base codon composition. PMID:10227203

Martínez-Mekler, G; Aldana, M; Cázarez-Bush, F; García-Pelayo, R; Cocho, G

1999-03-01

412

Codon randomization for rapid exploration of chemical space in thiopeptide antibiotic variants.  

PubMed

Thiopeptide antibiotics exhibit a profound level of chemical diversity that is installed through cascades of posttranslational modifications on ribosomal peptides. Here, we present a technique to rapidly explore the chemical space of the thiopeptide GE37468 through codon randomization, yielding insights into thiopeptide maturation as well as structure and activity relationships. In this incarnation of the methodology, we randomized seven residues of the prepeptide-coding region, enabling the generation of 133 potential thiopeptide variants. Variant libraries were subsequently queried in two ways. First, high-throughput MALDI-TOF mass spectrometry was applied to colony-level expressions to sample mutants that permitted full maturation of the antibiotic. Second, the activity of producing mutants was detected in an antibiotic overlay assay. In total, 29 of the 133 variants produced mature compound, 12 of which retained antibiotic activity and 1 that had improved activity. PMID:23261603

Young, Travis S; Dorrestein, Pieter C; Walsh, Christopher T

2012-12-21

413

p53 codon 72 polymorphism and Hematological Cancer Risk: An Update Meta-Analysis  

PubMed Central

Background Previous studies on the association of p53 codon 72 (Arg72Pro) polymorphism with hematological malignancies risk have produced conflicting results. The purpose of this meta-analysis is to define the effect of p53 Arg72Pro polymorphism on hematological malignancies risk. Methodology/Principal Findings Through searching PubMed databases (or hand searching) up to April 2012 using the following MeSH terms and keywords: “p53”, “codon 72” “polymorphism” and “leukemia”, or “lymphoma”, or “myeloma”, thirteen were identified as eligible articles in this meta-analysis for p53 Arg72Pro polymorphism (2,731 cases and 7, 356 controls), including nine studies on leukemia (1,266 cases and 4, 474 controls), three studies on lymphoma (1,359 cases and 2,652 controls), and one study on myeloma. The overall results suggested that p53 Arg72Pro polymorphism was not associated with hematological malignancies risk. In stratified analyses, significantly increased non-Hodgkin lymphomas risk was found in p53 Arg72Pro polymorphism heterozygote model (Arg/Pro vs. Arg/Arg: OR?=?1.18, 95%CI: 1.02–1.35) and dominant model (Arg/Pro+Pro/Pro vs. Arg/Arg: OR?=?1.18, 95%CI: 1.03–1.34), but no significant association was found between leukemia risk and p53 Arg72Pro polymorphism. Further studies showed no association between leukemia risk and p53 Arg72Pro polymorphism when stratified in subtypes of leukemias, ethnicities and sources of controls. Conclusions/Significance This meta-analysis indicates that the p53 Arg72Pro polymorphism may contribute to susceptibility to non-Hodgkin lymphomas.

Yuan, Guorong; Guo, Jing; Zhang, Zhizhong; Xie, Xinyou; Chen, Guangdi

2012-01-01

414

The Attenuated Genotype of Varicella-Zoster Virus Includes an ORF0 Transitional Stop Codon Mutation  

PubMed Central

Varicella-zoster virus (VZV) is the first of the human herpesviruses to be attenuated and subsequently approved as a live vaccine to prevent varicella and herpes zoster. Both the attenuated VZV vaccine, called vaccine Oka or vOka, and the parental strain pOka have been completely sequenced. Yet the specific determinants of attenuation are uncertain. The open reading frame (ORF) with the most single nucleotide polymorphisms (SNPs), ORF62, encodes the regulatory protein IE62, but IE62 studies have failed to define a specific SNP associated with attenuation. We have completed next-generation sequencing of the VZV Ellen genome, a strain known to be highly attenuated by its very limited replication in human skin xenografts in the SCID mouse model of VZV pathogenesis. A comparative analysis of the Ellen sequence with all other complete VZV sequences was extremely informative. In particular, an unexpected finding was a stop codon mutation in Ellen ORF0 (herpes simplex virus UL56 homolog) identical to one found in vOka, combined with the absence of polymorphisms in most Ellen ORFs that were known to be mutated in vOka. The mutated ORF0 protein was also imaged in both two dimensions and three dimensions by confocal microscopy. The probability of two VZV strains not connected by a recent common ancestor having an identical ORF0 SNP by chance would be 1 × 10?8, in other words, extremely unlikely. Taken together, these bioinformatics analyses strongly suggest that the stop codon ORF0 SNP is one of the determinants of the attenuation genotype of live VZV vaccines.

Peters, Geoffrey A.; Tyler, Shaun D.; Carpenter, John E.; Jackson, Wallen; Mori, Yasuko; Arvin, Ann M.

2012-01-01

415

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS  

PubMed Central

The ratio of divergence at nonsynonymous and synonymous sites, dN/dS, is a widely used measure in evolutionary genetic studies to investigate the extent to which selection modulates gene sequence evolution. Originally tailored to codon sequences of distantly related lineages, dN/dS represents the ratio of fixed nonsynonymous to synonymous differences. The impact of ancestral and lineage-specific polymorphisms on dN/dS, which we here show to be substantial for closely related lineages, is generally neglected in estimation techniques of dN/dS. To address this issue, we formulate a codon model that is firmly anchored in population genetic theory, derive analytical expressions for the dN/dS measure by Poisson random field approximation in a Markovian framework and validate the derivations by simulations. In good agreement, simulations and analytical derivations demonstrate that dN/dS is biased by polymorphisms at short time scales and that it can take substantial time for the expected value to settle at its time limit where only fixed differences are considered. We further show that in any attempt to estimate the dN/dS ratio from empirical data the effect of the intrinsic fluctuations of a ratio of stochastic variables, can even under neutrality yield extreme values of dN/dS at short time scales or in regions of low mutation rate. Taken together, our results have significant implications for the interpretation of dN/dS estimates, the McDonald–Kreitman test and other related statistics, in particular for closely related lineages.

Mugal, Carina F.; Wolf, Jochen B.W.; Kaj, Ingemar

2014-01-01

416

Role of p53 Codon 72 Arginine Allele in Cell Survival in vitro and in the Clinical Outcome of Patients with Advanced Breast Cancer  

Microsoft Academic Search

Background: The p53 codon 72 polymorphism, which results in either an arginine or proline residue, plays a different role in vitro and in vivo in cell survival and drug resistance. We verified, in vitro, the impact of the arginine allele on cell survival under normoxia and hypoxia, and investigated in vivo the role of p53 codon 72 arginine homozygosity in

I. Vannini; W. Zoli; A. Tesei; M. Rosetti; P. Sansone; G. Storci; A. Passardi; I. Massa; M. Ricci; D. Gusolfino; F. Fabbri; P. Ulivi; G. Brigliadori; D. Amadori; M. Bonafe

2008-01-01

417

The C-terminal amino acid sequence of nascent peptide is a major determinant of SsrA tagging at all three stop codons.  

PubMed Central

Recent studies on endogenous SsrA-tagged proteins have revealed that the tagging could occur at a position corresponding to the normal termination codon. During the study of SsrA-mediated Lacl tagging (Abo et al., EMBO J, 2000 19:3762-3769), we found that a variant Lacl (Lacl deltaC1) lacking the last C-terminal amino acid residue is efficiently tagged in a stop codon-dependent manner. SsrA tagging of Lacl deltaC1 occurred efficiently without Lacl binding to the lac operators at any one of three stop codons. The C-terminal (R)LESG peptide of Lacl deltaC1 was shown to trigger the SsrA tagging of an unrelated protein (CRP) when fused to its C terminus. Mass spectrometry analysis of the purified fusion proteins revealed that SsrA tagging occurs at a position corresponding to the termination codon. The alteration of the amino acid sequence but not the nucleotide sequence of the C-terminal portion eliminated the tagging. We also showed that the tagging-provoking sequences cause an efficient translational readthrough at UGA but not UAA codons. In addition, we found that C-terminal dipeptides known to induce an efficient translation readthrough could cause an efficient tagging at stop codons. We conclude that the amino acid sequence of nascent polypeptide prior to stop codons is a major determinant for the SsrA tagging at all three stop codons.

Sunohara, Takafumi; Abo, Tatsuhiko; Inada, Toshifumi; Aiba, Hiroji

2002-01-01

418

Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code  

Microsoft Academic Search

The nucleotide frequencies in the second codon positions of genes are remarkably different for the coding regions that correspond to different secondary structures in the encoded proteins, namely, helix, ?-strand and aperiodic structures. Indeed, hydrophobic and hydrophilic amino acids are encoded by codons having U or A, respectively, in their second position. Moreover, the ?-strand structure is strongly hydrophobic, while

Maria Luisa Chiusano; Fernando Alvarez-Valin; Massimo Di Giulio; Giuseppe D'Onofrio; Gaetano Ammirato; Giovanni Colonna; Giorgio Bernardi

2000-01-01

419