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1

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria  

E-print Network

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria Haruo SUZUKI 21 June 2008; accepted 24 September 2008) Abstract Synonymous codon usage varies both between sources of variation in synonymous codon usage among genes and provides a way to identify horizontally

Forney, Larry J.

2

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria  

E-print Network

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria Haruo SUZUKI 21 June 2008; accepted 24 September 2008; published online 21 October 2008) Abstract Synonymous codon) is widely used to identify major sources of variation in synonymous codon usage among genes and provides

Top, Eva

3

Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1  

PubMed Central

Two species of the DNA virus Torque teno sus virus (TTSuV), TTSuV1 and TTSuV2, have become widely distributed in pig-farming countries in recent years. In this study, we performed a comprehensive analysis of synonymous codon usage bias in 41 available TTSuV2 coding sequences (CDS), and compared the codon usage patterns of TTSuV2 and TTSuV1. TTSuV codon usage patterns were found to be phylogenetically conserved. Values for the effective number of codons (ENC) indicated that the overall extent of codon usage bias in both TTSuV2 and TTSuV1 was not significant, the most frequently occurring codons had an A or C at the third codon position. Correspondence analysis (COA) was performed and TTSuV2 and TTSuV1 sequences were located in different quadrants of the first two major axes. A plot of the ENC revealed that compositional constraint was the major factor determining the codon usage bias for TTSuV2. In addition, hierarchical cluster analysis of 41 TTSuV2 isolates based on relative synonymous codon usage (RSCU) values suggested that there was no association between geographic distribution and codon bias of TTSuV2 sequences. Finally, the comparison of RSCU for TTSuV2, TTSuV1 and the corresponding host sequence indicated that the codon usage pattern of TTSuV2 was similar to that of TTSuV1. However the similarity was low for each virus and its host. These conclusions provide important insight into the synonymous codon usage pattern of TTSuV2, as well as better understangding of the molecular evolution of TTSuV2 genomes. PMID:24303050

Dai, Dingzhen

2013-01-01

4

Comparison of correspondence analysis methods for synonymous codon usage in bacteria.  

PubMed

Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA. PMID:18940873

Suzuki, Haruo; Brown, Celeste J; Forney, Larry J; Top, Eva M

2008-12-01

5

Correlation matrix for quartet codon usage  

NASA Astrophysics Data System (ADS)

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

Frappat, L.; Sciarrino, A.; Sorba, P.

2005-06-01

6

Sum rules of codon usage probabilities  

E-print Network

In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A comparison with experimental data shows that the prediction is satisfied within about 5 %.

Frappat, L; Sorba, Paul

2003-01-01

7

Sum rules for codon usage probabilities  

NASA Astrophysics Data System (ADS)

In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A comparison between the theoretical predictions and the experimental data shows a satisfactory agreement.

Frappat, L.; Sciarrino, A.; Sorba, P.

2003-05-01

8

Codon Usage Domains over Bacterial Chromosomes  

E-print Network

Codon Usage Domains over Bacterial Chromosomes Marc Bailly-Bechet1 , Antoine Danchin2 , Mudassar Laboratory, University of Kent, Canterbury, Kent, United Kingdom The geography of codon bias distributions to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One

Kent, University of

9

Evolution of codon usage in bacteria.  

E-print Network

??Initially, this thesis investigates patterns of intragenomic codon usage within the genome of the Delta Proteobacterium Bdellovibrio bacteriovorus. Correspondence analyses revealed the primary factor influencing… (more)

Henry, Ian

2007-01-01

10

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency  

E-print Network

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency Wenfeng Qian1 , Jian-Rong Yang1 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

Zhang, Jianzhi

11

Universality and Shannon entropy of codon usage  

NASA Astrophysics Data System (ADS)

The distribution functions of codon usage probabilities, computed over all the available GenBank data for 40 eukaryotic biological species and five chloroplasts, are best fitted by the sum of a constant, an exponential, and a linear function in the rank of usage. For mitochondria the analysis is not conclusive. These functions are characterized by parameters that strongly depend on the total guanine and cytosine (GC) content of the coding regions of biological species. It is predicted that the codon usage is the same in all exonic genes with the same GC content. The Shannon entropy for codons, also strongly dependent on the exonic GC content, is computed.

Frappat, L.; Minichini, C.; Sciarrino, A.; Sorba, P.

2003-12-01

12

Evolution of Codon Usage Bias in Drosophila  

Microsoft Academic Search

We first review what is known about patterns of codon usage bias in Drosophila and make the following points: (i) Drosophila genes are as biased or more biased than those in microorganisms. (ii) The level of bias of genes and even the particular pattern of codon bias can remain phylogenetically invariant for very long periods of evolution. (iii) However, some

Jeffrey R. Powell; Etsuko N. Moriyama

1997-01-01

13

Studying Codon Usage: From sequence to function  

NASA Astrophysics Data System (ADS)

Protein coding sequences exhibit strong variances in the use of codons. Highly expressed genes such as those encoding ribosomal proteins use codons corresponding to the highly abundant tRNAs (``optimized codons''). High expression of heterologous genes also requires codon optimization, but even the codon usage of very weakly expressed genes tends to be far from random. To understand this biased choice of codon usage, we develop a theory based on the concept of ``ribosomal load.'' Ribosome is the key limiting commodity for rapidly growing organisms so that the use of ``non-optimal'' codons in any gene prolongs the translational elongation time, thus reducing the effective ribosome concentration. This presents a fitness cost, the magnitude of which depends on the amount of that protein being translated. We formulated and solved an evolution equation based on the above ingredients. This provides a quantitative relation between codon usage and protein abundance, which is found to be in good agreement with the available data for E.coli. This result suggests a convenient way to quantitatively predict protein abundances based on genome sequence data.

Hwa, Terry; Klumpp, Stefan; Dong, Jiajia

2007-03-01

14

Di-codon Usage for Gene Classification  

NASA Astrophysics Data System (ADS)

Classification of genes into biologically related groups facilitates inference of their functions. Codon usage bias has been described previously as a potential feature for gene classification. In this paper, we demonstrate that di-codon usage can further improve classification of genes. By using both codon and di-codon features, we achieve near perfect accuracies for the classification of HLA molecules into major classes and sub-classes. The method is illustrated on 1,841 HLA sequences which are classified into two major classes, HLA-I and HLA-II. Major classes are further classified into sub-groups. A binary SVM using di-codon usage patterns achieved 99.95% accuracy in the classification of HLA genes into major HLA classes; and multi-class SVM achieved accuracy rates of 99.82% and 99.03% for sub-class classification of HLA-I and HLA-II genes, respectively. Furthermore, by combining codon and di-codon usages, the prediction accuracies reached 100%, 99.82%, and 99.84% for HLA major class classification, and for sub-class classification of HLA-I and HLA-II genes, respectively.

Nguyen, Minh N.; Ma, Jianmin; Fogel, Gary B.; Rajapakse, Jagath C.

15

A Model of Codon Usage Bias  

NASA Astrophysics Data System (ADS)

The genetic code is degenerate; most amino acids can be encoded by from two to as many as six different codons. While one might expect these codons to be used with equal frequency, this turns out not to be the case---not only are some codons favored over others, but their usage can vary significantly between different genes in the same organism. Known causes of codon bias include differences in mutation rates as well as selection pressure related to the expression level of a gene, but the standard analysis methods can explain only a fraction of the observed codon usage variation. We here introduce an explicit model of codon usage bias, inspired by statistical physics. Combining this model with a maximum likelihood approach, we are able to clearly identify up to four different sources of bias in various genomes. We have applied the algorithm to Saccharomyces cerevisiae as well as 325 bacterial genomes, and in most cases our model explains essentially all observed variance.

Kloster, Morten; Tang, Chao

2007-03-01

16

Universality and Shannon entropy of codon usage  

E-print Network

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

Frappat, L; Sciarrino, A; Sorba, Paul

2003-01-01

17

An evolutionary perspective on synonymous codon usage in unicellular organisms  

Microsoft Academic Search

Summary Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift. Examination of the codon usage in 165Escherichia coli genes reveals a consistent trend of increasing bias with increasing gene expression level. Selection on codon usage appears to be unidirectional, so that the pattern seen in lowly expressed genes is

Paul M. Sharp; Wen-Hsiung Li

1986-01-01

18

Use and misuse of correspondence analysis in codon usage studies  

E-print Network

Use and misuse of correspondence analysis in codon usage studies Guy PerrieÁre* and Jean Thioulouse; Accepted August 22, 2002 ABSTRACT Correspondence analysis has frequently been used for codon usage studies but this method is often misused. Because amino acid composition exerts constraints on codon usage, it is common

Thioulouse, Jean

19

Genome Landscapes and Bacteriophage Codon Usage Julius B. Lucks1  

E-print Network

Genome Landscapes and Bacteriophage Codon Usage Julius B. Lucks1 , David R. Nelson1,2 , Grzegorz R exhibit unequal usage of synonymous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes

Plotkin, Joshua B.

20

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly  

E-print Network

Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high

Herbeck, Joshua

21

Codon Usage and Selection on Proteins Joshua B. Plotkin,1  

E-print Network

Codon Usage and Selection on Proteins Joshua B. Plotkin,1 Jonathan Dushoff,2 Michael M. Desai,3 on proteins on the basis of their synonymous codon usage (Plotkin and Dushoff 2003; Plotkin et al. 2004). Here the expected fre- quencies of synonymous codons as a function of the strength of selection on amino acids

Plotkin, Joshua B.

22

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

23

Genome-wide analysis of codon usage bias in Ebolavirus.  

PubMed

Ebola virus (EBOV) is a member of the family Filoviridae and its genome consists of a 19-kb, single-stranded, negative sense RNA. EBOV is subdivided into five distinct species with different pathogenicities, being Zaire ebolavirus (ZEBOV) the most lethal species. The interplay of codon usage among viruses and their hosts is expected to affect overall viral survival, fitness, evasion from host's immune system and evolution. In the present study, we performed comprehensive analyses of codon usage and composition of ZEBOV. Effective number of codons (ENC) indicates that the overall codon usage among ZEBOV strains is slightly biased. Different codon preferences in ZEBOV genes in relation to codon usage of human genes were found. Highly preferred codons are all A-ending triplets, which strongly suggests that mutational bias is a main force shaping codon usage in ZEBOV. Dinucleotide composition also plays a role in the overall pattern of ZEBOV codon usage. ZEBOV does not seem to use the most abundant tRNAs present in the human cells for most of their preferred codons. PMID:25445348

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

2015-01-22

24

Analysis of synonymous codon usage pattern in duck circovirus.  

PubMed

Duck circovirus (DuCV) disease causes a long-term immunosuppressive and multiple secondary infection in ducks. In this study, relative synonymous codon usage (RSCU) values, nucleotide contents and effective number of codon (ENC) values were calculated and compared among open reading frames (ORFs) of 53 DuCV genomes. The results reveal that most of the codons are ended with C and the overall bias is not remarkable in DuCV. A comparative analysis of codon contents and ENC values indicates that mutation pressure is the most significant factor responsible for the evolutional processes of codon usage bias in DuCV. However, other factors, such as composition constraints, translation selection, hydrophobicity and aromaticity should not be ignored. Finally principal component analysis (PCA) and hierarchical clustering method were performed based on RSCU. The significant difference of codon usage bias exists in DuCV-1 and DuCV-2 genotypes, but codon usage pattern of DuCV from the different epidemic areas or subtypes fails to influence the formation of codon usage bias. Analysis of the relationship of synonymous codon usage variation based on the two genotypes suggests that DuCV-2 is more conservative than DuCV-1, which may because of recombination events. Moreover, there are distinct differences in the degree of codon usage pattern evolution in different function genes, rep and cap. Therefore, the genotypes, subtypes and different functional genes also relate to the pattern of synonymous codon usage. The main objective of this study is to provide some sight into synonymous codon usage characteristics and the evolutionary relationship of DuCV. PMID:25497833

Xu, Yu; Jia, Renyong; Zhang, Zhilong; Lu, Yanyan; Wang, Mingshu; Zhu, Dekang; Chen, Shun; Liu, Mafeng; Yin, Zhongqiong; Cheng, Anchun

2015-02-25

25

The Effect of Multiple Evolutionary Selections on Synonymous Codon Usage of Genes in the Mycoplasma bovis Genome  

PubMed Central

Mycoplasma bovis is a major pathogen causing arthritis, respiratory disease and mastitis in cattle. A better understanding of its genetic features and evolution might represent evidences of surviving host environments. In this study, multiple factors influencing synonymous codon usage patterns in M. bovis (three strains’ genomes) were analyzed. The overall nucleotide content of genes in the M. bovis genome is AT-rich. Although the G and C contents at the third codon position of genes in the leading strand differ from those in the lagging strand (p<0.05), the 59 synonymous codon usage patterns of genes in the leading strand are highly similar to those in the lagging strand. The over-represented codons and the under-represented codons were identified. A comparison of the synonymous codon usage pattern of M. bovis and cattle (susceptible host) indicated the independent formation of synonymous codon usage of M. bovis. Principal component analysis revealed that (i) strand-specific mutational bias fails to affect the synonymous codon usage pattern in the leading and lagging strands, (ii) mutation pressure from nucleotide content plays a role in shaping the overall codon usage, and (iii) the major trend of synonymous codon usage has a significant correlation with the gene expression level that is estimated by the codon adaptation index. The plot of the effective number of codons against the G+C content at the third codon position also reveals that mutation pressure undoubtedly contributes to the synonymous codon usage pattern of M. bovis. Additionally, the formation of the overall codon usage is determined by certain evolutionary selections for gene function classification (30S protein, 50S protein, transposase, membrane protein, and lipoprotein) and translation elongation region of genes in M. bovis. The information could be helpful in further investigations of evolutionary mechanisms of the Mycoplasma family and heterologous expression of its functionally important proteins. PMID:25350396

Zhou, Jian-hua; Ding, Yao-zhong; He, Ying; Chu, Yue-feng; Zhao, Ping; Ma, Li-ya; Wang, Xin-jun; Li, Xue-rui; Liu, Yong-sheng

2014-01-01

26

The influence of translational selection on codon usage in fishes from the family Cyprinidae.  

PubMed

In this paper, the main factors shaping codon usage in three species of fishes that belong to the family Cyprinidae (namely Brachidanio rerio, Cyprinus carpio, and Carassius auratus) are reported. Correspondence analysis (COA), a commonly used multivariate statistical approach, was used to analyze codon usage bias. Our results show that the main trend is strongly correlated with the GC(3) content at silent sites of each sequence. On the other hand, the second axis discriminates between presumed highly and lowly expressed genes, a result that is confirmed by the distribution of matching expressed sequence tags (ESTs) along that axis. Translational selection appears, therefore, to influence synonymous codon usage in these fishes. The comparison of codon usages of the sequences displaying the extreme values on the second axis indicates that several codons are significantly incremented among the heavily expressed sequences. Interestingly, several of these triplets are not only shared by the three fishes but also by Xenopus laevis, another cold-blooded vertebrate in which translational selection influences codon choices. We postulate that natural selection was operative for codon usage in the last common ancestor of these fishes and Xenopus, and will probably be detected in cold-blooded vertebrates in general. Finally, we raise the possibility that the same phenomena will be found among warm-blooded vertebrates. PMID:14604802

Romero, Héctor; Zavala, Alejandro; Musto, Héctor; Bernardi, Giorgio

2003-10-23

27

Efficient translation initiation dictates codon usage at gene start  

PubMed Central

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

28

Analysis of a shift in codon usage in Drosophila.  

PubMed

In order to gain further insight into a shift in codon usage first observed in Drosophila willistoni we have analyzed seven genes in six species in the lineage leading to D. willistoni. This lineage contains the willistoni and saltans species groups. Sequences were obtained from GenBank or newly sequenced for this study. All species studied showed significant difference in codon usage compared to D. melanogaster for about one third of all amino acids. Within the willistoni/saltans lineage, codon usage is homogeneous, indicating that the shift in codon usage occurred prior to the diversification of extant species in this lineage which we estimate to date to about 20 million years ago. Thus the shift is old and has been stable. We also examined introns from these genes and the G/C composition at four-fold degenerate sites in an effort to detect a change in mutation bias. There is little or no evidence for a difference in mutation bias compared to D. melanogaster. We also considered whether relaxed selection (possibly due to reduced population sizes) or reduced recombination (due to numerous naturally occurring inversions) could account for the shift and concluded these factors alone are insufficient to explain the patterns observed. A change in the relative abundance of isoaccepting tRNAs is one of the few explanations that can account for the observations. Particularly intriguing is the fact that the greatest changes in codon usage have occurred for amino acids with two-fold C/T ending codons for which it is known that posttranscriptional modification occurs in tRNAs from a G in the wobble position to Queuosine that changes optimal binding from C to a slight preference for U. However, we do not argue that this shift was adaptive in nature, rather it may be an example of a "frozen accident." PMID:15008418

Powell, Jeffrey R; Sezzi, Erminia; Moriyama, Etsuko N; Gleason, Jennifer M; Caccone, Adalgisa

2003-01-01

29

Symmetry and Codon Usage Correlations in the Genetic Code  

E-print Network

The ratios of the codon usage in the quartets and sextets for the vertebrate series exhibit a correlated behaviour which fits naturally in the framework of the crystal basis model of the genetic code. Moreover the observed universal behaviour of these suitably normalized ratios can be easily explained.

Frappat, L; Sorba, Paul

1998-01-01

30

Similarity analysis of DNA sequences based on codon usage  

NASA Astrophysics Data System (ADS)

Based on the codon usage, we introduce an alternative approach to characterize and compare DNA sequences, which requires neither graphical representation and calculations of invariants of higher order matrices nor multiple sequence alignment. The utility of our approach is illustrated by an examination of the similarities/dissimilarities among the DNA sequence of full ?-globin genes of 10 species.

Li, Chun; Yu, Xiaoqing; Helal, Nadia

2008-06-01

31

The Selection-Mutation-Drift Theory of Synonymous Codon Usage  

Microsoft Academic Search

It is argued that the bias in synonymous codon usage observed in unicellular organisms is due to a balance between the forces of selection and mutation in a finite population, with greater bias in highly expressed genes reflecting stronger selection for efficiency of translation. A population genetic model is developed taking into account population size and selective differences between synonymous

Michael Bulmer

1991-01-01

32

Codon Usage Etsuko N Moriyama, University of Nebraska, Lincoln, Nebraska, USA  

E-print Network

Codon Usage Etsuko N Moriyama, University of Nebraska, Lincoln, Nebraska, USA email: emoriyama2@unl) are encoded by more than one codon. Codons encoding the same amino acid are called synonymous codons. Both in prokaryotic and eukaryotic genes, the synonymous codons are not used with equal frequencies. Introduction 0102

Moriyama, Etsuko

33

Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic Hong Qin*,1  

E-print Network

1 Intragenic spatial patterns of codon usage bias in prokaryotic and eukaryotic genomes Hong Qin*,1 distribution of synonymous codon usage bias in four prokaryotic (Escherichia coli, Bacillus subtilis pattern using isotonic regression, we show that in yeast and prokaryotic genomes, codon usage bias

Wu, Wei-Biao

34

Tissue-specific codon usage and the expression of human genes  

E-print Network

Tissue-specific codon usage and the expression of human genes Joshua B. Plotkin* , Harlan Robins report systematic differences in synonymous codon usage between genes selectively expressed in six adult human tissues. Furthermore, we show that the codon usage of brain-specific genes has been selectively

Plotkin, Joshua B.

35

Physica A 353 (2005) 365387 Codon usage trajectories and 7-cluster structure  

E-print Network

Physica A 353 (2005) 365­387 Codon usage trajectories and 7-cluster structure of 143 complete is estimated for bacterial genomes. We show that codon usage of bacterial genomes is a multi-linear function genomes and the other one for archaea). Description of these two codon-usage trajectories is the third

36

An Example in Kleisli: Codon Usage Extraction Made Easy Jiren Wang and Limsoon Wong  

E-print Network

An Example in Kleisli: Codon Usage Extraction Made Easy Jiren Wang and Limsoon Wong Bio,limsoong@krdl.org.sg 19 March 1999 Codon usage information was useful to many molecular biologists in designing from public DNA sequence databases and could com­ pute their codon usage. Second, we wanted

Wong, Limsoon

37

Evolutionary Patterns of Codon Usage in the Chloroplast Gene rbcL Dennis P. Wall,1  

E-print Network

Evolutionary Patterns of Codon Usage in the Chloroplast Gene rbcL Dennis P. Wall,1 Joshua T of codon usage bias in the chloroplast gene rbcL us- ing a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chlo- roplast genomic nucleotide content, as an attempt

Herbeck, Joshua

38

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

E-print Network

A PECULIAR CODON USAGE PATTERN REVEALED AFTER REMOVING THE EFFECT OF DNA METHYLATION Xuhua Xia, codon usage, genome, genomics Summary DNA methylation and deamination increases the CT mutation rate in CpG dinucleotides, especially in vertebrate genomes. This has profound effect on codon usage

Xia, Xuhua

39

Codon Usage Patterns in Cytochrome Oxidase I Across Multiple Insect Orders Joshua T. Herbeck,1  

E-print Network

Codon Usage Patterns in Cytochrome Oxidase I Across Multiple Insect Orders Joshua T. Herbeck,1 John December 2002 / Accepted: 16 December 2002 Abstract. Synonymous codon usage bias is deter- minedDNA in insects, we analyzed patterns of codon usage across a phylogeny of 88 insect species spanning 12 orders

Herbeck, Joshua

40

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage  

E-print Network

Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage Ziheng Yang* and Rasmus Nielsen *Department of Biology, Galton Laboratory, University, Denmark Current models of codon substitution are formulated at the levels of nucleotide substitution

Nielsen, Rasmus

41

Developmental Stage and Level of Codon Usage Bias in Drosophila  

PubMed Central

Codon usage bias (CUB) is a ubiquitous observation in molecular evolution. As a model, Drosophila has been particularly well-studied and indications show that selection at least partially controls codon usage, probably through selection for translational efficiency. Although many aspects of Drosophila CUB have been studied, this is the first study relating codon usage to development in this holometabolous insect with very different life stages. Here we ask the question: What developmental stage of Drosophila melanogaster has the greatest CUB? Genes with maximum expression in the larval stage have the greatest overall CUB when compared with embryos, pupae, and adults. (The same pattern was observed in Drosophila pseudoobscura, see Supplementary Material online.) We hypothesize this is related to the very rapid growth of larvae, placing increased selective pressure to produce large amounts of protein: a 300-fold increase requiring an approximate doubling of protein content every 10 h. Genes with highest expression in adult males and early embryos, stages with the least de novo protein synthesis, display the least CUB. These results are consistent with the hypothesis that CUB is caused (at least in part) by selection for efficient protein production. This seems to hold on the individual gene level (highly expressed genes are more biased than lowly expressed genes) as well as on a more global scale where genes with maximum expression during times of very rapid growth and protein synthesis are more biased than genes with maximum expression during times of low growth. PMID:18755761

Mason, Christopher E.; White, Kevin P.; Powell, Jeffrey R.

2008-01-01

42

Copyright 0 1996 by the Genetics Society of America Maximizing Transcription Efficiency Causes Codon Usage Bias  

E-print Network

Codon Usage Bias Xuhua Xia Museum of Natural Science and Department of Zoology and Physiology, LouisianaRNA, this rate in turn depends on the concentration ofribosomes and mRNA. Thus, patterns of codon usage presentedwith the prediction that the most frequently used ribonuclec- tide at the third codon sitesin m

Xia, Xuhua

43

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome  

E-print Network

Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome Hila-abundance tRNAs are often also at high demand since they correspond to preferred codons in genomes. Thus in the codon usage of the transcriptome across different conditions in several organisms by inspecting

Pilpel, Yitzhak

44

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

PubMed Central

We present a systematic computational framework, eCodonOpt, for designing parental DNA sequences for directed evolution experiments through codon usage optimization. Given a set of homologous parental proteins to be recombined at the DNA level, the optimal DNA sequences encoding these proteins are sought for a given diversity objective. We find that the free energy of annealing between the recombining DNA sequences is a much better descriptor of the extent of crossover formation than sequence identity. Three different diversity targets are investigated for the DNA shuffling protocol to showcase the utility of the eCodonOpt framework: (i) maximizing the average number of crossovers per recombined sequence; (ii) minimizing bias in family DNA shuffling so that each of the parental sequence pair contributes a similar number of crossovers to the library; and (iii) maximizing the relative frequency of crossovers in specific structural regions. Each one of these design challenges is formulated as a constrained optimization problem that utilizes 0–1 binary variables as on/off switches to model the selection of different codon choices for each residue position. Computational results suggest that many-fold improvements in the crossover frequency, location and specificity are possible, providing valuable insights for the engineering of directed evolution protocols. PMID:12034828

Moore, Gregory L.; Maranas, Costas D.

2002-01-01

45

Patterns of Synonymous Codon Usage on Human Metapneumovirus and Its Influencing Factors  

PubMed Central

Human metapneumovirus (HMPV) is an important agent of acute respiratory tract infection in children, while its pathogenicity and molecular evolution are lacking. Herein, we firstly report the synonymous codon usage patterns of HMPV genome. The relative synonymous codon usage (RSCU) values, effective number of codon (ENC) values, nucleotide contents, and correlation analysis were performed among 17 available whole genome of HMPV, including different genotypes. All preferred codons in HMPV are ended with A/U nucleotide and exhibited a great association with its high proportion of these two nucleotides in their genomes. Mutation pressure rather than natural selection is the main influence factor that determines the bias of synonymous codon usage in HMPV. The complementary pattern of codon usage bias between HMPV and human cell was observed, and this phenomenon suggests that host cells might be also act as an important factor to affect the codon usage bias. Moreover, the codon usage biases in each HMPV genotypes are separated into different clades, which suggest that phylogenetic distance might involve in codon usage bias formation as well. These analyses of synonymous codon usage bias in HMPV provide more information for better understanding its evolution and pathogenicity. PMID:23193361

Zhong, Qiao; Xu, Weidong; Wu, Yuanjian; Xu, Hongxing

2012-01-01

46

Analysing codon usage bias of cyprinid herpesvirus 3 and adaptation of this virus to the hosts.  

PubMed

The codon usage patterns of open reading frames (ORFs) in cyprinid herpesvirus 3 (CyHV-3) have been investigated in this study. The high correlation between GC12 % and GC3 % suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage and base component in the CyHV-3, while mutational pressure effect results from the high correlation between GC3 % and the first principal axis of principle component analysis (Axis 1) on the relative synonymous codon usage (RSCU) value of the viral functional genes. However, the interaction between the absolute codon usage bias and GC3 % suggests that other selections take part in the formation of codon usage, except for the mutational pressure. It is noted that the similarity degree of codon usage between the CyHV-3 and goldfish, Carassius auratus (L.), is higher than that between the virus and common carp, Cyprinus carpio L., suggesting that the goldfish plays a more important role than the common carp in codon usage pattern of the CyHV-3. The study of codon usage in CyHV-3 can provide some evidence about the molecular evolution of the virus. It can also enrich our understanding about the relationship between the CyHV-3 and its hosts by analysing their codon usage patterns. PMID:25491502

Ma, Y P; Liu, Z X; Hao, L; Ma, J Y; Liang, Z L; Li, Y G; Ke, H

2014-12-01

47

Synonymous Codon Usage in Escherichia coli: Selection for Translational Nina Stoletzki* and Adam Eyre-Walker  

E-print Network

Synonymous Codon Usage in Escherichia coli: Selection for Translational Accuracy Nina StoletzkiNational Evolutionary Synthesis Center, Durham, North Carolina In many organisms, selection acts on synonymous codons of proofreading, or to maximize the accuracy of translation. Using several data sets, we find evidence that codon

Eyre-Walker, Adam

48

The Evolution of Biased Codon and Amino Acid Usage in Nematode Genomes Asher D. Cutter,1  

E-print Network

The Evolution of Biased Codon and Amino Acid Usage in Nematode Genomes Asher D. Cutter,1 James D, United Kingdom Despite the degeneracy of the genetic code, whereby different codons encode the same amino acid, alternative codons and amino acids are utilized nonrandomly within and between genomes

Cutter, Asher D.

49

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

Microsoft Academic Search

Codon usage bias varies considerably among genomes and even within the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation (OXPHOS) is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred when both interactional genomes

Zheng Sun; Liang Ma; Robert W. Murphy; Xiansheng Zhang; Dawei Huang

2008-01-01

50

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

51

Species Based Synonymous Codon Usage in Fusion Protein Gene of Newcastle Disease Virus  

PubMed Central

Newcastle disease is highly pathogenic to poultry and many other avian species. However, the Newcastle disease virus (NDV) has also been reported from many non-avian species. The NDV fusion protein (F) is a major determinant of its pathogenicity and virulence. The functionalities of F gene have been explored for the development of vaccine and diagnostics against NDV. Although the F protein is well studied but the codon usage and its nucleotide composition from NDV isolated from different species have not yet been explored. In present study, we have analyzed the factors responsible for the determination of codon usage in NDV isolated from four major avian host species. The F gene of NDV is analyzed for its base composition and its correlation with the bias in codon usage. Our result showed that random mutational pressure is responsible for codon usage bias in F protein of NDV isolates. Aromaticity, GC3s, and aliphatic index were not found responsible for species based synonymous codon usage bias in F gene of NDV. Moreover, the low amount of codon usage bias and expression level was further confirmed by a low CAI value. The phylogenetic analysis of isolates was found in corroboration with the relatedness of species based on codon usage bias. The relationship between the host species and the NDV isolates from the host does not represent a significant correlation in our study. The present study provides a basic understanding of the mechanism involved in codon usage among species. PMID:25479071

Kumar, Chandra Shekhar; Kumar, Sachin

2014-01-01

52

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. PMID:23029152

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

2012-01-01

53

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. PMID:22014033

2011-01-01

54

Comparative genome analysis of six malarial parasites using codon usage bias based tools  

PubMed Central

Codon usage bias (CUB) is an omnipresent phenomenon, which occurs in nearly all organisms. Previous studies of codon bias in Plasmodium species were based on a limited dataset. This study uses whole genome datasets for comparative genome analysis of six Plasmodium species using CUB and other related methods for the first time. Codon usage bias, compositional variation in translated amino acid frequency, effective number of codons and optimal codons are analyzed for P.falciparum, P.vivax, P.knowlesi, P.berghei, P.chabaudii and P.yoelli. A plot of effective number of codons versus GC3 shows their differential codon usage pattern arises due to a combination of mutational and translational selection pressure. The increased relative usage of adenine and thymine ending optimal codons in highly expressed genes of P.falciparum is the result of higher composition biased pressure, and usage of guanine and cytosine bases at third codon position can be explained by translational selection pressure acting on them. While higher usage of adenine and thymine bases at third codon position in optimal codons of P.vivax highlights the role of translational selection pressure apart from composition biased mutation pressure in shaping their codon usage pattern. The frequency of those amino acids that are encoded by AT ending codons are significantly high in P.falciparum due to action of high composition biased mutational pressure compared with other Plasmodium species. The CUB variation in the three rodent parasites, P.berghei, P.chabaudii and P.yoelli is strikingly similar to that of P.falciparum. The simian and human malarial parasite, P.knowlesi shows a variation in codon usage bias similar to P.vivax but on closer study there are differences confirmed by the method of Principal Component Analysis (PCA). Abbreviations CDS - Coding sequences, GC1 - GC composition at first site of codon, GC2 - GC composition at second site of codon, GC3 - GC composition at third site of codon, Ala - Alanine, Arg - Arginine, Asn - Asparagine, Asp - Aspartic acid, Cys - Cysteine, Gln - Glutamine Glu - Glutamic acid Gly - Glycine His - Histidine Ile - Isoleucine Leu - Leucine Lys - Lysine Met - Methionine Phe - Phenylalanine Pro - Proline Ser - Serine Thr - Threonine Trp - Tryptophan Tyr - Tyrosine Val - Valine. PMID:23275725

Yadav, Manoj Kumar; Swati, D

2012-01-01

55

SCUMBLE: a method for systematic and accurate detection of codon usage bias by maximum likelihood estimation  

PubMed Central

The genetic code is degenerate—most amino acids can be encoded by from two to as many as six different codons. The synonymous codons are not used with equal frequency: not only are some codons favored over others, but also their usage can vary significantly from species to species and between different genes in the same organism. Known causes of codon bias include differences in mutation rates as well as selection pressure related to the expression level of a gene, but the standard analysis methods can account for only a fraction of the observed codon usage variation. We here introduce an explicit model of codon usage bias, inspired by statistical physics. Combining this model with a maximum likelihood approach, we are able to clearly identify different sources of bias in various genomes. We have applied the algorithm to Saccharomyces cerevisiae as well as 325 prokaryote genomes, and in most cases our model explains essentially all observed variance. PMID:18495752

Kloster, Morten; Tang, Chao

2008-01-01

56

Estimating selection intensity on synonymous codon usage in a nonequilibrium population.  

PubMed

Codon usage bias is the nonrandom use of synonymous codons for the same amino acid. Most population genetic models of codon usage evolution assume that the population is at mutation-selection-drift equilibrium. Natural populations, however, frequently deviate from equilibrium, often because of recent demographic changes. Here, we construct a matrix model that includes the effects of a recent change in population size on estimates of selection on preferred vs. unpreferred codons. Our results suggest that patterns of synonymous polymorphisms affecting codon usage can be quite erratic after such a change; statistical methods that fail to take demographic effects into account can then give incorrect estimates of important parameters. We propose a new method that can accurately estimate both demographic and codon usage parameters. The method also provides a simple way of testing for the effects of covariates such as gene length and level of gene expression on the intensity of selection, which we apply to a large Drosophila melanogaster polymorphism data set. Our analyses of twofold degenerate codons reveal that (i) selection acts in favor of preferred codons, (ii) there is mutational bias in favor of unpreferred codons, (iii) shorter genes and genes with higher expression levels are under stronger selection, and (iv) there is little evidence for a recent change in population size in the Zimbabwe population of D. melanogaster. PMID:19620398

Zeng, Kai; Charlesworth, Brian

2009-10-01

57

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. PMID:24707212

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

2014-01-01

58

Three-dimensional eukaryotic genomic organization is strongly correlated with codon usage expression and function.  

PubMed

It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of three-dimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture. PMID:25510862

Diament, Alon; Pinter, Ron Y; Tuller, Tamir

2014-01-01

59

Expression Pattern and, Surprisingly, Gene Length Shape Codon Usage in Caenorhabditis, Drosophila, and Arabidopsis  

Microsoft Academic Search

We measured the expression pattern and analyzed codon usage in 8,133, 1,550, and 2,917 genes, respectively, from Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana. In those three species, we observed a clear correlation between codon usage and gene expression levels and showed that this correlation is not due to a mutational bias. This provides direct evidence for selection on silent

Laurent Duret; Dominique Mouchiroud

1999-01-01

60

A Major Controversy in Codon-Anticodon Adaptation Resolved by a New Codon Usage Index  

PubMed Central

Two alternative hypotheses attribute different benefits to codon-anticodon adaptation. The first assumes that protein production is rate limited by both initiation and elongation and that codon-anticodon adaptation would result in higher elongation efficiency and more efficient and accurate protein production, especially for highly expressed genes. The second claims that protein production is rate limited only by initiation efficiency but that improved codon adaptation and, consequently, increased elongation efficiency have the benefit of increasing ribosomal availability for global translation. To test these hypotheses, a recent study engineered a synthetic library of 154 genes, all encoding the same protein but differing in degrees of codon adaptation, to quantify the effect of differential codon adaptation on protein production in Escherichia coli. The surprising conclusion that “codon bias did not correlate with gene expression” and that “translation initiation, not elongation, is rate-limiting for gene expression” contradicts the conclusion reached by many other empirical studies. In this paper, I resolve the contradiction by reanalyzing the data from the 154 sequences. I demonstrate that translation elongation accounts for about 17% of total variation in protein production and that the previous conclusion is due to the use of a codon adaptation index (CAI) that does not account for the mutation bias in characterizing codon adaptation. The effect of translation elongation becomes undetectable only when translation initiation is unrealistically slow. A new index of translation elongation ITE is formulated to facilitate studies on the efficiency and evolution of the translation machinery. PMID:25480780

Xia, Xuhua

2015-01-01

61

On the Limitations of Using Ribosomal Genes as References for the Study of Codon Usage: A Rebuttal  

E-print Network

On the Limitations of Using Ribosomal Genes as References for the Study of Codon Usage: A Rebuttal our finding that the identity of optimal codons in different genomes follows a set of clear rules Genetics paper stand. This provides us with an opportunity to bring up an aspect of how codon usage has

Petrov, Dmitri

62

1999 Oxford University Press16421649 Nucleic Acids Research, 1999, Vol. 27, No. 7 Proteome composition and codon usage in  

E-print Network

composition and codon usage in spirochaetes: species-specific and DNA strand-specific mutational biases in codon usage and amino acid composition patterns that are significantly different between genes encoded.pallidum having a much higher G+C content than B.burgdorferi. These changes in amino acid and codon compositions

Paris-Sud XI, Université de

63

Evidence for Stabilizing Selection on Codon Usage in Chromosomal Rearrangements of Drosophila pseudoobscura  

PubMed Central

There has been a renewed interest in investigating the role of stabilizing selection acting on genome-wide traits such as codon usage bias. Codon bias, when synonymous codons are used at unequal frequencies, occurs in a wide variety of taxa. Standard evolutionary models explain the maintenance of codon bias through a balance of genetic drift, mutation and weak purifying selection. The efficacy of selection is expected to be reduced in regions of suppressed recombination. Contrary to observations in Drosophila melanogaster, some recent studies have failed to detect a relationship between the recombination rate, intensity of selection acting at synonymous sites, and the magnitude of codon bias as predicted under these standard models. Here, we examined codon bias in 2798 protein coding loci on the third chromosome of D. pseudoobscura using whole-genome sequences of 47 individuals, representing five common third chromosome gene arrangements. Fine-scale recombination maps were constructed using more than 1 million segregating sites. As expected, recombination was demonstrated to be significantly suppressed between chromosome arrangements, allowing for a direct examination of the relationship between recombination, selection, and codon bias. As with other Drosophila species, we observe a strong mutational bias away from the most frequently used codons. We find the rate of synonymous and nonsynonymous polymorphism is variable between different amino acids. However, we do not observe a reduction in codon bias or the strength of selection in regions of suppressed recombination as expected. Instead, we find that the interaction between weak stabilizing selection and mutational bias likely plays a role in shaping the composition of synonymous codons across the third chromosome in D. pseudoobscura. PMID:25326424

Fuller, Zachary L.; Haynes, Gwilym D.; Zhu, Dianhui; Batterton, Matthew; Chao, Hsu; Dugan, Shannon; Javaid, Mehwish; Jayaseelan, Joy C.; Lee, Sandra; Li, Mingmei; Ongeri, Fiona; Qi, Sulan; Han, Yi; Doddapaneni, Harshavardhan; Richards, Stephen; Schaeffer, Stephen W.

2014-01-01

64

Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences  

Microsoft Academic Search

Viruses differ markedly in their specificity toward host organisms. Here, we test the level of general sequence adaptation that viruses display toward their hosts. We compiled a representative data set of viruses that infect hosts ranging from bacteria to humans. We consider their respective amino acid and codon usages and compare them among the viruses and their hosts. We show

Iris Bahir; Menachem Fromer; Yosef Prat; Michal Linial

2009-01-01

65

Is DNA Code Periodicity Only Due to CUF - Codons Usage Frequency?  

Microsoft Academic Search

The triplet code for proteins and functional RNA has been either from the universal pattern of ancient RNA (- HI) [1], with a key role of an uneven codon usage frequency (CUF) in the periodic patterns origination, or a reading frame monitoring device (RFMD -H2) [2- 4]. HI has lately been upheld [1] but in a single sequence sensitive way

Mariusz Zoltowski; Nicolaus Copernicus

2007-01-01

66

[Comparative studies on codon usage bias of Ganoderma lucidum based on analysis of genomic and transcriptomic data].  

PubMed

Codon usage bias is an important characteristic of genetic information transfer in organisms. Analysis of codon usage bias of different species is important for understanding the rules on genetic information transfer. The previous method for analysis of codon usage bias is mainly based on genomic data. However, this method is greatly limited, because the genome sequences of higher organisms are still not available up to now. In this study, we found that we could obtain the same optimal codons of Ganoderma lucidum (Curtis: Fr.) P. Karst based on its whole genomic data or large-scale transcriptomic data from its liquid-cultured hyphae, primordium and fruiting body, separately. This result indicated the feasibility to understand the codon usage bias based on the large-scale transcriptomic data. By calculating the proportion of rare codons of Escherichia coli and Saccharomyces cerevisiae in 26 terpene synthases (TS) of G. lucidum, we found that the rare codons of S. cerevisiae have a higher proportion in TS genes, while the rare codons of E. coli have relatively lower, suggesting that the TS genes of G. lucidum are possibly more difficult to be expressed in S. cerevisiae than in E. coli. Chemical synthesis of TS genes according to the yeast optimal codons will be an effective way to solve the problem on the mismatch of gene codon bias between the foreign genes and the host strain. PMID:25518336

Zhu, Xiao-Xuan; Zhu, Ying-Jie; Song, Jing-Yuan; Sun, Chao; Chen, Shi-Lin

2014-09-01

67

Effective population size does not predict codon usage bias in mammals.  

PubMed

Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (N e), with selection on CUB operating less efficiently in species with small N e. Here, we specifically ask whether variation in N e predicts differences in CUB in mammals and report two main findings. First, across 41 mammalian genomes, CUB was not correlated with two indirect proxies of N e (body mass and generation time), even though there was statistically significant evidence of selection shaping CUB across all species. Interestingly, autosomal genes showed higher codon usage bias compared to X-linked genes, and high-recombination genes showed higher codon usage bias compared to low recombination genes, suggesting intraspecific variation in N e predicts variation in CUB. Second, across six mammalian species with genetic estimates of N e (human, chimpanzee, rabbit, and three mouse species: Mus musculus, M. domesticus, and M. castaneus), N e and CUB were weakly and inconsistently correlated. At least in mammals, interspecific divergence in N e does not strongly predict variation in CUB. One hypothesis is that each species responds to a unique distribution of selection coefficients, confounding any straightforward link between N e and CUB. PMID:25505518

Kessler, Michael D; Dean, Matthew D

2014-10-01

68

Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights  

PubMed Central

The purpose of this study was to investigate the balance between transfer ribonucleic acid (tRNA) supply and demand in retrovirus-infected cells, seeking the best targets for antiretroviral therapy based on the hypothetical tRNA Inhibition Therapy (TRIT). Codon usage and tRNA gene data were retrieved from public databases. Based on logistic principles, a therapeutic score (T-score) was calculated for all sense codons, in each retrovirus-host system. Codons that are critical for viral protein translation, but not as critical for the host, have the highest T-score values. Theoretically, inactivating the cognate tRNA species should imply a severe reduction of the elongation rate during viral mRNA translation. We developed a method to predict tRNA species critical for retroviral protein synthesis. Four of the best TRIT targets in HIV-1 and HIV-2 encode Large Hydrophobic Residues (LHR), which have a central role in protein folding. One of them, codon CUA, is also a TRIT target in both HTLV-1 and HTLV-2. Therefore, a drug designed for inactivating or reducing the cytoplasmatic concentration of tRNA species with anticodon TAG could attenuate significantly both HIV and HTLV protein synthesis rates. Inversely, replacing codons ending in UA by synonymous codons should increase the expression, which is relevant for DNA vaccine design. PMID:24151425

Frias, Diego; Monteiro-Cunha, Joana P.; Mota-Miranda, Aline C.; Fonseca, Vagner S.; de Oliveira, Tulio; Galvao-Castro, Bernardo; Alcantara, Luiz C. J.

2013-01-01

69

Selection at the amino acid level can influence synonymous codon usage: implications for the study of codon adaptation in plastid genes.  

PubMed Central

A previously employed method that uses the composition of noncoding DNA as the basis of a test for selection between synonymous codons in plastid genes is reevaluated. The test requires the assumption that in the absence of selective differences between synonymous codons the composition of silent sites in coding sequences will match the composition of noncoding sites. It is demonstrated here that this assumption is not necessarily true and, more generally, that using compositional properties to draw inferences about selection on silent changes in coding sequences is much more problematic than commonly assumed. This is so because selection on nonsynonymous changes can influence the composition of synonymous sites (i.e., codon usage) in a complex manner, meaning that the composition biases of different silent sites, including neutral noncoding DNA, are not comparable. These findings also draw into question the commonly utilized method of investigating how selection to increase translation accuracy influences codon usage. The work then focuses on implications for studies that assess codon adaptation, which is selection on codon usage to enhance translation rate, in plastid genes. A new test that does not require the use of noncoding DNA is proposed and applied. The results of this test suggest that far fewer plastid genes display codon adaptation than previously thought. PMID:11560910

Morton, B R

2001-01-01

70

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

71

Evolutionary forces in shaping the codon and amino acid usages in Blochmannia floridanus.  

PubMed

Endosymbiotic relationship has great effect on ecological system. Codon and amino acid usages bias of endosymbiotic bacteria Blochmannia floridanus (whose host is an ant Camponotus floridanus) was investigated using experimentally known genes of this organism. Correspondence Analysis on RSCU values show that there exists only one single explanatory major axis that is linked to the strand specific mutational biases. Majority of the genes have a tendency to concentrate on the leading strand, which may be related to the adaptive property related to the replication mechanisms. Amino acid usages were markedly different between the highly and lowly expressed genes in this organism and in particular, GC rich amino acids were found to occur significantly higher in highly expressed genes than the lowly expressed genes. Comparative analyses of the orthologous genes of Escherichia coli and Blochmannia floridanus show that highly expressed genes are significantly more conserved than lowly expressed genes. Based on our results we concluded that strand specific mutational bias is strongly operational in selecting the codon usage in this organism. Replicational-transcriptional selection can be invoked from the presence of majority of highly expressed genes in the leading strand. Conservation of GC rich amino acids in the highly expressed genes to its ancestor is the major source of variation in amino acid usages in the organism. Hydrophobicity of the genes is the second major source in differentiating the genes according to their amino acid usages in this organism. PMID:15214801

Banerjee, T; Basak, S; Gupta, S K; Ghosh, T C

2004-08-01

72

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

PubMed Central

The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-optimal codons. Moreover, genes encoding proteins that cycle at the protein level exhibit non-optimal codon preferences. Remarkably, cell cycle-regulated genes expressed in different phases display different codon preferences. Here, we show empirically that transfer RNA (tRNA) expression is indeed highest in the G2 phase of the cell cycle, consistent with the non-optimal codon usage of genes expressed at this time, and lowest toward the end of G1, reflecting the optimal codon usage of G1 genes. Accordingly, protein levels of human glycyl-, threonyl-, and glutamyl-prolyl tRNA synthetases were found to oscillate, peaking in G2/M phase. In light of our findings, we propose that non-optimal (wobbly) matching codons influence protein synthesis during the cell cycle. We describe a new mathematical model that shows how codon usage can give rise to cell-cycle regulation. In summary, our data indicate that cells exploit wobbling to generate cell cycle-dependent dynamics of proteins. PMID:22373820

Frenkel-Morgenstern, Milana; Danon, Tamar; Christian, Thomas; Igarashi, Takao; Cohen, Lydia; Hou, Ya-Ming; Jensen, Lars Juhl

2012-01-01

73

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. PMID:23921637

Roller, Maša; Luci?, Vedran; Nagy, István; Perica, Tina; Vlahovi?ek, Kristian

2013-01-01

74

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. PMID:19131380

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

75

Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Rasmus Nielsen,* Vanessa L. Bauer DuMont, Melissa J. Hubisz, and Charles F. Aquadro  

E-print Network

Maximum Likelihood Estimation of Ancestral Codon Usage Bias Parameters in Drosophila Rasmus Nielsen a likelihood method for estimating codon usage bias parameters along the lineages of a phylogeny. The method is an extension of the classical codon-based models used for estimating dN/dS ratios along the lineages

Nielsen, Rasmus

76

Large-scale genomic analysis of codon usage in dengue virus and evaluation of its phylogenetic dependence.  

PubMed

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

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

2014-01-01

77

Is DNA code periodicity only due to CUF-codons usage frequency?  

PubMed

The triplet code for proteins and functional RNA has been either from the universal pattern of ancient RNA (-H1) [1], with a key role of an uneven codon usage frequency (CUF) in the periodic patterns origination, or a reading frame monitoring device (RFMD -H2) [2- 4]. H1 has lately been upheld [1] but in a single sequence sensitive way [1]. Since H1 and H2 are not mutually exclusive [2, 3, 4], a single sequence-wise sensitive approach by a resonant recognition model (RRM) has become the attempt described in this paper to challenge H1 and H2 in eukaryotes case as a novelty. In the RRM model [5, 6, 7] two bio-molecules interact favorably provided they both obey a common frequency and opposite phases consensus in their delocalized electron energy (DEE-) distributions [5]. Hence it has been possible to learn how well the DEE-s of the mRNA and of the ribosome match each other at 1/3 Hz - that applied to both the original and the CUF preserving randomly shuffled genomic data across the well known Bursét and Guigo collection of 570 coding vertebrates' genes. The matching of RRM patterns reduces to harmonics phase comparison of the relevant DEE-s, a task by a digital phase locked loop (DPLL) [8, 9, and 10]. The DPLL phase control to meet the RRM phase matching case is quantified into a small number of classes to describe the mRNA-ribosome interaction in a categorical way. PMID:18002222

Zoltowski, Mariusz

2007-01-01

78

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

PubMed

The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. These genomes had GC contents that ranged from 13.5% to 74.9%. We analyzed the distance of base frequencies at the three codon positions, codon frequencies, and amino acid compositions across genomes with respect to the differences in the GC content of these prokaryotic species. We found that although the phylogenetic lineages were remote among some species, a similar genomic GC content forced them to adopt similar base usage patterns at the three codon positions, codon usage patterns, and amino acid usage patterns. Our work demonstrates that in prokaryotic genomes: a) base usage, codon usage, and amino acid usage change with GC content with a linear correlation; b) the distance of each usage has a linear correlation with the GC content difference; and c) GC content is more essential than phylogenetic lineage in determining base usage, codon usage, and amino acid usage. This work is exceptional in that we adopted intuitively graphic methods for all analyses, and we used these analyses to examine as many as 2670 prokaryotes. We hope that this work is helpful for understanding common features in the organization of microbial genomes. PMID:25255224

Zhou, Hui-Qi; Ning, Lu-Wen; Zhang, Hui-Xiong; Guo, Feng-Biao

2014-01-01

79

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

80

Viral Proteins Originated De Novo by Overprinting Can Be Identified by Codon Usage: Application to the “Gene Nursery” of Deltaretroviruses  

PubMed Central

A well-known mechanism through which new protein-coding genes originate is by modification of pre-existing genes, e.g. by duplication or horizontal transfer. In contrast, many viruses generate protein-coding genes de novo, via the overprinting of a new reading frame onto an existing (“ancestral”) frame. This mechanism is thought to play an important role in viral pathogenicity, but has been poorly explored, perhaps because identifying the de novo frames is very challenging. Therefore, a new approach to detect them was needed. We assembled a reference set of overlapping genes for which we could reliably determine the ancestral frames, and found that their codon usage was significantly closer to that of the rest of the viral genome than the codon usage of de novo frames. Based on this observation, we designed a method that allowed the identification of de novo frames based on their codon usage with a very good specificity, but intermediate sensitivity. Using our method, we predicted that the Rex gene of deltaretroviruses has originated de novo by overprinting the Tax gene. Intriguingly, several genes in the same genomic region have also originated de novo and encode proteins that regulate the functions of Tax. Such “gene nurseries” may be common in viral genomes. Finally, our results confirm that the genomic GC content is not the only determinant of codon usage in viruses and suggest that a constraint linked to translation must influence codon usage. PMID:23966842

Pavesi, Angelo; Magiorkinis, Gkikas; Karlin, David G.

2013-01-01

81

Codon usage trajectories and 7-cluster structure of 143 complete bacterial genomic sequences  

NASA Astrophysics Data System (ADS)

Three results are presented. First, we prove the existence of a universal 7-cluster structure in all 143 completely sequenced bacterial genomes available in Genbank in August 2004, and explained its properties. The 7-cluster structure is responsible for the main part of sequence heterogeneity in bacterial genomes. In this sense, our 7 clusters is the basic model of bacterial genome sequence. We demonstrated that there are four basic “pure” types of this model, observed in nature: “parallel triangles”, “perpendicular triangles”, degenerated case and the flower-like type. Second, we answered the question: how big are the position-specific information and the contribution connected with correlations between nucleotide. The accuracy of the mean-field (context-free) approximation is estimated for bacterial genomes. We show that codon usage of bacterial genomes is a multi-linear function of their genomic G+C-content with high accuracy (more precisely, by two similar functions, one for eubacterial genomes and the other one for archaea). Description of these two codon-usage trajectories is the third result. All 143 cluster animated 3D-scatters are collected in a database and is made available on our web-site: http://www.ihes.fr/ ?zinovyev/7clusters .

Gorban, Alexander; Popova, Tatyana; Zinovyev, Andrey

2005-08-01

82

Mammalian expression levels of cellulase and xylanase genes optimised by human codon usage are not necessarily higher than those optimised by the extremely biased approach.  

PubMed

Xylanase gene xynB, cellulase genes egxA and bgl4 were subjected to codon optimisation using two opposing strategies. One was designated the 'one amino acid-one codon' approach, which employs only the codon most used by humans for each amino acid. The other one is referred to as the "humanised" codon usage method, which selects synonymous codons for each amino acid according to the human codon usage table to mimic patterns used in humans. Protein expression levels in mammalian cell lines from each sequence were measured using fluorescence-activated cell sorting, western blotting and enzymatic activity assay. The results indicate that compared with the humanised codon usage method, the relatively simple 'one amino acid-one codon' approach could enhance heterologous protein expression in mammalian cells without apparent drawbacks. PMID:24966044

Liu, Zhiguo; Sun, Yanxia; Feng, Tao; Ji, Qianqian; Cong, Peiqing; Chen, Yaosheng; He, Zuyong

2014-11-01

83

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. PMID:21335530

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

2011-01-01

84

Use of molecular beacons to probe for messenger RNA release from ribosomes during 5'-translational blockage by consecutive low-usage codons in Escherichia coli  

NASA Astrophysics Data System (ADS)

In `5'-translational blockage,' significantly reduced yields of proteins are synthesized in Escherichia coli when consecutive low-usage codons are inserted near translation starts of messages (with reduced or no effect when these same codons are inserted downstream). We tested the hypothesis that ribosomes encountering these low-usage codons prematurely release the mRNA. RNA from polysome gradients was fractionated into pools of polysomes, monosomes and ribosomes-free. New hybridization probes, called `molecular beacons,' and standard slot-blots, were used to detect test messages containing either consecutive low-usage AGG (arginine) or synonymous high-usage CGU insertions near the 5' end. The results show an approximately twofold increase in the ratio of free to bound mRNA when the low-usage codons were present compared to high-usage codons. In contrast, there was no difference in the ratio of free to bound mRNA when consecutive low-usage CUA or high-usage CUG (leucine) codons were inserted, or when the arginine codons were inserted near the 3' end. These data indicate that at least some mRNA is released from ribosomes during 5'-translational blockage by arginine but not leucine codons, and they support proposals that premature termination of translation can occur in some conditions in vivo in the absence of a stop codon.

Gao, Wenwu; Tyagi, Sanjay; Kramer, Fred R.; Goldman, Emanuel

2000-03-01

85

Mosquito vitellogenin genes: Comparative sequence analysis, gene duplication, and the role of rare synonymous codon usage in regulating expression.  

PubMed

Comparative sequence analysis of mosquito vitellogenin (Vg) genes was carried out to gain a better understanding of their evolution. The genomic clones of vitellogenin genes were isolated and sequenced from all three subfamilies of the family Culicidae including Culicinae (Aedes aegypti, Ochlerotatus atropalpus, Ae. polynesiensis, Ae. albopictus, Ochlerotatus triseriatus and Culex quinquefasciatus), Toxorhynchitinae (Toxorhynchites amboinensis), and Anophelinae (Anopheles albimanus). Genomic clones of vitellogenin genes Vg-B and Vg-C were isolated from Ae. aegypti and sequenced. A comparison of Vg-B and Vg-C, with the previously characterized vitellogenin gene, Vg-A1, suggests that Vg-A1 and Vg-B probably arose by a recent gene duplication, and Vg-C apparently diverged from the two other members of the gene family in an earlier gene duplication event. Two vitellogenin genes orthologous to Vg-C were cloned from a Cx. quinquefasciatus DNA library, one of which is truncated at the N-terminal end. Single vitellogenin genes, orthologous to Vg-C, were cloned from the An. albimanus and Tx. amboinensis libraries. Incomplete sequences orthologous to Vg-B and Vg-C were isolated from the Oc. atropalpus library. Only partial sequences were isolated from Ae. polynesiensis, Ae. albopictus and Oc. triseriatus. Inferred phylogenetic relationships based on analysis of these sequences suggest that Vg-C was the ancestral gene and that a recent gene duplication gave rise to Vg-A1 and Vg-B after the separation of the genus Aedes. The deduced amino acid composition of mosquito vitellogenin proteins exhibits higher tyrosine and phenylalanine composition than other mosquito proteins except for the hexamerin storage proteins. Analysis of vitellogenin coding sequences showed that a majority of amino acid substitutions were due to conserved and moderately conserved changes suggesting that the vitellogenins are under moderately selective constrains to maintain tertiary structure. The vitellogenin genes of the three anautogenous mosquitoes, that require a blood meal to develop eggs, had very high synonymous codon usage biases similar to highly expressed genes of other organisms. On the other hand, the vitellogenin genes of autogenous mosquitoes, that develop at least one batch of eggs without a blood meal, exhibited low synonymous codon usage bias. An unusual pattern of synonymous codon usage was observed in the first 15 amino acid residues encoding the signal peptide in the vitellogenin genes, where a high number of rarely used synonymous codons are present. It is hypothesized that rare synonymous codons have selectively accumulated in the signal peptide region to down-regulate the rate of translation initiation in the absence of a blood meal. Real-time PCR gene expression experiments showed that all three Ae. aegypti vitellogenin genes were highly expressed after a blood meal, and expressed in non-blood-fed females, males, larvae and pupae at trace levels. Sequences were deposited in GenBank (accession numbers: Ae. aegypti Vg-B, AY380797, Vg-C, AY373377; Oc. atropalpus Vg-B, AY691321, Vg-C, AY691322; Ae. polynesiensis Vg-A1, AY691318, Vg-B, AY691319, Vg-C, AY691320; Ae. albopictus Vg-A1, AY691316, Vg-C, AY691317; Oc. triseriatus Vg-C, AY691323; Cx. quinquefasciatus Vg-C1, AY691324, Vg-C2, AY691325; Tx. amboinensis Vg-C, AY691326; An. albimanus Vg-C, AY691327). PMID:20337554

Isoe, Jun; Hagedorn, Henry H

2007-01-01

86

Mosquito Vitellogenin Genes: Comparative Sequence Analysis, Gene Duplication, and the Role of Rare Synonymous Codon Usage in Regulating Expression  

PubMed Central

Comparative sequence analysis of mosquito vitellogenin (Vg) genes was carried out to gain a better understanding of their evolution. The genomic clones of vitellogenin genes were isolated and sequenced from all three subfamilies of the family Culicidae including Culicinae (Aedes aegypti, Ochlerotatus atropalpus, Ae. polynesiensis, Ae. albopictus, Ochlerotatus triseriatus and Culex quinquefasciatus), Toxorhynchitinae (Toxorhynchites amboinensis), and Anophelinae (Anopheles albimanus). Genomic clones of vitellogenin genes Vg-B and Vg-C were isolated from Ae. aegypti and sequenced. A comparison of Vg-B and Vg-C, with the previously characterized vitellogenin gene, Vg-A1, suggests that Vg-A1 and Vg-B probably arose by a recent gene duplication, and Vg-C apparently diverged from the two other members of the gene family in an earlier gene duplication event. Two vitellogenin genes orthologous to Vg-C were cloned from a Cx. quinquefasciatus DNA library, one of which is truncated at the N-terminal end. Single vitellogenin genes, orthologous to Vg-C, were cloned from the An. albimanus and Tx. amboinensis libraries. Incomplete sequences orthologous to Vg-B and Vg-C were isolated from the Oc. atropalpus library. Only partial sequences were isolated from Ae. polynesiensis, Ae. albopictus and Oc. triseriatus. Inferred phylogenetic relationships based on analysis of these sequences suggest that Vg-C was the ancestral gene and that a recent gene duplication gave rise to Vg-A1 and Vg-B after the separation of the genus Aedes. The deduced amino acid composition of mosquito vitellogenin proteins exhibits higher tyrosine and phenylalanine composition than other mosquito proteins except for the hexamerin storage proteins. Analysis of vitellogenin coding sequences showed that a majority of amino acid substitutions were due to conserved and moderately conserved changes suggesting that the vitellogenins are under moderately selective constrains to maintain tertiary structure. The vitellogenin genes of the three anautogenous mosquitoes, that require a blood meal to develop eggs, had very high synonymous codon usage biases similar to highly expressed genes of other organisms. On the other hand, the vitellogenin genes of autogenous mosquitoes, that develop at least one batch of eggs without a blood meal, exhibited low synonymous codon usage bias. An unusual pattern of synonymous codon usage was observed in the first 15 amino acid residues encoding the signal peptide in the vitellogenin genes, where a high number of rarely used synonymous codons are present. It is hypothesized that rare synonymous codons have selectively accumulated in the signal peptide region to down-regulate the rate of translation initiation in the absence of a blood meal. Real-time PCR gene expression experiments showed that all three Ae. aegypti vitellogenin genes were highly expressed after a blood meal, and expressed in non-blood-fed females, males, larvae and pupae at trace levels. Sequences were deposited in GenBank (accession numbers: Ae. aegypti Vg-B, AY380797, Vg-C, AY373377; Oc. atropalpus Vg-B, AY691321, Vg-C, AY691322; Ae. polynesiensis Vg-A1, AY691318, Vg-B, AY691319, Vg-C, AY691320; Ae. albopictus Vg-A1, AY691316, Vg-C, AY691317; Oc. triseriatus Vg-C, AY691323; Cx. quinquefasciatus Vg-C1, AY691324, Vg-C2, AY691325; Tx. amboinensis Vg-C, AY691326; An. albimanus Vg-C, AY691327). PMID:20337554

Isoe, Jun; Hagedorn, Henry H.

2007-01-01

87

Contrasting Codon Usage Patterns and Purifying Selection at the Mating Locus in Putatively Asexual Alternaria Fungal Species  

PubMed Central

Sexual reproduction in heterothallic ascomycete fungi is controlled by a single mating-type locus called MAT1 with two alternate alleles or idiomorphs, MAT1-1 and MAT1-2. These alleles lack sequence similarity and encode different transcriptional regulators. A large number of phytopathogenic fungi including Alternaria spp. are considered asexual, yet still carry expressed MAT1 genes. The molecular evolution of Alternaria MAT1 was explored using nucleotide diversity, nonsynonymous vs. synonymous substitution (dn/ds) ratios and codon usage statistics. Likelihood ratio tests of site-branch models failed to detect positive selection on MAT1-1-1 or MAT1-2-1. Codon-site models demonstrated that both MAT1-1-1 and MAT1-2-1 are under purifying selection and significant differences in codon usage were observed between MAT1-1-1 and MAT1-2-1. Mean GC content at the third position (GC3) and effective codon usage (ENC) were significantly different between MAT1-1-1 and MAT1-2-1 with values of 0.57 and 48 for MAT1-1-1 and 0.62 and 46 for MAT1-2-1, respectively. In contrast, codon usage of Pleospora spp. (anamorph Stemphylium), a closely related Dothideomycete genus, was not significantly different between MAT1-1-1 and MAT1-2-1. The purifying selection and biased codon usage detected at the MAT1 locus in Alternaria spp. suggest a recent sexual past, cryptic sexual present and/or that MAT1 plays important cellular role(s) in addition to mating. PMID:21625561

Stewart, Jane E.; Kawabe, Masato; Abdo, Zaid; Arie, Tsutomu; Peever, Tobin L.

2011-01-01

88

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

E-print Network

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

Namiko Mitarai; Kim Sneppen; Steen Pedersen

2008-09-25

89

Mitochondrial phylogenomics of early land plants: mitigating the effects of saturation, compositional heterogeneity, and codon-usage bias.  

PubMed

Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the remaining land plants but without support. These analyses indicate that the inference of an early-branching moss lineage based on the nucleotide data is caused by convergent compositional biases. Accommodating among-site amino acid compositional heterogeneity (CAT-model) yields no support for the optimal resolution of liverwort as sister to the rest of land plants, suggesting that the robust inference of the liverwort position in homogeneous analyses may be due in part to compositional biases among sites. All analyses support a paraphyletic bryophytes with hornworts composing the sister-group to tracheophytes. We conclude that while genomic data may generate highly supported phylogenetic trees, these inferences may be artifacts. We suggest that phylogenomic analyses should assess the possible impact of potential biases through comparisons of protein-coding gene data and their amino acid translations by evaluating the impact of substitutional saturation, synonymous substitutions, and compositional biases through data deletion strategies and by analyzing the data using heterogeneous composition models. We caution against relying on any one presentation of the data (nucleotide or amino acid) or any one type of analysis even when analyzing large-scale data sets, no matter how well-supported, without fully exploring the effects of substitution models. PMID:25070972

Liu, Yang; Cox, Cymon J; Wang, Wei; Goffinet, Bernard

2014-11-01

90

Mutational bias is the driving force for shaping the synonymous codon usage pattern of alternatively spliced genes in rice (Oryza sativa L.).  

PubMed

Alternative splicing plays important roles in diverse aspects of plant development, metabolism, and stress responses. However, the regulatory mechanisms of alternative splicing of genes still remain incompletely elucidated, especially in plants. In this study, the synonymous codon usage pattern of alternatively spliced (AS) genes in rice was firstly explored using the combination of correspondence analysis (CA), internal CA, correlation and ANOVA analyses. The results show that alternatively and non-alternatively spliced (non-AS) genes have similar tendency for overall codon usage, but exhibit significant difference in 58 out of 64 codons. AS and non-AS genes are both under strong purifying selection, but the former ones have significant lower mutation rate and are prone to be enriched towards the chromosomal ends. In the group of AS genes, the variability in synonymous codon usage between genes is mainly due to the variations in GC content, CDS length, as well as gene functions. Mutational bias that accounts for 25.85 % of the total codon usage variability plays a major role in shaping the codon usage pattern of AS genes. In contrast, no obvious evidence is found for the contributions of translational selection, AS types, the conservation of AS events, and numbers of AS variants to the codon usage divergence between AS genes. These findings may be useful for further understanding the mechanisms of origination, differentiation and regulation of alternatively spliced genes in plants. PMID:25407289

Liu, Qingpo; Hu, Haichao; Wang, Hong

2014-11-19

91

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

PubMed

Mitochondria from diverse phyla, including protozoa, fungi, higher plants, and humans, import tRNAs from the cytosol in order to ensure proper mitochondrial translation. Despite the broad occurrence of this process, our understanding of tRNA import mechanisms is fragmentary, and crucial questions about their regulation remain unanswered. In the unicellular green alga Chlamydomonas, a precise correlation was found between the mitochondrial codon usage and the nature and amount of imported tRNAs. This led to the hypothesis that tRNA import might be a dynamic process able to adapt to the mitochondrial genome content. By manipulating the Chlamydomonas mitochondrial genome, we introduced point mutations in order to modify its codon usage. We find that the codon usage modification results in reduced levels of mitochondrial translation as well as in subsequent decreased levels and activities of respiratory complexes. These effects are linked to the consequential limitations of the pool of tRNAs in mitochondria. This indicates that tRNA mitochondrial import cannot be rapidly regulated in response to a novel genetic context and thus does not appear to be a dynamic process. It rather suggests that the steady-state levels of imported tRNAs in mitochondria result from a co-evolutive adaptation between the tRNA import mechanism and the requirements of the mitochondrial translation machinery. PMID:23028354

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

2012-09-01

92

Codon usage correlations and crystal basis model of the genetic code  

NASA Astrophysics Data System (ADS)

The ratios of the codon frequencies for the amino acids coded by four or by six codons in the genetic code exhibit a correlated behaviour for 29 biological species. The analyzed species are such that the whole codon number, determined from the available coding sequences, is larger than about 100000. This correlation fits naturally in the framework of the crystal basis model of the genetic code (Frappat L., Sciarrino A. and Sorba P., Phys. Lett. A, 250 (1998) 214).

Chiusano, M. L.; Frappat, L.; Sorba, P.; Sciarrino, A.

2001-07-01

93

Codon usage between genomes is constrained by genome-wide mutational processes  

Microsoft Academic Search

Analysis of genome-wide codon bias shows that only two parameters effectively differentiate the genome-wide codon bias of 100 eubacterial and archaeal organisms. The first parameter correlates with genome GC content, and the second parameter correlates with context-dependent nucleotide bias. Both of these parameters may be calculated from intergenic sequences. Therefore, genome-wide codon bias in eubacteria and archaea may be predicted

Swaine L. Chen; William Lee; Alison K. Hottes; Lucy Shapiro; Harley H. McAdams

2004-01-01

94

Codon usage tabulated from international DNA sequence databases: status for the year 2000  

Microsoft Academic Search

The frequencies of each of the 257 468 complete protein coding sequences (CDSs) have been compiled from the taxonomical divisions of the GenBank DNA sequence database. The sum of the codons used by 8792 organisms has also been calculated. The data files can be obtained from the anonymous ftp sites of DDBJ, Kazusa and EBI. A list of the codon

Yasukazu Nakamura; Takashi Gojobori; Toshimichi Ikemura

2000-01-01

95

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

PubMed

Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages. PMID:22943112

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

2012-12-01

96

Evolution of the Adh locus in the Drosophila willistoni group: the loss of an intron, and shift in codon usage.  

PubMed

We report here the DNA sequence of the alcohol dehydrogenase gene (Adh) cloned from Drosophila willistoni. The three major findings are as follows: (1) Relative to all other Adh genes known from Drosophila, D. willistoni Adh has the last intron precisely deleted; PCR directly from total genomic DNA indicates that the deletion exists in all members of the willistoni group but not in any other group, including the closely related saltans group. Otherwise the structure and predicted protein are very similar to those of other species. (2) There is a significant shift in codon usage, especially compared with that in D. melanogaster Adh. The most striking shift is from C to U in the wobble position (both third and first position). Unlike the codon-usage-bias pattern typical of highly biased genes in D. melanogaster, including Adh, D. willistoni has nearly 50% G + C in the third position. (3) The phylogenetic information provided by this new sequence is in agreement with almost all other molecular and morphological data, in placing the obscura group closer to the melanogaster group, with the willistoni group farther distant but still clearly within the subgenus Sophophora. PMID:8336545

Anderson, C L; Carew, E A; Powell, J R

1993-05-01

97

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

PubMed

The mosquito Aedes aegypti is the primary vector of dengue virus (DENV) infection in most of the subtropical and tropical countries. Besides DENV, yellow fever virus (YFV) is also transmitted by A. aegypti. Susceptibility of A. aegypti to West Nile virus (WNV) has also been confirmed. Although studies have indicated correlation of codon bias between flaviviridae and their animal/insect hosts, it is not clear if codon sequences have any relation to susceptibility of A. aegypti to DENV, YFV and WNV. In the current study, usages of codon context sequences (codon pairs for neighboring amino acids) of the vector (A. aegypti) genome as well as the flaviviral genomes are investigated. We used bioinformatics methods to quantify codon context bias in a genome-wide manner of A. aegypti as well as DENV, WNV and YFV sequences. Mutual information statistics was applied to perform bicluster analysis of codon context bias between vector and flaviviral sequences. Functional relevance of the bicluster pattern was inferred from published microarray data. Our study shows that codon context bias of DENV, WNV and YFV sequences varies in a bicluster manner with that of specific sets of genes of A. aegypti. Many of these mosquito genes are known to be differentially expressed in response to flaviviral infection suggesting that codon context sequences of A. aegypti and the flaviviruses may play a role in the susceptible interaction between flaviviruses and this mosquito. The bias in usages of codon context sequences likely has a functional association with susceptibility of A. aegypti to flaviviral infection. The results from this study will allow us to conduct hypothesis-driven tests to examine the role of codon context bias in evolution of vector-virus interactions at the molecular level. PMID:24838953

Behura, Susanta K; Severson, David W

2014-10-01

98

TRENDS IN CODON AND AMINO ACID USAGE IN HUMAN PATHOGEN TROPHERYMA WHIPPLEI, THE ONLY KNOWN  

E-print Network

replicational-transcriptional selection, translational control and other physico-chemical properties of the gene pressure has little influence on the amino acid usage, for which the mean hydropathy level and aromaticity-style, the amino acid usage in highly expressed gene products of T. whipplei follows the cost

Wong, Limsoon

99

/ http://www.sciencemag.org/content/early/recent / 26 September 2013 / Page 1 / 10.1126/science.1241934 Codon usage is biased in natural genes and can strongly affect heterolo-  

E-print Network

.1241934 Codon usage is biased in natural genes and can strongly affect heterolo- gous expression (1). Many organisms are enriched for poorly-adapted codons at the N terminus of genes (2­5). Several studies suggest that these codons slow ribosomal elongation during initiation and lead to increased translational efficiency (2, 4

Church, George M.

100

Codon usage determines the mutational robustness, evolutionary capacity and virulence of an RNA virus  

PubMed Central

Summary RNA viruses exist as dynamic and diverse populations shaped by constant mutation and selection. Yet little is known about how the mutant spectrum contributes to virus evolvability and pathogenesis. Because several codon choices are available for a given amino acid, a central question concerns whether viral sequences have evolved to optimize not only the protein coding consensus, but also the DNA/RNA sequences accessible through mutation. Here we directly test this hypothesis by comparing wild type poliovirus to synthetic viruses carrying reengineered capsid sequences with hundreds of synonymous mutations. Strikingly, such rewiring of the population's mutant network reduced its robustness and attenuated the virus in an animal model of infection. We conclude that the position of a virus in sequence space defines its mutant spectrum, evolutionary trajectory, and pathogenicity. This organizing principle for RNA virus populations confers tolerance to mutations and facilitates replication and spread within the dynamic host environment. PMID:23159052

Lauring, Adam S.; Acevedo, Ashley; Cooper, Samantha B.; Andino, Raul

2012-01-01

101

Codon usage determines the mutational robustness, evolutionary capacity, and virulence of an RNA virus.  

PubMed

RNA viruses exist as dynamic and diverse populations shaped by constant mutation and selection. Yet little is known about how the mutant spectrum contributes to virus evolvability and pathogenesis. Because several codon choices are available for a given amino acid, a central question concerns whether viral sequences have evolved to optimize not only the protein coding consensus, but also the DNA/RNA sequences accessible through mutation. Here we directly test this hypothesis by comparing wild-type poliovirus to synthetic viruses carrying re-engineered capsid sequences with hundreds of synonymous mutations. Strikingly, such rewiring of the population's mutant network reduced its robustness and attenuated the virus in an animal model of infection. We conclude that the position of a virus in sequence space defines its mutant spectrum, evolutionary trajectory, and pathogenicity. This organizing principle for RNA virus populations confers tolerance to mutations and facilitates replication and spread within the dynamic host environment. PMID:23159052

Lauring, Adam S; Acevedo, Ashley; Cooper, Samantha B; Andino, Raul

2012-11-15

102

Nucleotide sequence of a macronuclear DNA molecule coding for alpha-tubulin from the ciliate Stylonychia lemnae. Special codon usage: TAA is not a translation termination codon.  

PubMed Central

The gene-sized macronuclear DNA of the hypotrichous ciliate Stylonychia lemnae contains two size classes of DNA molecules (1.85 and 1.73 kbp) coding for alpha-tubulin. Each macronucleus contains about 55000 copies of the 1.85 kbp molecules and about 17000 copies of the 1.73 kbp DNA molecules. Five macronuclear molecules of these sequences were cloned and sequenced, one, from the 1.85 kbp size class in its entirety. The 5 sequences fell into two classes suggesting that Stylonychia lemnae contains at least two different alpha-tubulin genes. All 5 clones show the codon TAA in the same nucleotide positions of the coding region. In this position the TAA codon cannot function as a translational stop codon and we suggest that this codon codes for the amino acid glutamine. The nucleotide sequence of the coding region as well as the encoded amino acid sequence is highly conserved compared to alpha-tubulin genes from vertebrates. The noncoding regions show several putative transcription-regulatory sequences as well as sequences presumably functioning as replication origins. Images PMID:2987795

Helftenbein, E

1985-01-01

103

Codon Evolution Mechanisms and Models  

E-print Network

Codon Evolution Mechanisms and Models EDITED BY Gina M. Cannarozzi University of Bern, Switzerland;CHAPTER 13 Measuring codon usage bias Alexander Roth, Maria Anisimova, and Gina M. Cannarozzi 13 triplets (or codons) to amino acids. Synonymous codons translate to the same amino acid and are indistin

Anisimova, Maria

104

Gene Expression Levels Are Correlated with Synonymous Codon Usage, Amino Acid Composition, and Gene Architecture in the Red Flour Beetle, Tribolium castaneum  

PubMed Central

Gene expression levels correlate with multiple aspects of gene sequence and gene structure in phylogenetically diverse taxa, suggesting an important role of gene expression levels in the evolution of protein-coding genes. Here we present results of a genome-wide study of the influence of gene expression on synonymous codon usage, amino acid composition, and gene structure in the red flour beetle, Tribolium castaneum. Consistent with the action of translational selection, we find that synonymous codon usage bias increases with gene expression. However, the correspondence between tRNA gene copy number and optimal codons is weak. At the amino acid level, translational selection is suggested by the positive correlation between tRNA gene numbers and amino acid usage, which is stronger for highly expressed genes. In addition, there is a clear trend for increased use of metabolically cheaper, less complex amino acids as gene expression increases. tRNA gene numbers also correlate negatively with amino acid size/complexity (S/C) score indicating the coupling between translational selection and selection to minimize the use of large/complex amino acids. Interestingly, the analysis of 10 additional genomes suggests that the correlation between tRNA gene numbers and amino acid S/C score is widespread and might be explained by selection against negative consequences of protein misfolding. At the level of gene structure, three major trends are detected: 1) complete coding region length increases across low and intermediate expression levels but decreases in highly expressed genes; 2) the average intron size shows the opposite trend, first decreasing with expression, followed by a slight increase in highly expressed genes; and 3) intron density remains nearly constant across all expression levels. These changes in gene architecture are only in partial agreement with selection favoring reduced cost of biosynthesis. PMID:22826459

Williford, Anna; Demuth, Jeffery P.

2012-01-01

105

What Drives Codon Choices in Human Genes?  

Microsoft Academic Search

Synonymous codon usage is biased and the bias seems to be different in different organisms. Factors with proposed roles in causing codon bias include degree and timing of gene expression, codon – anticodon inter actions, transcription and translation rate and fidelity, codon context, and global and local G + C content. We offer a new perspective and new methods for

Samuel Karlin; Jan Mrázek

1996-01-01

106

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.

Julie Yu

2008-01-01

107

A Comparison of English Teachers' Own Usage with Their Attitudes Toward Usage.  

ERIC Educational Resources Information Center

In spoken and written situations which focused the teachers' attentions on information rather than on their language, samples of 100 English teachers' actual language were obtained with respect to five debatable usages: "everybody...their,""reason...is because,""who" as an object pronoun, "will/would" with the first person subject to express…

Johnson, Robert Spencer

108

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

109

Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates.  

E-print Network

??Although synonymous codon usage in mammals has been investigated for decades, thereare still controversial interpretations of the observed results. Selectionism cannot explainthe strong regularities in… (more)

Nabiyouni, Maryam

2011-01-01

110

Computational identification of rare codons of Escherichia coli based on codon pairs preference  

PubMed Central

Background Codon bias is believed to play an important role in the control of gene expression. In Escherichia coli, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engineering operations. Previous studies have confirmed the existence of codon pair's preference in many genomes, but the underlying cause of this bias has not been well established. Here we focus on the patterns of rarely-used synonymous codons. A novel method was introduced to identify the rare codons merely by codon pair bias in Escherichia coli. Results In Escherichia coli, we defined the "rare codon pairs" by calculating the frequency of occurrence of all codon pairs in coding sequences. Rare codons which are disliked in genes could make great contributions to forming rare codon pairs. Meanwhile our investigation showed that many of these rare codon pairs contain termination codons and the recognized sites of restriction enzymes. Furthermore, a new index (Frare) was developed. Through comparison with the classical indices we found a significant negative correlation between Frare and the indices which depend on reference datasets. Conclusions Our approach suggests that we can identify rare codons by studying the context in which a codon lies. Also, the frequency of rare codons (Frare) could be a useful index of codon bias regardless of the lack of expression abundance information. PMID:20109184

2010-01-01

111

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. PMID:22707716

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

2012-01-01

112

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

113

A Comparison of Usage Evaluation and Inspection Methods for Assessing Groupware Usability  

E-print Network

A Comparison of Usage Evaluation and Inspection Methods for Assessing Groupware Usability Michelle@cs.usask.ca; saul@cpsc.ucalgary.ca ABSTRACT Many researchers believe that groupware can only be evaluated- consuming. Others believe that it is more practical to evaluate groupware through usability inspection

Greenberg, Saul

114

Variation in synonymous codon use and DNA polymorphism within the Drosophila genome  

E-print Network

Variation in synonymous codon use and DNA polymorphism within the Drosophila genome N. BIERNE* & A, Se`te, France Introduction It is now widely accepted that weak selection for codon usage is acting analyses suggest that selection for codon usage is currently active in D. simulans (Akashi & Schaeffer

Eyre-Walker, Adam

115

RESEARCH Open Access The role of codon selection in regulation of  

E-print Network

RESEARCH Open Access The role of codon selection in regulation of translation efficiency deduced is affected by a diversity of parameters, including secondary structure of the transcript and its codon usage. Here we examine the effects of codon usage on translation efficiency by re-analysis of previously

Pilpel, Yitzhak

116

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the  

E-print Network

Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models Ronald Jansen1 , Harmen J compositional bias, in terms of codon usage. Two widely used numerical indices, the codon adaptation index (CAI

Gerstein, Mark

117

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

118

Current Biology 16, 20532057, October 24, 2006 2006 Elsevier Ltd All rights reserved DOI 10.1016/j.cub.2006.08.067 Selection Intensity on Preferred Codons  

E-print Network

.1016/j.cub.2006.08.067 Report Selection Intensity on Preferred Codons Correlates with Overall Codon Usage Summary Adaptive codon usage provides evidence of natural selection in one of its most subtle forms: a fitness ben- efit of one synonymous codon relative to another. Co- don usage bias is evident in the coding

Cutter, Asher D.

119

Preferred and avoided codon pairs in three domains of life  

PubMed Central

Background Alternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons – neighboring nucleotides and neighboring codons – can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserved the codon context preferences in different organisms are. We analyzed 138 organisms (bacteria, archaea and eukaryotes) to find conserved patterns of codon pairs. Results After removing the effects of single codon usage and dipeptide biases we discovered a set of neighboring codons for which avoidances or preferences were conserved in all three domains of life. Such biased codon pairs could be divided into subtypes on the basis of the nucleotide patterns that influence the bias. The most frequently avoided type of codon pair was nnUAnn. We discovered that 95.7% of avoided nnUAnn type patterns contain out-frame UAA or UAG triplets on the sense and/or antisense strand. On average, nnUAnn codon pairs are more frequently avoided in ORFeomes than in genomes. Thus we assume that translational selection plays a major role in the avoidance of these codon pairs. Among the preferred codon pairs, nnGCnn was the major type. Conclusion Translational selection shapes codon pair usage in protein coding sequences by rules that are common to all three domains of life. The most frequently avoided codon pairs contain the patterns nnUAnn, nnGGnn, nnGnnC, nnCGCn, GUCCnn, CUCCnn, nnCnnA or UUCGnn. The most frequently preferred codon pairs contain the patterns nnGCnn, nnCAnn or nnUnCn. PMID:18842120

Tats, Age; Tenson, Tanel; Remm, Maido

2008-01-01

120

Rare codons regulate KRas oncogenesis  

PubMed Central

Summary Oncogenic mutations in the small Ras GTPases KRas, HRas, or NRas render the encoded proteins constitutively GTP-bound and active, which promote cancer [1]. Ras proteins share ~85% amino acid identity [2], are activated by [3] and signal through [4] the same proteins, and can exhibit functional redundancy [5][6]. Nevertheless, manipulating expression or activation of each isoform yields different cellular responses [7–10] and tumorigenic phenotypes [11–13], even when different ras genes are expressed from the same locus [6]. We now report a novel regulatory mechanism hardwired into the very sequence of RAS genes that underlies how such similar proteins impact tumorigenesis differently. Specifically, despite their high sequence similarity, KRAS is poorly translated compared to HRAS due to enrichment in genomically underrepresented, or rare, codons. Converting rare to common codons increased KRas expression and tumorigenicity to mirror that of HRas. Furthermore, in a genome-wide survey similar gene pairs with opposing codon bias were identified that not only manifested dichotomous protein expression, but were also enriched in key signaling protein classes and pathways. Thus, synonymous nucleotide differences affecting codon usage account for differences between HRas and KRas expression and function, and may represent a broader regulation strategy in cell signaling. PMID:23246410

Lampson, Benjamin L.; Pershing, Nicole L.K.; Prinz, Joseph A.; Lacsina, Joshua R.; Marzluff, William F.; Nicchitta, Christopher V.; MacAlpine, David M.; Counter, Christopher M.

2013-01-01

121

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

122

Codon Optimization Increases Steady-State mRNA Levels in Aspergillus oryzae Heterologous Gene Expression  

Microsoft Academic Search

We investigated the effect of codon optimization on the expression levels of heterologous proteins in Aspergillus oryzae, using the mite allergen De rf7a s amodel protein. A codon-optimized Der f 7 gene was synthesized according to the frequency of codon usage in A. oryzae by recursive PCR. Both native and optimized Der f 7 genes were expressed under the control

Masafumi Tokuoka; Mizuki Tanaka; Kazuhisa Ono; Shinobu Takagi; Takahiro Shintani; Katsuya Gomi

2008-01-01

123

Evidence for codon bias selection at the pre-mRNA level in eukaryotes  

E-print Network

Evidence for codon bias selection at the pre-mRNA level in eukaryotes Erik Willie and Jacek York, NY 10021, USA We investigated codon usage patterns across eukaryotic exons. We have shown that in humans codon preference varies with distance from the splice sites. This is consistent

Majewski, Jacek

124

ArticleFastTrack Good Codons, Bad Transcript: Large Reductions in  

E-print Network

ArticleFastTrack Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness@oeb.harvard.edu. Associate editor: Helen Piontkivska Abstract Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely encoded by a specific subset of possible codons. Within individual genes

125

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

126

ITG-Fachgruppe Bio-Informationstheorie "Gene Regulation and Information Theory" Halle/Saale, Germany, April 17-19, 2013 Codon-Based Distance Matrix  

E-print Network

/Saale, Germany, April 17-19, 2013 Codon-Based Distance Matrix using a Modified Empirical Codon Mutation Matrix Understand the mapping of 64 codons to 20 amino acids. 828 800 955 6288 21.1appendix Important Licensing to the ochre termination triplet and Stop (amb) refers to the amber. Codon Usage Table* Second Position Half

Henkel, Werner

127

Genome-Wide Patterns of Codon Bias Are Shaped by Natural Selection in the Purple Sea Urchin, Strongylocentrotus purpuratus  

PubMed Central

Codon usage bias has been documented in a wide diversity of species, but the relative contributions of mutational bias and various forms of natural selection remain unclear. Here, we describe for the first time genome-wide patterns of codon bias at 4623 genes in the purple sea urchin, Strongylocentrotus purpuratus. Preferred codons were identified at 18 amino acids that exclusively used G or C at third positions, which contrasted with the strong AT bias of the genome (overall GC content is 36.9%). The GC content of third positions and coding regions exhibited significant correlations with the magnitude of codon bias. In contrast, the GC content of introns and flanking regions was indistinguishable from the genome-wide background, which suggested a limited contribution of mutational bias to synonymous codon usage. Five distinct clusters of genes were identified that had significantly different synonymous codon usage patterns. A significant correlation was observed between codon bias and mRNA expression supporting translational selection, but this relationship was driven by only one highly biased cluster that represented only 8.6% of all genes. In all five clusters preferred codons were evolutionarily conserved to a similar degree despite differences in their synonymous codon usage distributions and magnitude of codon bias. The third positions of preferred codons in two codon usage groups also paired significantly more often in stems than in loops of mRNA secondary structure predictions, which suggested that codon bias might also affect mRNA stability. Our results suggest that mutational bias has played a minor role in determining codon bias in S. purpuratus and that preferred codon usage may be heterogeneous across different genes and subject to different forms of natural selection. PMID:23637123

Kober, Kord M.; Pogson, Grant H.

2013-01-01

128

Journal of Theoretical Biology 239 (2006) 417434 A model of protein translation including codon bias, nonsense errors,  

E-print Network

Journal of Theoretical Biology 239 (2006) 417­434 A model of protein translation including codon a heterogeneous medium, the mRNA transcript. Our results show that the heterogeneity of the codon translation errors and codon usage bias can have a large effect on the probability that a ribosome will completely

Wagner, Andreas

129

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. PMID:22698086

2012-01-01

130

Codon Distributions in DNA  

E-print Network

The codons, sixtyfour in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency-versus-rank of the codons. These distributions are characterised by parameters that are almost universal, i.e., gene independent. There is but a small part that depends on the gene. We present the theory to calculate the universal (gene-independent) part. The part that is gene-specific, however, has undetermined overlaps and fluctuations.

Som, A; Chakrabarti, J; Bandyopadhyay, D

2001-01-01

131

Codon distributions in DNA  

NASA Astrophysics Data System (ADS)

The codons, 64 in number, are distributed over the coding parts of DNA sequences. The distribution function is the plot of frequency versus rank of the codons. These distributions are characterized by parameters that are almost universal, i.e., gene independent. There is but a small part that depends on the gene. We present the theory to calculate the universal (gene-independent) part. The part that is gene-specific, however, has undetermined overlaps and fluctuations.

Som, A.; Chattopadhyay, S.; Chakrabarti, J.; Bandyopadhyay, D.

2001-05-01

132

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. PMID:24583580

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-01-01

133

Effect of codon-optimized E. coli signal peptides on recombinant Bacillus stearothermophilus maltogenic amylase periplasmic localization, yield and activity.  

PubMed

Recombinant proteins can be targeted to the Escherichia coli periplasm by fusing them to signal peptides. The popular pET vectors facilitate fusion of target proteins to the PelB signal. A systematic comparison of the PelB signal with native E. coli signal peptides for recombinant protein expression and periplasmic localization is not reported. We chose the Bacillus stearothermophilus maltogenic amylase (MA), an industrial enzyme widely used in the baking and brewing industry, as a model protein and analyzed the competence of seven, codon-optimized, E. coli signal sequences to translocate MA to the E. coli periplasm compared to PelB. MA fusions to three of the signals facilitated enhanced periplasmic localization of MA compared to the PelB fusion. Interestingly, these three fusions showed greatly improved MA yields and between 18- and 50-fold improved amylase activities compared to the PelB fusion. Previously, non-optimal codon usage in native E. coli signal peptide sequences has been reported to be important for protein stability and activity. Our results suggest that E. coli signal peptides with optimal codon usage could also be beneficial for heterologous protein secretion to the periplasm. Moreover, such fusions could even enhance activity rather than diminish it. This effect, to our knowledge has not been previously documented. In addition, the seven vector platform reported here could also be used as a screen to identify the best signal peptide partner for other recombinant targets of interest. PMID:25038884

Samant, Shalaka; Gupta, Gunja; Karthikeyan, Subbulakshmi; Haq, Saiful F; Nair, Ayyappan; Sambasivam, Ganesh; Sukumaran, Sunilkumar

2014-09-01

134

Usage Data for Electronic Resources: A Comparison between Locally Collected and Vendor-Provided Statistics.  

ERIC Educational Resources Information Center

Vendor-provided electronic resource usage statistics are not currently standardized across vendors. This study investigates the feasibility of using locally collected data to check the reliability of vendor-provided data. Vendor-provided data were compared with local data collected from North Carolina State University (NCSU) Libraries' Web…

Duy, Joanna; Vaughan, Liwen

2003-01-01

135

A comparison of two methods to assess the usage of mobile hand-held communication devices.  

PubMed

ABSTRACT Objective: The purposes of this study were to: 1) examine agreement between self-reported measures of mobile device use and direct measures of use, and 2) understand how respondents thought about their device use when they provided self-reports. Methods: Self-reports of six categories of device use were obtained using a previously developed questionnaire, and direct measures of use were collected using a custom logging application (n = 47). Bland-Altman analyses were used to examine agreement between the two measurement approaches. Interviews targeted participants' experiences completing the device use section of the questionnaire. Results: Self-reports of use on a typical day last week overestimated logged use; overestimates tended to be low at low average usage times, and became more variable as usage time increased. Self-reports of use yesterday also exceeded logged use, however the degree of overestimation was less than for a typical day last week. Six themes were identified from interviews, including the thought process used by participants to arrive at usage and the ease of reporting usage. Discussion: It is challenging for respondents of this questionnaire to provide accurate self-reports of use. The source of this challenge may be attributed to the intrinsic difficulty of estimating use, partly due to the multiple functions of the devices as well as the variability of use both within a day and a week. Conclusion: Research investigating the relationship between device use and health outcomes should include a logging application to examine exposure simultaneously with self-reports to better understand the sources of hazardous exposures. PMID:25436479

Berolo, Sophia; Steenstra, Ivan; Amick, Benjamin C; Wells, Richard P

2014-12-01

136

Usage data for electronic resources: A comparison between locally collected and vendor-provided statistics  

Microsoft Academic Search

Vendor-provided electronic resource usage statistics are not currently standardized across vendors. This study investigated the feasibility of using locally collected data to check the reliability of vendor-provided data. Vendor-provided data were compared with local data collected from the NCSU Libraries’ Web servers. The study finds that the two types of data correlate well in terms of use patterns, but that

Joanna Duy; Liwen Vaughan

2003-01-01

137

Codon Preference Optimization Increases Heterologous PEDF Expression  

PubMed Central

Pigment epithelium-derived factor (PEDF) is widely known for its neurotrophic and antiangiogenic functions. Efficacy studies of PEDF in animal models are limited because of poor heterologous protein yields. Here, we redesigned the human PEDF gene to preferentially match codon frequencies of E coli without altering the amino acid sequence. Following de novo synthesis, codon optimized PEDF (coPEDF) and the wtPEDF genes were cloned into pET32a containing a 5? thioredoxin sequence (Trx) and the recombinant Trx-coPEDF or Trx-wtPEDF fusion constructs expressed in native and two tRNA augmented E coli hosts - BL21-CodonPlus(DE3)-RIL and BL21-CodonPlus(DE3)-RP, carrying extra copies of tRNAarg,ile,leu and tRNAarg,pro genes , respectively. Trx-PEDF fusion proteins were isolated using Ni-NTA metal affinity chromatography and PEDF purified after cleavage with factor X?. Protein purity and identity were confirmed by western blot, MALDI-TOF, and UV/CD spectral analyses. Expression of the synthetic gene was ?3.4 fold greater (212.7 mg/g; 62.1 mg/g wet cells) and purified yields ?4 fold greater (41.1 mg/g; 11.3 mg/g wet cell) than wtPEDF in the native host. A small increase in expression of both genes was observed in hosts supplemented with rare tRNA genes compared to the native host but expression of coPEDF was ?3 fold greater than wtPEDF in both native and codon-bias-adjusted E coli strains. ?Gs at ?3 to +50 of the Trx site of both fusion genes were ?3.9 kcal/mol. Functionally, coPEDF was equally as effective as wtPEDF in reducing oxidative stress, promoting neurite outgrowth, and blocking endothelial tube formation. These findings suggest that while rare tRNA augmentation and mRNA folding energies can significantly contribute to increased protein expression, preferred codon usage, in this case, is advantageous to translational efficiency of biologically active PEDF in E coli. This strategy will undoubtedly fast forward studies to validate therapeutic utility of PEDF in vivo. PMID:21152082

Gvritishvili, Anzor G.; Leung, Kar Wah; Tombran-Tink, Joyce

2010-01-01

138

Genetic features of a translation initiation system composed of IRES element, nucleotide context surrounding the initiation codon, and translation initiation region of classical swine fever virus RNA.  

PubMed

Nucleotide and codon usage are typically examined to investigate viral evolution. In this study, we analyzed the genetic information of 46 strains of classical swine fever virus (CSFV) RNA, nucleotide usage in the internal ribosome entry site (IRES), the nucleotide context surrounding the initiation codon, and synonymous codon usage in the translation initiation region. Phylogenetic analysis of the IRES element indicated that the genetic diversity of this element is generally similar to the phylogenetic clusters of CSFV genotypes. Nucleotides surrounding the initiation codon of CSFV RNA were generally more stable (ACAUGGCACAUGGAGUUG) compared to the internal AUG in the CSFV coding sequence. The second codon position after the initiation codon was generally selected to be GAG, which has lower tRNA abundance in pigs than its synonymous member (GAA). Regarding the synonymous codon usage bias in the CSFV translation initiation region, some codons showing low tRNA abundance in pigs are more frequently located in the translation initiation region than in the open reading frame of CSFV. Although CSFV, similarly to other RNA viruses, has a high mutation rate in nature, the regulatory features of nucleotide and synonymous codon usage of the IRES element, the nucleotide context surrounding the initiation codon and the translation initiation region in CSFV RNA have been 'branded' in the system of translation initiation to accommodate gene expression mediated by the cap-independent translation mechanism. PMID:25526200

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

2014-01-01

139

A Generalized Mechanistic Codon Model  

PubMed Central

Models of codon evolution have attracted particular interest because of their unique capabilities to detect selection forces and their high fit when applied to sequence evolution. We described here a novel approach for modeling codon evolution, which is based on Kronecker product of matrices. The 61 × 61 codon substitution rate matrix is created using Kronecker product of three 4 × 4 nucleotide substitution matrices, the equilibrium frequency of codons, and the selection rate parameter. The entities of the nucleotide substitution matrices and selection rate are considered as parameters of the model, which are optimized by maximum likelihood. Our fully mechanistic model allows the instantaneous substitution matrix between codons to be fully estimated with only 19 parameters instead of 3,721, by using the biological interdependence existing between positions within codons. We illustrate the properties of our models using computer simulations and assessed its relevance by comparing the AICc measures of our model and other models of codon evolution on simulations and a large range of empirical data sets. We show that our model fits most biological data better compared with the current codon models. Furthermore, the parameters in our model can be interpreted in a similar way as the exchangeability rates found in empirical codon models. PMID:24958740

Zaheri, Maryam; Dib, Linda; Salamin, Nicolas

2014-01-01

140

Usage Bibliometrics  

NASA Astrophysics Data System (ADS)

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

Kurtz, Michael J.; Bollen, Johan

2010-01-01

141

Codon Evolution Mechanisms and Models  

E-print Network

;CHAPTER 2 Parametric models of codon evolution Maria Anisimova 2.1 Basic Markov models of codon described using Markov models. This chapter focuses on parametric models--models that describe the evolution-diagonal entries minus one--to enable scaling). In contrast to DNA models, the first amino acid substitution models

Anisimova, Maria

142

Kenyan medicinal plants used as antivenin: a comparison of plant usage  

Microsoft Academic Search

The success of snake bite healers is vaguely understood in Kenya, partly due to their unknown materia medica and occult-mystical nature of their practice. A comparison is made of plants used in snake bite treatments by two culturally distinct African groups (the Kamba and Luo). Thirty two plants used for snakebite treatment are documented. The majority of the antidotes are

Bethwell O Owuor; Daniel P Kisangau

2006-01-01

143

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

144

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

PubMed

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. PMID:24104350

Mitarai, Namiko; Pedersen, Steen

2013-10-01

145

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

146

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

E-print Network

Messenger RNA 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 messenger RNA (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 sequences and sequences where the synonymous codons were swapped randomly. By simulating translation of 87 genes, we demonstrate that the wild type 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.

Namiko Mitarai; Steen Pedersen

2013-09-04

147

Timing is everything: unifying codon translation rates and nascent proteome behavior.  

PubMed

Experiments have demonstrated that changing the rate at which the ribosome translates a codon position in an mRNA molecule's open reading frame can alter the behavior of the newly synthesized protein. That is, codon translation rates can govern nascent proteome behavior. We emphasize that this phenomenon is a manifestation of the nonequilibrium nature of cotranslational processes, and as such, there exist theoretical tools that offer a potential means to quantitatively predict the influence of codon translation rates on the broad spectrum of nascent protein behaviors including cotranslational folding, aggregation, and translocation. We provide a review of the experimental evidence for the impact that codon translation rates can have, followed by a discussion of theoretical methods that can describe this phenomenon. The development and application of these tools are likely to provide fundamental insights into protein maturation and homeostasis, codon usage bias in organisms, the origins of translation related diseases, and new rational design methods for biotechnology and biopharmaceutical applications. PMID:25486504

Nissley, Daniel A; O'Brien, Edward P

2014-12-31

148

Cue usage in volleyball: a time course comparison of elite, intermediate and novice female players.  

PubMed

This study compared visual search strategies in adult female volleyball players of three levels. Video clips of the attack of the opponent team were presented on a large screen and participants reacted to the final pass before the spike. Reaction time, response accuracy and eye movement patterns were measured. Elite players had the highest response accuracy (97.50 ± 3.5%) compared to the intermediate (91.50 ± 4.7%) and novice players (83.50 ± 17.6%; p<0.05). Novices had a remarkably high range of reaction time but no significant differences were found in comparison to the reaction time of elite and intermediate players. In general, the three groups showed similar gaze behaviour with the apparent use of visual pivots at moments of reception and final pass. This confirms the holistic model of image perception for volleyball and suggests that expert players extract more information from parafoveal regions. PMID:25609887

Vansteenkiste, P; Vaeyens, R; Zeuwts, L; Philippaerts, R; Lenoir, M

2014-12-01

149

CUE USAGE IN VOLLEYBALL: A TIME COURSE COMPARISON OF ELITE, INTERMEDIATE AND NOVICE FEMALE PLAYERS  

PubMed Central

This study compared visual search strategies in adult female volleyball players of three levels. Video clips of the attack of the opponent team were presented on a large screen and participants reacted to the final pass before the spike. Reaction time, response accuracy and eye movement patterns were measured. Elite players had the highest response accuracy (97.50 ± 3.5%) compared to the intermediate (91.50 ± 4.7%) and novice players (83.50 ± 17.6%; p<0.05). Novices had a remarkably high range of reaction time but no significant differences were found in comparison to the reaction time of elite and intermediate players. In general, the three groups showed similar gaze behaviour with the apparent use of visual pivots at moments of reception and final pass. This confirms the holistic model of image perception for volleyball and suggests that expert players extract more information from parafoveal regions. PMID:25609887

Vaeyens, R; Zeuwts, L; Philippaerts, R; Lenoir, M

2014-01-01

150

Efficient codon optimization with motif engineering  

E-print Network

Efficient codon optimization with motif engineering Anne Condon and Chris Thachuk Department-native host organisms. Codon opti- mization supports translational efficiency of the desired protein product, by exchanging codons which are rarely found in the host organism with more frequently observed codons. Motif

Condon, Anne

151

Asociaciones Trasformacion de codons a aminoacidos  

E-print Network

Asociaciones Trasformaci´on de codons a amino´acidos Ficheros Parte de Algoritmos, de la asignatura´on de codons a amino´acidos Ficheros Contenido 1 Asociaciones 2 Trasformaci´on de codons a amino codons a amino´acidos Ficheros Conceptos generales Frecuentemente es necesario establecer asociaciones

Giménez, Domingo

152

A NEW INFORMATICS METHOD FOR MEASURING SYNONYMOUS CODON USAGE BIAS  

E-print Network

@ornl.gov Environmental Sciences Division Oak Ridge National Laboratory Oak Ridge, TN 37831 DONG XU xud@ornl.gov Life Sciences Division Oak Ridge National Laboratory Oak Ridge, TN 37831 JIZHONG ZHOU zhouj@ornl.gov Environmental Sciences Division Oak Ridge National Laboratory Oak Ridge, TN 37831 ABSTRACT Most of the current

153

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. PMID:24884412

2014-01-01

154

Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle  

E-print Network

Codon Bias Signatures, Organization of Microorganisms in Codon Space, and Lifestyle A. Carbone,* F, 91440 Bures-sur-Yvette, France New and simple numerical criteria based on a codon adaptation index microbial genomes, even those for which little biological information is known, and a codon bias signature

Carbone, Alessandra

155

Point Counter Point UAR Codons for Glutamine  

E-print Network

Point Counter Point UAR Codons for Glutamine P.J. Keeling and W.F. Doolittle (1996) reported that UAR (TAR) codons incorporate glutamine in Hexamiti- dae. They state that ``the particular variation became the sole chain termination codon and UAA and UAG were removed from the terminator sites

Keeling, Patrick

156

Worksheet Usage, Reading Achievement, Classes' Lack of Readiness, and Science Achievement: A Cross-Country Comparison  

ERIC Educational Resources Information Center

Instructional written materials play important roles as teachers' agents in effective teaching practices. Worksheets are one of the most frequently used materials. In this exploratory study, the relationships between worksheet usage and science achievement in 32 countries were examined through the use of TIMSS and PIRLS data and multiple…

Lee, Che-Di

2014-01-01

157

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

158

Diverse expression levels of two codon-optimized genes that encode human papilloma virus type 16 major protein L1 in Hansenula polymorpha.  

PubMed

Two versions of an optimized gene that encodes human papilloma virus type 16 major protein L1 were designed according to the codon usage frequency of Pichia pastoris. Y16 was highly expressed in both P. pastoris and Hansenula polymorpha. M16 expression was as efficient as that of Y16 in P. pastoris, but merely detectable in H. polymorpha even though transcription levels of M16 and Y16 were similar. H. polymorpha had a unique codon usage frequency that contains many more rare codons than Saccharomyces cerevisiae or P. pastoris. These findings indicate that even codon-optimized genes that are expressed well in S. cerevisiae and P. pastoris may be inefficiently expressed in H. polymorpha; thus rare codons must be avoided when universal optimized gene versions are designed to facilitate expression in a variety of yeast expression systems, especially H. polymorpha is involved. PMID:24563290

Liu, Cunbao; Yang, Xu; Yao, Yufeng; Huang, Weiwei; Sun, Wenjia; Ma, Yanbing

2014-05-01

159

Society of Systematic Biologists How Can Third Codon Positions Outperform First and Second Codon Positions in Phylogenetic  

E-print Network

Society of Systematic Biologists How Can Third Codon Positions Outperform First and Second Codon-836Xonline DOI: 10.1080/10635150500481473 How Can Third Codon Positions Outperform First and Second Codon.?Greater phylogenetic signal is often found in parsimony-based analyses of third codon positions of protein-coding genes

Webb, Colleen

160

Comparison between oral and vaginal estrogen usage in inadequate endometrial patients for frozen-thawed blastocysts transfer  

PubMed Central

Endometrial preparation with exogenous estrogen is a common practice in frozen-thawed embryo transfer (FET) cycles. The objective of this study was to compare the clinical outcomes of two endometrial preparation groups, oral estradiol valerate tablets (OEV) group versus vaginal estradiol (VE) tablets group, in inadequate endometrium patients. This retrospective, single-center, cohort study of patients undergoing FET treatment between Jan. 2012 and Jun. 2013, at an academic IVF center, included 247 patients (cycles) with endometrial thickness < 8 mm on day 13 of the hormone replacement cycle: OEV group included 69 patients (cycles) who received continuous OEV from day 1 onwards up to the day of progesterone supplement, while VE group included 178 patients (cycles) who taken OEV from day 1 to day 12, and used VE tablets from day 13 till the day of progesterone supplement. Patients in VE group required more days and higher dosage of estradiol, but had thinner endometrium on the day of transfer. However, the increase of endometrial thickness was more, when compared to OEV-treated patients. The implantation rate and pregnancy rate were, though not significantly, higher in VE group. Conclusions: Longer time of administration and higher dosage of estradiol usage did not have adverse effects on the clinical pregnancy rate. VE tablets may promote endometrial development and pregnancy success in FET cycles could not verify. Further study is needed to confirm the vaginal estradiol action on frozen-thawed embryo transfer cycles. PMID:25400786

Liao, Xiuhua; Li, Zhou; Dong, Xiyuan; Zhang, Hanwang

2014-01-01

161

Assessment of work-integrated learning: comparison of the usage of a grading rubric by supervising radiographers and teachers  

PubMed Central

IntroductionProfessional work-integrated learning (WIL) that integrates the academic experience with off-campus professional experience placements is an integral part of many tertiary courses. Issues with the reliability and validity of assessment grades in these placements suggest that there is a need to strengthen the level of academic rigour of placements in these programmes. This study aims to compare the attitudes to the usage of assessment rubrics of radiographers supervising medical imaging students and teachers supervising pre-service teachers. MethodsWIL placement assessment practices in two programmes, pre-service teacher training (Avondale College of Higher Education, NSW) and medical diagnostic radiography (Faculty of Health Sciences, University of Sydney, NSW), were compared with a view to comparing assessment strategies across these two different educational domains. Educators (course coordinators) responsible for teaching professional development placements of teacher trainees and diagnostic radiography students developed a standards-based grading rubric designed to guide assessment of students’ work during WIL placement by assessors. After ?12 months of implementation of the rubrics, assessors’ reaction to the effectiveness and usefulness of the grading rubric was determined using a specially created survey form. Data were collected over the period from March to June 2011. Quantitative and qualitative data found that assessors in both programmes considered the grading rubric to be a vital tool in the assessment process, though teacher supervisors were more positive about the benefits of its use than the radiographer supervisors. ResultsBenefits of the grading rubric included accuracy and consistency of grading, ability to identify specific areas of desired development and facilitation of the provision of supervisor feedback. The use of assessment grading rubrics is of benefit to assessors in WIL placements from two very different teaching programmes. ConclusionRadiographers appear to need more training in the rubric's use, whereas teachers are found to generally use it appropriately. There are implications drawn from this finding that are applicable to health science and medical education in general.

Kilgour, Andrew J; Kilgour, Peter W; Gerzina, Tania; Christian, Beverly

2014-01-01

162

Codon Constraints on Closed 2D Shapes  

E-print Network

Codons are simple primitives for describing plane curves. They thus are primarily image-based descriptors. Yet they have the power to capture important information about the 3-D world, such as making part boundaries ...

Richards, Whitman

1984-05-01

163

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. PMID:22997484

Castro-Chavez, Fernando

2011-01-01

164

Selection on Codon Bias Ruth Hershberg and Dmitri A. Petrov  

E-print Network

Selection on Codon Bias Ruth Hershberg and Dmitri A. Petrov Department of Biological Sciences-4197/08/1201-0287$20.00 Key Words codon bias, selection, evolution Abstract In a wide variety of organisms, synonymous codons are used with dif- ferent frequencies, a phenomenon known as codon bias. Population genetic studies have

Petrov, Dmitri

165

Rare Codons Cluster Thomas F. Clarke IV, Patricia L. Clark*  

E-print Network

Rare Codons Cluster Thomas F. Clarke IV, Patricia L. Clark* Department of Chemistry & Biochemistry by more than one codon. These synonymous codons are not used with equal frequency: in every organism, some codons are used more commonly, while others are more rare. Though the encoded protein sequence

Clark, Patricia L.

166

RESEARCH ARTICLE Open Access Context-dependent codon partition models  

E-print Network

RESEARCH ARTICLE Open Access Context-dependent codon partition models provide significant increases is often hampered by the computational burdens associated with full codon models. Lately, codon partition models have been proposed as a viable alternative, mimicking the substitution behaviour of codon models

Gent, Universiteit

167

Transcription, Translation and Mutation Given this list of codons  

E-print Network

Transcription, Translation and Mutation GenBio1 Fall 2011 Given this list of codons: Consider no special meaning except in the context of questions 2 and 3. The key here is to identify the start codon (UAG) and begin translating after that until a stop codon is hit. Remember that codons are non

Prestwich, Ken

168

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

169

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. PMID:17957249

Akashi, Hiroshi; Goel, Piyush; John, Anoop

2007-01-01

170

Eur. J. Biochem. 145, 359-364 (1984) Yeast tRNAAsp:codon and wobble codon-anticodon interactions  

E-print Network

Eur. J. Biochem. 145, 359-364 (1984) 0FEBS 1984 Yeast tRNAAsp:codon and wobble codon)- EJB 840754 The conformations of the ribotrinucleoside bisphosphates GpApC and GpApU, the codon and wobble codon for aspartic acid respectively, bound to yeast tRNAAspin solution, have been examined

Clore, G. Marius

171

The codon information index: a quantitative measure of the information provided by the codon bias  

NASA Astrophysics Data System (ADS)

The genetic code is redundant, as there are about three times more codons than amino acids. Because of this redundancy, a given amino acid can be specified by different codons, which are therefore considered synonymous. Despite being synonymous, however, such codons are used with different frequencies, a phenomenon known as codon bias. The origin and roles of the codon bias have not yet been fully clarified, although it is clear that it can affect the efficiency, accuracy and regulation of the translation process. In order to provide a tool to address these issues, we introduce here the codon information index (CII), which represents a measure of the amount of information stored in mRNA sequences through the codon bias. The calculation of the CII requires solely the knowledge of the mRNA sequences, without any other additional information. We found that the CII is highly correlated with the tRNA adaptation index (tAI), even if the latter requires the knowledge of the tRNA pool of an organism. We anticipate that the CII will represent a useful tool to study quantitatively the relationship between the information provided by the codon bias and various aspects of the translation process, thus identifying those aspects that are most influenced by it.

Caniparoli, Luca; Marsili, Matteo; Vendruscolo, Michele

2013-04-01

172

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

173

REVISITING THE CODON ADAPTATION INDEX FROM A WHOLE-GENOME PERSPECTIVE  

E-print Network

REVISITING THE CODON ADAPTATION INDEX FROM A WHOLE-GENOME PERSPECTIVE: GENE EXPRESSION, CODON BIAS of nucleotides, called codons. The four nucleotides (A, T, C, G) define 64 codons used in the cell. Codons are not uniformly employed in the cell, but at the contrary, certain codons are preferred and we speak about codon

Carbone, Alessandra

174

Codon thermoelectric signature in molecular junctions  

NASA Astrophysics Data System (ADS)

The thermoelectric power of trimer oligonucleotides connected in between metallic contacts at different temperatures is theoretically studied. The obtained analytical expressions reveal the existence of important resonance effects leading to a significant thermopower enhancement for certain characteristic energies which depend on the specific electronic structure of considered codons. This result suggests the existence of a thermoelectric signature for different triplet associations of biological interest.

Maciá, Enrique

2010-07-01

175

CpG Usage in RNA Viruses: Data and Hypotheses  

PubMed Central

CpG repression in RNA viruses has been known for decades, but a reasonable explanation has not yet been proposed to explain this phenomenon. In this study, we calculated the CpG odds ratio of all RNA viruses that have available genome sequences and analyzed the correlation with their genome polarity, base composition, synonymous codon usage, phylogenetic relationship, and host. The results indicated that the viral base composition, synonymous codon usage and host selection were the dominant factors that determined the CpG bias in RNA viruses. CpG usage variation between the different viral groups was caused by different combinations of these pressures, which also differed from each other in strength. The consistent under-representation of CpG usage in ?ssRNA viruses is determined predominantly by base composition, which may be a consequence of the U/A preferred mutation bias of ?ssRNA viruses, whereas the CpG usage of +ssRNA viruses is affected greatly by their hosts. As a result, most +ssRNA viruses mimic their hosts' CpG usage. Unbiased CpG usage in dsRNA viruses is most likely a result of their dsRNA genome, which allows the viruses to escape from the host-driven CpG elimination pressure. CpG was under-represented in all reverse-transcribing viruses (RT viruses), suggesting that DNA methylation is an important factor affecting the CpG usage of retroviruses. However, vertebrate-infecting RT viruses may also suffer host' CpG elimination pressure that also acts on +ssRNA viruses, which results in further under-representation of CpG in the vertebrate-infecting RT viruses. PMID:24086312

Cheng, Xiaofei; Virk, Nasar; Chen, Wei; Ji, Shuqin; Ji, Shuxian; Sun, Yuqiang; Wu, Xiaoyun

2013-01-01

176

Exploring iPhone Usage: The Influence of Socioeconomic Differences on Smartphone Adoption, Usage and Usability  

E-print Network

Exploring iPhone Usage: The Influence of Socioeconomic Differences on Smartphone Adoption, Usage applications are installed and used. We present a longitudinal study of 34 iPhone 3GS users. 24 perceived the usability of their iPhones poorly in comparison to the other groups. We further discuss

Zhong, Lin

177

A common periodic table of codons and amino acids  

Microsoft Academic Search

A periodic table of codons has been designed where the codons are in regular locations. The table has four fields (16 places in each) one with each of the four nucleotides (A, U, G, C) in the central codon position. Thus, AAA (lysine), UUU (phenylalanine), GGG (glycine), and CCC (proline) were placed into the corners of the fields as the

J. C. Biro; B. Benyo; C. Sansom; Á Szlávecz; G Fördös; T Micsik; Z Benyó

2003-01-01

178

RESEARCH Open Access Stop codons in bacteria are not selectively  

E-print Network

RESEARCH Open Access Stop codons in bacteria are not selectively equivalent Inna S Povolotskaya1 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

Paris-Sud XI, Université de

179

The significance of nucleotides within DNA codons: a quantitative approach.  

E-print Network

The significance of nucleotides within DNA codons: a quantitative approach. Alejandro Guerra amino acids coded by triplets of nucleotides (codons) in the Genetic Code, ap- pears to depend on the nucleotide position within a codon, as well as its physico-chemical features. Although differ- ent orders

Guerra Hernández, Alejandro

180

All-codon scanning identifies p53 cancer rescue mutations  

E-print Network

All-codon scanning identifies p53 cancer rescue mutations Roberta Baronio1 , Samuel A. Danziger1 with modified properties. We describe the fast and simple All- Codon Scanning (ACS) strategy that creates a defined gene library wherein each individual codon within a specific target region is changed into all

Lathrop, Richard H.

181

Synonymous Codon Bias is Related to Selection for Translational Accuracy?  

E-print Network

Synonymous Codon Bias is Related to Selection for Translational Accuracy? Adam Eyre- Walker of synonymous codon bias is shown to be positively correlated to gene length in Escherichia co/i genes which length, selection in favor of codons which increase accuracy should be greater in longer genes, and long

Eyre-Walker, Adam

182

Termination Out of the 64 Nucleotide Combinations Possible for a Codon, ___________________,  

E-print Network

Termination Out of the 64 Nucleotide Combinations Possible for a Codon, ___________________, Rather ___________________________ When the Ribosome Reaches a Stop Codon, the Signal is Read to Stop Translation and Release the Polypeptide ______________________________ The Stop Codons __________________________, UAG is the Amber Codon

Cutler, Chris

183

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

184

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...

185

The Comparative Method Rules! Codon Volatility Cannot Detect Positive Darwinian Selection Using a Single Genome Sequence  

E-print Network

The Comparative Method Rules! Codon Volatility Cannot Detect Positive Darwinian Selection Using called ``codon volatility,'' defined for each codon as the ratio between the number of nonsynonymous codons that differ from the codon under study at a single nucleotide position and the number of sense

Graur, Dan

186

Mitochondrial ND Genes: Relevance of Codon Usage to Semen Quality in Men.  

E-print Network

??Studies have discovered higher frequencies of single nucleotide polymorphisms (SNPs) in different mitochondrial genes are associated with subnormozoospermia. However, the frequencies of SNPs in ND1… (more)

Khan, Sadia Jihan

2006-01-01

187

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

188

A whole-genome analysis of premature termination codons.  

PubMed

We sequenced the genomes of ten unrelated individuals and identified heterozygous stop codon-gain variants in protein-coding genes: we then sequenced their transcriptomes and assessed the expression levels of the stop codon-gain alleles. An ANOVA showed statistically significant differences between their expression levels (p=4×10(-16)). This difference was almost entirely accounted for by whether the stop codon-gain variant had a second, non-protein-truncating function in or near an alternate transcript: stop codon-gains without alternate functions were generally not found in the cDNA (p=3×10(-5)). Additionally, stop codon-gain variants in two intronless genes were not expressed, an unexpected outcome given previous studies. In this study, stop codon-gain variants were either well expressed in all individuals or were never expressed. Our finding that stop codon-gain variants were generally expressed only when they had an alternate function suggests that most naturally occurring stop codon-gain variants in protein-coding genes are either not transcribed or have their transcripts destroyed. PMID:21803148

Cirulli, Elizabeth T; Heinzen, Erin L; Dietrich, Fred S; Shianna, Kevin V; Singh, Abanish; Maia, Jessica M; Goedert, James J; Goldstein, David B

2011-11-01

189

Codon Capture and Ambiguous Intermediate Scenarios of Genetic Code Evolution  

E-print Network

Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.

Yamashita, Tatsuro

2011-01-01

190

Rare codons capacitate Kras-driven de novo tumorigenesis.  

PubMed

The KRAS gene is commonly mutated in human cancers, rendering the encoded small GTPase constitutively active and oncogenic. This gene has the unusual feature of being enriched for rare codons, which limit protein expression. Here, to determine the effect of the rare codon bias of the KRAS gene on de novo tumorigenesis, we introduced synonymous mutations that converted rare codons into common codons in exon 3 of the Kras gene in mice. Compared with control animals, mice with at least 1 copy of this Krasex3op allele had fewer tumors following carcinogen exposure, and this allele was mutated less often, with weaker oncogenic mutations in these tumors. This reduction in tumorigenesis was attributable to higher expression of the Krasex3op allele, which induced growth arrest when oncogenic and exhibited tumor-suppressive activity when not mutated. Together, our data indicate that the inherent rare codon bias of KRAS plays an integral role in tumorigenesis. PMID:25437878

Pershing, Nicole L K; Lampson, Benjamin L; Belsky, Jason A; Kaltenbrun, Erin; MacAlpine, David M; Counter, Christopher M

2014-12-01

191

Robotics and Energy Usage  

E-print Network

It is commonly assumed that the use of robots in an industrial plant will cut energy usage, because robots require no heat, light, or air conditioning in their work space. However, in analyzing industrial installations, we have found that...

Hershey, R. L.; Fenton, S. E.; Letzt, A. M.

1983-01-01

192

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

193

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

194

MODIS Collection 6 aerosol products: Comparison between Aqua's e-Deep Blue, Dark Target, and "merged" data sets, and usage recommendations  

NASA Astrophysics Data System (ADS)

The Moderate Resolution Imaging Spectroradiometer (MODIS) Atmospheres data product suite includes three algorithms applied to retrieve midvisible aerosol optical depth (AOD): the Enhanced Deep Blue (DB) and Dark Target (DT) algorithms over land, and a DT over-water algorithm. All three have been refined in the recent "Collection 6" (C6) MODIS reprocessing. In particular, DB has been expanded to cover vegetated land surfaces as well as brighter desert/urban areas. Additionally, a new "merged" data set which draws from all three algorithms is included in the C6 products. This study is intended to act as a point of reference for new and experienced MODIS data users with which to understand the global and regional characteristics of the C6 DB, DT, and merged data sets, based on MODIS Aqua data. This includes validation against Aerosol Robotic Network (AERONET) observations at 111 sites, focused toward regional and categorical (surface/aerosol type) analysis. Neither algorithm consistently outperforms the other, although in many cases the retrieved AOD and the level of its agreement with AERONET are very similar. In many regions the DB, DT, and merged data sets are all suitable for quantitative applications, bearing in mind that they cannot be considered independent, while in other cases one algorithm does consistently outperform the other. Usage recommendations and caveats are thus somewhat complicated and regionally dependent.

Sayer, A. M.; Munchak, L. A.; Hsu, N. C.; Levy, R. C.; Bettenhausen, C.; Jeong, M.-J.

2014-12-01

195

A novel ?-thalassemia frameshift mutation: codon 8 (-C).  

PubMed

We report a novel ?-thalassemia (?-thal) point mutation detected during newborn screening for hemoglobinopathies. Sequence analyses identified a frameshift mutation at codon 8 (-C) in exon 1 of the ?2-globin gene. This mutation causes an ?(+)-thal phenotype. PMID:22242813

Tang, Hai-Shen; Zhou, Jian-Ying; Xie, Xing-Mei; Li, Ru; Liao, Can; Li, Dong-Zhi

2012-01-01

196

20. WEST CONFEDERATE AVENUE BRIDGE SPANNING CODON'S RUN, ARCH DETAIL ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

20. WEST CONFEDERATE AVENUE BRIDGE SPANNING CODON'S RUN, ARCH DETAIL SHOWING BRICK ARCH FOR MAIN SPAN AND STONE VOUSSOIRS. VIEW W. - Gettysburg National Military Park Tour Roads, Gettysburg, Adams County, PA

197

Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast  

E-print Network

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 ...

Jungreis, Irwin

198

Evidence of efficient stop codon readthrough in four mammalian genes  

E-print Network

Stop codon readthrough is used extensively by viruses to expand their gene expression. Until recent discoveries in Drosophila, only a very limited number of readthrough cases in chromosomal genes had been reported. Analysis ...

Loughran, Gary

199

Primary SIVsm isolates use the CCR5 coreceptor from sooty mangabeys naturally infected in west Africa: a comparison of coreceptor usage of primary SIVsm, HIV-2, and SIVmac.  

PubMed

Genetically divergent strains of simian immunodeficiency virus (SIV) from macaques (mac), chimpanzees, and sooty mangabeys (SM) efficiently used rhesus and human CCR5 (R5), but not CXCR4 (xR4), for cell entry. Thus far, however, no studies have characterized primary SIVsm strains for their use of coreceptors derived from their own natural host. Coreceptor usage of two primary, blood-derived SIVsm isolates, SIVsmSL92b and SIVsmFNS from naturally infected sooty mangabeys, was determined. Primary SIVsm efficiently used SM-CCR5 expressed on HOS.CD4 and U87.CD4 cells. Sequence polymorphisms in CCR5 found in four sooty mangabeys did not alter viral entry. Unlike primary rhesus blood-derived R5-tropic SIVmac251, primary SM blood-derived R5-tropic SIVsm was strongly CD4 dependent. The SM-CXCR4 gene was fully functional for xR4-tropic primate lentiviruses, but was not used by primary SIVsm. Therefore, the lack of xR4 tropism among naturally occurring SIVsm strains was not due to CxCR4 gene defects in the natural host. SIVmac derived from four macaques with AIDS also did not use macaque- or SM-derived CXCR4, showing that xR4 tropism did not develop during progression to disease as for humans infected with HIV-1. Three of four primary HIV-2 strains used CCR5 from human, sooty mangabey, and macaque. The fourth, HIV-27924A, obtained from a patient with AIDS, was xR4-tropic. Because SIVmac is most closely related to HIV-2, SIVmac might be expected to rnimic tropisms of HIV-2 infections. However, the correlation between xR4 tropism and AIDS may be a species-specific phenomenon limited to humans. The R5-tropic primary SIVsm and HIV-2 strains grew in CCR5-negative human PBMC, consistent with their use of non-CCR5 coreceptors. However, primary SIVsmSL92b did not use non-CCR5 coreceptors efficiently. The two primary SIVsm isolates replicated poorly in CEMx174 cells, which do not express CCR5, compared to CCR5-positive PM1 cells. SIVmac grew equally well in both cell lines. The findings show that SM-chemokine receptors are fully functional for virus entry and that multicoreceptor tropism is a common property of primary lentiviruses within the SIVsm/HIV-2 subfamily. PMID:9656999

Chen, Z; Gettie, A; Ho, D D; Marx, P A

1998-06-20

200

A Model of Proto-Anti-Codon RNA Enzymes Requiring L-Amino Acid Homochirality  

E-print Network

A Model of Proto-Anti-Codon RNA Enzymes Requiring L-Amino Acid Homochirality Albert Erives Received natural amino acid units of polypeptides using a universal scheme of triplet nucleotide ``codons) the absence of any codons for D-amino acids; (ii) the odd combination of alternate codon patterns for some

Erives, Albert J.

201

Adaptation studied with the self-consistent codon index: genomic spaces, metabolic network  

E-print Network

Adaptation studied with the self-consistent codon index: genomic spaces, metabolic network are formed out of 20 amino-acids which are coded in triplets of nucleotides, called codons. The four nucleotides (A, T, C, G) define 64 codons used in the cell. Codons are not uniformly employed in the cell

Carbone, Alessandra

202

Phylogenetic Inference with Weighted Codon Evolutionary Alexis Criscuolo Christian J. Michel  

E-print Network

Phylogenetic Inference with Weighted Codon Evolutionary Distances Alexis Criscuolo Ã? Christian J evolutionary distances from a codon- based alignment based on a codon evolutionary model. The method first computes a standard distance matrix for each of the three codon positions. Then these three distance

Michel, Christian

203

All-codon scanning identifies p53 cancer rescue mutations  

PubMed Central

In vitro scanning mutagenesis strategies are valuable tools to identify critical residues in proteins and to generate proteins with modified properties. We describe the fast and simple All-Codon Scanning (ACS) strategy that creates a defined gene library wherein each individual codon within a specific target region is changed into all possible codons with only a single codon change per mutagenesis product. ACS is based on a multiplexed overlapping mutagenesis primer design that saturates only the targeted gene region with single codon changes. We have used ACS to produce single amino-acid changes in small and large regions of the human tumor suppressor protein p53 to identify single amino-acid substitutions that can restore activity to inactive p53 found in human cancers. Single-tube reactions were used to saturate defined 30-nt regions with all possible codon changes. The same technique was used in 20 parallel reactions to scan the 600-bp fragment encoding the entire p53 core domain. Identification of several novel p53 cancer rescue mutations demonstrated the utility of the ACS approach. ACS is a fast, simple and versatile method, which is useful for protein structure–function analyses and protein design or evolution problems. PMID:20581117

Baronio, Roberta; Danziger, Samuel A.; Hall, Linda V.; Salmon, Kirsty; Hatfield, G. Wesley; Lathrop, Richard H.; Kaiser, Peter

2010-01-01

204

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. PMID:24655606

2014-01-01

205

Cloning and expression of a codon-optimized gene encoding the influenza A virus nucleocapsid protein in Lactobacillus casei.  

PubMed

Lactic acid bacteria (LAB) species are envisioned as promising vehicles for the mucosal delivery of therapeutic and prophylactic molecules, including the development of oral vaccines. In this study, we report on the expression of a synthetic nucleocapsid (NP) gene of influenza A virus in Lactobacillus casei. The NP gene was re-designed based on the tRNA pool and the codon usage preference of L. casei BL23. The codon-optimized NP gene was then cloned and expressed in L. casei RCEID02 under the control of a constitutive promoter, that of the lactate dehydrogenase (ldh) gene. The synthetic NP gene was further expressed in L. casei EM116 under the control of an inducible promoter, that of the structural gene of nisin (nisA) from Lactococcus lactis. Based on Western blot analysis, the specific protein band of NP, with a molecular mass of 56.0 kDa, was clearly detected in both expression systems. Thus, our study demonstrates the success of expressing a codon-optimized influenza A viral gene in L. casei. The suitability of the recombinant LAB strains for immunization purposes is currently under evaluation. PMID:24400527

Suebwongsa, Namfon; Panya, Marutpong; Namwat, Wises; Sookprasert, Saovaluk; Redruello, Begoña; Mayo, Baltasar; Alvarez, Miguel A; Lulitanond, Viraphong

2013-06-01

206

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. PMID:24809485

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

2014-01-01

207

Telemedicine Usage and Potentials  

Microsoft Academic Search

Telemedicine has been in use for many years and it is the use of telecommunications technologies to consult with remote physician. In this paper, we shed light on telemedicine in terms of the common usage and the future potentials of the technology with some examples.

Yang Xiao; Daisuke Takahashi; Fei Hu

2007-01-01

208

Reduced amino acid specificity of mammalian tyrosyl-tRNA synthetase is associated with elevated mistranslation of Tyr codons.  

PubMed

Quality control operates at different steps in translation to limit errors to approximately one mistranslated codon per 10,000 codons during mRNA-directed protein synthesis. Recent studies have suggested that error rates may actually vary considerably during translation under different growth conditions. Here we examined the misincorporation of Phe at Tyr codons during synthesis of a recombinant antibody produced in tyrosine-limited Chinese hamster ovary (CHO) cells. Tyr to Phe replacements were previously found to occur throughout the antibody at a rate of up to 0.7% irrespective of the identity or context of the Tyr codon translated. Despite this comparatively high mistranslation rate, no significant change in cellular viability was observed. Monitoring of Phe and Tyr levels revealed that changes in error rates correlated with changes in amino acid pools, suggesting that mischarging of tRNA(Tyr) with noncognate Phe by tyrosyl-tRNA synthetase was responsible for mistranslation. Steady-state kinetic analyses of CHO cytoplasmic tyrosyl-tRNA synthetase revealed a 25-fold lower specificity for Tyr over Phe as compared with previously characterized bacterial enzymes, consistent with the observed increase in translation error rates during tyrosine limitation. Functional comparisons of mammalian and bacterial tyrosyl-tRNA synthetase revealed key differences at residues responsible for amino acid recognition, highlighting differences in evolutionary constraints for translation quality control. PMID:24828507

Raina, Medha; Moghal, Adil; Kano, Amanda; Jerums, Mathew; Schnier, Paul D; Luo, Shun; Deshpande, Rohini; Bondarenko, Pavel V; Lin, Henry; Ibba, Michael

2014-06-20

209

SPRING 2005 Brand usage guidelines  

E-print Network

ISSUE 1 SPRING 2005 Brand usage guidelines #12;#12;DURHAM UNIVERSITY BRAND USAGE GUIDELINES As you with confidence and modernity. Introducing the new marque THE NEW MARQUE #12;DURHAM UNIVERSITY BRAND USAGEmm WIDE LARGE MARQUE for use over 75mm wide #12;DURHAM UNIVERSITY BRAND USAGE GUIDELINES Depending

Wirosoetisno, Djoko

210

Modeling Usage: Techniques and Tools  

Microsoft Academic Search

Usage modeling seeks to provide end users with a usable - that is, effective, efficient, and satisfactory - interactive product. In a usage-centered development process, users must understand what they need to perform their work tasks. Various techniques exist for collecting and documenting what is understood about the user and future system usage. From the wealth of techniques, we've chosen

Catharina Riedemann; Regine Freitag

2009-01-01

211

Nursing documentation usage analysis.  

PubMed

This project investigated the use of electronic patient documentation in the work context of VA nurses, guided by cognitive work analysis methodology. Prominent themes in nursing workflow and documentation usage identifed in previous research were summarized and presented in detail to a focus group of practicing nurses. The group validated a need for integrated access to order, prescription and document information. A wire frame solution was developed and presented in a second group meeting for evaluation and feedback. PMID:18998895

Robertson, Cindy; Robertson, Cynthia L; Efthimiadis, Efthimis N; Hammond, Kenric W

2008-01-01

212

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

PubMed Central

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 (MSD), mutual information (MI), normalized mutual information (NMI), pattern intensity (PI), normalized cross-correlation (NCC) and entropy of the difference (EDI). 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 1 of the 5 patient studies, and with external-surrogate based correction in 3 out of 5 patients. In the remaining patient study there was little motion and all methods yielded similar visual image quality. PMID:24107647

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

2014-01-01

213

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

SciTech Connect

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

Zhang Weici [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Xiao Weihua [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China) and School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012 (China)]. E-mail: xiaow@ustc.edu.cn; Wei Haiming [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China); Zhang Jian [School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012 (China); Tian Zhigang [Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027 (China) and School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250012 (China)]. E-mail: tzg@ustc.edu.cn

2006-10-13

214

A model for codon position bias in RNA editing  

E-print Network

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

Liu, T; Liu, Tsunglin; Bundschuh, Ralf

2005-01-01

215

A model for codon position bias in RNA editing  

NASA Astrophysics Data System (ADS)

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

Bundschuh, Ralf; Liu, Tsunglin

2006-03-01

216

Model for Codon Position Bias in RNA Editing  

NASA Astrophysics Data System (ADS)

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

Liu, Tsunglin; Bundschuh, Ralf

2005-08-01

217

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

218

The Complete Mitochondrial Genome of the Pink Stem Borer, Sesamia inferens, in Comparison with Four Other Noctuid Moths  

PubMed Central

The complete 15,413-bp mitochondrial genome (mitogenome) of Sesamia inferens (Walker) (Lepidoptera: Noctuidae) was sequenced and compared with those of four other noctuid moths. All of the mitogenomes analyzed displayed similar characteristics with respect to gene content, genome organization, nucleotide comparison, and codon usages. Twelve-one protein-coding genes (PCGs) utilized the standard ATN, but the cox1 gene used CGA as the initiation codon; cox1, cox2, and nad4 genes had the truncated termination codon T in the S. inferens mitogenome. All of the tRNA genes had typical cloverleaf secondary structures except for trnS1(AGN), in which the dihydrouridine (DHU) arm did not form a stable stem-loop structure. Both the secondary structures of rrnL and rrnS genes inferred from the S. inferens mitogenome closely resembled those of other noctuid moths. In the A+T-rich region, the conserved motif “ATAGA” followed by a long T-stretch was observed in all noctuid moths, but other specific tandem-repeat elements were more variable. Additionally, the S. inferens mitogenome contained a potential stem-loop structure, a duplicated 17-bp repeat element, a decuplicated segment, and a microsatellite “(AT)7”, without a poly-A element upstream of the trnM in the A+T-rich region. Finally, the phylogenetic relationships were reconstructed based on amino acid sequences of mitochondrial 13 PCGs, which support the traditional morphologically based view of relationships within the Noctuidae. PMID:22949858

Chai, Huan-Na; Du, Yu-Zhou

2012-01-01

219

Notational usage modulates attention networks in binumerates.  

PubMed

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. PMID:24904366

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

2014-01-01

220

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. PMID:24904366

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

2014-01-01

221

Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae  

PubMed Central

In-frame stop codons normally signal termination during mRNA translation, but they can be read as ‘sense’ (readthrough) depending on their context, comprising the 6 nt preceding and following the stop codon. To identify novel contexts directing readthrough, under-represented 5? and 3? stop codon contexts from Saccharomyces cerevisiae were identified by genome-wide survey in silico. In contrast with the nucleotide bias 3? of the stop codon, codon bias in the two codon positions 5? of the termination codon showed no correlation with known effects on stop codon readthrough. However, individually, poor 5? and 3? context elements were equally as effective in promoting stop codon readthrough in vivo, readthrough which in both cases responded identically to changes in release factor concentration. A novel method analysing specific nucleotide combinations in the 3? context region revealed positions +1,2,3,5 and +1,2,3,6 after the stop codon were most predictive of termination efficiency. Downstream of yeast open reading frames (ORFs), further in-frame stop codons were significantly over-represented at the +1, +2 and +3 codon positions after the ORF, acting to limit readthrough. Thus selection against stop codon readthrough is a dominant force acting on 3?, but not on 5?, nucleotides, with detectable selection on nucleotides as far downstream as +6 nucleotides. The approaches described can be employed to define potential readthrough contexts for any genome. PMID:15602002

Williams, I.; Richardson, J.; Starkey, A.; Stansfield, I.

2004-01-01

222

Codon-optimized Human Sodium Iodide Symporter (opt-hNIS) as a Sensitive Reporter and Efficient Therapeutic Gene.  

PubMed

To generate a more efficient in vivo reporter and therapeutic gene, we optimized the coding sequence of the human sodium/iodide symporter (NIS) gene by replacing NIS DNA codons from wild type to new codons having the highest usage in human gene translation. The Codon Adaptation Index (CAI), representing the number of codons effective for human expression, was much improved (0.79 for hNIS, 0.97 for opt-hNIS). Both wild-type (hNIS) and optimized human NIS (opt-hNIS) were cloned into pcDNA3.1 and pMSCV vectors for transfection. Various cancer cell lines such as thyroid (TPC-1, FRO, B-CPAP), breast (MDA-MB-231), liver (Hep3B), cervical (HeLa), and glioma (U87MG) were transfected with pcDNA3.1/hNIS or pcDNA3.1/opt-hNIS. (125)I uptake by opt-hNIS-expressing cells was 1.6 ~ 2.1 times higher than uptake by wild-type hNIS-expressing cells. Stable cell lines were also established by retroviral transduction using pMSCV/hNIS or pMSCV/opt-hNIS, revealing higher NIS protein levels and (125)I uptake in opt-hNIS-expressing cells than in hNIS-expressing cells. Moreover, scintigraphic images from cell plates and mouse xenografts showed stronger signals from opt-hNIS-expressing cells than hNIS-expressing cells, and radioactivity uptake by opt-hNIS-expressing tumors was 2.3-fold greater than that by hNIS-expressing tumors. To test the efficacy of radioiodine therapy, mouse xenograft models were established with cancer cells expressing hNIS or opt-hNIS. (131)I treatment reduced tumor sizes of hNIS- and opt-hNIS-expressing tumors to 0.57- and 0.27- fold, respectively, compared to their sizes before therapy, suggesting an improved therapeutic effect of opt-hNIS. In summary, this study shows that codon optimization strongly increases hNIS protein levels and radioiodine uptake, thus supporting opt-hNIS as a more sensitive reporter and efficient therapeutic gene. PMID:25553100

Kim, Young-Hwa; Youn, Hyewon; Na, Juri; Hong, Kee-Jong; Kang, Keon Wook; Lee, Dong Soo; Chung, June-Key

2015-01-01

223

Codon-optimized Human Sodium Iodide Symporter (opt-hNIS) as a Sensitive Reporter and Efficient Therapeutic Gene  

PubMed Central

To generate a more efficient in vivo reporter and therapeutic gene, we optimized the coding sequence of the human sodium/iodide symporter (NIS) gene by replacing NIS DNA codons from wild type to new codons having the highest usage in human gene translation. The Codon Adaptation Index (CAI), representing the number of codons effective for human expression, was much improved (0.79 for hNIS, 0.97 for opt-hNIS). Both wild-type (hNIS) and optimized human NIS (opt-hNIS) were cloned into pcDNA3.1 and pMSCV vectors for transfection. Various cancer cell lines such as thyroid (TPC-1, FRO, B-CPAP), breast (MDA-MB-231), liver (Hep3B), cervical (HeLa), and glioma (U87MG) were transfected with pcDNA3.1/hNIS or pcDNA3.1/opt-hNIS. 125I uptake by opt-hNIS-expressing cells was 1.6 ~ 2.1 times higher than uptake by wild-type hNIS-expressing cells. Stable cell lines were also established by retroviral transduction using pMSCV/hNIS or pMSCV/opt-hNIS, revealing higher NIS protein levels and 125I uptake in opt-hNIS-expressing cells than in hNIS-expressing cells. Moreover, scintigraphic images from cell plates and mouse xenografts showed stronger signals from opt-hNIS-expressing cells than hNIS-expressing cells, and radioactivity uptake by opt-hNIS-expressing tumors was 2.3-fold greater than that by hNIS-expressing tumors. To test the efficacy of radioiodine therapy, mouse xenograft models were established with cancer cells expressing hNIS or opt-hNIS. 131I treatment reduced tumor sizes of hNIS- and opt-hNIS-expressing tumors to 0.57- and 0.27- fold, respectively, compared to their sizes before therapy, suggesting an improved therapeutic effect of opt-hNIS. In summary, this study shows that codon optimization strongly increases hNIS protein levels and radioiodine uptake, thus supporting opt-hNIS as a more sensitive reporter and efficient therapeutic gene. PMID:25553100

Kim, Young-Hwa; Youn, Hyewon; Na, Juri; Hong, Kee-Jong; Kang, Keon Wook; Lee, Dong Soo; Chung, June-Key

2015-01-01

224

Codon-based mutagenesis using dimer-phosphoramidites  

Microsoft Academic Search

A new approach for the synthesis of randomized DNA sequences containing the 20 codons corresponding to all natural amino acids is described. The strategy is based on the use of dinucleotide phosphoramidite building blocks within a resin-splitting procedure. Through this protocol, a minimal number of seven dimers is sufficient to encode all 20 natural amino acids. This synthesis procedure is

Philippe Neuner; Riccardo Cortese; Paolo Monaci

1998-01-01

225

Resolving Discrepancy between Nucleotides and Amino Acids in Deep-Level Arthropod Phylogenomics: Differentiating Serine Codons in 21-Amino-Acid Models  

PubMed Central

Background In a previous study of higher-level arthropod phylogeny, analyses of nucleotide sequences from 62 protein-coding nuclear genes for 80 panarthopod species yielded significantly higher bootstrap support for selected nodes than did amino acids. This study investigates the cause of that discrepancy. Methodology/Principal Findings The hypothesis is tested that failure to distinguish the serine residues encoded by two disjunct clusters of codons (TCN, AGY) in amino acid analyses leads to this discrepancy. In one test, the two clusters of serine codons (Ser1, Ser2) are conceptually translated as separate amino acids. Analysis of the resulting 21-amino-acid data matrix shows striking increases in bootstrap support, in some cases matching that in nucleotide analyses. In a second approach, nucleotide and 20-amino-acid data sets are artificially altered through targeted deletions, modifications, and replacements, revealing the pivotal contributions of distinct Ser1 and Ser2 codons. We confirm that previous methods of coding nonsynonymous nucleotide change are robust and computationally efficient by introducing two new degeneracy coding methods. We demonstrate for degeneracy coding that neither compositional heterogeneity at the level of nucleotides nor codon usage bias between Ser1 and Ser2 clusters of codons (or their separately coded amino acids) is a major source of non-phylogenetic signal. Conclusions The incongruity in support between amino-acid and nucleotide analyses of the forementioned arthropod data set is resolved by showing that “standard” 20-amino-acid analyses yield lower node support specifically when serine provides crucial signal. Separate coding of Ser1 and Ser2 residues yields support commensurate with that found by degenerated nucleotides, without introducing phylogenetic artifacts. While exclusion of all serine data leads to reduced support for serine-sensitive nodes, these nodes are still recovered in the ML topology, indicating that the enhanced signal from Ser1 and Ser2 is not qualitatively different from that of the other amino acids. PMID:23185239

Zwick, Andreas; Regier, Jerome C.; Zwickl, Derrick J.

2012-01-01

226

High-level production of yeast (Schwanniomyces occidentalis) phytase in transgenic rice plants by a combination of signal sequence and codon modification of the phytase gene.  

PubMed

This study was designed to produce yeast (Schwanniomyces occidentalis) phytase in rice with a view to future applications in the animal feed industry. To achieve high-level production, chimeric genes with the secretory signal sequence of the rice chitinase-3 gene were constructed using either the original full-length or N-truncated yeast phytase gene, or a modified gene whose codon usage was changed to be more similar to that of rice, and then introduced into rice (Oryza sativa L.). When the original phytase genes were used, the phytase activity in the leaves of transgenic rice was of the same level as in wild-type plants, whose mean value was 0.039 U/g fresh weight (g-FW) (1 U of activity was defined as 1 micromol P released per min at 37 degrees C). In contrast, the enzyme activity was increased markedly when codon-modified phytase genes were introduced: up to 4.6 U/g-FW of leaves for full-length codon-modified phytase, and 10.6 U/g-FW for truncated codon-modified phytase. A decrease in the optimum temperature and thermal stability was observed in the truncated heterologous enzyme, suggesting that the N-terminal region plays an important role in enzymatic properties. In contrast, the optimum temperature and pH of full-length heterologous phytase were indistinguishable from those of the benchmark yeast phytase, although the heterologous enzyme was less glycosylated. Full-length heterologous phytase in leaf extract showed extreme stability. These results indicate that codon modification, combined with the use of a secretory signal sequence, can be used to produce substantial amounts of yeast phytase, and possibly any phytases from various organisms, in an active and stable form. PMID:17168898

Hamada, Akira; Yamaguchi, Ken-ichi; Ohnishi, Naoto; Harada, Michiko; Nikumaru, Seiya; Honda, Hideo

2005-01-01

227

Basic Usage of Signal Generator Basic Usage of Oscilloscope  

E-print Network

Topics: Basic Usage of Signal Generator Basic Usage of Oscilloscope Capacitor Required Equipment and Components: CRO (Cathode Ray Oscilloscope) Breadboard DC power supply Resistors Function Generator Capacitor Information: Signal Generators A signal generator is an electronic instrument that generates repeating voltage

Ã?nay, Devrim

228

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. PMID:23396971

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

2013-01-01

229

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

E-print Network

Prokaryotic Gene Finding Based on Physicochemical Characteristics of Codons Calculated from An ab initio model for gene prediction in prokaryotic genomes is proposed based on physicochemical prediction in prokaryotic genomes based on a set of three physicochemical characteristics of codons--by codon

Jayaram, Bhyravabotla

230

Context effects on misreading and suppression at UAG codons in human cells  

SciTech Connect

This study investigates the effect of the 3{prime} codon context on the efficiency of nonsense supression and compares the results from mammalian tissue culture cells with that of Escherichia coli. When tRNA products within the cell recognize a nonsense codon, the function of the codon is suppressed, which affects protein synthesis. 52 refs., 6 figs.

Phillips-Jones, M.K.; Hill, L.S.J.; Atkinson, J.; Martin, R. [Univ. of Sheffield (United Kingdom)

1995-12-01

231

Oligonucleotide Design and Codon Optimization for PCR-based Gene Synthesis  

E-print Network

Oligonucleotide Design and Codon Optimization for PCR-based Gene Synthesis by Paul Jamesen Steiner Chairman, Department Committee on Graduate eses #12;#12;Oligonucleotide Design and Codon Optimization sequences can encode the same protein. If the primary concern is a protein sequence, codons can be changed

Williams, Brian C.

232

Activation of K-RAS by co-mutation of codons 19 and 20 is transforming  

E-print Network

. The majority of activating mutations in K-RAS are located in codons 12 and 13. In a human colorectal cancer we identified a novel K-RAS co-mutation that altered codons 19 and 20 resulting in transitions at both codons (L19F/T20A) in the same allele. Using focus...

Naguib, Adam; Wilson, Catherine H; Adams, David J; Arends, Mark J

2011-03-03

233

Evolving Protein Motifs Using a Stochastic Regular Language with Codon-Level Probabilities  

E-print Network

Evolving Protein Motifs Using a Stochastic Regular Language with Codon-Level Probabilities Brian J. The motifs use a stochastic regular expression language that uses codon-level probabilities within conserved is that uniform probabil- ity distributions are used for converved sets or masks of codons. For example

Fernandez, Thomas

234

Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts  

E-print Network

Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts Alessandra spectrum of related phage species. Based on a large-scale codon bias analysis of 116 DNA phages hosted that phage genomes are almost always under codon selective pressure imposed by translationally biased hosts

Carbone, Alessandra

235

Lie superalgebras and the multiplet structure of the genetic code. I. Codon representations  

E-print Network

Lie superalgebras and the multiplet structure of the genetic code. I. Codon representations Michael that the degeneracy of the genetic code, i.e., the phenomenon that different codons base triplets of DNA. In the present paper, we give the complete list of all typical codon representations typical 64-dimensional irre

Forger, Frank Michael

236

amino-acid pair distances15 . Subdivision of ratmousehuman codon triplets into classes  

E-print Network

amino-acid pair distances15 . Subdivision of rat­mouse­human codon triplets into classes that negative selection at a codon switches off and on at random moments. The expected waiting times (in units negative selection in rat and mouse lineages were fr and fm, respectively, at a two-substitution codon P0

Cai, Long

237

RESEARCH ARTICLE Open Access Increased incidence of rare codon clusters at 5'  

E-print Network

RESEARCH ARTICLE Open Access Increased incidence of rare codon clusters at 5' and 3' gene termini be affected by the use of rare versus common codons within the mRNA transcript. Results: Here, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes

Clark, Patricia L.

238

LETTER TO THE EDITOR The effect of nonsense codons on splicing  

E-print Network

LETTER TO THE EDITOR The effect of nonsense codons on splicing: A genomic analysis XIANG ZHANG that the recognition of in-frame nonsense codons is used generally for exon identification during pre-mRNA splicing. However, nonsense codon frequencies in pseudo exons and in regions flanking 5 splice sites are no greater

Tong, Liang

239

PRIMITIVE MOLECULAR MACHINE SCENARIO FOR THE ORIGIN OF THE THREE BASE CODON COMPOSITION  

E-print Network

PRIMITIVE MOLECULAR MACHINE SCENARIO FOR THE ORIGIN OF THE THREE BASE CODON COMPOSITION G. MARTÍNEZ codon composition. 1. Introduction In this work we address the fundamental question, associated with the origin of the genetic code: why are there three bases per codon in the translation to protein process? We

Aldana, Maximino

240

A Case For Codons in Evolutionary Algorithms Joshua Gilbert, Maggie Eppstein  

E-print Network

A Case For Codons in Evolutionary Algorithms Joshua Gilbert, Maggie Eppstein Dept. of Computer. The method is inspired by the biological genetic code and utilizes a many-to-one, codon-based, genotype-to- phenotype translation scheme. A genetic algorithm was implemented with this codon-based representation using

Eppstein, Margaret J.

241

A model for codon position bias in RNA editing Tsunglin Liu and Ralf Bundschuh  

E-print Network

A model for codon position bias in RNA editing Tsunglin Liu and Ralf Bundschuh Department polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose

Bundschuh, Ralf

242

DOI: 10.1002/cbic.201402104 A Bacterial Strain with a Unique Quadruplet Codon  

E-print Network

DOI: 10.1002/cbic.201402104 A Bacterial Strain with a Unique Quadruplet Codon Specifying Non. Schultz*[a] The addition of noncanonical amino acids to the genetic code requires unique codons not assigned to the 20 canonical amino acids. Among the 64 triplet codons, only the three non- sense "stop

Church, George M.

243

Expanding the Genetic Code: Selection of Efficient Suppressors of Four-base Codons and Identification  

E-print Network

Expanding the Genetic Code: Selection of Efficient Suppressors of Four-base Codons and Identification of ``Shifty'' Four-base Codons with a Library Approach in Escherichia coli Thomas J. Magliery2 , J devised a general strategy to select tRNAs with the ability to suppress four-base codons from a library

Magliery, Thomas J.

244

Translation efficiency is determined by both codon bias and folding energy  

E-print Network

Translation efficiency is determined by both codon bias and folding energy Tamir Tullera,b,1 studies have suggested that codon bias is the most important determinant of translation efficiency. There is a significant association between codon bias and translation efficiency across all endoge- nous genes in E. coli

Ruppin, Eytan

245

General Rules for Optimal Codon Choice Ruth Hershberg*, Dmitri A. Petrov  

E-print Network

General Rules for Optimal Codon Choice Ruth Hershberg*, Dmitri A. Petrov Department of Biology, Stanford University, Stanford, California, United States of America Abstract Different synonymous codons governing the identities of favored codons in different organisms remain obscure. In fact, it is not known

Petrov, Dmitri

246

KRAS codon 61, 146 and BRAF mutations predict resistance to cetuximab plus irinotecan in KRAS codon 12 and 13 wild-type metastatic colorectal cancer  

Microsoft Academic Search

Background:KRAS codons 12 and 13 mutations predict resistance to anti-EGFR monoclonal antibodies (moAbs) in metastatic colorectal cancer. Also, BRAF V600E mutation has been associated with resistance. Additional KRAS mutations are described in CRC.Methods:We investigated the role of KRAS codons 61 and 146 and BRAF V600E mutations in predicting resistance to cetuximab plus irinotecan in a cohort of KRAS codons 12

F Loupakis; A Ruzzo; C Cremolini; B Vincenzi; L Salvatore; D Santini; G Masi; I Stasi; E Canestrari; E Rulli; I Floriani; K Bencardino; N Galluccio; V Catalano; G Tonini; M Magnani; G Fontanini; F Basolo; A Falcone; F Graziano

2009-01-01

247

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

248

Computer Usage and Student Performance.  

ERIC Educational Resources Information Center

This study presents exploratory evidence to prove that student computer usage is correlated with academic performance using course grades as an academic performance measure. No conclusive evidence was found to indicate student performance and computing are related, but a significant relationship between course instructor and computer usage was…

Willits, Stephen; Clancy, Donald K.

1984-01-01

249

KRAS codon 12 mutations occur very frequently in pancreatic adenocarcinomas  

Microsoft Academic Search

DNAs from human pancreatic adenocarcinomas were analyzed for the presence of mutations in codons 12, 13 and 61 of the NRAS, KRAS and HRAS gene. Formalin-fixed and paraffin-embedded tissue was used directly in an in vitro amplification reaction to expand the relevant RAS sequences. The mutations were detected by selective hybridization using mutation-specific synthetic oligonucleotides. In 28 of the 30

Vincent T. H. B. M. Smit; Angelina J. M. Boot; Alida M. M. Smits; Gert Jan Fleuren; Cees J. Cornelisse; Johannes L. Bos

1988-01-01

250

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. PMID:24885062

2014-01-01

251

Selection of AUG initiation codons differs in plants and animals.  

PubMed Central

The influence of the nucleotide at position -3 relative to the AUG initiation codon on the initiation of protein synthesis was studied in two different in vitro translation systems using synthetic mRNAs. The four mRNAs, transcribed from cDNAs directed by an SP6 promoter, were identical except for mutations at nucleotide -3. In each case, translation of mRNAs produced a single protein of Mr = 12,600. Relative translational efficiencies showed a hierarchy in the reticulocyte lysate system (100, 85, 61 and 38% for A, G, U and C in position -3, respectively) but no differences in the wheat germ system. Differential mRNA degradation or polypeptide chain elongation were excluded as causes of the differences observed in translation in the reticulocyte lysate. mRNA competition increased the differences observed in translational efficiencies in reticulocyte lysate but showed no effect in wheat germ. Analysis of 61 plant and 209 animal mRNA sequences revealed qualitative and quantitative differences between the consensus sequences surrounding AUG initiation codons. Whereas the consensus sequence for animals was CACCAUG that for plants was AACAAUGGC. Both the structural and functional findings suggest that the factors which select AUG initiation codons in plants and animals differ significantly. Images Fig. 2. Fig. 3. Fig. 4. Fig. 5. PMID:3556162

Lütcke, H A; Chow, K C; Mickel, F S; Moss, K A; Kern, H F; Scheele, G A

1987-01-01

252

A Study of the Purine/Pyrimidine Codon Occurrence with a Reduced Centered Variable and an Evaluation  

E-print Network

A Study of the Purine/Pyrimidine Codon Occurrence with a Reduced Centered Variable 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

Michel, Christian

253

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

254

Co-variation of tRNA Abundance and Codon Usage in Escherichia coli at Different Growth Rates  

Microsoft Academic Search

We have used two-dimensional polyacrylamide gel electrophoresis to fractionate tRNAs fromEscherichia coli. A sufficiently high degree of resolution was obtained for 44 out of 46 tRNA species inE. colito be resolved into individual electrophoretic components. These isolated components were identified by hybridization to tRNA-specific oligonucle otide probes. Systematic measurements of the abundance of each individual tRNA isoacceptor inE. coli, grown

Hengjiang Dong; Lars Nilsson; Charles G. Kurland

1996-01-01

255

Partial Optimization of the 5-Terminal Codon Increased a Recombination Porcine Pancreatic Lipase (opPPL) Expression in Pichia pastoris  

PubMed Central

Pancreatic lipase plays a key role in intestinal digestion of feed fat, and is often deficient in young animals such as weaning piglets. The objective of this study was to express and characterize a partial codon optimized porcine pancreatic lipase (opPPL). A 537 bp cDNA fragment encoding N-terminus amino acid residue of the mature porcine pancreatic lipase was synthesized according to the codon bias of Pichia pastoris and ligated to the full-length porcine pancreatic lipase cDNA fragment. The codon optimized PPL was cloned into the pPICZ?A (Invitrogen, Beijing, China) vector. After the resultant opPPL/pPICZ?? plasmid was transformed into P.pastoris, the over-expressed extracellular opPPL containing a His-tag to the C terminus was purified using Ni Sepharose affinity column (GE Healthcare, Piscataway, NJ, USA), and was characterized against the native enzyme (commercial PPL from porcine pancreas, Sigma). The opPPL exhibited a molecular mass of approximately 52 kDa, and showed optimal temperature (40°C), optimal pH (8.0), Km (0.041 mM), and Vmax (2.008 µmol.mg protein ?1.min?1) similar to those of the commercial enzyme with p-NPP as the substrate. The recombinant enzyme was stable at 60°C, but lost 80% (P<0.05) of its activity after exposure to heat ?60°C for 20 min. The codon optimization increased opPPL yield for ca 4 folds (146 mg.L?1 vs 36 mg.L?1) and total enzyme activity increased about 5 folds (1900 IU.L?1 vs 367 IU.L?1) compared with those native naPPL/pPICZ?? tranformant. Comparison of gene copies and mRNA profiles between the two strains indicated the increased rePPL yields may partly be ascribed to the increased protein translational efficiency after codon optimization. In conclusion, we successfully optimized 5-terminal of porcine pancreatic lipase encoding gene and over-expressed the gene in P. pastoris as an extracellular, functional enzyme. The recombination enzyme demonstrates a potential for future use as an animal feed additive for animal improvement. PMID:25544987

Zhao, Hua; Chen, Dan; Tang, Jiayong; Jia, Gang; Long, Dingbiao; Liu, Guangmang; Chen, Xiaoling; Shang, Haiying

2014-01-01

256

Why Are Translationally SubOptimal Synonymous Codons Used in Escherichia coli ?  

Microsoft Academic Search

.   Natural selection favors certain synonymous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous polymorphisms\\u000a to test three hypotheses for the existence of translationally sub-optimal codons: (1) selection is a relatively weak force,\\u000a so there is a balance between mutation, selection, and drift; (2) at some

Nick G. C. Smith; Adam Eyre-Walker

2001-01-01

257

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

PubMed Central

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

2012-01-01

258

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

259

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

260

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. PMID:11453067

Lim, V I; Curran, J F

2001-01-01

261

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

262

Modeling Educational Usage of Facebook  

ERIC Educational Resources Information Center

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…

Mazman, Sacide Guzin; Usluel, Yasemin Kocak

2010-01-01

263

Usage in Contemporary American Dictionaries  

ERIC Educational Resources Information Center

An editorialized report of data accumulated in a study of current American practice in the treatment of problems of usage in general purpose dictionaries. Their descriptive objectivity is characterized as "that of the blind men examining the elephant." Such practices reveal little change from that of Samuel Johnson's 1755 English Dictionary. (AMH)

Creswell, Thomas J.

1977-01-01

264

Usage centric green performance indicators  

Microsoft Academic Search

Energy effciency of data centers is gaining importance as energy consumption and carbon footprint awareness are rising. Green Performance Indicators (GPIs) provide measurable means to assess the energy effciency of a resource or system. Most of the metrics commonly used today measure the energy effciency potential of a resource, system or application usage, rather than the energy effciency of the

Doron Chen; Ealan Henis; Ronen I. Kat; Dmitry Sotnikov; Cinzia Cappiello; Alexandre Mello Ferreira; Barbara Pernici; Monica Vitali; Tao Jiang; Jia Liu; Alexander Kipp

2011-01-01

265

Refining the Balance of Attenuation and Immunogenicity of Respiratory Syncytial Virus by Targeted Codon Deoptimization of Virulence Genes  

PubMed Central

ABSTRACT Respiratory syncytial virus (RSV) is the most important pathogen for lower respiratory tract illness in children for which there is no licensed vaccine. Live-attenuated RSV vaccines are the most clinically advanced in children, but achieving an optimal balance of attenuation and immunogenicity is challenging. One way to potentially retain or enhance immunogenicity of attenuated virus is to mutate virulence genes that suppress host immune responses. The NS1 and NS2 virulence genes of the RSV A2 strain were codon deoptimized according to either human or virus codon usage bias, and the resulting recombinant viruses (dNSh and dNSv, respectively) were rescued by reverse genetics. RSV dNSh exhibited the desired phenotype of reduced NS1 and NS2 expression. RSV dNSh was attenuated in BEAS-2B and primary differentiated airway epithelial cells but not in HEp-2 or Vero cells. In BALB/c mice, RSV dNSh exhibited a lower viral load than did A2, and yet it induced slightly higher levels of RSV-neutralizing antibodies than did A2. RSV A2 and RSV dNSh induced equivalent protection against challenge strains A/1997/12-35 and A2-line19F. RSV dNSh caused less STAT2 degradation and less NF-?B activation than did A2 in vitro. Serial passage of RSV dNSh in BEAS-2B cells did not result in mutations in the deoptimized sequences. Taken together, RSV dNSh was moderately attenuated, more immunogenic, and equally protective compared to wild-type RSV and genetically stable. PMID:25249281

Meng, Jia; Lee, Sujin; Hotard, Anne L.

2014-01-01

266

Why Are Translationally Sub-Optimal Synonymous Codons Used in Escherichia coli?  

E-print Network

Why Are Translationally Sub-Optimal Synonymous Codons Used in Escherichia coli? Nick G.C. Smith, Adam Eyre-Walker Centre for the Study of Evolution and School of Biological Sciences, University still be referred to as a sub-optimal codon.Correspondence to: N.G.C. Smith; email: n.g.c.smith

Eyre-Walker, Adam

267

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

268

Association between p53 Codon 72 (Arg72Pro) Polymorphism and Primary Open-Angle Glaucoma in Iranian Patients  

PubMed Central

Background: Glaucomatous neuropathy is a type of cell death due to apoptosis. The p53 gene is one of the regulatory genes of apoptosis. Recently, the association between the p53 gene encoding for proline at codon 72 and primary open-angle glaucoma (POAG) has been studied in some ethnic groups. This study is the first association analysis of POAG and p53 codon 72 polymorphism in Iranian patients. Methods: A cohort of 65 unrelated patients with POAG (age range from 12-62 years, mean ± SD of 40.16 ± 17.51 years) and 65 unrelated control subjects (without glaucoma, age range of 14-63 years, mean ± SD of 35.64 ± 13.61 years) were selected. In Iranian POAG patients and normal healthy controls, the p53 codon 72 polymorphism in exon 4 was amplified using polymerase chain reaction. The amplified DNA fragments were digested with the BstUI restriction enzyme, and the digestion patterns were used to identify the alleles for the polymorphic site. Results: Comparisons revealed significant differences in allele and genotype frequencies of Pro72Arg between POAG patients and control group. A higher risk of POAG was associated with allele Pro (OR = 2.1, 95% CI = 1.2–3.4) and genotype Pro/Pro (OR = 3.9, 95% CI = 0.13-12.7). Conclusion: The p53 Pro72 allele was more frequent in Iranian POAG patients than in the control group (P<0.05). The present findings show that the individuals with the Pro/Pro genotype may be more likely to develop POAG. However, additional studies are necessary to confirm this association. PMID:25605490

Neamatzadeh, Hossein; Soleimanizad, Reza; Zare-Shehneh, Masoud; Gharibi, Saba; Shekari, Abolfazl; Bahman Rahimzadeh, Amir

2015-01-01

269

ModelOMatic: Fast and Automated Model Selection between RY, Nucleotide, Amino Acid, and Codon Substitution Models.  

PubMed

Molecular phylogenetics is a powerful tool for inferring both the process and pattern of evolution from genomic sequence data. Statistical approaches, such as maximum likelihood and Bayesian inference, are now established as the preferred methods of inference. The choice of models that a researcher uses for inference is of critical importance, and there are established methods for model selection conditioned on a particular type of data, such as nucleotides, amino acids, or codons. A major limitation of existing model selection approaches is that they can only compare models acting upon a single type of data. Here, we extend model selection to allow comparisons between models describing different types of data by introducing the idea of adapter functions, which project aggregated models onto the originally observed sequence data. These projections are implemented in the program ModelOMatic and used to perform model selection on 3722 families from the PANDIT database, 68 genes from an arthropod phylogenomic data set, and 248 genes from a vertebrate phylogenomic data set. For the PANDIT and arthropod data, we find that amino acid models are selected for the overwhelming majority of alignments; with progressively smaller numbers of alignments selecting codon and nucleotide models, and no families selecting RY-based models. In contrast, nearly all alignments from the vertebrate data set select codon-based models. The sequence divergence, the number of sequences, and the degree of selection acting upon the protein sequences may contribute to explaining this variation in model selection. Our ModelOMatic program is fast, with most families from PANDIT taking fewer than 150 s to complete, and should therefore be easily incorporated into existing phylogenetic pipelines. ModelOMatic is available at https://code.google.com/p/modelomatic/. PMID:25209223

Whelan, Simon; Allen, James E; Blackburne, Benjamin P; Talavera, David

2015-01-01

270

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias  

PubMed Central

As a result of the redundancy of the genetic code, adjacent pairs of amino acids can be encoded by as many as 36 different pairs of synonymous codons. A species-specific “codon pair bias” provides that some synonymous codon pairs are used more or less frequently than statistically predicted. We synthesized de novo large DNA molecules using hundreds of over- or underrepresented synonymous codon pairs to encode the poliovirus capsid protein. Underrepresented codon pairs caused decreased rates of protein translation, and polioviruses containing such amino acid–independent changes were attenuated in mice. Polioviruses thus customized were used to immunize mice and provided protective immunity after challenge. This “death by a thousand cuts” strategy could be generally applicable to attenuating many kinds of viruses. PMID:18583614

Coleman, J. Robert; Papamichail, Dimitris; Skiena, Steven; Futcher, Bruce; Wimmer, Eckard; Mueller, Steffen

2009-01-01

271

Charging from sampled network usage  

Microsoft Academic Search

IP flows have heavy-tailed packet and byte size distributions. This make them poor candidates for uniform sampling---i.e. selecting 1 in N flows---since omission or inclusion of a large flow can have a large effect on estimated total traffic. Flows selected in this manner are thus unsuitable for use in usage sensitive billing. We propose instead using a size-dependent sampling scheme

Nick G. Duffield; Carsten Lund; Mikkel Thorup

2001-01-01

272

Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S. cerevisiae  

E-print Network

Leaky termination at premature stop codons antagonizes nonsense-mediated mRNA decay in S termination is primarily determined by a tetranucleotide termi- nation signal consisting of the stop codon and the first nucleotide immediately 3 of the stop codon. We found that the upf1 mutation, like the [PSI

Bedwell, David M.

273

A Pattern Matching Algorithm for Codon Optimization and CpG Motif-Engineering in DNA Expression Vectors  

E-print Network

A Pattern Matching Algorithm for Codon Optimization and CpG Motif- Engineering in DNA Expression for Advanced Scientific Research Jakkur, Bangalore, India udaykumar@jncasr.ac.in Abstract Codon optimization is the length of the amino acid sequence. Based on this, we develop a software tool. Key Words: Codon

Mukherjee, Amar

274

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

275

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

276

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

277

High level production of ?-galactosidase exhibiting excellent milk-lactose degradation ability from Aspergillus oryzae by codon and fermentation optimization.  

PubMed

A ?-galactosidase gene from Aspergillus oryzae was engineered utilizing codon usage optimization to be constitutively and highly expressed in the Pichia pastoris SMD1168H strain in a high-cell-density fermentation. After fermentation for 96 h in a 50-L fermentor using glucose and glycerol as combined carbon sources, the recombinant enzyme in the culture supernatant had an activity of 4,239.07 U mL(-1) with o-nitrophenyl-?-D-galactopyranoside as the substrate, and produced a total of extracellular protein content of 7.267 g L(-1) in which the target protein (6.24 g L(-1)) occupied approximately 86 %. The recombinant ?-galactosidase exhibited an excellent lactose hydrolysis ability. With 1,000 U of the enzyme in 100 mL milk, 92.44 % lactose was degraded within 24 h at 60 °C, and the enzyme could also accomplish the hydrolysis at low temperatures of 37, 25, and 10 °C. Thus, this engineered strain had significantly higher fermentation level of A. oryzae lactase than that before optimization and the ?-galactosidase may have a good application potential in whey and milk industries. PMID:24435763

Zhao, Qianqian; Liu, Fei; Hou, Zhongwen; Yuan, Chao; Zhu, Xiqiang

2014-03-01

278

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. PMID:23812587

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

2013-01-01

279

Use of the UGA Terminator as a Tryptophan Codon in Yeast Mitochondria  

Microsoft Academic Search

We propose that the UGA terminator regularly occurs as a tryptophan codon in yeast mitochondrial DNA. This conclusion is based on the sequence analysis of mitochondrial DNA regions coding for structural genes of cytochrome b, cytochrome oxidase, and the ATPase.

Giuseppe Macino; Gloria Coruzzi; Francisco G. Nobrega; May Li; Alexander Tzagoloff

1979-01-01

280

Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models  

E-print Network

We develop novel methods for comparative genomics analysis of protein-coding genes using phylogenetic codon models, in pursuit of two main lines of biological investigation: First, we develop PhyloCSF, an algorithm based ...

Lin, Michael F. (Michael Fong-Jay)

2012-01-01

281

18. WEST CONFEDERATE AVENUE BRIDGE SPANNING CODON'S RUN, BUILT 189x. ...  

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

18. WEST CONFEDERATE AVENUE BRIDGE SPANNING CODON'S RUN, BUILT 189x. NOTE STRAIGHT ASHLAR COURSING AND RAISED KEYSTONES. VIEW NW. - Gettysburg National Military Park Tour Roads, Gettysburg, Adams County, PA

282

Lack of correlation between p53 codon 72 polymorphism and anal cancer risk  

PubMed Central

AIM: To investigate the potential role of p53 codon 72 polymorphism as a risk factor for development of anal cancer. METHODS: Thirty-two patients with invasive anal carcinoma and 103 healthy blood donors were included in the study. p53 codon 72 polymorphism was analyzed in blood samples through polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing. RESULTS: The relative frequency of each allele was 0.60 for Arg and 0.40 for Pro in patients with anal cancer, and 0.61 for Arg and 0.39 for Pro in normal controls. No significant differences in distribution of the codon 72 genotypes between patients and controls were found. CONCLUSION: These results do not support a role for the p53 codon 72 polymorphism in anal carcinogenesis. PMID:19777616

Contu, Simone S; Agnes, Grasiela; Damin, Andrea P; Contu, Paulo C; Rosito, Mário A; Alexandre, Claudio O; Damin, Daniel C

2009-01-01

283

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. PMID:25036224

Brown, Paul A.; Lemaitre, Evelyne; Briand, François-Xavier; Courtillon, Céline; Guionie, Olivier; Allée, Chantal; Toquin, Didier; Bayon-Auboyer, Marie-Hélène; Jestin, Véronique; Eterradossi, Nicolas

2014-01-01

284

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 PMID:2185223

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

1990-01-01

285

A mechanism for stop codon recognition by the ribosome: a bioinformatic approach.  

PubMed Central

Protein synthesis in ribosomes requires two kinds of tRNAs: initiation and elongation. The former initiates the process (formylmethionine tRNA in prokaryotes and special methionine tRNA in eukaryotes). The latter participates in the synthesis proper, recognizing the sense codons. Synthesis is also assisted by special proteins: initiation, elongation, and termination factors. The termination factors are necessary to recognize stop codons (UAG, UGA, and UAA) and to release the complete protein chain from the elongation tRNA preceding a stop codon. No termination tRNA capable of recognizing stop codons by their anticodons is known. The termination factors are thought to do this. In the large ribosomal RNA, we found two sites that, like tRNAs, contain the anticodon hairpin but with triplets complementary to stop codons. One site is hairpin 69 from domain IV; the other site is hairpin 89, domain V. By analogy, we call them termination tRNAs: Ter-tRNA1 and Ter-tRNA2, respectively, even though they transport no amino acids, and suggest that they directly pair to stop codons. The termination factors only aid in this recognition, making it specific and reliable. A strong argument in favor of our hypothesis comes from vertebrate mitochondria. They are known to acquire two new stop codons, AGA and AGG. In the standard code, these are two out of six arginine codons. We revealed that the corresponding anticodons, UCU and CCU, have evolved in Ter-tRNA1 of these mitochondria. PMID:11780625

Ivanov, V; Beniaminov, A; Mikheyev, A; Minyat, E

2001-01-01

286

Regional Codon Randomization: Defining a TATA-Binding Protein Surface Required for RNA Polymerase III Transcription  

Microsoft Academic Search

The TATA-binding protein (TBP) is required for transcription by all three nuclear RNA polymerases. TBP was subjected to regional codon randomization, a codon-based mutagenesis method that generates complex yet compact protein libraries. Analysis of 186 temperature-sensitive TBP mutants yielded 65 specifically defective in transcription by RNA polymerase III (Pol III). These mutants map to a limited TBP surface that may

Brendan P. Cormack; Kevin Struhl

1993-01-01

287

Cotranslational insertion of selenocysteine into formate dehydrogenase from Escherichia coli directed by a UGA codon  

SciTech Connect

The structural gene (fdhF) for the 80-kDa selenopolypeptide of formate dehydrogenase from Escherichia coli contains an in-frame UGA codon at amino acid position 140 that is translated. Translation of gene fusions between N-terminal parts of fdhF with lacZ depends on the availability of selenium in the medium when the hybrid gene contains the UGA codon; it is independent of the presence of selenium when an fdhF portion upstream of the UGA position is fused to lacZ. Transcription does not require the presence of selenium in either case. By localized mutagenesis, the UGA codon was converted into serine (UCA) and cysteine (UGC and UGU) codons. Each mutagion relieved the selenium dependency of fdhF mRNA translation. Selenium incorporation was completely abolished in the case of the UCA insertion and was reduced to about 10% when the UGA was replaced by a cysteine codon. Insertion of UCA yielded an inactive fdhF gene product, while insertion of UGC and UGU resulted in polypeptides with lowered activities as components in the system formerly known as formate hydrogenlyase. Altogether the results indicate that the UGA codon at position 140 directs the cotranslational insertion of selenocysteine into the fdhF polypeptide chain.

Zinoni, F.; Birkmann, A.; Leinfelder, W.; Boeck, A.

1987-05-01

288

EART 265 Lecture Notes: Energy Energy Usage  

E-print Network

EART 265 Lecture Notes: Energy Energy Usage US per capita energy usage is 10 kW. This represents 1/4 of the worldwide energy usage, and with 1/20th of the world population gives a global average power consumption of 2 kW. Euro- pean countries tend to use less energy per capita by a factor of 2. China's per capita

Nimmo, Francis

289

Human SNPs resulting in premature stop codons and protein truncation  

PubMed Central

Single nucleotide polymorphisms (SNPs) constitute the most common type of genetic variation in humans. SNPs introducing premature termination codons (PTCs), herein called X-SNPs, can alter the stability and function of transcripts and proteins and thus are considered to be biologically important. Initial studies suggested a strong selection against such variations/mutations. In this study, we undertook a genome-wide systematic screening to identify human X-SNPs using the dbSNP database. Our results demonstrated the presence of 28 X-SNPs from 28 genes with known minor allele frequencies. Eight X-SNPs (28.6 per cent) were predicted to cause transcript degradation by nonsense-mediated mRNA decay. Seventeen X-SNPs (60.7 per cent) resulted in moderate to severe truncation at the C-terminus of the proteins (deletion of > 50 per cent of the amino acids). The majority of the X-SNPs (78.6 per cent) represent commonly occurring SNPs, by contrast with the rarely occurring disease-causing PTC mutations. Interestingly, X-SNPs displayed a non-uniform distribution across human populations: eight X-SNPs were reported to be prevalent across three different human populations, whereas six X-SNPs were found exclusively in one or two population(s). In conclusion, we have systematically investigated human SNPs introducing PTCs with respect to their possible biological consequences, distributions across different human populations and evolutionary aspects. We believe that the SNPs reported here are likely to affect gene/protein function, although their biological and evolutionary roles need to be further investigated. PMID:16595072

2006-01-01

290

Modeling Long-Term Search Engine Usage  

Microsoft Academic Search

Search engines are key components in the online world and the choice of search engine is an important determinant of the user experience. In this work we seek to model user behaviors and determine key variables that af- fect search engine usage. In particular, we study the engine usage behavior of more than ten thousand users over a period of

Ryen W. White; Ashish Kapoor; Susan T. Dumais

2010-01-01

291

Physical Educators' Technology Competencies and Usage  

ERIC Educational Resources Information Center

The purpose of this study was to examine K-12 physical education teachers' perceptions of ability and usage of technology. Physical educators (n = 114) completed the Physical Education Technology Usage Survey assessing their perceived technology competency, how and why they utilize technology, challenges they face in implementing technology, and…

Woods, Marianne L.; Goc Karp, Grace; Miao, Hui; Perlman, Dana

2008-01-01

292

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

293

Abnormal Web Usage Control by Proxy Strategies.  

ERIC Educational Resources Information Center

Approaches to designing a proxy server with Web usage control and to making the proxy server effective on local area networks are proposed to prevent abnormal Web access and to prioritize Web usage. A system is implemented to demonstrate the approaches. The implementation reveals that the proposed approaches are effective, such that the abnormal…

Yu, Hsiang-Fu; Tseng, Li-Ming

2002-01-01

294

A Wheelchair Usage Monitoring\\/Logging System  

Microsoft Academic Search

Real life information on wheelchair usage is important for investigating the effectiveness of certain features, evaluate users' performance, and eventually improve the safety and reliability of wheelchairs. The purpose of the study is to develop a wheelchair usage monitoring\\/logging system that travels with wheelchair users in their daily activity settings and collects data independently. The system consists of a wheel

Dan Ding; Elizabeth Leister; Rory A. Cooper; Donald Spaeth; Rosemarie Cooper; Annmarie Kelleher; Michael L. Boninger

2005-01-01

295

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates  

NASA Astrophysics Data System (ADS)

It has been observed for several proteins that slowing down the rate at which individual codons are translated can increase their probability of cotranslational protein folding, while speeding up codon translation can decrease it. Here we investigate whether or not this inverse relationship between translation speed and the cotranslational folding probability is a general phenomenon or if other scenarios are possible. We first derive chemical kinetic equations that relate individual codon translation rates to the probability that a domain will fold, populate an intermediate or misfold, and examine the cotranslational folding scenarios that are possible within these models. We find that speeding up codon translation through misfolding-prone segments can, in some cases, increase the folding probability of a domain immediately before the nascent protein is released from the ribosome and decrease its chances of misfolding. Thus, for some proteins fast-translating codons could be as important as slow-translating codons in coordinating cotranslational protein folding.

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

2014-01-01

296

The effect of tRNA levels on decoding times of mRNA codons  

PubMed Central

The possible effect of transfer ribonucleic acid (tRNA) concentrations on codons decoding time is a fundamental biomedical research question; however, due to a large number of variables affecting this process and the non-direct relation between them, a conclusive answer to this question has eluded so far researchers in the field. In this study, we perform a novel analysis of the ribosome profiling data of four organisms which enables ranking the decoding times of different codons while filtering translational phenomena such as experimental biases, extreme ribosomal pauses and ribosome traffic jams. Based on this filtering, we show for the first time that there is a significant correlation between tRNA concentrations and the codons estimated decoding time both in prokaryotes and in eukaryotes in natural conditions (?0.38 to ?0.66, all P values <0.006); in addition, we show that when considering tRNA concentrations, codons decoding times are not correlated with aminoacyl-tRNA levels. The reported results support the conjecture that translation efficiency is directly influenced by the tRNA levels in the cell. Thus, they should help to understand the evolution of synonymous aspects of coding sequences via the adaptation of their codons to the tRNA pool. PMID:25056313

Dana, Alexandra; Tuller, Tamir

2014-01-01

297

The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons.  

PubMed

According to Crick's wobble hypothesis, tRNAs with uridine at the wobble position (position 34) recognize A- and G-, but not U- or C-ending codons. However, U in the wobble position is almost always modified, and Salmonella enterica tRNAs containing the modified nucleoside uridine-5-oxyacetic acid (cmo(5)U34) at this position are predicted to recognize U- (but not C-) ending codons, in addition to A- and G-ending codons. We have constructed a set of S. enterica mutants with only the cmo(5)U-containing tRNA left to read all four codons in the proline, alanine, valine, and threonine family codon boxes. From the phenotypes of these mutants, we deduce that the proline, alanine, and valine tRNAs containing cmo(5)U read all four codons including the C-ending codons, while the corresponding threonine tRNA does not. A cmoB mutation, leading to cmo(5)U deficiency in tRNA, was introduced. Monitoring A-site selection rates in vivo revealed that the presence of cmo(5)U34 stimulated the reading of CCU and CCC (Pro), GCU (Ala), and GUC (Val) codons. Unexpectedly, cmo(5)U is critical for efficient decoding of G-ending Pro, Ala, and Val codons. Apparently, whereas G34 pairs with U in mRNA, the reverse pairing (U34-G) requires a modification of U34. PMID:17942742

Näsvall, S Joakim; Chen, Peng; Björk, Glenn R

2007-12-01

298

Introns are cis effectors of the nonsense-codon-mediated reduction in nuclear mRNA abundance.  

PubMed Central

The translation of human triosephosphate isomerase (TPI) mRNA normally terminates at codon 249 within exon 7, the final exon. Frameshift and nonsense mutations of the type that cause translation to terminate prematurely at or upstream of codon 189 within exon 6 reduce the level of nuclear TPI mRNA to 20 to 30% of normal by a mechanism that is not a function of the distance of the nonsense codon from either the translation initiation or termination codon. In contrast, frameshift and nonsense mutations of another type that cause translation to terminate prematurely at or downstream of codon 208, also within exon 6, have no effect on the level of nuclear TPI mRNA. In this work, quantitations of RNA that derived from TPI alleles in which nonsense codons had been generated between codons 189 and 208 revealed that the boundary between the two types of nonsense codons resides between codons 192 and 195. The analysis of TPI gene insertions and deletions indicated that the positional feature differentiating the two types of nonsense codons is the distance of the nonsense codon upstream of intron 6. For example, the movement of intron 6 to a position downstream of its normal location resulted in a concomitant downstream movement of the boundary between the two types of nonsense codons. The analysis of intron 6 mutations indicated that the intron 6 effect is stipulated by the 88 nucleotides residing between the 5' and 3' splice sites. Since the deletion of intron 6 resulted in only partial abrogation of the nonsense codon-mediated reduction in the level of TPI mRNA, other sequences within TPI pre-mRNA must function in the effect. One of these sequences may be intron 2, since the deletion of intron 2 also resulted in partial abrogation of the effect. In experiments that switched introns 2 and 6, the replacement of intron 6 with intron 2 was of no consequence to the effect of a nonsense codon within either exon 1 or exon 6. In contrast, the replacement of intron 2 with intron 6 was inconsequential to the effect of a nonsense codon in exon 6 but resulted in partial abrogation of a nonsense codon in exon 1. Images PMID:8065363

Cheng, J; Belgrader, P; Zhou, X; Maquat, L E

1994-01-01

299

Three suppressor mutations which cure a mitochondrial RNA maturase deficiency occur at the same codon in the open reading frame of the nuclear NAM2 gene.  

PubMed Central

Dominant mutations of the nuclear NAM2 gene are able to compensate for a deficiency of the maturase encoded by the fourth intron of the mitochondrial cytochrome b gene. We have determined the complete nucleotide sequence of the NAM2-1 suppressor allele. The results of S1 nuclease protection experiments show that two overlapping poly(A)+ RNAs are transcribed from the gene using different promoters. The longer transcript contains two open reading frames (ORFs), a long ORF which could encode a protein of 894 amino acids, mol. wt 102,000 daltons, and a short ORF of 51 codons which is omitted from the shorter transcript. The wild-type nam2+ and two other suppressor alleles, NAM2-6 and NAM2-7, have been cloned. A comparison of the sequence of the wild-type and the three suppressor alleles shows that on three separate occasions the same codon specifying glycine was mutated (once to serine and twice to cysteine). Finally sequence comparisons identified two regions in the long ORF, distinct from the position of the suppressor mutations, that could correspond to binding domains for a nucleotide and a nucleic acid. Images Fig. 3. Fig. 4. Fig. 6. PMID:3034607

Labouesse, M; Herbert, C J; Dujardin, G; Slonimski, P P

1987-01-01

300

47 CFR 22.907 - Coordination of channel usage.  

Code of Federal Regulations, 2011 CFR

...2011-10-01 false Coordination of channel usage. 22.907 Section 22.907...Service § 22.907 Coordination of channel usage. Licensees in the Cellular...coordinate, with the appropriate parties, channel usage at each transmitter...

2011-10-01

301

47 CFR 22.907 - Coordination of channel usage.  

Code of Federal Regulations, 2013 CFR

...2013-10-01 false Coordination of channel usage. 22.907 Section 22.907...Service § 22.907 Coordination of channel usage. Licensees in the Cellular...coordinate, with the appropriate parties, channel usage at each transmitter...

2013-10-01

302

Sense codon emancipation for proteome-wide incorporation of noncanonical amino acids: rare isoleucine codon AUA as a target for genetic code expansion  

PubMed Central

One of the major challenges in contemporary synthetic biology is to find a route to engineer synthetic organisms with altered chemical constitution. In terms of core reaction types, nature uses an astonishingly limited repertoire of chemistries when compared with the exceptionally rich and diverse methods of organic chemistry. In this context, the most promising route to change and expand the fundamental chemistry of life is the inclusion of amino acid building blocks beyond the canonical 20 (i.e. expanding the genetic code). This strategy would allow the transfer of numerous chemical functionalities and reactions from the synthetic laboratory into the cellular environment. Due to limitations in terms of both efficiency and practical applicability, state-of-the-art nonsense suppression- or frameshift suppression-based methods are less suitable for such engineering. Consequently, we set out to achieve this goal by sense codon emancipation, that is, liberation from its natural decoding function – a prerequisite for the reassignment of degenerate sense codons to a new 21st amino acid. We have achieved this by redesigning of several features of the post-transcriptional modification machinery which are directly involved in the decoding process. In particular, we report first steps towards the reassignment of 5797 AUA isoleucine codons in Escherichia coli using efficient tools for tRNA nucleotide modification pathway engineering. PMID:24433543

Bohlke, Nina; Budisa, Nediljko

2014-01-01

303

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

304

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

305

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

306

Reducing the Energy Usage of Office Applications  

Microsoft Academic Search

In this paper, we demonstrate how component-based middlewarecan reduce the energy usage of closed-source applications. Werst describe how the Puppeteer system exploits well-dened interfacesexported by applications to modify their behavior. We then present adetailed study of the energy usage of Microsoft's PowerPoint applicationand show that adaptive policies can reduce energy expenditure by 49%in some instances. In addition, we use the

Jason Flinn; Eyal De Lara; Mahadev Satyanarayanan; Dan S. Wallach; Willy Zwaenepoel

2001-01-01

307

Web Usage Mining Via Fuzzy Logic Techniques  

Microsoft Academic Search

With the increment of users and information on the Web, mining processes inspired in the traditional data mining ones have\\u000a been developed. This new recent area of investigation is called Web Mining. Within this area, we study the analysis of web\\u000a log files in what is called Web Usage Mining. Different techniques of mining to discover usage patterns from web

Víctor H. Escobar-jeria; Maria J. Martín-bautista; Daniel Sánchez; María Amparo Vila Miranda

2007-01-01

308

Predicting energy usage in a supermarket  

E-print Network

PREDICTING ENERGY USAGE IN A SUPERMARKET A Thesis by DEREK WAYNE SCHROCK Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE December 1989 Major... Subject: Mechanical Engineering PREDICTING ENERGY USAGE IN A SUPERMARKET by DEREK WAYNE SCHROCK Approved as to style and content by: David . Claridge (Chair of Comtnittee) Dennis L. O'Neal (Member) B. on us sell (Member) Walter L. Bradle (Head...

Schrock, Derek Wayne

1989-01-01

309

Nonsense ?-thalassemia mutation at codon 37 (TGG>TGA), detected for the first time in three Turkish cases.  

PubMed

Thalassemias are genetically heterogeneous group of disorders with reduced or absent production of globin. ?-Thalassemia major can be caused by homozygosity or compound heterozygosity for ?-globin gene mutation. Here we report, for the first time in Turkey, three cases who carry the nonsense ?-thalassemia (?-thal) mutation at codon 37 (TGG>TGA; Trp?Stop) causing premature stop codon. PMID:22385009

Bozdogan, Sevcan Tug; Unsal, Cagatay; Erkman, Hakan; Genc, Ahmet; Yuregir, Ozge Ozalp; Muslumanoglu, Muhammed Hamza; Aslan, Huseyin

2012-01-01

310

CoDoNS: Replacing the DNS Hierarchy Venugopalan Ramasubramanian (Rama)  

E-print Network

CoDoNS: Replacing the DNS Hierarchy with Peers Venugopalan Ramasubramanian (Rama) Emin Gün Sirer Computer Science Dept., Cornell University #12;Why change the DNS? · DNS is largely successful ­ Two performance ­ Security #12;DNS: Problems · Poor availability ­ 80% of domain names bottle-necked at 2 servers

Sirer, Emin Gun

311

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

312

Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus  

E-print Network

Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus), has led to the identification of five antibody-combining regions, or epitopes, of the HA protein. Epitopic residues exhibit greater variability, higher ratios of re- placement to silent mutations

Plotkin, Joshua B.

313

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation  

PubMed Central

Ribosome profiling data report on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate-reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation. PMID:25538139

Pop, Cristina; Rouskin, Silvi; Ingolia, Nicholas T; Han, Lu; Phizicky, Eric M; Weissman, Jonathan S; Koller, Daphne

2014-01-01

314

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

315

Association between the p21 Codon 31 A1 (arg) Allele and Lung Cancer  

Microsoft Academic Search

In previous investigations p53 polymorphisms and haplotypes have been found to be associated with different types of cancer. In this paper the codon 31 polymorphism of the p53-inducible protein p21 was studied in 144 Swedish lung cancer patients and two different control groups: 95 patients with chronic obstructive pulmonary disease (COPD) and 761 healthy controls. An increased frequency of the

A. Själander; R. Birgander; A. Rannug; A.-K. Alexandrie; G. Tornling; G. Beckman

1996-01-01

316

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons  

PubMed Central

Until now the most efficient solution to align nucleotide sequences containing open reading frames was to use indirect procedures that align amino acid translation before reporting the inferred gap positions at the codon level. There are two important pitfalls with this approach. Firstly, any premature stop codon impedes using such a strategy. Secondly, each sequence is translated with the same reading frame from beginning to end, so that the presence of a single additional nucleotide leads to both aberrant translation and alignment. We present an algorithm that has the same space and time complexity as the classical Needleman-Wunsch algorithm while accommodating sequencing errors and other biological deviations from the coding frame. The resulting pairwise coding sequence alignment method was extended to a multiple sequence alignment (MSA) algorithm implemented in a program called MACSE (Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons). MACSE is the first automatic solution to align protein-coding gene datasets containing non-functional sequences (pseudogenes) without disrupting the underlying codon structure. It has also proved useful in detecting undocumented frameshifts in public database sequences and in aligning next-generation sequencing reads/contigs against a reference coding sequence. MACSE is distributed as an open-source java file executable with freely available source code and can be used via a web interface at: http://mbb.univ-montp2.fr/macse. PMID:21949676

Ranwez, Vincent; Harispe, Sébastien; Delsuc, Frédéric; Douzery, Emmanuel J. P.

2011-01-01

317

Expanded use of sense codons is regulated by modified cytidines in tRNA  

PubMed Central

Codon use among the three domains of life is not confined to the universal genetic code. With only 22 tRNA genes in mammalian mitochondria, exceptions from the universal code are necessary for proper translation. A particularly interesting deviation is the decoding of the isoleucine AUA codon as methionine by the one mitochondrial-encoded tRNAMet. This tRNA decodes AUA and AUG in both the A- and P-sites of the metazoan mitochondrial ribosome. Enrichment of posttranscriptional modifications is a commonly appropriated mechanism for modulating decoding rules, enabling some tRNA functions while restraining others. In this case, a modification of cytidine, 5-formylcytidine (f5C), at the wobble position-34 of human mitochondrial () enables expanded decoding of AUA, resulting in a deviation in the genetic code. Visualization of the codon•anticodon interaction by X-ray crystallography revealed that recognition of both A and G at the third position of the codon occurs in the canonical Watson–Crick geometry. A modification-dependent shift in the tautomeric equilibrium toward the rare imino-oxo tautomer of cytidine stabilizes the f5C34•A base pair geometry with two hydrogen bonds. PMID:23781103

Cantara, William A.; Murphy, Frank V.; Demirci, Hasan; Agris, Paul F.

2013-01-01

318

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.  

PubMed

Ribosome profiling data report on the distribution of translating ribosomes, at steady-state, with codon-level resolution. We present a robust method to extract codon translation rates and protein synthesis rates from these data, and identify causal features associated with elongation and translation efficiency in physiological conditions in yeast. We show that neither elongation rate nor translational efficiency is improved by experimental manipulation of the abundance or body sequence of the rare AGG tRNA. Deletion of three of the four copies of the heavily used ACA tRNA shows a modest efficiency decrease that could be explained by other rate-reducing signals at gene start. This suggests that correlation between codon bias and efficiency arises as selection for codons to utilize translation machinery efficiently in highly translated genes. We also show a correlation between efficiency and RNA structure calculated both computationally and from recent structure probing data, as well as the Kozak initiation motif, which may comprise a mechanism to regulate initiation. PMID:25538139

Pop, Cristina; Rouskin, Silvi; Ingolia, Nicholas T; Han, Lu; Phizicky, Eric M; Weissman, Jonathan S; Koller, Daphne

2014-01-01

319

Analysis and comparison of nucleotide sequences encoding the genes for (NiFe) and (NiFeSe) hydrogenases from Desulfovibrio gigas and Desulfovibrio baculatus  

SciTech Connect

The nucleotide sequences encoding the (NiFe) hydrogenase from Desulfovibrio gigas and the (NiFeSe) hydrogenase from Desulfovibrio baculatus were analyzed by the codon usage method of Staden and McLachlan. The reported reading frames were found to contain regions of low codon probability which are matched by more probable sequences in other frames. Renewed nucleotide sequencing showed the probable frames to be correct. The corrected sequences of the two small and large subunits share a significant degree of sequence homology. The small subunit, which contains 10 conserved cysteine residues, is likely to coordinate at least 2 iron-sulfur clusters, while the finding of a selenocystein codon (TGA) near the 3{prime} end of the (NiFeSe) large-subunit gene matched by a regular cysteine codon (TGC) in the (NiFe) large subunit gene indicates the presence of some of the ligands to the active-site nickel in the large subunit.

Voordouw, G. (Univ. of Calgary, Alberta (Canada)); Menon, N.K.; LeGall, J.; Euisung Choi; Peck, H.D. Jr.; Przybyla, A.E. (Univ. of Georgia, Athens (United States))

1989-05-01

320

A Single IRES Containing a G-quartet RNA Structure Drives FGF-2 Gene Expression at Four Alternative Translation Initiation Codons  

E-print Network

Alternative Translation Initiation Codons Sophie Bonnal1 , Céline Schaeffer2 , Laurent Créancier1,3 , Simone growth factor 2 (FGF-2) mRNA contains four CUG and one AUG translation initiation codons. While the 5'-end proximal CUG codon is initiated by a cap-dependent translation process, the other four initiation

Paris-Sud XI, Université de

321

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

322

Association of sporadic Creutzfeldt-Jakob disease with homozygous genotypes at PRNP codons 129 and 219 in the Korean population.  

PubMed

Human prion protein gene (PRNP) is considered an important gene in determining the incidence of human transmissible spongiform encephalopathies or prion diseases. Polymorphisms of PRNP at codon 129 in Europeans and codon 219 in Japanese may play an important role in the susceptibility to sporadic Creutzfeldt-Jakob disease (CJD); data regarding codon 129 in the Japanese population have led to divergent interpretations. In order to determine which, if any, of the PRNP genotypes in Korean people are associated with sporadic CJD, we examined the genotype and allelic distributions of human PRNP polymorphisms in 150 patients with sporadic CJD. All Korean sporadic CJD patients were Met/Met at codon 129, Glu/Glu at codon 219 and undeleted at the octarepeat region of PRNP. Our study showed significant differences in genotype frequency of PRNP at codon 129 (chi 2=8.8998, P=0.0117) or 219 (chi 2=12.6945, P=0.0004) between sporadic CJD and normal controls. Furthermore, the genotype frequency of the heterozygotes for codons 129 and/or 219 showed a significant difference between the normal population and sporadic CJD patients (chi 2=21.0780, P<0.0001). PMID:16217673

Jeong, Byung-Hoon; Lee, Kyung-Hee; Kim, Nam-Ho; Jin, Jae-Kwang; Kim, Jae-Il; Carp, Richard I; Kim, Yong-Sun

2005-12-01

323

Manufacturing developments to reduce strategic materials usage  

SciTech Connect

Manufacturing development programs to reduce the usage in gas turbine engines are examined. Several programs which provided significant of cobalt, titanium, and tantalum results in reducing raw materials requirements, that have been reduced to practice are described. The programs include forging and casting complex parts to near net shape, recycling of machining scrap and used parts, repair and refurbishment of damaged or worn parts, and component retirement for cause. In addition to reduction of strategic material usage, the programs resulted in lower cost parts due to reduced material input requirements and less machining.

Allen, M.M.; Halfpap, D.S.; Siegel, M.A.

1984-04-01

324

Amino-acid substitutions at codon 13 of the N-ras oncogene in human acute myeloid leukaemia  

NASA Astrophysics Data System (ADS)

DNAs from four out of five patients with acute myeloid leukaemia (AML) tested by an in vivo selection assay in nude mice using transfected mouse NIH 3T3 cells were found to contain an activated N-ras oncogene. Using a set of synthetic oligonucleotide probes, we have detected a mutation at codon 13 in all four genes. The same codon is mutated in an additional AML DNA that is positive in the focus-formation assay on 3T3 cells. DNA from the peripheral blood of one patient in remission does not contain a codon 13 mutation.

Bos, Johannes L.; Toksoz, Deniz; Marshall, Christopher J.; Verlaan-de Vries, Matty; Veeneman, Gerrit H.; van der Eb, Alex J.; van Boom, Jacques H.; Janssen, Johannes W. G.; Steenvoorden, Ada C. M.

1985-06-01

325

Lie Superalgebras and the Multiplet Structure of the Genetic Code I: Codon Representations  

E-print Network

It has been proposed that the degeneracy of the genetic code,i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In the initial work of Hornos & Hornos this picture was developed in the framework of simple Lie algebras. Here, we explore the possibility of explaining the degeneracy of the genetic code using basic classical Lie superalgebras, whose representation theory is sufficiently well understood, at least as far as typical representations are concerned. In the present paper, we give the complete list of all typical codon representations (typical 64 -dimensional irreducible representations), whereas in the second part, we shall present the corresponding branching rules and discuss which of them reproduce the multiplet structure of the genetic code.

F. M. Forger; R. S. Sachse

1998-08-04

326

Lie superalgebras and the multiplet structure of the genetic code. I. Codon representations  

NASA Astrophysics Data System (ADS)

It has been proposed by Hornos and Hornos [Phys. Rev. Lett. 71, 4401-4404 (1993)] that the degeneracy of the genetic code, i.e., the phenomenon that different codons (base triplets) of DNA are transcribed into the same amino acid, may be interpreted as the result of a symmetry breaking process. In their work, this picture was developed in the framework of simple Lie algebras. Here, we explore the possibility of explaining the degeneracy of the genetic code using basic classical Lie superalgebras, whose representation theory is sufficiently well understood, at least as far as typical representations are concerned. In the present paper, we give the complete list of all typical codon representations (typical 64-dimensional irreducible representations), whereas in the second part, we shall present the corresponding branching rules and discuss which of them reproduce the multiplet structure of the genetic code.

Forger, Michael; Sachse, Sebastian

2000-08-01

327

[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

328

Recent Developments in Web Usage Mining Research  

Microsoft Academic Search

Web Usage Mining is that area of Web Mining which deals with the extraction of interesting knowledge from logging information produced by web servers. In this paper, we present a survey of the recent developments in this area that is receiving increasing attention from the Data Mining community. Web Mining (29) is that area of Data Mining which deals with

Federico Michele Facca; Pier Luca Lanzi

2003-01-01

329

VEHICLE USAGE AGREEMENT DEPARTMENT OF BIOLOGICAL SCIENCE  

E-print Network

VEHICLE USAGE AGREEMENT DEPARTMENT OF BIOLOGICAL SCIENCE All drivers of vehicles must certify to the following: 1. I certify that I have a valid driver's license appropriate for the vehicle type and will abide belts. 2. I have read and understand the vehicle operating policies and procedures as defined

Ronquist, Fredrik

330

Congestion rents allocation based on transmission usage  

Microsoft Academic Search

In this paper, an allocation method for the congestion rents is presented. The method is based on the use of generalized generation distribution factors (GGDFs) and generalized load distribution factors (GLDFs). These factors are employed to quantify the usage of the transmission system by considering the day-ahead market outcome. Under this allocation scheme, the system conditions are still reflected in

Guillermo Bautista; Victor H. Quintana

2003-01-01

331

Permlyzer: Analyzing Permission Usage in Android Applications  

E-print Network

, the Android system implements an install-time permission mecha- nism to provide users with an opportunity security/privacy sensitive oper- ations. Therefore, Android enforces a permission-based mech- anismPermlyzer: Analyzing Permission Usage in Android Applications Wei Xu, Fangfang Zhang, and Sencun

Zhu, Sencun

332

CONSUMER PANACEA OVER INTERNET USAGE IN PAKISTAN  

Microsoft Academic Search

The present age is the era of information technology and everywhere microwaves are scattered. Everybody wants to explore itself with this information technology and happenings taking place of Internet for the purpose of education, awareness, entertainment and especially interaction with strangers. In Pakistan, the awareness of internet usage is increasing and people are gaining knowledge about online buying and selling.

Bilal AFSAR; Jawaria Andleeb QURESHI; Asim REHMAN; Rehmat Ullah BANGASH

2011-01-01

333

The Scope of Usage-Based Theory  

PubMed Central

Usage-based approaches typically draw on a relatively small set of cognitive processes, such as categorization, analogy, and chunking to explain language structure and function. The goal of this paper is to first review the extent to which the “cognitive commitment” of usage-based theory has had success in explaining empirical findings across domains, including language acquisition, processing, and typology. We then look at the overall strengths and weaknesses of usage-based theory and highlight where there are significant debates. Finally, we draw special attention to a set of culturally generated structural patterns that seem to lie beyond the explanation of core usage-based cognitive processes. In this context we draw a distinction between cognition permitting language structure vs. cognition entailing language structure. As well as addressing the need for greater clarity on the mechanisms of generalizations and the fundamental units of grammar, we suggest that integrating culturally generated structures within existing cognitive models of use will generate tighter predictions about how language works. PMID:23658552

Ibbotson, Paul

2013-01-01

334

Vertical File Usage: A Comparative Study.  

ERIC Educational Resources Information Center

Since recorded usage of vertical files in a university library does not always indicate actual needs of patrons, a study was conducted on the use of a collection of 20,000 pamphlets over a three-year period (1972-75). Data were collected from circulation records and from a questionnaire circulated with each pamphlet. Three subject areas had the…

Wells, Dorothy P.

335

Nutritional supplements usage by Portuguese athletes.  

PubMed

In this study, we determined the prevalence of nutritional supplements (NS) usage, the type of supplements used, the reasons for usage, and the source of nutritional advice among Portuguese athletes. Two hundred ninety-two athletes (68 % male, 12 - 37 years old) from 13 national sports federations completed a questionnaire that sought information on socio-demographics, sports data, and NS usage. Most athletes (66 %) consumed NS, with a median consumption of 4 supplements per athlete. The most popular supplements included multivitamins/minerals (67 %), sport drinks (62 %), and magnesium (53 %). Significant differences for the type of NS consumed were found between gender and age groups and the number of weekly training hours. Most athletes used NS to accelerate recovery (63 %), improve sports performance (62 %), and have more energy/reduce fatigue (60 %). Athletes sought advice on supplementation mainly from physicians (56 %) and coaches (46 %). Age and gender were found to influence reasons for use and the source of information. Reasons for NS usage were supported scientifically in some cases (e. g., muscle gain upon protein supplementation), but others did not have a scientific basis (e. g., use of glutamine and magnesium). Given the high percentage of NS users, there is an urgent need to provide athletes with education and access to scientific and unbiased information, so that athletes can make assertive and rational choices about the utilization of these products. PMID:24220164

Sousa, Mónica; Fernandes, Maria João; Moreira, Pedro; Teixeira, Vítor Hugo

2013-01-01

336

Web usage of the GP bibliography  

Microsoft Academic Search

A recent upgrade to the Genetic Programming bibliography enables monitoring of its www usage. Downloads are dominated by automated software robotic agents (web bots), particularly Yahoo and other search engine spiders. These are very variable and cast doubt that some world wide web hits statistics relate to people. Some 62% of GP papers are on line. PDF is twice as

William B. Langdon

2006-01-01

337

Nutrition label usage of Chinese consumers  

Microsoft Academic Search

Though the Pacific-rim countries like China, Hong Kong and ASEAN countries will soon constitute an economic power comparable to that of North America and Europe, most of the empirical work on food labelling is related to the US and UK consumers. Research into nutrition label usage in a Chinese socio-cultural context is not found. To redress this imbalance, this study

Wai-sum Siu; Tina Man-yi Tsoi

1998-01-01

338

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

339

Jadeite: Improving API Documentation Using Usage Information  

E-print Network

Jadeite: Improving API Documentation Using Usage Information Abstract Jadeite is a new Javadoc-like API documentation sys- tem that takes advantage of multiple users' aggregate experience to reduce difficulties that programmers have learning new APIs. Previous studies have shown that programmers often

Myers, Brad A.

340

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

341

Codon-modifications and an endoplasmic reticulum-targeting sequence additively enhance expression of an Aspergillus phytase gene in transgenic canola.  

PubMed

Transgenic plants offer advantages for biomolecule production because plants can be grown on a large scale and the recombinant macromolecules can be easily harvested and extracted. We introduced an Aspergillus phytase gene into canola (Brassica napus) (line 9412 with low erucic acid and low glucosinolates) by Agrobacterium-mediated transformation. Phytase expression in transgenic plant was enhanced with a synthetic phytase gene according to the Brassica codon usage and an endoplasmic reticulum (ER) retention signal KDEL that confers an ER accumulation of the recombinant phytase. Secretion of the phytase to the extracellular fluid was also established by the use of the tobacco PR-S signal peptide. Phytase accumulation in mature seed accounted for 2.6% of the total soluble proteins. The enzyme can be glycosylated in the seeds of transgenic plants and retain a high stability during storage. These results suggest a commercial feasibility of producing a stable recombinant phytase in canola at a high level for animal feed supplement and for reducing phosphorus eutrophication problems. PMID:16249870

Peng, Ri-He; Yao, Quan-Hong; Xiong, Ai-Sheng; Cheng, Zong-Ming; Li, Yi

2006-03-01

342

High Molecular Mass Forms of Basic Fibroblast Growth Factor are Initiated by Alternative CUG Codons  

Microsoft Academic Search

A 6.75-kilobase human hepatoma-derived basic fibroblast growth factor (bFGF) cDNA was cloned and sequenced. An amino-terminal sequence generated from a purified hepatoma bFGF was found to correspond to the nucleotide sequence and to begin 8 amino acids upstream from the putative methionine start codon thought to initiate a 154-amino acid bFGF translation product. This sequence suggests that a form of

Herve Prats; Mourad Kaghad; Anne Catherine Prats; Michael Klagsbrun; Jean Michel Lelias; Philippe Liauzun; Pascale Chalon; Jean Pierre Tauber; Francois Amalric; John A. Smith; Daniel Caput

1989-01-01

343

p53 Codon 72 polymorphism in oral exfoliated cells in a Sudanese population.  

PubMed

Earlier studies have investigated the tumor suppressor gene p53 as a co-factor in the development of oral squamous cell carcinoma (OSCC). Our previous studies have indicated that chronic use of Sudanese snuff (toombak) and the presence of human papilloma virus (HPV) may be involved in the high prevalence of OSCC in Sudan. This study investigated the prevalence of p53 codon 72 polymorphism in brush biopsies obtained from a Sudanese population. A total of 174 individuals were included in the study; chronic toombak users (n=152) and non-users (n=22). DNA was extracted from all the samples and genotyped for the codon 72 polymorphism by polymerase chain reaction/restriction fragment length polymorphism. The Arg/Pro genotype was found in 53% of the 174 study participants, compared to 21% found with Arg/Arg and 26% found with Pro/Pro. Stratifying by toombak use, 28 (18%), 45 (29%) and 79 (52%) of the 152 samples from toombak users had Arg/Arg, Pro/Pro and Arg/Pro respectively, compared to 9 (41%), 0 (0%) and 13 (59%) found in the 22 samples from non users. The differences between the samples from toombak users and non users in Arg/Arg and Pro/Pro codon 72 polymorphism and HPV infection were statistically significant (p<0.05). Our study indicated that a high prevalence of the genotype Arg/Pro at the p53 codon 72 may contribute to susceptibility to OSCC, especially in combination with the use of carcinogenic tobacco-specific nitrosamine (TSNA)-rich toombak. Our observations warrant an in-depth study for understanding the role of p53 polymorphism in human oral cancers. PMID:22210716

Sand, Lars; Jalouli, Miranda M; Jalouli, Jamshid; Sapkota, Dipak; Ibrahim, Salah O

2012-01-01

344

Mechanism of codon recognition by transfer RNA studied with oligonucleotides larger than triplets.  

PubMed Central

The binding of yeast tRNAPhe to UUCA, UUCC, UUCCC, UUCUUCU, U4, U5, U6 and U7 was analysed by fluorescence temperature jump and equilibrium sedimentation measurements. In all cases the two observed relaxation processes can be assigned to alpha) an intramolecular conformation change of the anticodon loop and beta) preferential binding of the oligonucleotides to one of the anticodon conformations. The anticodon loop transition is associated with inner sphere complexation of Mg2+ and proceeds with rate constants of about 10(3) s-1. The rate constants of oligonucleotide binding are between 4 and 10 X 10(6) M-1s-1 and reflect an increase of the association rate with the number of binding sites compensated to some degree by electrostatic repulsion in the preequilibrium complex. Neither temperature jump nor equilibrium sedimentation experiments provided evidence for UUCA or UUCC induced tRNA dimerisation, although UUC binding leads to strong tRNA dimerisation under equivalent conditions. The results obtained for the longer oligonucleotides are similar. In the case of UUCUUCU with its two potential binding sites for tRNAPhe there was no evidence for the formation of 'ternary' complexes. Apparently tRNAPhe binds preferentially to the second UUC of this 'messenger' and forms additional contacts with residues on either side of the codon. Some evidence for the formation of ternary complexes is obtained for U6 and U7, although the extent of this reaction remains very small. Our results demonstrate that the mode of tRNA binding to a codon is strongly influenced by residues next to the codon. The formation of cooperative contacts between tRNA molecules at adjacent codons apparently requires support by a catalyst adjusting an appropriate conformation of messenger and tRNA molecules. PMID:4011439

Labuda, D; Striker, G; Grosjean, H; Porschke, D

1985-01-01

345

Polymorphisms in codon 31 of p21 and cervical cancer susceptibility in Korean women  

Microsoft Academic Search

The aim of this study was to determine whether the codon 31 genotype of p21 might be associated with an increased risk of cervical cancer development in Korean women. We used tissue derived from patients with invasive cervical cancer (ICC) (n=111, composed of two histologic groups: squamous cell carcinoma (n=67) and adenocarcinoma (n=44)), cervical intraepithelial neoplasia (CIN) III (n=101), and

Ju-Won Roh; Moon-Hong Kim; Jae-Weon Kim; Noh-Hyun Park; Yong-Sang Song; Soon-Beom Kang; Hyo-Pyo Lee

2001-01-01

346

A deviant mitochondrial genetic code in prymnesiophytes (yellow-algae): UGA codon for tryptophan.  

PubMed

The sequence of a representative mitochondrial gene COXI, encoding cytochrome c oxidase subunit I, was determined in five species that cover all the orders of the Prymnesiophyta with the exception of the Pavlovales. Through this analysis, we noticed that the 'stop' codon UGA appears frequently and, specifically, at conserved tryptophan (Trp) sites of the gene. We showed these sites were not edited in the corresponding mRNA in one of these species, Isochrysis galbana. Therefore, it is most likely that the UGA codon is used for Trp, and not as a stop codon, in prymnesiophytes. All the analyzed prymnesiophytes made a tight cluster on the COXI phylogenetic tree which includes representative species of green-algae, land plants, yellow-green algae, eustigmatophytes and a red-alga. This suggests a monophyletic origin for the prymnesiophytes. The same deviant genetic code, i.e. UGA for Trp, has also been found in the red-alga, Chondrus crispus. In spite of the fact that this red-alga and the prymnesiophytes, share the same deviant genetic code for Trp, close affinity between the two groups was not statistically supported by the phylogenetic analysis of COXI sequences. PMID:9342410

Hayashi-Ishimaru, Y; Ehara, M; Inagaki, Y; Ohama, T

1997-10-01

347

Mismatch repair at stop codons is directed independent of GATC methylation on the Escherichia coli chromosome  

NASA Astrophysics Data System (ADS)

The mismatch repair system (MMR) corrects replication errors that escape proofreading. Previous studies on extrachromosomal DNA in Escherichia coli suggested that MMR uses hemimethylated GATC sites to identify the newly synthesized strand. In this work we asked how the distance of GATC sites and their methylation status affect the occurrence of single base substitutions on the E. coli chromosome. As a reporter system we used a lacZ gene containing an early TAA stop codon. We found that occurrence of point mutations at this stop codon is unaffected by GATC sites located more than 115 base pairs away. However, a GATC site located about 50 base pairs away resulted in a decreased mutation rate. This effect was independent of Dam methylation. The reversion rate of the stop codon increased only slightly in dam mutants compared to mutL and mutS mutants. We suggest that unlike on extrachromosomal DNA, GATC methylation is not the only strand discrimination signal for MMR on the E. coli chromosome.

Sneppen, Kim; Semsey, Szabolcs

2014-12-01

348

Recognition of the amber UAG stop codon by release factor RF1  

SciTech Connect

We report the crystal structure of a termination complex containing release factor RF1 bound to the 70S ribosome in response to an amber (UAG) codon at 3.6-{angstrom} resolution. The amber codon is recognized in the 30S subunit-decoding centre directly by conserved elements of domain 2 of RF1, including T186 of the PVT motif. Together with earlier structures, the mechanisms of recognition of all three stop codons by release factors RF1 and RF2 can now be described. Our structure confirms that the backbone amide of Q230 of the universally conserved GGQ motif is positioned to contribute directly to the catalysis of the peptidyl-tRNA hydrolysis reaction through stabilization of the leaving group and/or transition state. We also observe synthetic-negative interactions between mutations in the switch loop of RF1 and in helix 69 of 23S rRNA, revealing that these structural features interact functionally in the termination process. These findings are consistent with our proposal that structural rearrangements of RF1 and RF2 are critical to accurate translation termination.

Korostelev, Andrei; Zhu, Jianyu; Asahara, Haruichi; Noller, Harry F. (UCSC)

2010-08-23

349

Mismatch repair at stop codons is directed independent of GATC methylation on the Escherichia coli chromosome.  

PubMed

The mismatch repair system (MMR) corrects replication errors that escape proofreading. Previous studies on extrachromosomal DNA in Escherichia coli suggested that MMR uses hemimethylated GATC sites to identify the newly synthesized strand. In this work we asked how the distance of GATC sites and their methylation status affect the occurrence of single base substitutions on the E. coli chromosome. As a reporter system we used a lacZ gene containing an early TAA stop codon. We found that occurrence of point mutations at this stop codon is unaffected by GATC sites located more than 115 base pairs away. However, a GATC site located about 50 base pairs away resulted in a decreased mutation rate. This effect was independent of Dam methylation. The reversion rate of the stop codon increased only slightly in dam mutants compared to mutL and mutS mutants. We suggest that unlike on extrachromosomal DNA, GATC methylation is not the only strand discrimination signal for MMR on the E. coli chromosome. PMID:25475788

Sneppen, Kim; Semsey, Szabolcs

2014-01-01

350

Effect of Codon Optimisation on the Production of Recombinant Fish Growth Hormone in Pichia pastoris  

PubMed Central

This study was established to test the hypothesis of whether the codon optimization of fish growth hormone gene (FGH) based on P. pastoris preferred codon will improve the quantity of secreted rFGH in culture supernatant that can directly be used as fish feed supplements. The optimized FGH coding sequence (oFGH) and native sequence (nFGH) of giant grouper fish (Epinephelus lanceolatus) were cloned into P. pastoris expression vector (pPICZ?A) downstream of alcohol oxidase gene (AOX1) for efficient induction of extracellular rFGH by adding 1% of absolute methanol. The results showed that recombinant P. pastoris was able to produce 2.80 ± 0.27?mg of oFGH compared to 1.75 ± 0.25 of nFGH in one litre of culture supernatant. The total body weight of tiger grouper fingerlings fed with oFGH increased significantly at third (P < 0.05) and fourth weeks (P < 0.01) of four-week experiment period compared to those fed with nFGH. Both oFGH and nFGH significantly enhanced the final biomass and fish survival percentage. In conclusion, codon optimization of FGH fragment was useful to increase rFGH quantity in the culture supernatant of P. pastoris that can be directly used as fish feed supplements. Further studies are still required for large scale production of rFGH and practical application in aquaculture production. PMID:25147851

Rothan, Hussin A.; Ser Huy, Teh; Mohamed, Zulqarnain

2014-01-01

351

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 PMID:8730280

Dobbie, Z; Spycher, M; Mary, J L; Häner, M; Guldenschuh, I; Hürliman, R; Amman, R; Roth, J; Müller, H; Scott, R J

1996-01-01

352

Apolipoprotein B48 is the Product of a Messenger RNA with an Organ-Specific In-Frame Stop Codon  

Microsoft Academic Search

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 Gln2153 in

San-Hwan Chen; Geetha Habib; Chao-Yuh Yang; Zi-Wei Gu; Bo Rong Lee; Shi-Ai Weng; Steven R. Silberman; Sheng-Jian Cai; J. P. Deslypere; Maryvonne Rosseneu; Antonio M. Gotto; Wen-Hsiung Li; Lawrence Chan

1987-01-01

353

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

PubMed Central

While mRNA stability has been demonstrated to control rates of translation, generating both global and local synonymous codon biases in many unicellular organisms, this explanation cannot adequately explain why codon bias strongly tracks neighboring intergene GC content; suggesting that structural dynamics of DNA might also influence codon choice. Because minor groove width is highly governed by 3-base periodicity in GC, the existence of triplet-based codons might imply a functional role for the optimization of local DNA molecular dynamics via GC content at synonymous sites (?GC3). We confirm a strong association between GC3-related intrinsic DNA flexibility and codon bias across 24 different prokaryotic multiple whole-genome alignments. We develop a novel test of natural selection targeting synonymous sites and demonstrate that GC3-related DNA backbone dynamics have been subject to moderate selective pressure, perhaps contributing to our observation that many genes possess extreme DNA backbone dynamics for their given protein space. This dual function of codons may impose universal functional constraints affecting the evolution of synonymous and non-synonymous sites. We propose that synonymous sites may have evolved as an ‘accessory’ during an early expansion of a primordial genetic code, allowing for multiplexed protein coding and structural dynamic information within the same molecular context. PMID:25200075

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

2014-01-01

354

Historical review of medicinal plants’ usage  

PubMed Central

Healing with medicinal plants is as old as mankind itself. The connection between man and his search for drugs in nature dates from the far past, of which there is ample evidence from various sources: written documents, preserved monuments, and even original plant medicines. Awareness of medicinal plants usage is a result of the many years of struggles against illnesses due to which man learned to pursue drugs in barks, seeds, fruit bodies, and other parts of the plants. Contemporary science has acknowledged their active action, and it has included in modern pharmacotherapy a range of drugs of plant origin, known by ancient civilizations and used throughout the millennia. The knowledge of the development of ideas related to the usage of medicinal plants as well as the evolution of awareness has increased the ability of pharmacists and physicians to respond to the challenges that have emerged with the spreading of professional services in facilitation of man's life. PMID:22654398

Petrovska, Biljana Bauer

2012-01-01

355

Burnout and Humor Usage among Community College Nursing Faculty Members.  

ERIC Educational Resources Information Center

Assesses the correlation of burnout among community college nursing faculty members and their use of humor to mediate academic stress related to burnout. Differences in burnout between high versus low humor usage respondents showed a higher sense of personal accomplishment with high humor usage. Of those with low humor usage, workload was related…

Talbot, Laura A.

2000-01-01

356

Bibliometric Laws and Library Usage as Social Phenomena.  

ERIC Educational Resources Information Center

Presents literature review posing hypothesis: pattern of usage of library materials may be function of social stratification of scholarly activity. Concentration of scholarly productivity, articles on a subject in journals, citations, and library usage and citations as indicators of quality and library usage are discussed. A 115-item bibliography…

Bensman, Stephen J.

1982-01-01

357

Similarity measure to identify users' profiles in web usage mining  

E-print Network

Similarity measure to identify users' profiles in web usage mining Firas Abou Latif -- Nicolas information. It makes the website browsing process even harder. This paper addresses the web usage mining problématique ré- currente. Le Web Usage Mining, qui tente de résoudre ce problème, propose des techniques

Paris-Sud XI, Université de

358

File system usage in Windows NT 4.0  

Microsoft Academic Search

We have performed a study of the usage of the Windows NT File System through long-term kernel tracing. Our goal was to provide a new data point with respect to the 1985 and 1991 trace-based File System studies, to investigate the usage details of the Windows NT file system architecture, and to study the overall statistical behavior of the usage

Werner Vogels

1999-01-01

359

A usage coverage based approach for assessing product family design  

E-print Network

to mass production, then to lean production and finally to mass customization. Mass customization requires1 A usage coverage based approach for assessing product family design Jiliang WANG1 , Bernard analyzed the relations between usage context information and the design of products. A usage coverage model

Paris-Sud XI, Université de

360

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

361

Predictors of Bicycle Helmet Usage Among Seniors  

Microsoft Academic Search

This study identified predictors of bicycle helmet usage in a sample of seniors in Mesa, Arizona. Participants reported: days\\/week bicycling, usual duration, where biking occurred, helmet ownership, bicycle accidents, injuries, and age and gender. Descriptive, non-parametric statistics, and regression analysis were utilized. Seventy-four females and 123 males completed the survey. The mean age was 70.7(7.2) years. Respondents biked a mean

Timothy J. Bungum; Nicole W. Bungum

2003-01-01

362

Reducing Energy Usage in Extractive Distillation  

E-print Network

, .. ~ REDUCING ENERGY USAGE IN,EXTRACTIVE DISTILLATION A. C. Saxena V. A. Bhandari Polysar Limited Sarnia, Ontario, Canada Abstract Butadiene 1:3 is separated from other C. hydrocarbons by extractive distillation in a sieve plate tower... not affect tower stability and the operators h~,e adapted well to the new control strategy. INTRODUCTION For its rubber manufacturing operations at Sarnia, Ontario, Canada, Polysar Limited extracts butadiene 1:3 from a mixed C. hydrocarbon feed...

Saxena, A. C.; Bhandari, V. A.

363

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

364

Web Usage Mining: An Implementation View  

Microsoft Academic Search

\\u000a This paper describes the implementation of Web usage mining for DSpace server of NIT Rourkela. The DSpace log files have been\\u000a preprocessed to convert the data stored in them into a structured format. Thereafter, the general procedures for bot-removal\\u000a and session-identification from a Web log file have been applied with certain modifications pertaining to the DSpace log files.\\u000a Furthermore, analysis

Sathya Babu Korra; Saroj Kumar Panigrahy; Sanjay Kumar Jena

365

Web Usage Mining Proposition de Projet Long  

E-print Network

et d´eveloppement de composants de datamining Une fois que des acc`es `a des contenus web sont ´ecoutWeb Usage Mining Proposition de Projet Long 7 d´ecembre 2007 Contexte et objectifs du projet long la soci´et´e SopraGroup et de l'ENSEEIHT. Le but du projet est l'´etude et le d´eveloppement d

Grigoras, .Romulus

366

Predictors of bicycle helmet usage among seniors.  

PubMed

This study identified predictors of bicycle helmet usage in a sample of seniors in Mesa, Arizona. Participants reported: days/week bicycling, usual duration, where biking occurred, helmet ownership, bicycle accidents, injuries, and age and gender. Descriptive, non-parametric statistics, and regression analysis were utilized. Seventy-four females and 123 males completed the survey. The mean age was 70.7(7.2) years. Respondents biked a mean of 4.9(2.3) days per week and averaged 40.5 (32.5) minutes of riding per day. Eighty-two participants (41.6%) owned bicycle helmets and 55 (27.9%) were observed wearing helmets. Eighty-seven (44.2%) participants biked outside their retirement community and 25 (12.7%) reported an accident within the past year. Chi-square (2, N = 197) = 0.66, p = .72) indicated no differences in of male or female helmet usage. Those who rode outside the retirement communities (chi2(2, 197) = 22.6, p = .001) were more likely to wear helmets than counterparts. Logistic regression found age to be a predictor of bicycle helmet usage. PMID:12713072

Bungum, Timothy J; Bungum, Nicole W

2003-06-01

367

Limitations of the 'ambush hypothesis' at the single-gene scale: what codon biases are to blame?  

PubMed

Ribosomal frameshifting, a translational error, catastrophically alters the amino acid composition of the nascent protein by shifting the reading frame from the intended contiguous trinucleotide reading. Frameshift events waste energy and resources, and peptide products have unpredictable cytotoxic effects. The 'Ambush Hypothesis' (Seligmann and Pollock 2004, DNA Cell Biol 23:701-5) suggests there is a selective pressure favouring the evolution of out-of-frame ('hidden') stop codons. Although this hypothesis has gained empirical support through whole-genome studies, it is presently unknown whether it can be applied at a single-gene scale. Herein, we report such an investigation using the gene, polyketide synthase (PKS), among species of fungi. Contrary to expectation, genes presented with significantly lower number of hidden stop codons than expected in a selection-neutral model (p < 0.0005), suggesting both non-adherence to the ambush hypothesis as well as suppression of hidden stop codon evolution. It is known that there are multiple adaptive considerations determining codon selection during evolution, and that the information-holding potential of the genetic code is finite. We hypothesize that the reason for low hidden stops in PKS genes is due to competing 'codon biases' that are prioritized over the selective pressure favouring the emergence of hidden stops. Future studies of the ambush hypothesis in the context of other drivers of codon bias may allow this hypothesis to be molded into a comprehensive genetic theory that can be integrated within the broader genetic theory of codon bias and applied to the genetic code at any scale of analysis. PMID:25307067

Bertrand, Robert L; Abdel-Hameed, Mona; Sorensen, John L

2014-10-12

368

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

369

Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment  

SciTech Connect

Aminoacyl-tRNA synthetases (aaRSs) ensure faithful translation of mRNA into protein by coupling an amino acid to a set of tRNAs with conserved anticodon sequences. Here, we show that in mitochondria of Saccharomyces cerevisiae, a single aaRS (MST1) recognizes and aminoacylates two natural tRNAs that contain anticodon loops of different size and sequence. Besides a regular ?? with a threonine (Thr) anticodon, MST1 also recognizes an unusual ??, which contains an enlarged anticodon loop and an anticodon triplet that reassigns the CUN codons from leucine to threonine. Our data show that MST1 recognizes the anticodon loop in both tRNAs, but employs distinct recognition mechanisms. The size but not the sequence of the anticodon loop is critical for ?? recognition, whereas the anticodon sequence is essential for aminoacylation of ??. The crystal structure of MST1 reveals that, while lacking the N-terminal editing domain, the enzyme closely resembles the bacterial threonyl-tRNA synthetase (ThrRS). A detailed structural comparison with Escherichia coli ThrRS, which is unable to aminoacylate ??, reveals differences in the anticodon-binding domain that probably allow recognition of the distinct anticodon loops. Finally, our mutational and modeling analyses identify the structural elements in MST1 (e.g., helix {alpha}11) that define tRNA selectivity. Thus, MTS1 exemplifies that a single aaRS can recognize completely divergent anticodon loops of natural isoacceptor tRNAs and that in doing so it facilitates the reassignment of the genetic code in yeast mitochondria.

Ling, Jiqiang; Peterson, Kaitlyn M.; Simonovic, Ivana; Cho, Chris; Soll, Dieter; Simonovic, Miljan (Yale) [Yale; (UIC)

2014-03-12

370

Eight new mtDNA sequences of glass sponges reveal an extensive usage of +1 frameshifting in mitochondrial translation.  

PubMed

Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of +1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate the mechanism of frameshifting, we determined eight new complete or nearly complete mtDNA sequences from glass sponges and examined individual mitochondrial genes from three others. We found nine new instances of single nucleotide insertions in these sequences and analyzed them both comparatively and phylogenetically. The base insertions appear to have been gained and lost repeatedly in hexactinellid mt protein genes, suggesting no functional significance for the frameshifting sites. A high degree of sequence conservation, the presence of unusual tRNAs, and a distinct pattern of codon usage suggest the "out-of-frame pairing" model of translational frameshifting. Additionally, we provide evidence that relaxed selection pressure on glass sponge mtDNA - possibly a result of their low growth rates and deep-water lifestyle - has allowed frameshift insertions to be tolerated for hundreds of millions of years. Our study provides the first example of a phylogenetically diverse and extensive usage of translational frameshifting in animal mitochondrial coding sequences. PMID:24177232

Haen, Karri M; Pett, Walker; Lavrov, Dennis V

2014-02-10

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. PMID:24988409

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

372

Mechanism of PTC124 activity in cell-based luciferase assays of nonsense codon suppression  

PubMed Central

High-throughput screening (HTS) assays used in drug discovery frequently use reporter enzymes such as firefly luciferase (FLuc) as indicators of target activity. An important caveat to consider, however, is that compounds can directly affect the reporter, leading to nonspecific but highly reproducible assay signal modulation. In rare cases, this activity appears counterintuitive; for example, some FLuc inhibitors, acting through posttranslational Fluc reporter stabilization, appear to activate gene expression. Previous efforts to characterize molecules that influence luciferase activity identified a subset of 3,5-diaryl-oxadiazole-containing compounds as FLuc inhibitors. Here, we evaluate a number of compounds with this structural motif for activity against FLuc. One such compound is PTC124 {3-[5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl]benzoic acid}, a molecule originally identified in a cell-based FLuc assay as having nonsense codon suppression activity [Welch EM, et al., Nature (2007) 447:87–91]. We find that the potency of FLuc inhibition for the tested compounds strictly correlates with their activity in a FLuc reporter cell-based nonsense codon assay, with PTC124 emerging as the most potent FLuc inhibitor (IC50 = 7 ± 1 nM). However, these compounds, including PTC124, fail to show nonsense codon suppression activity when Renilla reniformis luciferase (RLuc) is used as a reporter and are inactive against the RLuc enzyme. This suggests that the initial discovery of PTC124 may have been biased by its direct effect on the FLuc reporter, implicating firefly luciferase as a molecular target of PTC124. Our results demonstrate the value of understanding potential interactions between reporter enzymes and chemical compounds and emphasize the importance of implementing the appropriate control assays before interpreting HTS results. PMID:19208811

Auld, Douglas S.; Thorne, Natasha; Maguire, William F.; Inglese, James

2009-01-01

373

P53 Codon 72 polymorphisms: A case-control study of gastric cancer and potential interactions  

PubMed Central

P53 codon 72 polymorphisms have been reported to be associated with cancers of the lung, esophagus and cervix. However, there have been no reports on the interaction of select risk factors and p53 codon 72 polymorphisms in gastric cancer susceptibility. 155 gastric cancer cases and 134 cancer-free controls were enrolled at the Memorial Sloan Kettering Cancer Center (MSKCC) from November 1992 to November 1994. The crude odds ratio (OR1) associated with the (Pro/Pro) polymorphism and the risk of gastric cancer was 1.27 (0.70–2.33). Adjusting for age, sex, race and education (OR2) and further adjusting for BMI, calories, sodium, smoking, vitamin C, fiber, alcohol, fat, and H. pylori status (OR3) did not yield significant results. Significant joint effects were associated with high fat consumption (OR1 = 2.61 (95% CI:1.13–6.06); OR2 = 2.85 (95% CI:1.14–7.15) for total cancers and for proximal tumors (OR1 = 2.56 (95%CI:1.00–6.54)). The low vitamin C intake/high-risk polymorphism group (Pro/Pro) had an OR1 of 4.82 (95% CI: 1.72–13.45) and the OR2 was 6.19 (95% CI: 2.08–18.40) for distal tumors. The point estimates were increased for interaction odds ratios but not statistically significant (OR1 = 4.25 (95% CI: 0.66–27.50); OR2 = 4.73 (95% CI: 0.67–33.43); OR3 = 5.55 (95% CI: 0.66–46.47)). Further studies specifically looking at proximal and distal tumors are required to confirm any potential interaction between the p53 codon 72 polymorphisms an environmental risk, in particular low dietary vitamin C and high fat consumption. PMID:16111803

Sul, James; Yu, Guo-Pei; Lu, Qing-Yi; Lu, Ming-Lan; Setiawan, Veronica Wendy; Wang, Ming-Rong; Guo, Chun Hua; Yu, Shun-Zhang; Mu, Lina; Cai, Lin; Kurtz, Robert C; Zhang, Zuo-Feng

2014-01-01

374

Significance of premature stop codons in env of simian immunodeficiency virus.  

PubMed Central

The location of the translational termination codon for the transmembrane protein (TMP) varies in three infectious molecular clones of simian immunodeficiency virus from macaques (SIVmac). The SIVmac251 and SIVmac142 infectious clones have premature stop signals that differ in location by one codon; transfection of these DNAs into human HUT-78 cells yielded virus with a truncated TMP (28 to 30 kilodaltons [kDa]). The SIVmac239 infectious clone does not have a premature stop codon in its TMP-coding region. Transfection of HUT-78 cells with this clone initially yielded virus with a full-length TMP (41 kDa). At 20 to 30 days posttransfection, SIVmac239 virus with a 41-kDa TMP gradually disappeared coincident with the emergence of a virus with a 28-kDa TMP. Virus production dramatically increased in parallel with the emergence of a virus with a 28-kDa TMP. Sequence analysis of viral DNAs from these cultures showed that premature stop codons arising by point mutation were responsible for the change in size of the TMP with time. A similar selective pressure for truncated forms of TMP was observed when the SIVmac239 clone was transfected into human peripheral blood lymphocytes (PBL). In contrast, no such selective pressure was observed in macaque PBL. When the SIVmac239 clone was transfected into macaque PBL and the resultant virus was serially passaged in macaque PBL, the virus replicated very well and maintained a 41-kDa TMP for 80 days in culture. Macaque monkeys were infected with SIVmac239 having a 28-kDa TMP; virus subsequently recovered from T4-enriched lymphocytes of peripheral blood showed only the 41-kDa form of TMP. These results indicate that the natural form of TMP in SIVmac is the full-length 41-kDa TMP, just as in human immunodeficiency virus type 1. Viruses with truncated forms of TMP appear to result from mutation and selection during propagation in unnatural human cells. Images PMID:2795718

Kodama, T; Wooley, D P; Naidu, Y M; Kestler, H W; Daniel, M D; Li, Y; Desrosiers, R C

1989-01-01

375

On Amino Acid and Codon Assignment in Algebraic Models for the Genetic Code  

NASA Astrophysics Data System (ADS)

We give a list of all possible schemes for performing amino acid and codon assignments in algebraic models for the genetic code, which are consistent with a few simple symmetry principles, in accordance with the spirit of the algebraic approach to the evolution of the genetic code proposed by Hornos and Hornos. Our results are complete in the sense of covering all the algebraic models that arise within this approach, whether based on Lie groups/Lie algebras, on Lie superalgebras or on finite groups.

Antoneli, Fernando; Forger, Michael; Gaviria, Paola A.; Hornos, José Eduardo M.

376

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

377

Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position.  

PubMed

Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex. The Crick wobble rules define, but do not explain, which base pairs are allowed/disallowed at the wobble position of this duplex. This work examines whether the H-bonded configurations of solitary RNA base pairs can in themselves help decide which base pairs are allowed at the wobble position during codon-anticodon pairing. Taking the purine-type bases guanine, hypoxanthine, queuine and adenine as anticodon wobble bases, H-bonded pairing energies and optimized configurations of numerous RNA base pairs are calculated in gas and modeled aqueous phase at the B3LYP/6-31 G(d,p) level. Calculated descriptors of alignment of these solitary base pairs are able to screen between allowed and disallowed base pairs for all cases studied here, except two cases which invoke base-sugar interactions in the codon wobble nucleoside. The exclusion of adenine from the anticodon wobble position cannot be explained on the basis of pairing facility or base pair geometry. These DFT results thus account for the specificity and degeneracy of the genetic code for all cases involving guanine, hypoxanthine and queuine as anticodon wobble bases. PMID:22399149

Das, Gunajyoti; Lyngdoh, R H Duncan

2012-08-01

378

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, S B L; Hing, W C; Tung, S Y; Park, T

2014-07-01

379

Nucleotide modifications and tRNA anticodon–mRNA codon interactions on the ribosome  

PubMed Central

We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo5U34 and m6A37. In tRNAVal, these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural analysis of the ribosomal decoding center. No prestructuring effect on the tRNA anticodon stem–loop from the two modifications could be observed, but we identified two mechanisms that may contribute to the expanded decoding capability by the modifications: The further reach of the cmo5U34 allows an alternative outer conformation to be formed for the noncognate base pairs, and the modification results in increased contacts between tRNA, mRNA, and the ribosome. PMID:22028366

Allnér, Olof; Nilsson, Lennart

2011-01-01

380

Structural insights into eRF3 and stop codon recognition by eRF1  

PubMed Central

Eukaryotic translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act cooperatively to ensure efficient stop codon recognition and fast polypeptide release. The crystal structures of human and Schizosaccharomyces pombe full-length eRF1 in complex with eRF3 lacking the GTPase domain revealed details of the interaction between these two factors and marked conformational changes in eRF1 that occur upon binding to eRF3, leading eRF1 to resemble a tRNA molecule. Small-angle X-ray scattering analysis of the eRF1/eRF3/GTP complex suggested that eRF1's M domain contacts eRF3's GTPase domain. Consistently, mutation of Arg192, which is predicted to come in close contact with the switch regions of eRF3, revealed its important role for eRF1's stimulatory effect on eRF3's GTPase activity. An ATP molecule used as a crystallization additive was bound in eRF1's putative decoding area. Mutational analysis of the ATP-binding site shed light on the mechanism of stop codon recognition by eRF1. PMID:19417105

Cheng, Zhihong; Saito, Kazuki; Pisarev, Andrey V.; Wada, Miki; Pisareva, Vera P.; Pestova, Tatyana V.; Gajda, Michal; Round, Adam; Kong, Chunguang; Lim, Mengkiat; Nakamura, Yoshikazu; Svergun, Dmitri I.; Ito, Koichi; Song, Haiwei

2009-01-01

381

Codon-optimized Luciola italica luciferase variants for mammalian gene expression in culture and in vivo.  

PubMed

Luciferases have proven to be useful tools in advancing our understanding of biologic processes. Having a multitude of bioluminescent reporters with different properties is highly desirable. We characterized codon-optimized thermostable green- and red-emitting luciferase variants from the Italian firefly Luciola italica for mammalian gene expression in culture and in vivo. Using lentivirus vectors to deliver and stably express these luciferases in mammalian cells, we showed that both variants displayed similar levels of activity and protein half-lives as well as similar light emission kinetics and higher stability compared to the North American firefly luciferase. Further, we characterized the red-shifted variant for in vivo bioluminescence imaging. Intramuscular injection of tumor cells stably expressing this variant into nude mice yielded a robust luciferase activity. Light emission peaked at 10 minutes post-d-luciferin injection and retained > 60% of signal at 1 hour. Similarly, luciferase activity from intracranially injected glioma cells expressing the red-shifted variant was readily detected and used as a marker to monitor tumor growth over time. Overall, our characterization of these codon-optimized luciferases lays the groundwork for their further use as bioluminescent reporters in mammalian cells. PMID:22418023

Maguire, Casey A; van der Mijn, Johannes C; Degeling, Marja H; Morse, Danielle; Tannous, Bakhos A

2012-02-01

382

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

383

Deriving Framework Usages Based on Behavioral Models  

NASA Astrophysics Data System (ADS)

One of the critical issue in framework-based software development is a huge introduction cost caused by technical gap between developers and users of frameworks. This paper proposes a technique for deriving framework usages to implement a given requirements specification. By using the derived usages, the users can use the frameworks without understanding the framework in detail. Requirements specifications which describe definite behavioral requirements cannot be related to frameworks in as-is since the frameworks do not have definite control structure so that the users can customize them to suit given requirements specifications. To cope with this issue, a new technique based on satisfiability problems (SAT) is employed to derive the control structures of the framework model. In the proposed technique, requirements specifications and frameworks are modeled based on Labeled Transition Systems (LTSs) with branch conditions represented by predicates. Truth assignments of the branch conditions in the framework models are not given initially for representing the customizable control structure. The derivation of truth assignments of the branch conditions is regarded as the SAT by assuming relations between termination states of the requirements specification model and ones of the framework model. This derivation technique is incorporated into a technique we have proposed previously for relating actions of requirements specifications to ones of frameworks. Furthermore, this paper discuss a case study of typical use cases in e-commerce systems.

Zenmyo, Teruyoshi; Kobayashi, Takashi; Saeki, Motoshi

384

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

385

Maternal Control Strategies, Maternal Language Usage and Children's Language Usage at Two Years  

ERIC Educational Resources Information Center

The present study determined whether parenting style, defined by control strategies varying in power-assertion mediated the established relation between maternal language usage (grammar and semantics) and child language (grammar, semantics and pragmatics) during toddlerhood (n = 60). Based upon their use of control strategies mothers were…

Taylor, Nicole; Donovan, Wilberta; Miles, Sally; Leavitt, Lewis

2009-01-01

386

Detection of codon 12 point mutations of K-ras gene from mouse lung adenocarcinoma by "enriched" PCR.  

SciTech Connect

PURPOSE: Recent studies have shown that chemical carcinogens induce a high frequency of point mutations in the K-ras oncogene from mouse lung tumors at codons 12, 13 and 61. These experiments were performed to identify K-ras mutations in tissues from control and radiation-exposed mice. MATERIALS AND METHODS: By modifying the technique of the 'enriched' polymerase chain reaction (PCR), it was possible to detect point mutations at codon 12 of the K-ras oncogene from 25-year-old paraffin-embedded normal lungs and lung adenocarcinomas from mice exposed to radiation. Together, a total of 120 lung tissues were screened for point mutations at codon 12 of the K-ras oncogene in this study. RESULTS: A significant increase in K-ras codon 12 point mutations was observed in the normal lungs from mice exposed to 24 once-weekly neutron irradiations (100%), compared with normal lungs from mice with sham-irradiation (50%) (p<0.05). Lung adenocarcinomas from mice receiving 24 once-weekly neutron irradiations also had a significantly higher frequency of K-ras codon 12 point mutations (100%) than the lung adenocarcinomas of mice receiving 24 or 60 once-weekly gamma-ray irradiations (50%), but the higher frequency was not significantly different from that in spontaneous lung adenocarcinomas from mice (75%; p > 0.05). The validity of the technique was confirmed by sequencing two of the mutants. In doing so, a K-ras 13(Asp) point mutation was observed. CONCLUSIONS: The data suggest that high-linear energy transfer (LET) neutron radiation was more effective than low-LET gamma-rays in inducing K-ras point mutations at codon 12 in the lungs of B6CF1 mice.

Zhang, Y.; Woloschak, G. E.; Center for Mechanistic Biology and Biotechnology

1998-07-01

387

Initiation codon selection is accomplished by a scanning mechanism without crucial initiation factors in Sindbis virus subgenomic mRNA.  

PubMed

Translation initiation of alphavirus subgenomic mRNA (sgmRNA) can occur in the absence of several initiation factors (eIFs) in infected cells; however, the precise translation mechanism is still poorly understood. In this study, we have examined the mechanism of initiation and AUG selection in Sindbis virus (SINV) sgmRNA. Our present findings suggest that sgmRNA is translated via a scanning mechanism, since the presence of a hairpin structure before the initiation codon hampers protein synthesis directed by this mRNA. In addition, translation is partially recovered when an in-frame AUG codon is placed upstream of this hairpin. This scanning process takes place without the participation of eIF4A and active eIF2. These results, combined with our findings through modifying the SINV sgmRNA leader sequence, do not support the possibility of a direct initiation from the start codon without previous scanning, or a shunting mechanism. Moreover, studies carried out with sgmRNAs containing two alternative AUG codons within a good context for translation reveal differences in AUG selection which are dependent on the cellular context and the phosphorylation state of eIF2?. Thus, initiation at the additional AUG is strictly dependent on active eIF2, whereas the genuine AUG codon can start translation following eIF2? inactivation. Collectively, our results suggest that SINV sgmRNA is translated by a scanning mechanism without the potential participation of crucial eIFs. A model is presented that explains the mechanism of initiation of mRNAs bearing two alternative initiation codons. PMID:25404563

Garcia-Moreno, Manuel; Sanz, Miguel Angel; Carrasco, Luis

2015-01-01

388

Human Upf Proteins Target an mRNA for Nonsense-Mediated Decay When Bound Downstream of a Termination Codon  

Microsoft Academic Search

Nonsense-mediated decay (NMD) rids eukaryotic cells of aberrant mRNAs containing premature termination codons. These are discriminated from true termination codons by downstream cis-elements, such as exon–exon junctions. We describe three novel human proteins involved in NMD, hUpf2, hUpf3a, and hUpf3b. While in HeLa cell extracts these proteins are complexed with hUpf1, in intact cells hUpf3a and hUpf3b are nucleocytoplasmic shuttling

Jens Lykke-Andersen; Mei-Di Shu; Joan A. Steitz

2000-01-01

389

Assistive devices: usage in patients with rheumatoid arthritis  

Microsoft Academic Search

We describe the usage of various assistive devices and identify factors associated with usage in patients with rheumatoid\\u000a arthritis (RA). A cross-sectional, multicentre study was performed in three outpatient rheumatology clinics in the Netherlands.\\u000a Two hundred forty patients with RA participated in the study. The main measures were questionnaires and a semi-structured\\u000a interview regarding the possession and usage of 21

I. G. de Boer; A. J. Peeters; H. K. Ronday; B. J. A. Mertens; T. W. J. Huizinga; T. P. M. Vliet Vlieland

2009-01-01

390

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

391

The AUG start codon of the Saccharomyces cerevisiae NFS1 gene can be substituted for by UUG without increased initiation of translation at  

E-print Network

increased initiation of translation at downstream codons Ju¨ rgen H. Nett, Jacques Kessl, Tina Wenz of the site for initiation of translation for the Saccharomyces cerevisiae NFS1 gene was examined using mRNA was translated in vitro using a reticulocyte system, initiation from the mutated codon

Trumpower, Bernard L.

392

Usage-Oriented Topic Maps Building Approach  

NASA Astrophysics Data System (ADS)

In this paper, we present a collaborative and incremental construction approach of multilingual Topic Maps based on enrichment and merging techniques. In recent years, several Topic Map building approaches have been proposed endowed with different characteristics. Generally, they are dedicated to particular data types like text, semi-structured data, relational data, etc. We note also that most of these approaches take as input monolingual documents to build the Topic Map. The problem is that the large majority of resources available today are written in various languages, and these resources could be relevant even to non-native speakers. Thus, our work is driven towards a collaborative and incremental method for Topic Map construction from textual documents available in different languages. To enrich the Topic Map, we take as input a domain thesaurus and we propose also to explore the Topic Map usage which means available potential questions related to the source documents.

Ellouze, Nebrasse; Lammari, Nadira; Métais, Elisabeth; Ben Ahmed, Mohamed

393

Mutation of the prion protein gene at codon 208 in familial Creutzfeldt-Jakob disease.  

PubMed

Four point mutations and one insertion within the prion protein (PrP) gene have been tightly linked to the development of inherited prion disease. We developed a denaturing gradient gel electrophoresis system that allowed us to screen the entire open reading frame of the PrP gene. Using this system, we found a new mutation of the PrP gene in a patient with pathologically confirmed Creutzfeldt-Jakob disease and a negative family history for dementia. DNA sequencing revealed an adenine substitution for guanine at the second position of codon 208, which results in the nonconservative substitution of histidine for arginine. The same PrP mutation was identified in another younger member of the pedigree but was not present in more than 200 alleles tested. Such findings suggest that the frequency of inherited prion disease might be higher than ascertained by clinical history alone. PMID:8909447

Mastrianni, J A; Iannicola, C; Myers, R M; DeArmond, S; Prusiner, S B

1996-11-01

394

Multiple start codons and phosphorylation result in discrete Rad52 protein species  

PubMed Central

The sequence of the Saccharomyces cerevisiae RAD52 gene contains five potential translation start sites and protein-blot analysis typically detects multiple Rad52 species with different electrophoretic mobilities. Here we define the gene products encoded by RAD52. We show that the multiple Rad52 protein species are due to promiscuous choice of start codons as well as post-translational modification. Specifically, Rad52 is phosphorylated both in a cell cycle-independent and in a cell cycle-dependent manner. Furthermore, phosphorylation is dependent on the presence of the Rad52 C terminus, but not dependent on its interaction with Rad51. We also show that the Rad52 protein can be translated from the last three start sites and expression from any one of them is sufficient for spontaneous recombination and the repair of gamma-ray-induced double-strand breaks. PMID:16707661

de Mayolo, Adriana Antúnez; Lisby, Michael; Erdeniz, Naz; Thybo, Tanja; Mortensen, Uffe H.; Rothstein, Rodney

2006-01-01

395

Distinguishing Regional from Within-Codon Rate Heterogeneity in DNA Sequence Alignments  

NASA Astrophysics Data System (ADS)

We present an improved phylogenetic factorial hidden Markov model (FHMM) for detecting two types of mosaic structures in DNA sequence alignments, related to (1) recombination and (2) rate heterogeneity. The focus of the present work is on improving the modelling of the latter aspect. Earlier papers have modelled different degrees of rate heterogeneity with separate hidden states of the FHMM. This approach fails to appreciate the intrinsic difference between two types of rate heterogeneity: long-range regional effects, which are potentially related to differences in the selective pressure, and the short-term periodic patterns within the codons, which merely capture the signature of the genetic code. We propose an improved model that explicitly distinguishes between these two effects, and we assess its performance on a set of simulated DNA sequence alignments.

Mantzaris, Alexander V.; Husmeier, Dirk

396

Functional studies of a germ-line polymorphism at codon 47 within the p53 gene  

SciTech Connect

A rare germ-line polymorphism in codon 47 of the p53 gene replaces the wild-type proline (CCG) with a serine (TCG). Restriction analysis of 101 human samples revealed the frequency of the rare allele to be 0% (n = 69) in Causasians and 4.7% (3/64, n = 32) among African-Americans. To investigate the consequence of this amino acid substitution, a cDNA construct (p53 mut47ser) containing the mutation was introduced into a lung adenocarcinoma cell line (Calu-6) that does not express p53. A growth suppression similar to that obtained after introduction of a wild-type p53 cDNA construct was observed, in contrast to the result obtained by introduction of p53 mut143ala. Furthermore, expression of neither p53 mut47ser nor wild-type p53 was tolerated by growing cells. In transient expression assays, both mut47ser and wild-type p53 activated the expression of a reporter gene linked to a p53 binding sequence (PG13-CAT) and inhibited the expression of the luciferase gene under the control of the Rous sarcoma virus promoter (RSVluc). In the same assay, mut143ala did not activate the expression of PG13-CAT and produced only a slight inhibitory effect on RSVluc. These findings indicate that the p53 variant with a serine at codon 47 should be considered as a rare germ-line polymorphism that does not alter the growth-suppression activity of p53. 30 refs., 3 figs., 3 tabs.

Felley-Bosco, E.; Weston, A.; Cawley, H.M.; Bennett, W.P.; Harris, C.C.

1993-09-01

397

Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants.  

PubMed

Surfactant protein A (SP-A), a molecule with roles in lung innate immunity and surfactant-related functions, is encoded by two genes in humans: SFTPA1 (SP-A1) and SFTPA2 (SP-A2). The mRNAs from these genes differ in their 5'-untranslated regions (5'-UTR) due to differential splicing. The 5'-UTR variant ACD' is exclusively found in transcripts of SP-A1, but not in those of SP-A2. Its unique exon C contains two upstream AUG codons (uAUGs) that may affect SP-A1 translation efficiency. The first uAUG (u1) is in frame with the primary start codon (p), but the second one (u2) is not. The purpose of this study was to assess the impact of uAUGs on SP-A1 expression. We employed RT-qPCR to determine the presence of exon C-containing SP-A1 transcripts in human RNA samples. We also used in vitro techniques including mutagenesis, reporter assays, and toeprinting analysis, as well as in silico analyses to determine the role of uAUGs. Exon C-containing mRNA is present in most human lung tissue samples and its expression can, under certain conditions, be regulated by factors such as dexamethasone or endotoxin. Mutating uAUGs resulted in increased luciferase activity. The mature protein size was not affected by the uAUGs, as shown by a combination of toeprint and in silico analysis for Kozak sequence, secondary structure, and signal peptide and in vitro translation in the presence of microsomes. In conclusion, alternative splicing may introduce uAUGs in SP-A1 transcripts, which in turn negatively affect SP-A1 translation, possibly affecting SP-A1/SP-A2 ratio, with potential for clinical implication. PMID:25326576

Tsotakos, Nikolaos; Silveyra, Patricia; Lin, Zhenwu; Thomas, Neal; Vaid, Mudit; Floros, Joanna

2015-01-01

398

Identification of a new ? chain variant at codons 22-25 (-9 nts) using the Sebia capillarys 2 electrophoresis system.  

PubMed

We have identified a new ? chain hemoglobin (Hb) variant in a Chinese family. Sequencing of the amplified ?2-globin gene revealed a 9 nucleotide (nt) deletion (-C GAG TAT GG) at codons 22-25, which results in a predicted ?-globin chain that is missing amino acid residues 23-25 (Glu-Tyr-Gly) and the formation of Hb Zhanjiang. PMID:21417576

Liao, Can; Zhou, Jian-Ying; Xie, Xing-Mei; Liu, Ying-Na; Chen, Li-He; Li, Dong-Zhi

2011-01-01

399

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

Microsoft Academic Search

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

Hiroshi Akashi; Piyush Goel; Anoop John; Justin Fay

2007-01-01

400

On the codon assignment of chain termination signals and the minimization of the effects of frameshift mutations  

E-print Network

It has been suggested that the minimization of the probability for lethal mutations is a major constraint shaping the genetic code, with the finding that the genetic code is highly protective against transition mutations. Here, we show that recent data on polymerase-induced frameshifts provide a rationale for the codon assignment of chain termination signals (CTS).

Jestin, J L

1997-01-01

401

Mutations of codon 918 in the RET proto-oncogene correlate to poor prognosis in sporadic medullary thyroid carcinomas  

SciTech Connect

The hereditary multiple endocrine neoplasia syndromes types 2A and B (MEN 2A and B) were recently linked to germline mutations in the RET proto-oncogene, altering one of five cysteine residues in exon 10 or 11 (MEN 2A), or substituting a methionine for a threonine at codon 918 in exon 16 (MEN 2B). The latter mutation also occurs somatically in some sporadic medullary thyroid carcinomas (MTC), and has in a previous study been correlated with a less favorable clinical outcome. In the present study, 46 MTCs were selected for investigation of the codon 918 mutation. The mutation was found in 29 tumors (63%), and was significantly correlated with a poor outcome, with regard to distant metastasis or tumor recurrence (p<10{sup 4}). Two tumors showed multifocal growth and C-cell hyperplasia, and these patients were therefore also investigated for germline mutations in exons 10, 11 and 16. The codon 918 mutation was found only in the tumors, thus of somatic origin. The RET codon 918 mutation may have prognostic impact, and therefore preoperative assessment may influence decision-making in the treatment of patients suffering from MTC. 13 refs., 1 fig., 1 tab.

Zedenius, J.; Svensson, A.; Baeckdahl, M.; Wallin, G. [Karolinska Hospital, Stockholm (Sweden)] [and others] [Karolinska Hospital, Stockholm (Sweden); and others

1995-10-01

402

A common dominant TLR5 stop codon polymorphism abolishes flagellin signaling and is associated with susceptibility to legionnaires' disease  

Microsoft Academic Search

Although Toll-like receptors (TLRs) are critical mediators of the immune response to pathogens, the influence of polymorphisms in this gene family on human susceptibility to infection is poorly understood. We demonstrated recently that TLR5 recognizes flagellin, a potent inflam- matory stimulus present in the flagellar structure of many bacteria. Here, we show that a common stop codon polymorphism in the

Thomas R. Hawn; Annelies Verbon; Kamilla D. Lettinga; Lue Ping Zhao; Shuying Sue Li; Richard J. Laws; Shawn J. Skerrett; Bruce Beutler; Lea Schroeder; Alex Nachman; Adrian Ozinsky; Kelly D. Smith; Alan Aderem

2003-01-01

403

Detection of human papillomavirus DNA and p53 codon 72 polymorphism in prostate carcinomas of patients from Argentina  

PubMed Central

Background Infections with high-risk human papillomaviruses (HPVs), causatively linked to cervical cancer, might also play a role in the development of prostate cancer. Furthermore, the polymorphism at codon 72 (encoding either arginine or proline) of the p53 tumor-suppressor gene is discussed as a possible determinant for cancer risk. The HPV E6 oncoprotein induces degradation of the p53 protein. The aim of this study was to analyse prostate carcinomas and hyperplasias of patients from Argentina for the presence of HPV DNA and the p53 codon 72 polymorphism genotype. Methods HPV DNA detection and typing were done by consensus L1 and type-specific PCR assays, respectively, and Southern blot hybridizations. Genotyping of p53 codon 72 polymorphism was performed both by allele specific primer PCRs and PCR-RFLP (Bsh1236I). Fischer's test with Woolf's approximation was used for statistical analysis. Results HPV DNA was detected in 17 out of 41 (41.5 %) carcinoma samples, whereas all 30 hyperplasia samples were HPV-negative. Differences in p53 codon 72 allelic frequencies were not observed, neither between carcinomas and hyperplasias nor between HPV-positive and HPV-negative carcinomas. Conclusion These results indicate that the p53 genotype is probably not a risk factor for prostate cancer, and that HPV infections could be associated with at least a subset of prostate carcinomas. PMID:16307686

Leiros, Gustavo J; Galliano, Silvia R; Sember, Mario E; Kahn, Tomas; Schwarz, Elisabeth; Eiguchi, Kumiko

2005-01-01

404

Association between genotypes at codon 171 and 136 of the prion protein gene and production traits in market lambs  

Technology Transfer Automated Retrieval System (TEKTRAN)

Scrapie is a transmissible spongiform encephalopathy of small ruminants for which infection is genetically controlled by commonly occurring polymorphisms in the gene encoding the normal prion protein precursor gene Prnp. Selection of sheep with the Prnp allele encoding arginine at codon 171 is rema...

405

The other codons: Nirenberg and the genetic code, 2D animationSite: DNA Interactive (www.dnai.org)  

NSDL National Science Digital Library

After the easy codons, exact triplets had to be made in order to finish deciphering the rest. Marshall Nirenberg and a group of scientists including Maxine Singer, Marianne Grunberg-Manago, Phil Leder were involved in this process. Har Gobind Khorana also worked on this problem.

2008-10-06

406

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

407

Elimination of redundant and stop codons during the chemical synthesis of degenerate oligonucleotides. Combinatorial testing on the chromophore region of the red fluorescent protein mKate.  

PubMed

Although some strategies have been reported for the elimination of stop and redundant codons during the chemical synthesis of degenerate oligonucleotides, incorporating an expensive cocktail of 20 trimer-phosphoramidites is currently a commonly employed and straightforward approach. As an alternative option, we describe here a cheaper strategy based on standard monomer-phosphoramidites and a simplified resin-splitting procedure. The accurate division of the resin, containing the growing oligonucleotide, into four columns represents the key step in this approach. The synthesis of the degenerate codon NDT in column 1, loaded with 60% of the resin, produces 12 codons, while a degenerate codon VMA in column 2, loaded with 30% of the resin, produces 6 codons. Codons ATG and TGG, independently synthesized in columns 3 and 4, respectively, and loaded with 5% each, completes the 20 different codons. The experimental frequency of each mutant codon in the library was assessed by randomizing 12 contiguous codons that encode for amino acids located in the chromophore region of the enhanced red fluorescent protein mKate-S158A. Furthermore, randomization of three contiguous codons that encode for the amino acids Phe62, Met63, and Tyr64, which are equivalent to Phe64, Ser65, and Tyr66 in GFP, gave rise to some red and golden yellow fluorescent mutants displaying interesting phenotypes and spectroscopic properties. The absorption and emission spectra of two of these mutants also suggested that the complete maturation of the red and golden yellow chromophores in mKate proceeds via the formation of a green-type chromophore and a cyan-type chromophore, respectively. PMID:23654278

Gaytán, Paul; Roldán-Salgado, Abigail

2013-08-16

408

A Multilingual Usage Consultation Tool Based on Internet Searching  

E-print Network

]: Miscellaneous General Terms Design Keywords Usage consultation, question answering, text mining. ABSTRACT We which verb is used with "jet lag" in English, he can simply type "jet lag" into a search en- gine and obtain usages such as "avoid jet lag" and "recover from jet lag" among various snippets of information

Nakagawa, Hiroshi

409

Understanding Mobile App Usage Patterns Using In-App Advertisements  

E-print Network

Understanding Mobile App Usage Patterns Using In-App Advertisements Alok Tongaonkar1 , Shuaifu Dai2. This has resulted in a growing need of the operators to understand the usage patterns of the mobile apps present a novel way of identifying Android apps in network traces using mobile in-app advertisements. Our

Song, Dawn

410

Furman University Justification of Business Usage of Cell Phone  

E-print Network

Furman University Justification of Business Usage of Cell Phone 1 Name/mo) $60.00 Unlimited $70.00 Texts (Optional) 1000/mo. $10.00 Data (Smart phone only) 2GB $30.00 4GB w Justification of Business Usage of Cell Phone 2 The type of cell phone coverage must be reasonably

411

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

412

ColourVis: exploring colour usage in paintings over time  

Microsoft Academic Search

The colour palette of painters over history has been of interest to many, including: art historians, archeologists, and art lovers. Colour usage in art changes from culture to culture and season to season and is often thought of as reflecting or inspiring mood and ambience. We present ColourVis: a visualization that supports exploration of colour usage in digital images. In

Jonathan Haber; Sean Lynch; Sheelagh Carpendale

2011-01-01

413

KOINOTITES: A Web Usage Mining Tool for Personalization  

E-print Network

KOINOTITES: A Web Usage Mining Tool for Personalization Dimitrios Pierrakos Inst. of Informatics@iit.demokritos.gr SUMMARY This paper presents the Web Usage Mining system KOINOTITES, which uses data mining techniques for the construction of user communities on the Web. User communities model groups of visitors in a Web site, who have

Paliouras, George

414

Software Dependability Evaluation Based on Markov Usage Models  

E-print Network

Software Dependability Evaluation Based on Markov Usage Models Walter J. Gutjahr Department for computing optimal state transition probabilities for software tests, based on a Markov usage model; this distribution may also be used in the more general context of structural statistical testing of software

Gutjahr, Walter

415

Personalized Power Saving Profiles Generation Analyzing Smart Device Usage Patterns  

E-print Network

-app advertisements consume up to 30% of the total power consumed by the application [1]. The Android operating system power saving profiles by analyzing individual usage patterns. The client is an Android app named "Power Monitor" running on the Android devices. It periodically records usage information from the devices

Gesbert, David

416

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

417

(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

418

A Genetic Algorithm Approach to Focused Software Usage Testing  

E-print Network

A Genetic Algorithm Approach to Focused Software Usage Testing Robert M. Patton, Annie S. Wu Orlando, FL, U.S.A. ABSTRACT Because software system testing typically consists of only a very small the test results from a limited amount of testing based on high-level usage models. It can also be very

Wu, Annie S.

419

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.

420

Kiwi: A Multilingual Usage Consultation Tool based on Internet Searching  

Microsoft Academic Search

We present a usage consultation tool based on Internet searching. When a user enters a string of words that he wants to find the usage for, the system sends a query to the search engine to obtain a corpus about the string. The corpus is statistically analyzed and results are displayed. As the system uses neither language-dependent analysis nor initial

Kumiko Tanaka-Ishii; Masato Yamamoto; Hiroshi Nakagawa

2003-01-01

421

Improving API Usage through Automatic Detection of Redundant Code  

E-print Network

Improving API Usage through Automatic Detection of Redundant Code David Kawrykow and Martin P Programming Interfaces (APIs). We have observed many cases where APIs are used in ways that are not the most effective. We developed a technique and tool support to automatically detect such patterns of API usage

Robillard, Martin

422

Detecting Inefficient API Usage David Kawrykow and Martin P. Robillard  

E-print Network

Detecting Inefficient API Usage David Kawrykow and Martin P. Robillard School of Computer Science (APIs). We have observed many cases where APIs are used in ways that are not efficient. We developed a technique to automatically detect inefficient API usage in software projects. The main hypothesis underlying

Robillard, Martin

423

What should we measure? Conceptualizing usage in health information exchange  

PubMed Central

Under the provisions of the Health Information Technology for Economic & Clinical Health act providers need to demonstrate their ‘meaningful use’ of electronic health record systems' health information exchange (HIE) capability. HIE usage is not a simple construct, but the choice of its measurement must attend to the users, context, and objectives of the system being examined. This review examined how usage is reported in the existing literature and also what conceptualizations of usage might best reflect the nature and objectives of HIE. While existing literature on HIE usage included a diverse set of measures, most were theoretically weak, did not attend to the interplay of measure, level of analysis and architectural strategy, and did not reflect how HIE usage affected the actual process of care. Attention to these issues will provide greater insight into the effects of previously inaccessible information on medical decision-making and the process of care. PMID:20442148

Jasperson, Jon

2010-01-01

424

Chemistry & Biology, Vol. 9, 237244, February, 2002, 2002 Elsevier Science Ltd. All rights reserved. PII S1074-5521(02)00094-7 Exploring the Limits of Codon and Anticodon Size  

E-print Network

reserved. PII S1074-5521(02)00094-7 Exploring the Limits of Codon and Anticodon Size tRNA species that have Department of Chemistry University of California ture, underused codons for which the cognate tRNA is in low abundance ("hungry" codons), and upstreamBerkeley, California 94720 3 Genomics Institute Shine

Magliery, Thomas J.

425

Web-based pathology practice examination usage  

PubMed Central

Context: General and subject specific practice examinations for students in health sciences studying pathology were placed onto a free public internet web site entitled web path and were accessed four clicks from the home web site menu. Subjects and Methods: Multiple choice questions were coded into. html files with JavaScript functions for web browser viewing in a timed format. A Perl programming language script with common gateway interface for web page forms scored examinations and placed results into a log file on an internet computer server. The four general review examinations of 30 questions each could be completed in up to 30 min. The 17 subject specific examinations of 10 questions each with accompanying images could be completed in up to 15 min each. The results of scores and user educational field of study from log files were compiled from June 2006 to January 2014. Results: The four general review examinations had 31,639 accesses with completion of all questions, for a completion rate of 54% and average score of 75%. A score of 100% was achieved by 7% of users, ?90% by 21%, and ?50% score by 95% of users. In top to bottom web page menu order, review examination usage was 44%, 24%, 17%, and 15% of all accessions. The 17 subject specific examinations had 103,028 completions, with completion rate 73% and average score 74%. Scoring at 100% was 20% overall, ?90% by 37%, and ?50% score by 90% of users. The first three menu items on the web page accounted for 12.6%, 10.0%, and 8.2% of all completions, and the bottom three accounted for no more than 2.2% each. Conclusions: Completion rates were higher for shorter 10 questions subject examinations. Users identifying themselves as MD/DO scored higher than other users, averaging 75%. Usage was higher for examinations at the top of the web page menu. Scores achieved suggest that a cohort of serious users fully completing the examinations had sufficient preparation to use them to support their pathology education. PMID:25337431

Klatt, Edward C.

2014-01-01

426

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

427

Monitoring seat feature usage among wheelchair users.  

PubMed

To help manage pressure ulcers and adjust posture, powered wheelchairs can be equipped with seat tilt and backrest recline features. Clinicians usually prescribe these features for wheelchair users who are vulnerable to pressure sores or have difficulty changing postures, but little data has been collected to determine whether or not, and what extent, these features are used. This study examined how wheelchair users use power wheelchair seat features such as seat tilt, backrest recline, and seat elevation, during typical daily activities. A Seat Feature Data Logger (SFDL) was attached to 11 subject's wheelchairs for 10-14 days to gather data regarding daily usage of these features. The results showed that while subjects did not always use large angles of tilt and recline as many clinicians recommend, these features were used frequently and their use resulted in lower peak pressures. The information collected by the SFDL allows for a novel and quantitative description of the effectiveness and use of power seat features, and can also be used as a clinical compliance tool. PMID:18002970

Ding, Dan; Cooper, Rory A; Cooper, Rosemarie; Kelleher, Annmarie

2007-01-01

428

Mass spectrometry approach and ELISA reveal the effect of codon optimization on N-linked glycosylation of HIV-1 gp120.  

PubMed

The genes encoding many viral proteins such as HIV-1 envelope glycoprotein gp120 have a tendency for codons that are poorly used by the human genome. Why these codons are frequently present in the HIV genome is not known. The presence of these codons limits expression of HIV-1 gp120 for biochemical studies. The poor codons are replaced by synonymous codons that are frequently present in the highly expressed human genes to overexpress this protein. Whether this codon optimization affects functional properties of gp120 such as its N-linked glycosylation is unknown. We applied a bottom-up mass-spectrometry-based workflow for the direct measurement of deglycosylated and unglycosylated peptides with putative N-linked glycosylation sites, that is, NxS/T motifs. Using this mass-spectrometry approach in combination with ELISA, it is found that codon optimization significantly reduces the frequency with which the dolichol pyrophosphate-linked oligosaccharide is added by the catalytic subunits of oligosaccharide transferase complex to the glycosylation sites. This reduction affects binding of glycan-dependent broadly neutralizing antibodies. These data are essential for biochemical studies of gp120 and successful development of a vaccine against HIV-1. Furthermore, they demonstrate a mass-spectrometry approach for studying the site-specific N-linked glycosylation efficiency of glycoproteins. PMID:25285362

Honarmand Ebrahimi, Kourosh; West, Graham M; Flefil, Ricardo

2014-12-01

429

Student Drug Usage and Self-Alienation.  

ERIC Educational Resources Information Center

Utilizing responses (a self administered, 15 item questionnaire) of a rural northeastern New England sample of junior high, senior high, and college students, correlation between legal and illegal drug use and perceived self-alienation was examined. Comparison was also made between users and nonusers. Legal users were defined as those who made at…

Fischler, Michael L.

430

Bioinformatic, structural, and functional analyses support release factor-like MTRF1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria  

PubMed Central

Vertebrate mitochondria use stop codons UAA and UAG decoded by the release factor (RF) MTRF1L and two reassigned arginine codons, AGA and AGG. A second highly conserved RF-like factor, MTRF1, which evolved from a gene duplication of an ancestral mitochondrial RF1 and not a RF2, is a good candidate for recognizing the nonstandard codons. MTRF1 differs from other RFs by having insertions in the two external loops important for stop codon recognition (tip of helix ?5 and recognition loop) and by having key substitutions that are involved in stop codon interactions in eubacterial RF/ribosome structures. These changes may allow recognition of the larger purine base in the first position of AGA/G and, uniquely for RFs, only of G at position 2. In contrast, residues that support A and G recognition in the third position in RF1 are conserved as would be required for recognition of AGA and AGG. Since an assay with vertebrate mitochondrial ribosomes has not been established, we modified Escherichia coli RF1 at the helix ?5 and recognition loop regions to mimic MTRF1. There was loss of peptidyl-tRNA hydrolysis activity with standard stop codons beginning with U (e.g., UAG), but a gain of activity with codons beginning with A (AAG in particular). A lower level of activity with AGA could be enhanced by solvent modification. These observations imply that MTRF1 has the characteristics to recognize A as the first base of a stop codon as would be required to decode the nonstandard codons AGA and AGG. PMID:20421313

Young, David J.; Edgar, Christina D.; Murphy, Jennifer; Fredebohm, Johannes; Poole, Elizabeth S.; Tate, Warren P.

2010-01-01

431

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

432

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

433

Comparisons of infant Escherichia coli isolates link genomic profiles with adaptation to the ecological niche  

PubMed Central

Background Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli. An important step toward achieving a more complete understanding of E.coli biology entails elucidating relationships between gene content and adaptation to the ecological niche. Results Here, we present genome comparisons of 16 E.coli strains that represent commensals and pathogens isolated from infants during a specific time period in Trondheim, Norway. Using differential gene content, we characterized enrichment profiles of the collection of strains relating to phylogeny, early vs. late colonization, pathogenicity and growth rate. We found clear gene content distinctions relating to the various grouping criteria. We also found that different categories of strains use different genetic elements for similar biological processes. The sequenced genomes included two pairs of strains where each pair was isolated from the same infant at different time points. One pair, in which the strains were isolated four months apart, showed maintenance of an early colonizer genome profile but also gene content and codon usage changes toward the late colonizer profile. Lastly, we placed our sequenced isolates into a broader genomic context by comparing them with 25 published E.coli genomes that represent a variety of pathotypes and commensal strains. This analysis demonstrated the importance of geography in shaping strain level gene content profiles. Conclusions Our results indicate a general pattern where alternative genetic pathways lead toward a consistent ecological role for E.coli as a species. Within this framework however, we saw selection shaping the coding repertoire of E.coli strains toward distinct ecotypes with different phenotypic properties. PMID:23384204

2013-01-01

434

Donor plasmid design for codon and single base genome editing using zinc finger nucleases.  

PubMed

In recent years, CompoZr zinc finger nuclease (ZFN) technology has matured to the point that a user-defined double strand break (DSB) can be placed at virtually any location in the human genome within 50 bp of a desired site. Such high resolution ZFN engineering is well within the conversion tract limitations demarcated by the mammalian DNA repair machinery, resulting in a nearly universal ability to create point mutations throughout the human genome. Additionally, new architectures for targeted nuclease engineering have been rapidly developed, namely transcription activator like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems, further expanding options for placement of DSBs. This new capability has created a need to explore the practical limitations of delivering plasmid-based information to the sites of chromosomal double strand breaks so that nuclease-donor methods can be widely deployed in fundamental and therapeutic research. In this chapter, we explore a ZFN-compatible donor design in the context of codon changes at an endogenous locus encoding the human RSK2 kinase. PMID:25408408

Pruett-Miller, Shondra M; Davis, Gregory D

2015-01-01

435

Structural Evidence for a Germline-Encoded T Cell Receptor - Major Histocompatibility Complex Interaction 'Codon'  

SciTech Connect

All complexes of T cell receptors (TCRs) bound to peptide-major histocompatibility complex (pMHC) molecules assume a stereotyped binding 'polarity', despite wide variations in TCR-pMHC docking angles. However, existing TCR-pMHC crystal structures have failed to show broadly conserved pairwise interaction motifs. Here we determined the crystal structures of two TCRs encoded by the variable {beta}-chain 8.2 (V{sub {beta}}8.2), each bound to the MHC class II molecule I-A{sup u}, and did energetic mapping of V{sub {alpha}} and V{sub {beta}} contacts with I-A{sup u}. Together with two previously solved structures of V{sub {beta}}8.2-containing TCR-MHC complexes, we found four TCR-I-A complexes with structurally superimposable interactions between the V{sub {beta}} loops and the I-A {alpha}-helix. This examination of a narrow 'slice' of the TCR-MHC repertoire demonstrates what is probably one of many germline-derived TCR-MHC interaction 'codons'.

Feng, D.; Bond, C.J.; Ely, L.K.; Maynard, J.; Garcia, K.C.

2009-06-02

436

Representation of DNA sequences in genetic codon context with applications in exon and intron prediction.  

PubMed

To apply digital signal processing (DSP) methods to analyze DNA sequences, the sequences first must be specially mapped into numerical sequences. Thus, effective numerical mappings of DNA sequences play key roles in the effectiveness of DSP-based methods such as exon prediction. Despite numerous mappings of symbolic DNA sequences to numerical series, the existing mapping methods do not include the genetic coding features of DNA sequences. We present a novel numerical representation of DNA sequences using genetic codon context (GCC) in which the numerical values are optimized by simulation annealing to maximize the 3-periodicity signal to noise ratio (SNR). The optimized GCC representation is then applied in exon and intron prediction by Short-Time Fourier Transform (STFT) approach. The results show the GCC method enhances the SNR values of exon sequences and thus increases the accuracy of predicting protein coding regions in genomes compared with the commonly used 4D binary representation. In addition, this study offers a novel way to reveal specific features of DNA sequences by optimizing numerical mappings of symbolic DNA sequences. PMID:25491390

Yin, Changchuan

2014-11-12

437

Premature termination codon read-through in the ABCC6 gene: potential treatment for pseudoxanthoma elasticum.  

PubMed

Pseudoxanthoma elasticum (PXE) is an autosomal recessive disorder manifesting with ectopic connective tissue mineralization, caused by mutations in the ABCC6 gene, with ~35% of all mutations being premature termination mutations. In this study, we investigated the therapeutic potential of the nonsense codon read-through-inducing drug, PTC124, in treating PXE. The ability of this drug to facilitate read-through of nonsense mutations was examined in HEK293 cells transfected with human ABCC6 expression constructs harboring seven different PXE-associated nonsense mutations, and was evaluated by immunofluorescence and In-Cell ELISA. Our data demonstrated that PTC124 did not exhibit cytotoxicity in concentrations up to 20??g?ml(-1), and the facilitated read-through varied not only with dose but also with sequence context. Considering the redundancy of the genetic code, it was postulated that in case of the most common recurrent nonsense mutation, p.R1141X, the read-through may result in substitution of the arginine 1,141 by glycine, tryptophan, or cysteine. Their potential pathogenicity was tested in a recently developed zebrafish messenger RNA (mRNA) rescue assay, and demonstrated that all three mRNA transcripts were able to rescue abcc6a morpholino-induced phenotype of zebrafish. Thus, our results suggest that read-through of nonsense mutations in ABCC6 by PTC124 may have potential for pharmacologic treatment of PXE. PMID:23702584

Zhou, Yong; Jiang, Qiujie; Takahagi, Shunsuke; Shao, Changxia; Uitto, Jouni

2013-12-01

438

Premature Termination Codon Read-Through in the ABCC6 Gene: Potential Treatment for Pseudoxanthoma Elasticum  

PubMed Central

Pseudoxanthoma elasticum (PXE) is an autosomal recessive disorder manifesting with ectopic connective tissue mineralization, caused by mutations in the ABCC6 gene, ~35% of all mutations being premature termination mutations. In this study, we investigated the therapeutic potential of the nonsense codon read-through-inducing drug, PTC124, in treating PXE. The ability of this drug to facilitate read-through of nonsense mutations was examined in HEK293 cells transfected with human ABCC6 expression constructs harboring seven different PXE associated nonsense mutations, and evaluated by immunofluorescence and In-Cell ELISA. Our data demonstrated that PTC124 did not exhibit cell toxicity in concentrations up to 40 µg/ml, and the facilitated read-through was not only dose dependent but also sequence context dependent. Considering the redundancy of the genetic code, it was postulated that in case of the most common recurrent nonsense mutation, p.R1141X, the read-through may result in substitution of the arginine 1141 by either glycine, tryptophan or cysteine. Their potential pathogenicity was tested in a recently developed zebrafish mRNA rescue assay, and demonstrated that all three mRNA transcripts were able to rescue abcc6a morpholino-induced phenotype of zebrafish. Thus, our results suggest that read-through of nonsense mutations in ABCC6 by PTC124 may have potential for pharmacologic treatment of PXE. PMID:23702584

Zhou, Yong; Jiang, Qiujie; Takahagi, Shunshuge; Shao, Changxia; Uitto, Jouni

2013-01-01

439

Dynamics of a genetic toggle switch at the nucleotide and codon levels  

NASA Astrophysics Data System (ADS)

We study the dynamics of a model stochastic two-gene switch at the nucleotide and codon levels. First, we show that its stability, the mean lifetime of the noisy attractors, differs from that of a model where transcription and translation elongation are modeled as single-step delayed events, indicating the need of detailed models to study the dynamics of switches. Next, we vary the coupling between the two genes by varying the affinity of repressor proteins to the promoters and measure the mutual information between the two proteins times series. We find that there is a degree of coupling that maximizes information propagation between the two genes. This is explained by the effects of the coupling on mean and entropy of RNA and protein numbers of each gene, as well as correlation, 2-tuple entropy between the two proteins numbers, and, finally, the stability of the noisy attractors. We also find that increasing the rate of translation initiation increases the correlation between RNA and protein numbers and between the two proteins, due to increased stability of the noisy attractors. Increasing the rate of transcription or decreasing RNA degradation causes opposite effects to the correlation between RNA and proteins of each gene and the stability of the noisy attractors. Finally, we add a sequence-dependent transcription pause site and show that both its probability of occurrence, as well as its mean time length, affects the dynamics of the switch, further demonstrating the dependence of the dynamics of this circuit on sequence level events.

Potapov, Ilya; Lloyd-Price, Jason; Yli-Harja, Olli; Ribeiro, Andre S.

2011-09-01

440

Genetic Analysis of Diversity within a Chinese Local Sugarcane Germplasm Based on Start Codon Targeted Polymorphism  

PubMed Central

In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation. PMID:24779012

Que, Youxiong; Pan, Yongbao; Lu, Yunhai; Yang, Cui; Yang, Yuting; Huang, Ning; Xu, Liping

2014-01-01

441

The First Report of a Homozygous Codons 9/10 (+T) ?-Thalassemia Mutation in a Turkish Patient.  

PubMed

Abstract For the first time in Turkey, we report a thalassemic patient with a homozygous codons 9/10 (+T) genotype. Currently, the patient is 3 years and 2 months old and received an initial transfusion at the age of 18 months. After being alloimmunized following this transfusion, he required frequent transfusions, every week to every other week. Although alloimmunization was controlled after methyl-prednisolone, intravenous immunoglobulin, plasmapheresis and rituximab, the transfusion requirements continued related to hypersplenism. Subsequent to splenectomy, transfusion requirements disappeared with average hemoglobin (Hb) levels around 11.0?g/dL. The mother underwent prenatal diagnosis (PND) when she became pregnant for the third time; this revealed a heterozygous codons 9/10 fetus. PMID:25572182

Unal, Sule; Chui, David H K; Luo, Hong-Yuan; Okur, Hamza; Oymak, Yesim; Gumruk, Fatma

2015-01-01

442

4-hydroxy estrogen induces DNA damage on codon 130/131 of PTEN in endometrial carcinoma cells.  

PubMed

Catechol estrogens, such as 4-hydroxyestradiol (4-OHE2), are estrogen metabolites that form DNA adducts and may induce mutations and subsequent cell transformation in mammary cells; however, little is known about their roles in endometrial carcinogenesis. Furthermore, it remains unclear whether 4-OHE2 is able to induce DNA damage on specific genes involved in carcinogenesis or a 'pro'-mutation status such as microsatellite instability (MSI). Therefore, we modified terminal transferase-dependent PCR by the application of a capillary sequencer to detect DNA damage at the single base level. Using this method, we demonstrated that 4-OHE2 directly induced DNA damage on codon 130/131 in exon 5 of PTEN, which is a mutation hot spot for PTEN in endometrial carcinoma. Whereas, both estradiol and 4-OHE2 treatment did not affect MSI status in immortalized endometrial glandular cells. 4-OHE2 might contribute to endometrial carcinogenesis by inducing PTEN mutation on codon 130/131. PMID:25449419

Ke, He; Suzuki, Akihisa; Miyamoto, Tsutomu; Kashima, Hiroyasu; Shiozawa, Tanri

2015-01-15

443

Vitamin D Receptor Translation Initiation Codon Polymorphism and Markers of Osteoporotic Risk in Older African-American Women  

Microsoft Academic Search

:   A polymorphism at the first of two potential translation initiation codons in the vitamin D receptor (VDR) gene defined by\\u000a the FokI restriction endonuclease has been associated with reduced bone mineral density (BMD) among Caucasian, Asian, and Mexican-American\\u000a women. We tested the hypothesis that the FokI polymorphism is related to markers of osteoporotic risk in 104 community-dwelling African-American women

J. M. Zmuda; J. A. Cauley; M. E. Danielson; T. M. Theobald; R. E. Ferrell

1999-01-01

444

Synonymous Codon Bias Is Not Caused by Mutation Bias in G1C-Rich Genes in Humans  

Microsoft Academic Search

It is has been suggested that synonymous codon bias is a consequence of mutation bias in mammals. We tested this hypothesis in humans using single-nucleotide polymorphism data. We found a pattern of polymorphism which was inconsistent with the mutation bias hypothesis in G1C-rich genes. However, the data were consistent with the action of natural selection or biased gene conversion. Similar

Nick G. C. Smith; Adam Eyre-Walker

445

The preliminary study of p53 codon 72 polymorphism and risk of cervical carcinoma in Gabonese women.  

PubMed

Cervical cancer is the leading cause of cancer-related death in Africa and the first most common cancer in Gabonese women due to infection of high-risk human papillomavirus (HPV). However, other cofactors such as genetic factors also come into play. A common polymorphism of the p53 codon 72 in exon 4 with two alleles encoding arginine or proline is known at this locus. The homozygous arginine form of this polymorphism has been associated with the development of cervical cancer as an increased genetic risk factor. However, the results are still controversial. This study aims to investigate whether the genotype distribution of p53 codon 72 may be a risk factor for cervical cancer among Gabonese women. Samples from 102 Gabonese women, 31 diagnosed with cervical cancer and 71 healthy controls, were used. HPV detection was done by nested PCR with MY09/11 and GP5+/6+ primers followed by sequencing for HPV genotyping. p53 codon 72 polymorphism determination was performed by allele-specific PCR assay. Viral DNA was detected in 87.1 % of cases and in 54.93 % of control. HPV 16 was the most predominant in cancer and controls cases. The distribution of Arg/Arg, Arg/Pro and Pro/Pro genotypes was 35.5, 51.6 and 12.9 % in the cervical cancer group and 22.5, 62 and 15.5 % in the control group. No significant association was found between polymorphism of p53 itself as well as in combination with HPV16/18 infection and risk of development of cervical cancer among Gabonese women. Thus, the polymorphism of p53 codon 72 in exon 4 does not seem to play a role in the development of cervical cancer among Gabonese women. PMID:25502079

Assoumou, Samira Zoa; Boumba, Anicet Luc M; Ndjoyi-Mbiguino, Angelique; Khattabi, Abdelkrim; Ennaji, Moulay Mustapha

2015-01-01

446

Presenile dementia and cerebral haemorrhage linked to a mutation at codon 692 of the ?-amyloid precursor protein gene  

Microsoft Academic Search

Several families with an early-onset form of familial Alzheimer's disease have been found to harbour mutations at a specific codon (717) of the gene for the beta-amyloid precursor protein (APP) on chromosome 21. We now report, a novel base mutation in the same exon of the APP gene which co-segregates in one family with presenile dementia and cerebral haemorrhage due

Lydia Hendriks; Duijn van C. M; Patrick Cras; Marc Cruts; Wim Van Hul; Frans van Harskamp; Andrew Warren; Melvin G. McInnis; Stylianos E. Antonarakis; Jean-Jacques Martin; Broeckhoven van C; A. Hofman

1992-01-01

447

Human basic fibroblast growth factor gene encodes four polypeptides: Three initiate translation from non-AUG codons  

Microsoft Academic Search

Human basic fibroblast growth factor (bFGF) is an angiogenic polypeptide mitogen present in a wide variety of mesoderm- and neuroectoderm-derived tissues. bFGF cDNA and genomic clones predict a 17.8-kDa (155-amino acid) gene product based on the presence of a single putative translational initiator ATG codon. However, a bFGF protein isolated from human placenta contains two additional amino acids NHâ-terminal to

R. Z. Florkiewicz; A. Sommer

1989-01-01

448

Apolipoprotein A-I deficiency due to a codon 84 nonsense mutation of the apolipoprotein A-I gene  

SciTech Connect

The molecular genetic defect of a female patient with apolipoprotein A-I (apoA-I) deficiency and premature atherosclerosis was examined. Her parents were first cousins. Her plasma density fraction from 1.063 to 1.21 g/ml contained no apoA-I on SDS/PAGE and no measurable high density lipoprotein cholesterol. Southern blot hybridization showed no gross abnormality to be present in the patient's apoA-I gene and homozygosity for a haplotype of restriction fragment length polymorphisms in the apoA-I gene region. Sequencing after amplification by PCR revealed a codon 84 nonsense mutation (CAG {r arrow} TAG, Gln {r arrow} stop) of exon 4 and a codon 37 missense mutation (GCC{r arrow} ACC, Ala {r arrow} Thr) of exon 3 in the patient's apoA-I gene. The data from dot-blot hybridization with allele-specific oligonucleotide probes indicated that she was homozygous for the apoA-I gene with regard to the two mutations. The codon 37 missense mutation was also detected in the apoA-I gene of 6 out of 60 controls, who all had normal levels of apoA-I and high density lipoprotein cholesterol, suggesting that the missense mutation is polymorphic and not associated with apoA-I deficiency. These finding indicate that homozygosity for the apoA-I gene with codon 84 nonsense mutation causes the deficiency of apoA-I and of high density lipoprotein cholesterol in the patient.

Matsunaga, Tomoyuki; Yanagi, Hisako; Hattori, Naoko; Yamakawa, Kimiko; Yamanouchi, Yasuko; Hamaguchi, Hideo (Univ. of Tsukuba (Japan)); Hiasa, Yoshikazu; Maeda, Toshihiro (Komatsushima Red Cross Hospital (Japan)); Tanaka, Isao; Obara, Takashi (Eisai Co., Ltd., Tsukuba (Japan))

1991-04-01

449

The association of a codon 136 PrP gene variant with the occurrence of natural scrapie  

Microsoft Academic Search

Summary Incidence of both experimental and natural scrapie in sheep has been associated with polymorphisms of the PrP gene. In case\\/ control studies the PrP allele which encodes valine at codon 136 (Val136) is found in 96–100% of naturally infected scrapie sheep of Shetland, Scottish Halfbred and Bleu du Maine breeds. In contrast, in healthy animals from the same flocks,

N. Hunter; W. Goldmann; G. Smith; J. Hope

1994-01-01

450

Expression of recombinant endochitinase from the Antarctic bacterium, Sanguibacter antarcticus KOPRI 21702 in Pichia pastoris by codon optimization  

Microsoft Academic Search

An endochitinase was previously purified and the gene was cloned from the psychrophilic Antarctic bacterium, Sanguibacter antarcticus (KCTC 13143). In the present study, recombinant endochitinase, rChi21702, was expressed using a yeast expression system (Pichia pastoris) and codon optimization. The expressed rChi21702 was purified by Phenyl-Sepharose column chromatography. Optimal expression yielded 1-mg purified enzyme from 1-L bioreactor culture. When p-NP-(GlcNAc)2 was

Sung Gu Lee; Hye Yeon Koh; Se Jong Han; Deuk Chae Na; Il-Chan Kim; Hong Kum Lee; Joung Han Yim

2010-01-01

451

Two Chinese pedigrees for adenomatous polyposis coli: new mutations at codon 1309 and predisposition to phenotypic variations.  

PubMed

Familial adenomatous polyposis (FAP) is an autosomal dominant inherited disease caused by a mutation in the adenomatous polyposis coli (APC) gene. Some studies have attempted to correlate mutations at codon 1309 with classic FAP (?100 colorectal polyps). We report two Chinese FAP pedigrees with new frameshift mutations at codon 1309, in which affected individuals manifest phenotypic variations. Comprehensive physical examinations were performed for all living individuals and the medical data of deceased patients were collected. Screening of the APC and human mutY homolog (MUTYH) genes for germline mutations was conducted by direct polymerase chain reaction (PCR) sequencing. In two pedigrees, a heterozygous deletion in exon 16 of the APC gene was present in all FAP patients but absent in the unaffected individuals. There were no changes to the MUTYH gene. The first pedigree, with a new frameshift mutation at c.3926_3930 del AAAAG (p. Glu1309Aspfs X4), exhibited obvious differences in the polyp number such that the proband manifested only three colorectal polyps, whereas another patients showed the symptoms of classic FAP. The second pedigree, also traced a new mutation at c.3922_3925 del AAAG (p. Glu1309Argfs X11). Although all of the patients presented with classic polyposis, one of them exhibited a delayed onset of colorectal cancer in his 50s. Two novel mutations at codon 1309 in two Chinese families suffering from FAP could enrich the germline mutation spectrum of the APC gene. Families of individuals might manifest different phenotypes, even with an identical codon 1309 mutation, unlike in previous studies. PMID:24664542

Liao, Dai-Xiang; Li, Bing; Du, Xue-Mei; Yu, Jun-Hui; Chang, Hong; Wu, Zhi-Qiang; Hao, Hao-Jie; Wang, You-Xin; Han, Wei-Dong; Cheng, Shu-Jun; Luo, Cheng-Hua

2014-09-01

452

VEHICLE USAGE LOG Department ________________________________________ Vehicle Homebase ____________________________ Week Ended (Sunday) _________________  

E-print Network

VEHICLE USAGE LOG Department ________________________________________ Vehicle Homebase ____________________________ Week Ended (Sunday) _________________ Door #____________ License Plate ____________________ Vehicle/Supplies (Enter Description such as grade sheets, artifacts, money, etc.) 6. Taking vehicle to Automotive Shop

Yang, Zong-Liang

453

A theoretical thermochemical study of solute-solvent dielectric effects in the displacement of codon-anticodon base pairs  

NASA Astrophysics Data System (ADS)

Quantum-chemical solvent effect theories describe the electronic structure of a molecular subsystem embedded in a solvent or other molecular environment. The solvation of biomolecules is important in molecular biology, since numerous processes involve proteins interacting in changing solvent-solute systems. In this theoretical study, we focus on mRNA-tRNA base pairs as a fundamental step in protein synthesis influenced by hydrogen bonding between two antiparallel trinucleotides, namely, the mRNA codon and tRNA anticodon. We use the mean reaction field theories, which describe electrostatic and polarization interactions between solute and solvent in the AAA, UUU, AAG, and UUC triplex sequences optimized in various solvent media such as water, dimethylsulfoxide, methanol, ethanol, and cyclopean using the self-consistent reaction field model. This process depends on either the reaction potential function of the solvent or charge transfer operators that appear in solute-solvent interaction. Because of codon and anticodon biological criteria, we performed nonempirical quantum-mechanical calculations at the BLYP and B3LYP/3-21G, 6-31G, and 6-31G* levels of theory in the gas phase and five solvents at three temperatures. Finally, to obtain more information, we calculated thermochemical parameters to find that the dielectric constant of solvents plays an important role in the displacement of amino acid sequences on codon-anticodon residues in proteins, which can cause some mutations in humans.

Monajjemi, M.; Razavian, M. H.; Mollaamin, F.; Naderi, F.; Honarparvar, B.

2008-12-01

454

Codon 104 variation of p53 gene provides adaptive apoptotic responses to extreme environments in mammals of the Tibet plateau  

PubMed Central

Mutational changes in p53 correlate well with tumorigenesis. Remarkably, however, relatively little is known about the role that p53 variations may play in environmental adaptation. Here we report that codon asparagine-104 (104N) and glutamic acid-104 (104E), respectively, of the p53 gene in the wild zokor (Myospalax baileyi) and root vole (Microtus oeconomus) are adaptively variable, meeting the environmental stresses of the Tibetan plateau. They differ from serine-104 (104S) seen in other rodents, including the lowland subterranean zokor Myospalax cansus, and from serine 106 (106S) in humans. Based on site-directed mutational analysis in human cell lines, the codon 104N variation in M. baileyi is responsible for the adaptive balance of the transactivation of apoptotic genes under hypoxia, cold, and acidic stresses. The 104E p53 variant in Microtus oeconomus suppresses apoptotic gene transactivation and cell apoptosis. Neither 104N nor 104E affects the cell-cycle genes. We propose that these variations in p53 codon 104 are an outcome of environmental adaptation and evolutionary selection that enhance cellular strategies for surviving the environmental stresses of hypoxia and cold (in M. baileyi and M. oeconomus) and hypercapnia (in M. baileyi) in the stressful environments of the Qinghai-Tibet plateau. PMID:24297887

Zhao, Yang; Ren, Ji-Long; Wang, Ming-Yang; Zhang, Sheng-Ting; Liu, Yu; Li, Min; Cao, Yi-Bin; Zu, Hu-Yue; Chen, Xiao-Cheng; Wu, Chung-I; Nevo, Eviatar; Chen, Xue-Qun; Du, Ji-Zeng

2013-01-01

455

Codon 104 variation of p53 gene provides adaptive apoptotic responses to extreme environments in mammals of the Tibet plateau.  

PubMed

Mutational changes in p53 correlate well with tumorigenesis. Remarkably, however, relatively little is known about the role that p53 variations may play in environmental adaptation. Here we report that codon asparagine-104 (104N) and glutamic acid-104 (104E), respectively, of the p53 gene in the wild zokor (Myospalax baileyi) and root vole (Microtus oeconomus) are adaptively variable, meeting the environmental stresses of the Tibetan plateau. They differ from serine-104 (104S) seen in other rodents, including the lowland subterranean zokor Myospalax cansus, and from serine 106 (106S) in humans. Based on site-directed mutational analysis in human cell lines, the codon 104N variation in M. baileyi is responsible for the adaptive balance of the transactivation of apoptotic genes under hypoxia, cold, and acidic stresses. The 104E p53 variant in Microtus oeconomus suppresses apoptotic gene transactivation and cell apoptosis. Neither 104N nor 104E affects the cell-cycle genes. We propose that these variations in p53 codon 104 are an outcome of environmental adaptation and evolutionary selection that enhance cellular strategies for surviving the environmental stresses of hypoxia and cold (in M. baileyi and M. oeconomus) and hypercapnia (in M. baileyi) in the stressful environments of the Qinghai-Tibet plateau. PMID:24297887

Zhao, Yang; Ren, Ji-Long; Wang, Ming-Yang; Zhang, Sheng-Ting; Liu, Yu; Li, Min; Cao, Yi-Bin; Zu, Hu-Yue; Chen, Xiao-Cheng; Wu, Chung-I; Nevo, Eviatar; Chen, Xue-Qun; Du, Ji-Zeng

2013-12-17

456

Phylotranscriptomics: saturated third codon positions radically influence the estimation of trees based on next-gen data.  

PubMed

Recent advancements in molecular sequencing techniques have led to a surge in the number of phylogenetic studies that incorporate large amounts of genetic data. We test the assumption that analyzing large number of genes will lead to improvements in tree resolution and branch support using moths in the superfamily Bombycoidea, a group with some interfamilial relationships that have been difficult to resolve. Specifically, we use a next-gen data set that included 19 taxa and 938 genes (?1.2M bp) to examine how codon position and saturation might influence resolution and node support among three key families. Maximum likelihood, parsimony, and species tree analysis using gene tree parsimony, on different nucleotide and amino acid data sets, resulted in largely congruent topologies with high bootstrap support compared with prior studies that included fewer loci. However, for a few shallow nodes, nucleotide and amino acid data provided high support for conflicting relationships. The third codon position was saturated and phylogenetic analysis of this position alone supported a completely different, potentially misleading sister group relationship. We used the program RADICAL to assess the number of genes needed to fix some of these difficult nodes. One such node originally needed a total of 850 genes but only required 250 when synonymous signal was removed. Our study shows that, in order to effectively use next-gen data to correctly resolve difficult phylogenetic relationships, it is necessary to assess the effects of synonymous substitutions and third codon positions. PMID:24148944

Breinholt, Jesse W; Kawahara, Akito Y

2013-01-01

457

Activating K-Ras mutations outwith ‘hotspot' codons in sporadic colorectal tumours – implications for personalised cancer medicine  

PubMed Central

Background: Response to EGFR-targeted therapies in colorectal cancer patients has been convincingly associated with Kirsten-Ras (K-Ras) mutation status. Current mandatory mutation testing for patient selection is limited to the K-Ras ‘hotspot' codons 12 and 13. Methods: Colorectal tumours (n=106) were screened for additional K-Ras mutations, phenotypes compared in transformation and Ras GTPase activating assays and gene and pathway changes induced by individual K-Ras mutants identified by microarray analysis. Taqman-based gene copy number and FISH analyses were used to investigate K-Ras gene amplification. Results: Four additional K-Ras mutations (Leu19Phe (1 out of 106 tumours), Lys117Asn (1 out of 106), Ala146Thr (7 out of 106) and Arg164Gln (1 out of 106)) were identified. Lys117Asn and Ala146Thr had phenotypes similar to the hotspot mutations, whereas Leu19Phe had an attenuated phenotype and the Arg164Gln mutation was phenotypically equivalent to wt K-Ras. We additionally identified a new K-Ras gene amplification event, present in approximately 2% of tumours. Conclusions: The identification of mutations outwith previously described hotspot codons increases the K-Ras mutation burden in colorectal tumours by one-third. Future mutation screening to facilitate optimal patient selection for treatment with EGFR-targeted therapies should therefore be extended to codon 146, and in addition should consider the unique molecular signatures associated with individual K-Ras mutations. PMID:20147967

Smith, G; Bounds, R; Wolf, H; Steele, R J C; Carey, F A; Wolf, C R

2010-01-01

458

Using Ontologies to Discover Domain-Level Web Usage Profiles  

Microsoft Academic Search

Usage patterns discovered through Web usage mining are ef- fective in capturing item-to-item and user-to-user relationships and sim- ilarities at the level of user sessions.Without the benefit of deeper do- main knowledge, such patterns provide little insight into the underlying reasons for which such items or users are grouped together.This can lead to a number of important shortcomings in personalization

Bamshad Mobasher

2002-01-01

459

Health Services Usage by Alaskan Injection Drug Users  

Microsoft Academic Search

Objectives: The purpose of this study was to explore health services usage among injection drug users in Anchorage, Alaska.Design: 645 participants were recruited as part of a federally funded study of needle exchanges. They completed a health services usage questionnaire that elicited information on use of a health care provider (physician or nurse) and emergency room services. Chi-square and t-tests

Grace L. Reynolds; Rebecca S. Wells; Dennis G. Fisher; Henry H. Cagle

2006-01-01

460

Generalization method of relationships among nucleotide sequences reveals an order in assimilation of amino acid codons during the isoacceptor tRNAs evolution  

SciTech Connect

A new method, generalization of relationships among the nucleotide sequences, has been used to analyze divergency both within and across the families of isoaccepting tRNAs. Dendrogram, depicting relations between tRNA sets with different amino acid specificities, presents the results of analysis. The method made it possible to interpret the dendrogram, as a reflection of final stage of the evolution of ambiguous molecules-adaptors to highly specific tRNAs. We have proposed a model of amino acid codons assimilation at this stage. According to the model, the final formation of specific adaptors was followed by assimilation of codon clusters (four codons, differing in the third position), the first dinucleotides of which were connected by transitions. Alternate steps along double-stranded coding DNA accompanied the establishment of tRNA sets with strict specificities. Complementary codons, to which specific adaptors were assigned at step the last, were involved into the process afterwards. 34 refs., 2 figs., 1 tab.

Chaley, M.B.; Korotkov, E.V. [Center Bioengineering, Moscow (Russian Federation)

1996-12-31