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1

Compositional nonrandomness upstream of start codons in archaebacteria  

Microsoft Academic Search

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

Anders Fuglsang

2004-01-01

2

Availability of a second upstream AUG can completely overcome inhibition of protein synthesis initiation engendered by mRNA secondary structure encompassing the start codon.  

PubMed

Secondary structure analysis of the mRNA from a nonproductive construct carrying the nonstructural gene 3 (NS3) of Japanese Encephalitis Virus revealed the presence of a potential 28 nucleotide long stem and loop beginning with the guanine of the initiation codon AUG that had a calculated stabilization energy of -13 kcal/mol (delta Gfzero). Provision of an additional AUG along with three codons upstream resulted in complete relief of inhibition. N-terminal amino acid sequence of the recombinant protein was consistent with initiation of protein synthesis having occurred from the upstream AUG. Similar levels of NS3 specific RNA in E. coli cells carrying the expressing and nonexpressing constructs and restoration of recombinant protein expression following deletion of segments beginning with the stem and loop confirmed the role of this structure in blocking expression at the level of translation initiation. Our approach exploits the ability of a ribosome in motion to open up downstream secondary structural elements of considerable stability and represents a novel and widely applicable strategy to overcome a block in translation initiation caused by mRNA secondary structure around the translation start site. PMID:9322762

Satchidanandam, V; Shivashankar, Y

1997-09-01

3

Efficient translation initiation dictates codon usage at gene start.  

PubMed

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

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

2013-01-01

4

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

Microsoft Academic Search

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

Rintaro Saito; Masaru Tomita

1999-01-01

5

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

PubMed Central

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

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

2013-01-01

6

Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a `weak' context of the start codon  

Microsoft Academic Search

Motivation: The context of the start codon (typically, AUG) and the features of the 5? Untranslated Regions (5? UTRs) are important for understanding translation regulation in eukaryotic mRNAs and for accurate prediction of the coding region in genomic and cDNA sequences. The presence of AUG triplets in 5? UTRs (upstream AUGs) might effect the initiation rate and, in the context

Igor B. Rogozin; Alexey V. Kochetov; Fyodor A. Kondrashov; Eugene V. Koonin; Luciano Milanesi

2001-01-01

7

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

PubMed Central

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

2014-01-01

8

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

PubMed Central

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

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

2012-01-01

9

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

PubMed

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

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

2012-12-01

10

Amino Termini of Many Yeast Proteins Map to Downstream Start Codons  

PubMed Central

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

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

2012-01-01

11

A Mutation in the 5?-UTR of IFITM5 Creates an In-Frame Start Codon and Causes Autosomal-Dominant Osteogenesis Imperfecta Type V with Hyperplastic Callus  

PubMed Central

Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disorder associated with bone fragility and susceptibility to fractures after minimal trauma. OI type V has an autosomal-dominant pattern of inheritance and is not caused by mutations in the type I collagen genes COL1A1 and COL1A2. The most remarkable and pathognomonic feature, observed in ?65% of affected individuals, is a predisposition to develop hyperplastic callus after fractures or surgical interventions. To identify the molecular cause of OI type V, we performed whole-exome sequencing in a female with OI type V and her unaffected parents and searched for de novo mutations. We found a heterozygous de novo mutation in the 5?-untranslated region of IFITM5 (the gene encoding Interferon induced transmembrane protein 5), 14 bp upstream of the annotated translation initiation codon (c.?14C>T). Subsequently, we identified an identical heterozygous de novo mutation in a second individual with OI type V by Sanger sequencing, thereby confirming that this is the causal mutation for the phenotype. IFITM5 is a protein that is highly enriched in osteoblasts and has a putative function in bone formation and osteoblast maturation. The mutation c.?14C>T introduces an upstream start codon that is in frame with the reference open-reading frame of IFITM5 and is embedded into a stronger Kozak consensus sequence for translation initiation than the annotated start codon. In vitro, eukaryotic cells were able to recognize this start codon, and they used it instead of the reference translation initiation signal. This suggests that five amino acids (Met-Ala-Leu-Glu-Pro) are added to the N terminus and alter IFITM5 function in individuals with the mutation.

Semler, Oliver; Garbes, Lutz; Keupp, Katharina; Swan, Daniel; Zimmermann, Katharina; Becker, Jutta; Iden, Sandra; Wirth, Brunhilde; Eysel, Peer; Koerber, Friederike; Schoenau, Eckhard; Bohlander, Stefan K.; Wollnik, Bernd; Netzer, Christian

2012-01-01

12

Start/stop codon like trinucleotides extensions in primate alpha satellites.  

PubMed

The centromeres remain "the final frontier" in unexplored segments of genome landscape in primate genomes, characterized by 2-5 Mb arrays of evolutionary rapidly evolving alpha satellite (AS) higher order repeats (HORs). Alpha satellites as specific noncoding sequences may be also significant in light of regulatory role of noncoding sequences. Using the Global Repeat Map (GRM) algorithm we identify in NCBI assemblies of chromosome 5 the species-specific alpha satellite HORs: 13mer in human, 5mer in chimpanzee, 14mer in orangutan and 3mers in macaque. The suprachromosomal family (SF) classification of alpha satellite HORs and surrounding monomeric alpha satellites is performed and specific segmental structure was found for major alpha satellite arrays in chromosome 5 of primates. In the framework of our novel concept of start/stop Codon Like Trinucleotides (CLTs) as a "new DNA language in noncoding sequences", we find characteristics and differences of these species in CLT extensions, in particular the extensions of stop-TGA CLT. We hypothesize that these are regulators in noncoding sequences, acting at a distance, and that they can amplify or weaken the activity of start/stop codons in coding sequences in protein genesis, increasing the richness of regulatory phenomena. PMID:23026763

Rosandi?, Marija; Glun?i?, Matko; Paar, Vladimir

2013-01-21

13

Examining weak protein-protein interactions in start codon recognition via NMR spectroscopy.  

PubMed

Weak protein-protein interactions are critical in numerous biological processes. Unfortunately, they are difficult to characterize due to the high concentrations required for the production and detection of the complex population. The inherent sensitivity of NMR spectroscopy to the chemical environment makes it an excellent tool to tackle this problem. NMR permits the exploration of interactions over a range of affinities, yielding essential insights into dynamic biological processes. The conversion of messanger RNA to protein is one such process that requires the coordinated association of many low-affinity proteins. During start codon recognition, eukaryotic initiation factors assemble into high-order complexes that bind messanger RNA and bring it to the ribosome for decoding. Many of the structures of the eukaryotic initiation factors have been determined; however, little is known regarding the weak binary complexes formed and their structure-function mechanisms. Herein, we use start codon recognition as a model system to review the relevant NMR methods for the characterization of weak interactions and the development of small molecule inhibitors. PMID:24393460

Luna, Rafael E; Akabayov, Sabine R; Ziarek, Joshua J; Wagner, Gerhard

2014-04-01

14

Reduce Manual Curation by Combining Gene Predictions from Multiple Annotation Engines, a Case Study of Start Codon Prediction  

PubMed Central

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

Ederveen, Thomas H. A.; Overmars, Lex; van Hijum, Sacha A. F. T.

2013-01-01

15

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.

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

2014-01-01

16

Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism.  

PubMed

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

17

Comprehensive Analysis of Transcript Start Sites in Ly49 Genes Reveals an Unexpected Relationship with Gene Function and a Lack Of Upstream Promoters  

PubMed Central

Comprehensive analysis of the transcription start sites of the Ly49 genes of C57BL/6 mice using the oligo-capping 5?-RACE technique revealed that the genes encoding the “missing self” inhibitory receptors, Ly49A, C, G, and I, were transcribed from multiple broad regions in exon 1, in the intron1/exon2 region, and upstream of exon -1b. Ly49E was also transcribed in this manner, and uniquely showed a transcriptional shift from exon1 to exon 2 when NK cells were activated in vitro with IL2. Remarkably, a large proportion of Ly49E transcripts was then initiated from downstream of the translational start codon. By contrast, the genes encoding Ly49B and Q in myeloid cells, the activating Ly49D and H receptors in NK cells, and Ly49F in activated T cells, were predominantly transcribed from a conserved site in a pyrimidine-rich region upstream of exon 1. An ?200 bp fragment from upstream of the Ly49B start site displayed tissue-specific promoter activity in dendritic cell lines, but the corresponding upstream fragments from all other Ly49 genes lacked detectable tissue-specific promoter activity. In particular, none displayed any significant activity in a newly developed adult NK cell line that expressed multiple Ly49 receptors. Similarly, no promoter activity could be found in fragments upstream of intron1/exon2. Collectively, these findings reveal a previously unrecognized relationship between the pattern of transcription and the expression/function of Ly49 receptors, and indicate that transcription of the Ly49 genes expressed in lymphoid cells is achieved in a manner that does not require classical upstream promoters.

Gays, Frances; Koh, Alan S. C.; Mickiewicz, Katarzyna M.; Aust, Jonathan G.; Brooks, Colin G.

2011-01-01

18

Transcription of a transposed trypanosome surface antigen gene starts upstream of the transposed segment.  

PubMed Central

The non-telomeric variant surface glycoprotein (VSG) genes in Trypanosoma brucei are activated by a duplicative transposition to a telomeric expression site. We have determined the 5' end of the transposed segment of the gene for VSG 117 and infer from comparison with similar data obtained by others that the crossover can occur at variable positions within short repeats present upstream of this gene and in the expression site. We have analysed nascent and steady state transcripts of the transposed gene and its neighbouring expression site DNA. The results indicate that transcription starts upstream of the transposed gene segment in the expression site and that transcripts are rapidly processed at specific points identified by protection of DNA-RNA hybrids against digestion by nuclease S1 or Exo VII. Hence, this gene appears to be activated by a process akin to promoter addition. Images Fig. 3. Fig. 4. Fig. 5.

De Lange, T; Kooter, J M; Luirink, J; Borst, P

1985-01-01

19

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

PubMed Central

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

Rentero, Carles; Puigdomenech, Pere

2006-01-01

20

Effect of the Codon Following the ATG Start Site on the Expression of Ovine Growth Hormone in Escherichia coli  

Microsoft Academic Search

For expression of ovine growth hormone (OGH) in inclusion bodies without an affinity histidine tag at either end of the protein, three clones, differing only in the second codon following the ATG start site, were constructed. Their expression was studied by SDS–PAGE followed by immunoblotting. Clone Ala.OGH (clone 1), beginning with Met.Ala.Phe.Pro … , did not show any expression. Clone

Niti Puri; K. B. C. Appa Rao; Swapna Menon; A. K. Panda; Gunjan Tiwari; L. C. Garg; S. M. Totey

1999-01-01

21

Evidence for involvement of trans-acting factors in selection of the AUG start codon during eukaryotic translational initiation.  

PubMed Central

The molecular mechanism with which an appropriate AUG codon is selected as the start site for translational initiation by eukaryotic ribosomes is not known. By using a cell-free translation system, small RNA molecules containing single AUG codons, surrounded by various nucleotide sequences, were tested for their abilities to interfere with the translation of a reporter mRNA. RNAs containing the AUG in an ACCAUGG context (Kozak consensus sequence) were able to inhibit translation of the reporter mRNA. In contrast, RNAs containing the AUG in a less favorable context for start site selection (for example, CAGAUGG) had no effect on the translation of the reporter mRNA. The effect mediated by the ACCAUGC-containing RNAs was not due to sequestration of ribosomal subunits or to particular structural features in these RNAs. To identify potential trans-acting factors that might be preferentially bound by ACCAUGG-containing RNAs, ACCAUGG- and CAGAUGC-containing RNAs with a single 4-thiouridine residue at the AUG were incubated with partially fractionated extracts, and AUG-binding proteins were identified after irradiation of the complexes with UV light and subsequent analysis by gel electrophoresis. The analysis (of such complexes in competition experiments revealed that proteins, approximately 50 and 100 kDa in size, were found to bind directly at the AUG codon embedded in the ACCAUGG motif. One of these proteins has been identified as the La autoantigen. These findings indicate that trans-acting factors may play a role in AUG start site selection during translational initiation.

McBratney, S; Sarnow, P

1996-01-01

22

Evidence for involvement of trans-acting factors in selection of the AUG start codon during eukaryotic translational initiation.  

PubMed

The molecular mechanism with which an appropriate AUG codon is selected as the start site for translational initiation by eukaryotic ribosomes is not known. By using a cell-free translation system, small RNA molecules containing single AUG codons, surrounded by various nucleotide sequences, were tested for their abilities to interfere with the translation of a reporter mRNA. RNAs containing the AUG in an ACCAUGG context (Kozak consensus sequence) were able to inhibit translation of the reporter mRNA. In contrast, RNAs containing the AUG in a less favorable context for start site selection (for example, CAGAUGG) had no effect on the translation of the reporter mRNA. The effect mediated by the ACCAUGC-containing RNAs was not due to sequestration of ribosomal subunits or to particular structural features in these RNAs. To identify potential trans-acting factors that might be preferentially bound by ACCAUGG-containing RNAs, ACCAUGG- and CAGAUGC-containing RNAs with a single 4-thiouridine residue at the AUG were incubated with partially fractionated extracts, and AUG-binding proteins were identified after irradiation of the complexes with UV light and subsequent analysis by gel electrophoresis. The analysis (of such complexes in competition experiments revealed that proteins, approximately 50 and 100 kDa in size, were found to bind directly at the AUG codon embedded in the ACCAUGG motif. One of these proteins has been identified as the La autoantigen. These findings indicate that trans-acting factors may play a role in AUG start site selection during translational initiation. PMID:8668168

McBratney, S; Sarnow, P

1996-07-01

23

Patterns of variation in DNA segments upstream of transcription start sites  

PubMed Central

It is likely that evolutionary differences among species are driven by sequence changes in regulatory regions. Likewise, polymorphisms in the promoter regions may be responsible for interindividual differences at the level of populations. We present an unbiased survey of genetic variation in 2-kb segments upstream of the transcription start sites of 28 protein-coding genes, characterized in five population groups of different geographic origin. On average, we found 9.1 polymorphisms and 8.8 haplotypes per segment with corresponding nucleotide and haplotype diversities of 0.082% and 58%, respectively. We characterized these segments through different summary statistics, Hardy-Weinberg equilibria fixation index (Fst) estimates, and neutrality tests, as well as by analyzing the distributions of haplotype allelic classes, introduced here to assess the departure from neutrality and examined by coalescent simulations under a simple population model, assuming recombinations or different demography. Our results suggest that genetic diversity in some of these regions could have been shaped by purifying selection and driven by adaptive changes in the other, thus explaining the relatively large variance in the corresponding genetic diversity indices loci. However, some of these effects could be also due to linkage with surrounding sequences, and the neutralists' explanations cannot be ruled out given uncertainty in the underlying demographic histories and the possibility of random effects due to the small size of the studied segments. Hum Mutat 28(5), 441–450, 2007. © 2007 Wiley-Liss, Inc.

Labuda, Damian; Labbe, Catherine; Langlois, Sylvie; Lefebvre, Jean-Francois; Freytag, Virginie; Moreau, Claudia; Sawicki, Jakub; Beaulieu, Patrick; Pastinen, Tomi; Hudson, Thomas J; Sinnett, Daniel

2007-01-01

24

Secret Codon  

NSDL National Science Digital Library

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

Yu, Julie

2008-01-01

25

Potential of Start Codon Targeted (SCoT) markers for DNA fingerprinting of newly synthesized tritordeums and their respective parents.  

PubMed

Hexaploid tritordeum (H(ch)H(ch)AABB; 2n?=?42) results from the cross between Hordeum chilense (H(ch)H(ch); 2n?=?14) and cultivated durum wheat (Triticum turgidum ssp. durum (AABB; 2n?=?28). Morphologically, tritordeum resembles the wheat parent, showing promise for agriculture and wheat breeding. Start Codon Targeted (SCoT) polymorphism is a recently developed technique that generates gene-targeted markers. Thus, we considered it interesting to evaluate its potential for the DNA fingerprinting of newly synthesized hexaploid tritordeums and their respective parents. In this study, 60 SCoT primers were tested, and 18 and 19 of them revealed SCoT polymorphisms in the newly synthesized tritordeum lines HT27 and HT22, respectively, and their parents. An analysis of the presence/absence of bands among tritordeums and their parents revealed three types of polymorphic markers: (i) shared by tritordeums and one of their parents, (ii) exclusively amplified in tritordeums, and (iii) exclusively amplified in the parents. No polymorphism was detected among individuals of each parental species. Three SCoT markers were exclusively amplified in tritordeums of lines HT22 and HT27, being considered as polyploidization-induced rearrangements. About 70 % of the SCoT markers of H. chilense origin were not transmitted to the allopolyploids of both lines, and most of the SCoTs scored in the newly synthesized allopolyploids originated from wheat, reinforcing the potential use of tritordeum as an alternative crop. PMID:24733248

Cabo, Sandra; Ferreira, Luciana; Carvalho, Ana; Martins-Lopes, Paula; Martín, António; Lima-Brito, José Eduardo

2014-08-01

26

Start Codon Targeted (SCoT) marker reveals genetic diversity of Dendrobium nobile Lindl., an endangered medicinal orchid species.  

PubMed

Genetic variability in the wild genotypes of Dendrobium nobile Lindl. collected from different parts of Northeast India, was analyzed using a Start Codon Targeted (SCoT) marker system. A total of sixty individuals comprising of six natural populations were investigated for the existing natural genetic diversity. One hundred and thirty two (132) amplicons were produced by SCoT marker generating 96.21% polymorphism. The PIC value of the SCoT marker system was 0.78 and the Rp values of the primers ranged between 4.43 and 7.50. The percentage of polymorphic loci (Pp) ranging from 25% to 56.82%, Nei's gene diversity (h) from 0.08 to 0.15 with mean Nei's gene diversity of 0.28, and Shannon's information index (I) values ranging from 0.13 to 0.24 with an average value of 0.43 were recorded. The gene flow value (0.37) and the diversity among populations (0.57) demonstrated higher genetic variation among the populations. Analysis of molecular variance (AMOVA) showed 43.37% of variation within the populations, whereas 56.63% variation was recorded among the populations. Cluster analysis also reveals high genetic variation among the genotypes. Present investigation suggests the effectiveness of SCoT marker system to estimate the genetic diversity of D. nobile and that it can be seen as a preliminary point for future research on the population and evolutionary genetics of this endangered orchid species of medicinal importance. PMID:23939470

Bhattacharyya, Paromik; Kumaria, Suman; Kumar, Shrawan; Tandon, Pramod

2013-10-15

27

Mutation of the start codon in the FRDA1 gene: linkage analysis of three pedigrees with the ATG to ATT transversion points to a unique common ancestor  

Microsoft Academic Search

Friedreich ataxia (FRDA) is a progressive neurodegenerative disorder caused by loss-of-function mutations in the gene encoding\\u000a frataxin. Most patients with FRDA have trinucleotide repeat expansions in both alleles of the FRDA1 gene. In patients heterozygous\\u000a for the expansion the second allele may be inactivated by a point mutation. We identified the ATG?ATT (M1I) mutation of the\\u000a start codon in three

Christine Zühlke; Franco Laccone; Mireille Cossée; Alfried Kohlschütter; Michel Koenig; Eberhard Schwinger

1998-01-01

28

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

Microsoft Academic Search

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

Marilyn Kozak

1984-01-01

29

The antibiotic Furvina(R) targets the P-site of 30S ribosomal subunits and inhibits translation initiation displaying start codon bias  

PubMed Central

Furvina®, also denominated G1 (MW 297), is a synthetic nitrovinylfuran [2-bromo-5-(2-bromo-2-nitrovinyl)-furan] antibiotic with a broad antimicrobial spectrum. An ointment (Dermofural®) containing G1 as the only active principle is currently marketed in Cuba and successfully used to treat dermatological infections. Here we describe the molecular target and mechanism of action of G1 in bacteria and demonstrate that in vivo G1 preferentially inhibits protein synthesis over RNA, DNA and cell wall synthesis. Furthermore, we demonstrate that G1 targets the small ribosomal subunit, binds at or near the P-decoding site and inhibits its function interfering with the ribosomal binding of fMet-tRNA during 30S initiation complex (IC) formation ultimately inhibiting translation. Notably, this G1 inhibition displays a bias for the nature (purine vs. pyrimidine) of the 3?-base of the codon, occurring efficiently only when the mRNA directing 30S IC formation and translation contains the canonical AUG initiation triplet or the rarely found AUA triplet, but hardly occurs when the mRNA start codon is either one of the non-canonical triplets AUU or AUC. This codon discrimination by G1 is reminiscent, though of opposite type of that displayed by IF3 in its fidelity function, and remarkably does not occur in the absence of this factor.

Fabbretti, Attilio; Brandi, Letizia; Petrelli, Dezemona; Pon, Cynthia L.; Castanedo, Nilo R.; Medina, Ricardo; Gualerzi, Claudio O.

2012-01-01

30

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

PubMed

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

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

2000-05-15

31

GTG mutation in the start codon of the androgen receptor gene in a family of horses with 64,XY disorder of sex development.  

PubMed

Genetic sex in mammals is determined by the sex chromosomal composition of the zygote. The X and Y chromosomes are responsible for numerous factors that must work in close concert for the proper development of a healthy sexual phenotype. The role of androgens in case of XY chromosomal constitution is crucial for normal male sex differentiation. The intracellular androgenic action is mediated by the androgen receptor (AR), and its impaired function leads to a myriad of syndromes with severe clinical consequences, most notably androgen insensitivity syndrome and prostate cancer. In this paper, we investigated the possibility that an alteration of the equine AR gene explains a recently described familial XY, SRY?+ disorder of sex development. We uncovered a transition in the first nucleotide of the AR start codon (c.1A>G). To our knowledge, this represents the first causative AR mutation described in domestic animals. It is also a rarely observed mutation in eukaryotes and is unique among the >750 entries of the human androgen receptor mutation database. In addition, we found another quiet missense mutation in exon 1 (c.322C>T). Transcription of AR was confirmed by RT-PCR amplification of several exons. Translation of the full-length AR protein from the initiating GTG start codon was confirmed by Western blot using N- and C-terminal-specific antibodies. Two smaller peptides (25 and 14 amino acids long) were identified from the middle of exon 1 and across exons 5 and 6 by mass spectrometry. Based upon our experimental data and the supporting literature, it appears that the AR is expressed as a full-length protein and in a functional form, and the observed phenotype is the result of reduced AR protein expression levels. PMID:22095250

Révay, T; Villagómez, D A F; Brewer, D; Chenier, T; King, W A

2012-01-01

32

Rare variants analysis of neurexin-1? in autism reveals a novel start codon mutation affecting protein levels at synapses.  

PubMed

Neurexins are synaptic plasma membrane proteins encoded by three genes (NRXN1, -2, -3) with alternative promoters. Mutations in neurexin genes have been identified in different neurodevelopmental disorders, including autism. Recently, two point mutations altering the translation initiation site of NRXN1? (c.-3G>T and c.3G>T) have been described in patients with autism and mental retardation. In this study, we analyzed the NRXN1? gene in a sample of 153 patients with autism. We report the identification of a novel mutation, c.3G>A (p.Met1), affecting the translation initiation site. Expression analysis showed that the c.3G>A mutation switches the translation start site of NRXN1? to an in-frame downstream methionine and decreases synaptic levels of the mutant protein in cultured neurons. These data reinforce a role for synaptic defects of NRXN1? in neurodevelopmental disorders. PMID:24064682

Camacho-Garcia, Rafael J; Hervás, Amaia; Toma, Claudio; Balmaña, Noemí; Cormand, Bru; Martinez-Mir, Amalia; Scholl, Francisco G

2013-12-01

33

Comprehensive Analysis of Transcript Start Sites in Ly49 Genes Reveals an Unexpected Relationship with Gene Function and a Lack Of Upstream Promoters  

Microsoft Academic Search

Comprehensive analysis of the transcription start sites of the Ly49 genes of C57BL\\/6 mice using the oligo-capping 5?-RACE technique revealed that the genes encoding the “missing self” inhibitory receptors, Ly49A, C, G, and I, were transcribed from multiple broad regions in exon 1, in the intron1\\/exon2 region, and upstream of exon -1b. Ly49E was also transcribed in this manner, and

Frances Gays; Alan S. C. Koh; Katarzyna M. Mickiewicz; Jonathan G. Aust; Colin G. Brooks; Jason Barbour

2011-01-01

34

A Mutation in the Start Codon of ?-Crystallin D Leads to Nuclear Cataracts in the Dahl SS/Jr-Ctr Strain  

PubMed Central

Cataracts are a major cause of blindness. The most common forms of cataracts are age and UV related and develops mostly in the elderly, while congenital cataracts appear at birth or in early childhood. The Dahl salt-sensitive (SS/Jr) rat is an extensively used model of salt-sensitive hypertension that exhibits concomitant renal disease. In the mid 1980’s, cataracts appeared in a few animals in the Dahl S colony, presumably the result of a spontaneous mutation. The mutation was fixed and bred to establish the SS/Jr-Ctr substrain. The SS/Jr-Ctr substrain has been exclusively used by a single investigator to study the role of steroids and hypertension. Using a classical positional cloning approach, we localized the cataract gene with high-resolution to a less than 1 Mbp region on chromosome 9 using an F1 (SS/Jr-Ctr X SHR) X SHR backcross population. The 1 Mbp region contained only 13 genes, including 4 genes from the ?-crystallins (Cryg) gene family which are known to play a role in cataract formation. All of the ?-crystallins were sequenced and a novel point mutation in the start codon (ATG ? GTG) of the Crygd gene was identified which led to the complete absence of CRYGD protein in the eyes of the SS/Jr-Ctr strain. In summary, the identification of the genetic cause in this novel cataract model may provide an opportunity to better understand the development of cataracts, particularly in the context of hypertension.

Johnson, Ashley C.; Lee, Jonathan W.; Harmon, Ashlyn C.; Morris, Zaliya; Wang, Xuexiang; Fratkin, Jonathan; Rapp, John P.; Gomez-Sanchez, Elise; Garrett, Michael R.

2013-01-01

35

The in Vivo TRPV6 Protein Starts at a Non-AUG Triplet, Decoded as Methionine, Upstream of Canonical Initiation at AUG*  

PubMed Central

TRPV6 channels function as epithelial Ca2+ entry pathways in the epididymis, prostate, and placenta. However, the identity of the endogenous TRPV6 protein relies on predicted gene coding regions and is only known to a certain level of approximation. We show that in vivo the TRPV6 protein has an extended N terminus. Translation initiates at a non-AUG codon, at ACG, which is decoded by methionine and which is upstream of the annotated AUG, which is not used for initiation. The in vitro properties of channels formed by the extended full-length TRPV6 proteins and the so-far annotated and smaller TRPV6 are similar, but the extended N terminus increases trafficking to the plasma membrane and represents an additional scaffold for channel assembly. The increased translation of the smaller TRPV6 cDNA version may overestimate the in vivo situation where translation efficiency may represent an additional mechanism to tightly control the TRPV6-mediated Ca2+ entry to prevent deleterious Ca2+ overload.

Fecher-Trost, Claudia; Wissenbach, Ulrich; Beck, Andreas; Schalkowsky, Pascal; Stoerger, Christof; Doerr, Janka; Dembek, Anna; Simon-Thomas, Martin; Weber, Armin; Wollenberg, Peter; Ruppert, Thomas; Middendorff, Ralf; Maurer, Hans H.; Flockerzi, Veit

2013-01-01

36

Translation of chloroplast psbD mRNA in Chlamydomonas is controlled by a secondary RNA structure blocking the AUG start codon  

PubMed Central

Translation initiation represents a key step during regulation of gene expression in chloroplasts. Here, we report on the identification and characterization of three suppressor point mutations which overcome a translational defect caused by the deletion of a U-rich element in the 5?-untranslated region (5?-UTR) of the psbD mRNA in the green alga Chlamydomonas reinhardtii. All three suppressors affect a secondary RNA structure encompassing the psbD AUG initiation codon within a double-stranded region as judged by the analysis of site-directed chloroplast mutants as well as in vitro RNA mapping experiments using RNase H. In conclusion, the data suggest that these new element serves as a negative regulator which mediates a rapid shut-down of D2 synthesis.

Klinkert, Birgit; Elles, Ingolf; Nickelsen, Jorg

2006-01-01

37

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

PubMed Central

Background Codon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Although genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias. Methods and Principal Findings Here, we use bioinformatics approaches to analyze codon usage bias and codon context patterns in a genome-wide manner among 15 dipteran and 7 hymenopteran insect species. Results show that GAA is the most frequent codon in the dipteran species whereas GAG is the most frequent codon in the hymenopteran species. Data reveals that codons ending with C or G are frequently used in the dipteran genomes whereas codons ending with A or T are frequently used in the hymenopteran genomes. Synonymous codon usage orders (SCUO) vary within genomes in a pattern that seems to be distinct for each species. Based on comparison of 30 one-to-one orthologous genes among 17 species, the fruit fly Drosophila willistoni shows the least codon usage bias whereas the honey bee (Apis mellifera) shows the highest bias. Analysis of codon context patterns of these insects shows that specific codons are frequently used as the 3?- and 5?-context of start and stop codons, respectively. Conclusions Codon bias pattern is distinct between dipteran and hymenopteran insects. While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects. Also, codon context patterns vary among these species largely according to their phylogeny.

Behura, Susanta K.; Severson, David W.

2012-01-01

38

Nucleotide sequence of the LuxC gene and the upstream DNA from the bioluminescent system of Vibrio harveyi.  

PubMed Central

The nucleotide sequence of the luxC gene (1431 bp) and the upstream DNA (1049 bp) of the luminescent bacterium Vibrio harveyi has been determined. The luxC gene can be translated into a polypeptide of 55 kDa in excellent agreement with the molecular mass of the reductase polypeptide required for synthesis of the aldehyde substrate for the bioluminescent reaction. Analyses of codon usage showed a high frequency (1.9%) of the isoleucine codon, AUA, in the luxC gene compared to that found in Escherichia coli genes (0.2%) and its absence in the luxA, B and D genes. The low G/C content of the luxC gene and upstream DNA (38-39%) compared to that found in the other lux genes of V. harveyi (45%) was primarily due to a stretch of 500 nucleotides with only a 24% G/C content, extending from 200 bp inside lux C to 300 bp upstream. Moreover, an open reading frame did not extend for more than 48 codons between the luxC gene and 600 bp upstream at which point a gene transcribed in the opposite direction started. As the lux system in the luminescent bacterium, V. fischeri, contains a regulatory gene immediately upstream of luxC transcribed in the same direction, these results show that the organization and regulation of the lux genes have diverged in different luminescent bacteria.

Miyamoto, C M; Graham, A F; Meighen, E A

1988-01-01

39

Quantifying Position-Dependent Codon Usage Bias  

PubMed Central

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

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

2014-01-01

40

Amino-terminal extension generated from an upstream AUG codon is not required for mitochondrial import of yeast N2,N2-dimethylguanosine-specific tRNA methyltransferase.  

PubMed Central

The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The DNA sequence of the TRM1 locus and the 5' ends of mRNAs expressed from this gene have been determined. The majority of the 5' ends map within a large open reading frame between two in-frame ATGs at positions +1 and +49. A small fraction of the 5' ends are located upstream of the first ATG. Both AUGs of the TRM1 mRNAs are used to initiate translation, and two forms of N2,N2-dimethylguanosine-specific tRNA methyltransferase, which differ by an amino-terminal extension of 16 amino acids, are made. Mitochondrial tRNAs are modified when the initiation of translation is limited to one or the other of the AUGs, suggesting that the amino-terminal extension is not necessary for import of the protein into mitochondria. Mitochondrial targeting information must, therefore, be located in a region of N2,N2-dimethylguanosine-specific tRNA methyltransferase that is found in both forms of the enzyme. Images

Ellis, S R; Hopper, A K; Martin, N C

1987-01-01

41

Upstream Processing  

NSDL National Science Digital Library

This two page PDF, created by Northeast Biomanufacturing Center and Collaborative, discusses the key functions and tasks of a manufacturing technician (upstream). The document focuses mostly on: the work compliance with both EH&S and cGMPS, the cleanliness and maintenance of production areas, maintaining effective communication, the preparation of process materials, the preparation of equipment, performance of basic manufacturing operations, performing upstream manufacturing operations and performance sampling. Each one of these topics contains anywhere from five to fifteen different subtopics. The lists are meant to give a broad overview of each one of these topics.

2009-09-24

42

Two alternative ways of start site selection in human norovirus reinitiation of translation.  

PubMed

The calicivirus minor capsid protein VP2 is expressed via termination/reinitiation. This process depends on an upstream sequence element denoted termination upstream ribosomal binding site (TURBS). We have shown for feline calicivirus and rabbit hemorrhagic disease virus that the TURBS contains three sequence motifs essential for reinitiation. Motif 1 is conserved among caliciviruses and is complementary to a sequence in the 18 S rRNA leading to the model that hybridization between motif 1 and 18 S rRNA tethers the post-termination ribosome to the mRNA. Motif 2 and motif 2* are proposed to establish a secondary structure positioning the ribosome relative to the start site of the terminal ORF. Here, we analyzed human norovirus (huNV) sequences for the presence and importance of these motifs. The three motifs were identified by sequence analyses in the region upstream of the VP2 start site, and we showed that these motifs are essential for reinitiation of huNV VP2 translation. More detailed analyses revealed that the site of reinitiation is not fixed to a single codon and does not need to be an AUG, even though this codon is clearly preferred. Interestingly, we were able to show that reinitiation can occur at AUG codons downstream of the canonical start/stop site in huNV and feline calicivirus but not in rabbit hemorrhagic disease virus. Although reinitiation at the original start site is independent of the Kozak context, downstream initiation exhibits requirements for start site sequence context known for linear scanning. These analyses on start codon recognition give a more detailed insight into this fascinating mechanism of gene expression. PMID:24599949

Luttermann, Christine; Meyers, Gregor

2014-04-25

43

Codon optimizer: a freeware tool for codon optimization  

Microsoft Academic Search

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

Anders Fuglsang

2003-01-01

44

Converting nonsense codons into sense codons by targeted pseudouridylation.  

PubMed

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

Karijolich, John; Yu, Yi-Tao

2011-06-16

45

Efficient initiation of mammalian mRNA translation at a CUG codon.  

PubMed Central

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

Dasso, M C; Jackson, R J

1989-01-01

46

Codon usage in Giardia lamblia.  

PubMed

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

Char, S; Farthing, M J

1992-01-01

47

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

PubMed Central

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

Harms, E; Umbarger, H E

1987-01-01

48

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

PubMed Central

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

2013-01-01

49

Non-canonical translation start sites in the TMEM16A chloride channel?  

PubMed Central

TMEM16A is a plasma membrane protein with voltage- and calcium-dependent chloride channel activity. The role of the various TMEM16A domains in expression and function is poorly known. In a previous study, we found that replacing the first ATG of the TMEM16A coding sequence with a nonsense codon (M1X mutation), to force translation from the second ATG localized at position 117, only had minor functional consequences. Therefore, we concluded that this region is dispensable for TMEM16A processing and channel activity. We have now removed the first 116 codons from the TMEM16A coding sequence. Surprisingly, the expression of the resulting mutant, ?(1–116), resulted in complete loss of activity. We hypothesized that, in the mutant M1X, translation may start at a position before the second ATG, using a non-canonical start codon. Therefore, we placed an HA-epitope at position 89 in the M1X mutant. We found, by western blot analysis, that the HA-epitope can be detected, thus demonstrating that translation starts from an upstream non-ATG codon. We truncated the N-terminus of TMEM16A at different sites while keeping the HA-epitope. We found that stepwise shortening of TMEM16A caused an in parallel stepwise decrease in TMEM16A expression and function. Our results indicate that indeed the N-terminus of TMEM16A is important for its activity. The use of an alternative start codon appears to occur in a naturally-occurring TMEM16A isoform that is particularly expressed in human testis. Future experiments will need to address the role of normal and alternative amino-terminus in TMEM16A structure and function.

Sondo, Elvira; Scudieri, Paolo; Tomati, Valeria; Caci, Emanuela; Mazzone, Amelia; Farrugia, Gianrico; Ravazzolo, Roberto; Galietta, Luis J.V.

2014-01-01

50

Utilization of non-AUG initiation codons in a flow cytometric method for efficient selection of recombinant cell lines.  

PubMed

Here we describe a method that couples flow cytometric detection with the attenuated translation of a reporter protein to enable efficient selection of CHO clones producing high levels of recombinant proteins. In this system, a small cell surface reporter protein is expressed from an upstream open reading frame utilizing a non-AUG initiation (alternate start) codon. Due to the low translation initiation efficiency of this alternate start codon, the majority of translation initiation events occur at the first AUG of the downstream open reading frame encoding the recombinant protein of interest. While translation of the reporter is significantly reduced, the levels are sufficient for detection using flow cytometric methods and, in turn, predictive of protein expression from the gene of interest since both ORFs are translated from the same mRNA. Using this system, CHO cells have been sorted to obtain enriched pools producing significantly higher levels of recombinant proteins than the starting cell population and clones with significantly better productivity than those generated from limiting dilution cloning. This method also serves as an effective screening tool during clone expansion to enable resources to be focused solely on clones with both high and stable expression. PMID:21618473

Cairns, Victor R; DeMaria, Christine T; Poulin, Francis; Sancho, José; Liu, Ping; Zhang, Jin; Campos-Rivera, Juanita; Karey, Kenneth P; Estes, Scott

2011-11-01

51

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

PubMed

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

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

2001-09-01

52

Divergence in codon usage of Lactobacillus species.  

PubMed Central

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

Pouwels, P H; Leunissen, J A

1994-01-01

53

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

PubMed

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

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

2005-11-01

54

CodonO: codon usage bias analysis within and across genomes  

Microsoft Academic Search

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

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

2007-01-01

55

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency  

PubMed Central

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

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

2012-01-01

56

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

PubMed Central

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

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

2001-01-01

57

Extensive Transcript Diversity and Novel Upstream Open Reading Frame Regulation in Yeast  

PubMed Central

To understand the diversity of transcripts in yeast (Saccharomyces cerevisiae) we analyzed the transcriptional landscapes for cells grown under 18 different environmental conditions. Each sample was analyzed using RNA-sequencing, and a total of 670,446,084 uniquely mapped reads and 377,263 poly-adenylated end tags were produced. Consistent with previous studies, we find that the majority of yeast genes are expressed under one or more different conditions. By directly comparing the 5? and 3? ends of the transcribed regions, we find extensive differences in transcript ends across many conditions, especially those of stationary phase, growth in grape juice, and salt stimulation, suggesting differential choice of transcription start and stop sites is pervasive in yeast. Relative to the exponential growth condition (i.e., YPAD), transcripts differing at the 5? ends and 3? ends are predicted to differ in their annotated start codon in 21 genes and their annotated stop codon in 63 genes. Many (431) upstream open reading frames (uORFs) are found in alternate 5? ends and are significantly enriched in transcripts produced during the salt response. Mutational analysis of five genes with uORFs revealed that two sets of uORFs increase the expression of a reporter construct, indicating a role in activation which had not been reported previously, whereas two other uORFs decreased expression. In addition, RNA binding protein motifs are statistically enriched for alternate ends under many conditions. Overall, these results demonstrate enormous diversity of transcript ends, and that this heterogeneity is regulated under different environmental conditions. Moreover, transcript end diversity has important biological implications for the regulation of gene expression. In addition, our data also serve as a valuable resource for the scientific community.

Waern, Karl; Snyder, Michael

2013-01-01

58

Efficiency of reinitiation of translation on human immunodeficiency virus type 1 mRNAs is determined by the length of the upstream open reading frame and by intercistronic distance.  

PubMed Central

In this study, we examined the mechanism of translation of the human immunodeficiency virus type 1 tat mRNA in eucaryotic cells. This mRNA contains the tat open reading frame (ORF), followed by rev and nef ORFs, but only the first ORF, encoding tat, is efficiently translated. Introduction of premature stop codons in the tat ORF resulted in efficient translation of the downstream rev ORF. We show that the degree of inhibition of translation of rev is proportional to the length of the upstream tat ORF. An upstream ORF spanning 84 nucleotides was predicted to inhibit 50% of the ribosomes from initiating translation at downstream AUGs. Interestingly, the distance between the upstream ORF and the start codon of the second ORF also played a role in efficiency of downstream translation initiation. It remains to be investigated if these conclusions relate to translation of mRNAs other than human immunodeficiency virus type 1 mRNAs. The strong inhibition of rev translation exerted by the presence of the tat ORF may reflect the different roles of Tat and Rev in the viral life cycle. Tat acts early to induce high production of all viral mRNAs. Rev induces a switch from the early to the late phase of the viral life cycle, resulting in production of viral structural proteins and virions. Premature Rev production may result in entrance into the late phase in the presence of suboptimal levels of viral mRNAs coding for structural proteins, resulting in inefficient virus production.

Luukkonen, B G; Tan, W; Schwartz, S

1995-01-01

59

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

60

Conservation of a dual-start motif in P22 lysis gene regulation.  

PubMed

Gene 13 of bacteriophage P22 is functionally equivalent to lambda lysis gene S. Gene S codes for two products, the polypeptides S105 and S107, produced from translational initiation events at the third and first codon, respectively. We have shown that the two polypeptides have opposing functions in lysis: S105 is the lethal lysis effector, and S107 acts as an inhibitor of lysis (U. Bläsi, K. Nam, D. Hartz, L. Gold, and R. Young, EMBO J. 11:3501-3510, 1989). Gene 13 has a 108-codon reading frame and its product begins with a similar motif: Met-1-Lys-2-Lys-3-Met-4. Here, we present in vivo and in vitro evidence for the expression of a 13(108) and a 13(105) product and show that the lambda lysis control mechanisms is evolutionarily conserved in phage P22. In this case 13(108), like S107 in lambda, functions as the inhibitor of the lysis effector 13(105). Although the DNA sequences upstream of the S and 13 gene starts showed less homology, the same structural characteristics, i.e., stem-loop structures immediately upstream and about 10 codons downstream of the start region, were present in both reading frames. Using in vitro mutagenesis and toeprinting, we show that the upstream stem-loop structures of genes 13 and S, containing the Shine-Dalgarno sequence for initiations at Met-1, are interchangeable. Moreover, our data indicate that the stability of the secondary structures present in the translational initiation regions of genes S and 13 is set to create a particular ratio of initiation events at Met-1 and Met-3 or Met-4. The ratio of effector to inhibitor was much higher in P22 than in lambda. We propose that this reflects less transcriptional readthrough at the late terminator t(R) and suggests that the dual-start motif in genes 13 and S may be important for establishment of maintenance of the lysogenic state. PMID:2294085

Nam, K; Bläsi, U; Zagotta, M T; Young, R

1990-01-01

61

Conservation of a dual-start motif in P22 lysis gene regulation.  

PubMed Central

Gene 13 of bacteriophage P22 is functionally equivalent to lambda lysis gene S. Gene S codes for two products, the polypeptides S105 and S107, produced from translational initiation events at the third and first codon, respectively. We have shown that the two polypeptides have opposing functions in lysis: S105 is the lethal lysis effector, and S107 acts as an inhibitor of lysis (U. Bläsi, K. Nam, D. Hartz, L. Gold, and R. Young, EMBO J. 11:3501-3510, 1989). Gene 13 has a 108-codon reading frame and its product begins with a similar motif: Met-1-Lys-2-Lys-3-Met-4. Here, we present in vivo and in vitro evidence for the expression of a 13(108) and a 13(105) product and show that the lambda lysis control mechanisms is evolutionarily conserved in phage P22. In this case 13(108), like S107 in lambda, functions as the inhibitor of the lysis effector 13(105). Although the DNA sequences upstream of the S and 13 gene starts showed less homology, the same structural characteristics, i.e., stem-loop structures immediately upstream and about 10 codons downstream of the start region, were present in both reading frames. Using in vitro mutagenesis and toeprinting, we show that the upstream stem-loop structures of genes 13 and S, containing the Shine-Dalgarno sequence for initiations at Met-1, are interchangeable. Moreover, our data indicate that the stability of the secondary structures present in the translational initiation regions of genes S and 13 is set to create a particular ratio of initiation events at Met-1 and Met-3 or Met-4. The ratio of effector to inhibitor was much higher in P22 than in lambda. We propose that this reflects less transcriptional readthrough at the late terminator t(R) and suggests that the dual-start motif in genes 13 and S may be important for establishment of maintenance of the lysogenic state. Images FIG. 3 FIG. 4 FIG. 5

Nam, K; Blasi, U; Zagotta, M T; Young, R

1990-01-01

62

Biotechnology: Upstream Processing Associate  

NSDL National Science Digital Library

In this 2:31 video excerpted from Pathways to Technology, youâÂÂll learn about the role biotechnology plays in the fight against cancer. Roya Dirin is an upstream processing associate who works with cells, looking for proteins that can help treat cancer. Her first career was as a midwife, but she decided to switch fields because she wanted to help cure diseases. Roya explains how her community college biotechnology degree is just the first step in her new career. The video is accompanied by a background essay, standards alignment, and discussion questions. Users who sign up for a free account can download the video as well.

2012-05-23

63

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

PubMed Central

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

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

2012-01-01

64

CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models  

PubMed Central

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

Gil, Manuel; Zoller, Stefan; Anisimova, Maria

2013-01-01

65

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

PubMed

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

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

2013-06-01

66

Nucleotide sequence and transcriptional start site of the Methylobacterium organophilum XX methanol dehydrogenase structural gene  

SciTech Connect

The nucleotide sequence of a cloned 2.5-kilobase-pair SmaI fragment containing the methanol dehydrogenase (MDH) structural gene from Methylobacterium organophilum XX was determined. A single open reading frame with a coding capacity of 626 amino acids (molecular weight, 66,000) was identified on one stand, and N-terminal sequencing of purified MDH revealed that 27 of these residues constituted a putative signal peptide. Primer extension mapping of in vivo transcripts indicated that the start of mRNA synthesis was 160 to 170 base pairs upstream of the ATG codon. Northern (RNA) blot analysis further demonstrated that the transcript was 2.1 kilobase pairs in length and therefore appeared to encode only MDH.

Machlin, S.M.; Hanson, R.S. (Univ. of Minnesota, Navarre (USA))

1988-10-01

67

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

PubMed Central

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

Kliman, Richard M.

2014-01-01

68

Interferon-induced transcription of a gene encoding a 15-kDA protein depends on an upstream enhancer element  

SciTech Connect

A human gene encoding an interferon-induced 15-kDa protein has been isolated from a genomic library. The gene appears to be single-copy and is composed of two exons, the first of which contains the ATG translation initiation codon. In vitro nuclear run-on assays showed that the transcription rate of the gene is stimulated after interferon treatment. To analyze transcriptional regulatory sequences, the authors constructed recombinant plasmids for use in transient transfection assays of HeLa cells. Constructs containing 115 nucleotides 5' to the transcription initiation site were found to be fully inducible by interferon. Assays of deletion mutants identified a critical element for interferon induction located between -115 and -96, just upstream of the CCAAT box. Moreover, a DNA fragment including this region can confer interferon inducibility on a heterologous promoter (thymidine kinase) when cloned in either orientation upstream of the gene or downstream of the gene. These are properties characteristic of an enhancer element that is active only after treatment with interferon. This regulatory sequence may be shared by a group of interferon-induced genes, since a very similar sequence is present within the functional region near the RNA start site of another interferon-induced gene.

Reich, N.; Evans, B.; Levy, D.; Fahey, D.; Knight, E. Jr.; Darnell, J.E. Jr.

1987-09-01

69

Hidden coding potential of eukaryotic genomes: nonAUG started ORFs  

Microsoft Academic Search

It is widely considered that the vast majority of eukaryotic mRNAs contain only one open reading frame (ORF) and encode single protein. However, eukaryotic ribosomes can initiate translation at alternative start codons due to leaky scanning or reinitiation mechanisms that provides an opportunity to synthesize several protein products. Recent investigations also demonstrated that alternative translation from nonAUG start codons and

Alex V. Kochetov; Phani Deep Prayaga; Oxana A. Volkova; Ramasubbu Sankararamakrishnan

2012-01-01

70

Context specific misreading of phenylalanine codons  

Microsoft Academic Search

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

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

1989-01-01

71

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

72

Effect of Codon Message on Xylanase Thermal Activity*  

PubMed Central

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

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

2012-01-01

73

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

PubMed Central

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

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

2010-01-01

74

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

PubMed

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

Kliman, Richard M

2014-01-01

75

Start Young!  

ERIC Educational Resources Information Center

Discusses the importance of early interest in science and how effective it is on career choice in adult stages of life. Recommends starting mathematics and science activities in preschool and kindergarten. Describes how to create a career-oriented learning center in the classroom with examples of kitchen chemistry, nutrition/botany, zoology,…

Rubin, Penni

2002-01-01

76

The Effects of Codon Context on In Vivo Translation Speed  

PubMed Central

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

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

2014-01-01

77

Getting Started  

NSDL National Science Digital Library

Before starting any of the activities in this guide, we strongly recommend that you read the information in this section. Here we cover the critically important issues of how to handle amphibians and reptiles, and safety issues concerning these animals and field activities in general. We also discuss permits and regulations relating to the collecting, handling, and raising of herps. This free selection also includes the Table of Contents, Preface, and Introduction.

Krasny, Marianne E.; Schneider, Rebecca L.; Morreale, Steven J.

2001-01-01

78

Codon Usage and Selection on Proteins  

Microsoft Academic Search

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

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

2006-01-01

79

An Improved Implementation of Codon Adaptation Index  

PubMed Central

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

Xia, Xuhua

2007-01-01

80

VH4 codon signature for multiple sclerosis  

US Patent & Trademark Office Database

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

2013-03-12

81

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

PubMed Central

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

Shokrani, HR; Shayan, P; Eslami, A; Nabavi, R

2012-01-01

82

Single-stranded genomic architecture constrains optimal codon usage  

PubMed Central

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

Cardinale, Daniel J.; Duffy, Siobain

2011-01-01

83

Molecular evolution of synonymous codon usage in Populus  

Microsoft Academic Search

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

Pär K Ingvarsson; Umeå Plant

2008-01-01

84

Upstream open reading frames: Molecular switches in (patho)physiology  

PubMed Central

Conserved upstream open reading frames (uORFs) are found within many eukaryotic transcripts and are known to regulate protein translation. Evidence from genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of human diseases. A genetic mouse model has recently provided proof-of-principle support for the physiological relevance of uORF-mediated translational control in mammals. The targeted disruption of the uORF initiation codon within the transcription factor CCAAT/enhancer binding protein ? (C/EBP?) gene resulted in deregulated C/EBP? protein isoform expression, associated with defective liver regeneration and impaired osteoclast differentiation. The high prevalence of uORFs in the human transcriptome suggests that intensified search for mutations within 5? RNA leader regions may reveal a multitude of alterations affecting uORFs, causing pathogenic deregulation of protein expression.

Wethmar, Klaus; Smink, Jeske J; Leutz, Achim

2010-01-01

85

Stop codon reassignments in the wild.  

PubMed

The canonical genetic code is assumed to be deeply conserved across all domains of life with very few exceptions. By scanning 5.6 trillion base pairs of metagenomic data for stop codon reassignment events, we detected recoding in a substantial fraction of the >1700 environmental samples examined. We observed extensive opal and amber stop codon reassignments in bacteriophages and of opal in bacteria. Our data indicate that bacteriophages can infect hosts with a different genetic code and demonstrate phage-host antagonism based on code differences. The abundance and diversity of genetic codes present in environmental organisms should be considered in the design of engineered organisms with altered genetic codes in order to preclude the exchange of genetic information with naturally occurring species. PMID:24855270

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

2014-05-23

86

Upstream regulation of mycotoxin biosynthesis.  

PubMed

Mycotoxins are natural contaminants of food and feed products, posing a substantial health risk to humans and animals throughout the world. A plethora of filamentous fungi has been identified as mycotoxin producers and most of these fungal species belong to the genera Aspergillus, Fusarium, and Penicillium. A number of studies have been conducted to better understand the molecular mechanisms of biosynthesis of key mycotoxins and the regulatory cascades controlling toxigenesis. In many cases, the mycotoxin biosynthetic genes are clustered and regulated by one or more pathway-specific transcription factor(s). In addition, as biosynthesis of many secondary metabolites is coordinated with fungal growth and development, there are a number of upstream regulators affecting biosynthesis of mycotoxins in fungi. This review presents a concise summary of the regulation of mycotoxin biosynthesis, focusing on the roles of the upstream regulatory elements governing biosynthesis of aflatoxin and sterigmatocystin in Aspergillus. PMID:24377857

Yu, Jae-Hyuk; Alkhayyat, Fahad

2014-01-01

87

Comparative genomic analysis of novel conserved peptide upstream open reading frames in Drosophila melanogaster and other dipteran species  

PubMed Central

Background Upstream open reading frames (uORFs) are elements found in the 5'-region of an mRNA transcript, capable of regulating protein production of the largest, or major ORF (mORF), and impacting organismal development and growth in fungi, plants, and animals. In Drosophila, approximately 40% of transcripts contain upstream start codons (uAUGs) but there is little evidence that these are translated and affect their associated mORF. Results Analyzing 19,389 Drosophila melanogaster transcript annotations and 666,153 dipteran EST sequences we have identified 44 putative conserved peptide uORFs (CPuORFs) in Drosophila melanogaster that show evidence of negative selection, and therefore are likely to be translated. Transcripts with CPuORFs constitute approximately 0.3% of the total number of transcripts, a similar frequency to the Arabidopsis genome, and have a mean length of 70 amino acids, much larger than the mean length of plant CPuORFs (40 amino acids). There is a statistically significant clustering of CPuORFs at cytological band 57 (p = 10-5), a phenomenon that has never been described for uORFs. Based on GO term and Interpro domain analyses, genes in the uORF dataset show a higher frequency of ORFs implicated in mitochondrial import than the genome-wide frequency (p < 0.01) as well as methyltransferases (p < 0.02). Conclusion Based on these data, it is clear that Drosophila contain putative CPuORFs at frequencies similar to those found in plants. They are distinguished, however, by the type of mORF they tend to associate with, Drosophila CPuORFs preferentially occurring in transcripts encoding mitochondrial proteins and methyltransferases. This provides a basis for the study of CPuORFs and their putative regulatory role in mitochondrial function and disease.

Hayden, Celine A; Bosco, Giovanni

2008-01-01

88

Selection on codon bias in yeast: a transcriptional hypothesis.  

PubMed

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

Trotta, Edoardo

2013-11-01

89

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

PubMed

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

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

2014-07-01

90

Comparative Genomics of Trypanosomatid Pathogens using Codon Usage Bias  

PubMed Central

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

Rashmi, Mayank; Swati, D

2013-01-01

91

Upstream waves in Saturn's foreshock  

NASA Technical Reports Server (NTRS)

An analysis based on plasma and magnetic-field data obtained from Voyager 1 during its Saturn encounter is reported. The plasma data provided every 96 sec and magnetic-field data averaged over 48 sec are utilized. The evidence of upstream waves at Saturn are detected. The waves have a period, in the spacecraft frame, of about 550 sec and a relative amplitude larger than 0.3, are left- and right-hand elliptically polarized, and propagate at about 30 deg with respect to the average magnetic field. The appearance of the waves is correlated with the spacecraft being magnetically connected to the bow shock.

Bavassano Cattaneo, M. B.; Cattaneo, P.; Moreno, G.; Lepping, R. P.

1991-01-01

92

Codon 12 Region of Mouse K-ras Gene Is the Site for in vitro Binding of Transcription Factors GATA6 and NF-Y  

Microsoft Academic Search

Codon 12 of the K-ras gene is a generally recognized example of a mutational hot spot. By the approach of gel retardation and specific antibodies,\\u000a a double-stranded oligonucleotide corresponding to the codon 12 region of the mouse K-ras gene (from 20 to 50 bp with respect to the exon 1 start) was found to be a site for cooperative binding

E. V. Gorshkova; V. I. Kaledin; V. F. Kobzev; T. I. Merkulova

2005-01-01

93

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

PubMed Central

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

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

2014-01-01

94

RNA polymerase-binding and transcription initiation sites upstream of the methyl reductase operon of Methanococcus vannielii  

SciTech Connect

RNA polymerase, purified from Methanococcus vannielii, was shown by exonuclease III footprinting to bind to a 49-base pair (bp) region of DNA in the intergenic region upstream of mcrB. S1 nuclease protection experiments demonstrated that transcription initiation in vivo occurs within this region at 32 or 33 bp 5' to the ATG translation initiation codon of mcrB and 19 or 20 bp 3' to a TATA box.

Thomm, M.; Sherf, B.A.; Reeve, J.N.

1988-04-01

95

Synonymous codon usage pattern analysis of Hepatitis D virus.  

PubMed

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

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

2013-05-01

96

On Ribosome Load, Codon Bias and Protein Abundance  

PubMed Central

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

Klumpp, Stefan; Dong, Jiajia; Hwa, Terence

2012-01-01

97

Identification of an upstream activating sequence and an upstream repressible sequence of the pyruvate kinase gene of the yeast Saccharomyces cerevisiae.  

PubMed Central

To clarify carbon source-dependent control of the glycolytic pathway in the yeast Saccharomyces cerevisiae, we have initiated a study of transcriptional regulation of the pyruvate kinase gene (PYK). By deletion analysis of the 5'-noncoding region of the PYK gene, we have identified an upstream activating sequence (UASPYK1) located between 634 and 653 nucleotides upstream of the initiating ATG codon. The promoter activity of the PYK 5'-noncoding region was abolished when the sequence containing the UASPYK1 was deleted from the region. Synthetic UASPYK1 (26mer), in either orientation, was able to restore the transcriptional activity of UAS-depleted mutants when placed upstream of the TATA sequence located at -199 (ATG as +1). While the UASPYK1 was required for basal to intermediate levels of transcriptional activation, a sequence between -714 and -811 was found to be necessary for full activation. On the other hand, a sequence between -344 and -468 was found to be responsible for transcriptional repression of the PYK gene when yeast cells were grown on nonfermentable carbon sources. This upstream repressible sequence also repressed transcription, although to a lesser extent, when glucose was present in the medium. The possible mechanism for carbon source-dependent regulation of PYK expression through these cis-acting regulatory elements is discussed. Images

Nishizawa, M; Araki, R; Teranishi, Y

1989-01-01

98

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

Microsoft Academic Search

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

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

2006-01-01

99

Stop codons in bacteria are not selectively equivalent  

PubMed Central

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

2012-01-01

100

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

Microsoft Academic Search

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

Chang H Kim; Younghoon Oh; Tae H Lee

1997-01-01

101

A cross talk between codon usage bias in human oncogenes  

PubMed Central

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

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

2014-01-01

102

First analysis of synonymous codon usage in porcine circovirus.  

PubMed

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

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

2014-08-01

103

Experimental telemedicine network by extended upstream CATV  

Microsoft Academic Search

A type of tap-off upstream extension system is developed to provide high-speed upstream signal transmission by our experimental telemedicine network, which is composed of a wireless LAN and three CATV networks. Transmission tests conducted with this extension system show that 64QAM signals at the symbol rate of 5 Msymbols\\/sec can be transferred stably in the 260 MHz extended upstream band

Yuying Yang; M. Nakamura; S. Kubota; H. Shimizu

2003-01-01

104

Codon usage in bacteria: correlation with gene expressivity.  

PubMed Central

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

Gouy, M; Gautier, C

1982-01-01

105

Determinants of Initiation Codon Selection during Translation in Mammalian Cells  

PubMed Central

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

Matsuda, Daiki; Mauro, Vincent P.

2010-01-01

106

Codon usage bias in human cytomegalovirus and its biological implication.  

PubMed

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

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

2014-07-15

107

Directional Next-Generation RNA Sequencing and Examination of Premature Termination Codon Mutations in Endoglin/Hereditary Haemorrhagic Telangiectasia  

PubMed Central

Hereditary haemorrhagic telangiectasia (HHT) is a disease characterised by abnormal vascular structures, and most commonly caused by mutations in ENG, ACVRL1 or SMAD4 encoding endothelial cell-expressed proteins involved in TGF-? superfamily signalling. The majority of mutations reported on the HHT mutation database are predicted to lead to stop codons, either due to frameshifts or direct nonsense substitutions. The proportion is higher for ENG (67%) and SMAD4 (65%) than for ACVRL1 (42%), p < 0.0001. Here, by focussing on ENG, we report why conventional views of these mutations may need to be revised. Of the 111 stop codon-generating ENG mutations, on ExPASy translation, all except one were premature termination codons (PTCs), sited at least 50-55 bp upstream of the final exon-exon boundary of the main endoglin isoform, L-endoglin. This strongly suggests that the mutated RNA species will undergo nonsense-mediated decay. We provide new in vitro expression data to support dominant negative activity of stable truncated endoglin proteins but suggest these will not generate HHT: the single natural stop codon mutation in L-endoglin (sited within 50-55 nucleotides of the final exon-exon boundary) is unlikely to generate functional protein since it replaces the entire transmembrane domain, as would 8 further natural stop codon mutations, if the minor S-endoglin isoform were implicated in HHT pathogenesis. Finally, next-generation RNA sequencing data of 7 different RNA libraries from primary human endothelial cells demonstrate that multiple intronic regions of ENG are transcribed. The potential consequences of heterozygous deletions or duplications of such regions are discussed. These data support the haploinsufficiency model for HHT pathogenesis, explain why final exon mutations have not been detected to date in HHT, emphasise the potential need for functional examination of non-PTC-generating mutations, and lead to proposals for an alternate stratification system of mutational types for HHT genotype-phenotype correlations.

Govani, F.S.; Giess, A.; Mollet, I.G.; Begbie, M.E.; Jones, M.D.; Game, L.; Shovlin, C.L.

2013-01-01

108

AT2AT3profiling: A new look at synonymous codon usage  

Microsoft Academic Search

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

Wolfgang Pluhar

2006-01-01

109

The structure of the human dihydrolipoamide dehydrogenase gene (DLD) and its upstream elements  

SciTech Connect

The structural organization of the gene for the E[sub 3] subunit of the human [alpha]-ketoacid dehydrogenase complexes, dihydrolipoamide dehydrogenase (DLD), and its upstream elements have been determined by restriction endonuclease mapping and DNA sequence analysis of overlapping genomic clones. The gene is approximately 20 kb long. It contains 14 exons ranging in size from 69 to 780 bp and 13 introns ranging in size from 93 bp to l7.0 kb. All splice donor and acceptor sites conform to the GT/AG rule. The 5[prime] ends of mRNA transcripts upstream from the translation initiation codon were determined by primer extension assay. A [open quotes]CAAT box[close quotes]-like sequence is present at 39 bp upstream of the presumptive cap site and the 5[prime] flanking region has been sequenced up to 2.0 kb upstream. There are several sequences compatible with presumptive promoter elements, including an Sp1 binding site, a nuclear respiratory factor 1 site, two cyclic AMP response element binding sites, and a possible negative response element present in the insulin promoter. A 313-bp segment from -2076 to -1763 is 89% homologous to a recently described pTR5 repetitive element found in the human genome. 27 refs., 3 figs., 1 tab.

Feigenbaum, A.S.; Robinson, B.H. (Univ. of Toronto, Ontario (Canada))

1993-08-01

110

Analysis of codon usage and nucleotide composition bias in polioviruses  

Microsoft Academic Search

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

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

2011-01-01

111

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

PubMed Central

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

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

1994-01-01

112

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

PubMed Central

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

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

1994-01-01

113

The empirical codon mutation matrix as a communication channel  

PubMed Central

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

2014-01-01

114

Differential use of an in-frame translation initiation codon regulates human mu opioid receptor (OPRM1)  

Microsoft Academic Search

The pharmacological effects of morphine and morphine-like drugs are mediated primarily through the µ opioid receptor. Here\\u000a we show that differential use of an in-frame translational start codon in the 5?-untranslated region of the OPRM1 generates\\u000a different translational products in vivo and in vitro. The 5?-end of the OPRM1 gene is necessary for initiating the alternate\\u000a form and for subsequent

Kyu Young Song; Hack Sun Choi; Cheol Kyu Hwang; Chun Sung Kim; Ping-Yee Law; Li-Na Wei; Horace H. Loh

2009-01-01

115

Modular Innovations in Upstream Fish Passage.  

National Technical Information Service (NTIS)

This project examined design alternatives for the construction, equipping and operation of upstream fish passage facilities suitable for installation at small hydropower sites being developed or re-developed. These alternatives were examined for technical...

J. Truebe M. Drooker

1980-01-01

116

Mussel Assemblages Upstream from Three Kansas Resevoirs  

Microsoft Academic Search

During summers 1999 and 2000, we surveyed 40 sites in the Marais des Cygnes River (n=15), Fall River (n=13), and Elk River (n=12) in eastern Kansas, upstream from three reservoirs, to examine effects of reservoir inundation on upstream mussel assemblages. We recorded present and historically-occurring species plus 10 habitat variables at each site. We collected 1367 live mussels of 18

Matt Combes; David Edds

2005-01-01

117

Whistler waves observed upstream from collisionless shocks  

Microsoft Academic Search

Waves in the frequency range 0.5-4. Hz have been studied in the region upstream of the earth's bow shock with data from the flux-gate magnetic field experiment on Imp 6. Such waves are invariably detected adjacent to the shock, persisting upstream for intervals often less than a minute but occasionally of the order of many hours. Analysis of 150 examples

D. H. Fairfield

1974-01-01

118

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

Microsoft Academic Search

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

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

2010-01-01

119

Identification of stop codon readthrough genes in Saccharomyces cerevisiae.  

PubMed

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

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

2003-05-01

120

Codon Preference Optimization Increases Prokaryotic Cystatin C Expression  

PubMed Central

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

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

2012-01-01

121

Why Kids Start  

MedlinePLUS

... Home > Stop Smoking > About Smoking > Preventing Smoking Why Kids Start Almost 70% of adult smokers began smoking ... the time they turn 14. So why do kids start smoking in the first place? Their parents ...

122

Waves observed upstream of interplanetary shocks  

NASA Technical Reports Server (NTRS)

The properties of the waves that are present upstream of interplanetary, collisionless, quasi-parallel shocks are described. Two types of such waves have been detected, a higher frequency whistler mode wave and a lower frequency fast mode MHD wave. Both are typically circular or elliptically polarized right-hand waves which propagate along the ambient magnetic field with a 15 deg angle cone. The high frequency waves have sufficient group velocities to outrun the shock, and may be generated by cyclotron resonance with 100 eV to 1 keV shock electrons. The lower frequency waves must be generated locally by particles upstream of the shock, probably by 1-10 keV ions flowing away from the shock. Distinct changes in the spectra of upstream waves as a function of distance from the shock have been noted.

Tsurutani, B. T.; Smith, E. J.; Jones, D. E.

1983-01-01

123

Head Start Automation Manual.  

ERIC Educational Resources Information Center

The task for the National Data Management Project is to share technological capabilities with the Head Start Community in order to implement improved services for children and families involved in Head Start. Many Head Start programs have incorporated technology into their programs, including word processing, database management systems,…

Maryland Univ., College Park. Univ. Coll.

124

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

125

Estimating Selection on Synonymous Codon Usage from Noisy Experimental Data  

PubMed Central

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

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

2013-01-01

126

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

PubMed Central

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

2012-01-01

127

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

PubMed

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

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-06-01

128

Differential Codon Adaptation between dsDNA and ssDNA Phages in Escherichia coli  

PubMed Central

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

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-01-01

129

Cold start fuel\\/air mixture supply device for spark ignition internal combustion engines  

Microsoft Academic Search

A combined accelerator pump and cold start fuel\\/air mixture supply device has an automatic throttle valve in a mixture supply passage, a fuel control valve controlling flow of fuel drawn into the passage through an inlet upstream of the throttle valve, and an air valve upstream of the fuel inlet. A primary spring tends to seat the air valve. A

1984-01-01

130

Preferred codons and amino acid couples in hyperthermophiles  

PubMed Central

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

2002-01-01

131

Bacterial start site prediction  

Microsoft Academic Search

With the growing number of completely sequenced bacterial genes, accurate gene prediction in bacterial genomes remains an important problem. Although the existing tools predict genes in bacterial genomes with high overall accuracy, their ability to pinpoint the translation start site remains unsatisfactory. In this paper, we present a novel approach to bacterial start site prediction that takes into account multiple

Sridhar S. Hannenhalli; William S. Hayes; Artemis G. Hatzigeorgiou; James W. Fickett

1999-01-01

132

Aboriginal Head Start.  

ERIC Educational Resources Information Center

In Canada, about 100 Aboriginal Head Start (AHS) programs provide Aboriginal preschool children with a start in preparing for elementary school and an understanding of their Native culture. The involvement of parents, communities, and elders is key to the success of AHS. The AHS mission statement and seven guiding principles are presented. (SV)

Dunning, Paula

2000-01-01

133

Start with Science  

ERIC Educational Resources Information Center

The author has found over her 13 years of teaching that starting off the school year with a science investigation has been a great method to learn about her students, to engage them about science before the school year even starts, and to build a foundation for a year of engaging science experiences. This article describes four such activities…

Erickson, Susan

2012-01-01

134

Start at the End ...  

ERIC Educational Resources Information Center

Start at the end; that's the way to improve children's plans for investigations. Strange as it may seem, there are times when beginning at the beginning of an investigation is not the best way to start things off. To give children the opportunity to ask questions and plan what to do, sometimes it is best to get them first to consider others' data…

Goldsworthy, Anne

2005-01-01

135

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

PubMed Central

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

Suzuki, T; Ueda, T; Watanabe, K

1997-01-01

136

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

137

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

Microsoft Academic Search

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

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

1985-01-01

138

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

Microsoft Academic Search

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

Xuhua Xia

139

Control of eukaryotic protein synthesis by upstream open reading frames in the 5'-untranslated region of an mRNA.  

PubMed Central

Control of gene expression is achieved at various levels. Translational control becomes crucial in the absence of transcription, such as occurs in early developmental stages. One of the initiating events in translation is that the 40 S subunit of the ribosome binds the mRNA at the 5'-cap structure and scans the 5'-untranslated region (5'-UTR) for AUG initiation codons. AUG codons upstream of the main open reading frame can induce formation of a translation-competent ribosome that may translate and (i) terminate and re-initiate, (ii) terminate and leave the mRNA, resulting in down-regulation of translation of the main open reading frame, or (iii) synthesize an N-terminally extended protein. In the present review we discuss how upstream AUGs can control the expression of the main open reading frame, and a comparison is made with other elements in the 5'-UTR that control mRNA translation, such as hairpins and internal ribosome entry sites. Recent data indicate the flexibility of controlling translation initiation, and how the mode of ribosome entry on the mRNA as well as the elements in the 5'-UTR can accurately regulate the amount of protein synthesized from a specific mRNA.

Meijer, Hedda A; Thomas, Adri A M

2002-01-01

140

Comparison of Synonymous Codon Distribution Patterns of Bacteriophage and Host Genomes  

Microsoft Academic Search

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

Takashi KUNISAWA; Shigehiko KANAYA; Elizabeth KUTTER

1998-01-01

141

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

PubMed

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

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

2014-01-01

142

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

Microsoft Academic Search

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

Robert Friedman; Austin L. Hughes

2004-01-01

143

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

Microsoft Academic Search

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

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

2008-01-01

144

Following translation by single ribosomes one codon at a time  

Microsoft Academic Search

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

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

2008-01-01

145

Nonneutral GC3 and Retroelement Codon Mimicry in Phytophthora  

Microsoft Academic Search

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

Rays H. Y. Jiang; Francine Govers

2006-01-01

146

Rational protein sequence diversification by multi-codon scanning mutagenesis  

PubMed Central

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

Liu, Jia; Cropp, T. Ashton

2014-01-01

147

Computational codon optimization of synthetic gene for protein expression  

PubMed Central

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

2012-01-01

148

Translational Redefinition of UGA Codons Is Regulated by Selenium Availability*  

PubMed Central

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

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

2013-01-01

149

Psychiatric Advance Directives: Getting Started  

MedlinePLUS

... Home Getting Started National Resource Center on Psychiatric Advance Directives - Getting Started Getting Started Psychiatric advance directives (PADs) are relatively new legal instruments that may ...

150

Reselection of a Genomic Upstream Open Reading Frame in Mouse Hepatitis Coronavirus 5?-Untranslated-Region Mutants  

PubMed Central

An AUG-initiated upstream open reading frame (uORF) encoding a potential polypeptide of 3 to 13 amino acids (aa) is found within the 5? untranslated region (UTR) of >75% of coronavirus genomes based on 38 reference strains. Potential CUG-initiated uORFs are also found in many strains. The AUG-initiated uORF is presumably translated following genomic 5?-end cap-dependent ribosomal scanning, but its function is unknown. Here, in a reverse-genetics study with mouse hepatitis coronavirus, the following were observed. (i) When the uORF AUG-initiating codon was replaced with a UAG stop codon along with a U112A mutation to maintain a uORF-harboring stem-loop 4 structure, an unimpaired virus with wild-type (WT) growth kinetics was recovered. However, reversion was found at all mutated sites within five virus passages. (ii) When the uORF was fused with genomic (main) ORF1 by converting three in-frame stop codons to nonstop codons, a uORF-ORF1 fusion protein was made, and virus replicated at WT levels. However, a frameshifting G insertion at virus passage 7 established a slightly 5?-extended original uORF. (iii) When uAUG-eliminating deletions of 20, 30, or 51 nucleotides (nt) were made within stem-loop 4, viable but debilitated virus was recovered. However, a C80U mutation in the first mutant and an A77G mutation in the second appeared by passage 10, which generated alternate uORFs that correlated with restored WT growth kinetics. In vitro, the uORF-disrupting nondeletion mutants showed enhanced translation of the downstream ORF1 compared with the WT. These results together suggest that the uORF represses ORF1 translation yet plays a beneficial but nonessential role in coronavirus replication in cell culture.

Wu, Hung-Yi; Guan, Bo-Jhih; Su, Yu-Pin; Fan, Yi-Hsin

2014-01-01

151

Unusual codon usage bias in low expression genes of Vibrio cholerae  

PubMed Central

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

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

2008-01-01

152

10. DIABLO DAM: DETAIL OF TAINTOR GATES FROM UPSTREAM ON ...  

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

10. DIABLO DAM: DETAIL OF TAINTOR GATES FROM UPSTREAM ON NORTH END OF DAM, 1989. - Skagit Power Development, Diablo Dam, On Skagit River, 6.9 miles upstream from Newhalem, Newhalem, Whatcom County, WA

153

Upstream and Downstream Sound Radiation into a Moving Fluid.  

National Technical Information Service (NTIS)

An experimental demonstration of the influence of fluid motion in a duct on the sound pressure field radiated in the upstream and downstream directions from a stationary sound source is presented. The measured ratio between the upstream and downstream sou...

U. Ingard V. K. Singhal

1973-01-01

154

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

PubMed Central

Background KRAS mutations in codons 12 and 13 are established predictive biomarkers for anti-EGFR therapy in colorectal cancer. Previous studies suggest that KRAS codon 61 and 146 mutations may also predict resistance to anti-EGFR therapy in colorectal cancer. However, clinicopathological, molecular, and prognostic features of colorectal carcinoma with KRAS codon 61 or 146 mutation remain unclear. Methods We utilized a molecular pathological epidemiology database of 1267 colon and rectal cancers in the Nurse’s Health Study and the Health Professionals Follow-up Study. We examined KRAS mutations in codons 12, 13, 61 and 146 (assessed by pyrosequencing), in relation to clinicopathological features, and tumor molecular markers, including BRAF and PIK3CA mutations, CpG island methylator phenotype (CIMP), LINE-1 methylation, and microsatellite instability (MSI). Survival analyses were performed in 1067 BRAF-wild-type cancers to avoid confounding by BRAF mutation. Cox proportional hazards models were used to compute mortality hazard ratio, adjusting for potential confounders, including disease stage, PIK3CA mutation, CIMP, LINE-1 hypomethylation, and MSI. Results KRAS codon 61 mutations were detected in 19 cases (1.5%), and codon 146 mutations in 40 cases (3.2%). Overall KRAS mutation prevalence in colorectal cancers was 40% (=505/1267). Of interest, compared to KRAS-wild-type, overall, KRAS-mutated cancers more frequently exhibited cecal location (24% vs. 12% in KRAS-wild-type; P?codon, though statistical power was limited for codon 61 mutants. Neither KRAS codon 61 nor codon 146 mutation was significantly associated with clinical outcome or prognosis in univariate or multivariate analysis [colorectal cancer-specific mortality hazard ratio (HR)?=?0.81, 95% confidence interval (CI)?=?0.29-2.26 for codon 61 mutation; colorectal cancer-specific mortality HR?=?0.86, 95% CI?=?0.42-1.78 for codon 146 mutation]. Conclusions Tumors with KRAS mutations in codons 61 and 146 account for an appreciable proportion (approximately 5%) of colorectal cancers, and their clinicopathological and molecular features appear generally similar to KRAS codon 12 or 13 mutated cancers. To further assess clinical utility of KRAS codon 61 and 146 testing, large-scale trials are warranted.

2014-01-01

155

Monochromatic precursor starts  

NASA Astrophysics Data System (ADS)

Whistler precursors are discrete emissions that precede two-hop whistlers, starting shortly after the one-hop delay. More evidence is presented that the precursor and associated whistler propagate through the same duct, and observations of a new type of precursor are presented. This new precursor has a monochromatic precursor start (MPS) which may or may not trigger a riser. Although MPS's may be emissions entrained by power line radiation (PLR), phase analysis of the starting frequencies shows that they are not simply related to harmonics of the power line frequencies in the two conjugate regions (50 Hz in New Zealand, 60 Hz in Alaska). If the MPS is due to entrainment by PLR, then previous theories of precursor generation need not be discarded. Forward triggering of a precursor at a power line harmonic by a hybrid whistler may occur.

Rietveld, M. T.

1980-05-01

156

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

PubMed Central

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

2014-01-01

157

Whistler waves observed upstream from collisionless shocks  

NASA Technical Reports Server (NTRS)

Waves in the frequency range 0.5-4. Hz have been studied in the region upstream of the earth's bow shock with data from the flux-gate magnetic field experiment on Imp 6. Such waves are invariably detected adjacent to the shock, persisting upstream for intervals often less than a minute but occasionally of the order of many hours. Analysis of 150 examples of these waves during a 3-month interval indicates that propagation directions generally make angles of between 20 and 40 deg with the field direction. The waves as measured in the spacecraft frame of reference are either left- or right-hand-polarized with respect to the average field direction. The left-handed waves generally have lower frequencies than the right-handed waves, and the left-handed frequencies never exceed 2.5 Hz. The measured sense of polarization is found to depend on the propagation direction (or alternatively, the field direction) relative to the solar wind direction.

Fairfield, D. H.

1974-01-01

158

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

PubMed

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

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

2012-01-01

159

Starting in School  

ERIC Educational Resources Information Center

Through its signature initiative, Liberal Education and America's Promise (LEAP), the Association of American Colleges and Universities (AAC&U) is promoting a vision for learning that begins in school: Starting in School . . . Rigorous and rich curriculum focused on the essential learning outcomes; comprehensive, individualized, and…

Albertine, Susan

2012-01-01

160

Is Head Start Dying?  

ERIC Educational Resources Information Center

Analysis of problems faced by Head Start and its present status includes a review of its transfer from O.E.O. to H.E.W., its extensions, the Westinghouse Report, and other studies and articles. Decline in public interest and support is noted. (KW)

Sherman, Ann; And Others

1971-01-01

161

Expression of hepatocyte growth factor activator inhibitor type 2 (HAI-2) in human testis: identification of a distinct transcription start site for the HAI-2 gene in testis.  

PubMed

Hepatocyte growth factor activator inhibitor type 1 (HAI-1) and type 2 (HAI-2) are recently identified integral membrane Kunitz-type proteinase inhibitors. They have important regulatory roles in pericellular activation of hepatocyte growth factor/scatter factor (HGF/SF) which is critically involved in the development and regeneration of various tissues. Recent reports suggest that HGF/SF is also involved in testicular development and spermatogenesis. In this study, we analyzed the expression of HAIs in the testis. In human testis, HAI-2 was strongly expressed whereas HAI-1 mRNA was hardly detectable. Of interest was the observation that the mRNA size of HAI-2 was shorter in the testis (1.2 kb) than those in the other tissues such as placenta (1.5 kb). Subsequent experiments revealed that there are two major transcription start sites of the HAI-2 gene, which are -30 bp and -360 bp upstream from the translation initiation ATG codon. Although the latter site appeared to be mainly used in the placenta and other non-testicular organs, only the former site is used in testis, resulting in the -300 bp shorter mRNA. An immunohistochemical study using a specific monoclonal antibody raised against human HAI-2 protein indicated that HAI-2 is expressed exclusively in primary spermatocytes. These results suggest a distinct regulation of HAI-2 gene expression in testis and that HAI-2 may play a role in the process of spermatogenesis. PMID:12553733

Yamauchi, Masamichi; Itoh, Hiroshi; Naganuma, Seiji; Koono, Masashi; Hasui, Yoshihiro; Osada, Yukio; Kataoka, Hiroaki

2002-12-01

162

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

163

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

PubMed

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

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

2009-01-01

164

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

PubMed Central

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

2012-01-01

165

Site-directed mutagenesis of adeno-associated virus type 2 structural protein initiation codons: effects on regulation of synthesis and biological activity.  

PubMed Central

It has been shown that two of the three adeno-associated virus type 2 capsid proteins, B and C, are synthesized from a single spliced transcript. Protein C arises from an AUG codon at nucleotide 2810, whereas protein B is initiated by a unique eucaryotic initiation codon (ACG) that lies 65 triplets upstream from the C origin. The third capsid component, protein A, is synthesized from a second spliced transcript which uses an alternative 3' acceptor site. In this study we used oligonucleotide-directed mutagenesis to confirm the positions of the B initiation codon and the 3' acceptor sites for the alternatively spliced B/C and A protein messages. We also located definitively the protein A initiation codon, an AUG triplet mapping to nucleotide 2203. Mutagenesis of the B initiator permitted a direct test of the effect of increased B initiator strength on the translational efficiencies of the B and C proteins. It was found that conversion of the relatively inefficient protein B initiator (ACG) to an AUG enhanced the level of B synthesis while abolishing the synthesis of C from its downstream AUG initiator. Protein C synthesis thus depends on the strength of the B initiator, i.e., the relatively higher levels of C (approximately 20-fold greater than B) must result from frequent readthrough of the weak B initiator. Finally, we examined the abilities of mutants deficient in the synthesis of A, B, or C to produce infectious virions. We found that at least two of the structural proteins, B and C, are required for the production of infectious virions and that sequestration of single-stranded adeno-associated virus genomes from the pool of replicating DNA molecules does not occur in the absence of either of these proteins. Images

Muralidhar, S; Becerra, S P; Rose, J A

1994-01-01

166

Anomalous upstream retroflection in the agulhas current.  

PubMed

The Agulhas current, the major western boundary current of the Southern Hemisphere, plays a crucial role in the water mass balance ofthe world oceans by controlling the transfer of thernocline water from the Indian to the Atlantic ocean systems. The main mechanism for such transfer is through the shedding of large rings of warm water at the Agulhas retroflection south ofAfrica. On the basis ofsatellite imagery and drifter tracks, anomalous reversals ofthe current are observed to occur far upstream of its characteristic retroflection location. The observations agree with results of an inertial jet model ofthe current. These anomalous reversals probably cause abrupt and major changes in the fluxes south ofAfrica and thus in the rate of ring shedding. This unusual flow bimodality in a major component of the global ocean heat transport system could have important climatic implications. PMID:17842430

Lutjeharms, J R; van Ballegooyen, R C

1988-06-24

167

The Vitamin D Receptor (VDR) Start Codon Polymorphism in Primary Hyperparathyroidism and Parathyroid VDR Messenger Ribonucleic Acid Levels  

Microsoft Academic Search

Vitamin D regulates parathyroid cell proliferation and secretion of PTH. Increased prevalence of the polymorphic vitamin D receptor (VDR) alleles b, a, and T has been reported in sporadic primary hyperparathyroidism (PHPT), suggesting that these genetic variants may predispose to the disease. Recently, another polymorphism in the VDR gene was related to bone mineral density, and this VDR-FokI polymorphism causes

PAMELA CORREA; JONAS RASTAD; PETER SCHWARZ; GUNNAR WESTIN; ANDREAS KINDMARK; EWA LUNDGREN; GORAN ÅKERSTROM; TOBIAS CARLING

168

Premature Stop Codon in MMP20 Causing Amelogenesis Imperfecta  

PubMed Central

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

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

2009-01-01

169

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

Microsoft Academic Search

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

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

2003-01-01

170

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

Microsoft Academic Search

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

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

2006-01-01

171

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

PubMed Central

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

Hatfield, D; Rice, M

1978-01-01

172

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

PubMed

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

Parisien, Marc; Yi, Chengqi; Pan, Tao

2012-03-01

173

When to Start Antiretroviral Therapy  

MedlinePLUS

... circumstances. What factors influence the decision to start ART? The following factors influence the decision to start ... an important factor in deciding when to start ART? A CD4 count measures the number of CD4 ...

174

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

PubMed

Mutation and selection are two major forces causing codon usage biases. How these two forces influence the codon usages in green plant mitochondrial genomes has not been well investigated. In the present study, we surveyed five bryophyte mitochondrial genomes to reveal their codon usage patterns as well as the determining forces. Three interesting findings were made. First, comparing to Chara vulgaris, an algal species sister to all extant land plants, bryophytes have more G, C-ending codon usages in their mitochondrial genes. This is consistent with the generally higher genomic GC content in bryophyte mitochondria, suggesting an increased mutational pressure toward GC. Second, as indicated by Wright's Nc-GC3s plot, mutation, not selection, is the major force affecting codon usages of bryophyte mitochondrial genes. However, the real mutational dynamics seem very complex. Context-dependent analysis indicated that nucleotide at the 2nd codon position would slightly affect synonymous codon choices. Finally, in bryophyte mitochondria, tRNA genes would apply a weak selection force to fine-tune the synonymous codon frequencies, as revealed by data of Ser4-Pro-Thr-Val families. In summary, complex mutation and weak selection together determined the codon usages in bryophyte mitochondrial genomes. PMID:21106008

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

2010-12-01

175

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

176

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

177

Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs  

PubMed Central

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

Beier, Hildburg; Grimm, Michael

2001-01-01

178

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

PubMed Central

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

2011-01-01

179

StartUpNation  

NSDL National Science Digital Library

It would seem that more and more people are interested in developing their own business, and a number of websites are dedicated to helping these persons achieve that goal. One valuable website in that realm is StartUpNation. Created by Jeff and Rich Sloan, the site contains a well-designed homepage that includes links to sections dedicated to areas of interest to the prospective entrepreneur, including those that deal with customer service and creating strategic marketing plans. A good place to start is the âÂÂLean from the Expertsâ area, located on the left-hand side of the homepage. Here, visitors can learn from successful individuals, such as Glenn Coggeshell of Black Dot Coffee. Along the same side, visitors can also read about how to choose a business for themselves and also how to plan to make this business a reality. In keeping with the times, the site also affords users the opportunity to sign up for RSS feeds and the ability to listen (and download) a number of podcasts.

180

Heat shock responsiveness analysis of Athsp70b upstream region  

Microsoft Academic Search

A 1431-bp upstream fragment of Athsp70b was cloned via PCR amplification and expressed in onion epidermis by particle bombardment. Furthermore, the progressive deletions\\u000a of the Athsp70b upstream fragment linked to the ?-glucuronidase (GUS) coding region were performed. Then, a stable GUS expression was analyzed\\u000a in tobacco BY2 cells and Arabidopsis. Our present results showed that about a 500-bp region upstream

H. L. Song; Q. Wei; J. Yu; B. K. Kuai

2008-01-01

181

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

182

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

PubMed Central

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

Medori, R; Tritschler, H J

1993-01-01

183

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

PubMed Central

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

Lim, V I; Curran, J F

2001-01-01

184

Upstream/downstream: Issues in environmental ethics  

SciTech Connect

Upstream/Downstream reminds us that there are four issues that are more or less distinctive to environmental ethics. First, and most distinctively, environmental issues involve the standing of nonhuman living things and systems. Thus, environmental politics is only partly a clash among the interest of the parties involved; it often involves actions on behalf of the existence rights of nonhuman life forms. Second, environmental ethics concern the intergenerational distribution of benefits more explicitly than do most other ethical issues, which brings out serious weaknesses in legal frameworks that rely on claims for damages. Third, the complexity and indirectness of many environmental impacts introduces a high degree of uncertainty and thus technical as well as ethical issues of prudent behavior. Specifically, where science may not fully reveal environmental risks, should development proceed; should analysis proceed if it is known to have a Pollyanna bias Fourth, insofar as environmental damage is typically done to common property, and thus its regulation is generally a matter for governmental regulation, the obligations of private actors to make sacrifices beyond what government requires is at issue - an issue that one would expect to be taken up at length in the other volumes.

Scherer, D. (ed.)

1991-01-01

185

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

PubMed

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

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

1993-12-15

186

Minnesota: Early Head Start Initiatiive  

ERIC Educational Resources Information Center

Minnesota provides supplemental state funding to existing federal Head Start and Early Head Start (EHS) grantees to increase their capacity to serve additional infants, toddlers, and pregnant women. The initiative was started in 1997 when the state legislature earmarked $1 million of the general state Head Start supplemental funds for children…

Center for Law and Social Policy, Inc. (CLASP), 2012

2012-01-01

187

Codon-based encoding for DNA sequence analysis.  

PubMed

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

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

2014-06-01

188

Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast  

PubMed Central

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

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

2013-01-01

189

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

Microsoft Academic Search

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

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

2001-01-01

190

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

PubMed Central

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

Devaraj, Aishwarya; Fredrick, Kurt

2010-01-01

191

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

Microsoft Academic Search

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

CHRISTIAN J. MICHEL

1989-01-01

192

Interorganizational IT investments and the value upstream relational capital  

Microsoft Academic Search

Purpose – The focus of this article is upstream relational capital, the intangible value of a firm's business relations with its suppliers. The paper aims to propose and test a valuation model of an organization's upstream relational capital that incorporates the leveraging impact of IT investments. Design\\/methodology\\/approach – A survey was carried out of 159 CEOs in the wireless telecommunication

Pierre-Majorique Léger

2010-01-01

193

Collisionless shocks and upstream waves and particles - Introductory remarks  

NASA Technical Reports Server (NTRS)

A qualitative account is presented of collisionless shock theory in relation to the problem of upstream waves and particles. Particular attention is given to parallel shocks in high-beta plasmas, the relation of upstream phenomena to local shock structure, and Fermi acceleration.

Kennel, C. F.

1981-01-01

194

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

Microsoft Academic Search

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

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

2004-01-01

195

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

PubMed Central

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

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-01-01

196

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

Microsoft Academic Search

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

Fran Supek; Kristian Vlahovicek

2005-01-01

197

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

Microsoft Academic Search

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

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

2010-01-01

198

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

199

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

200

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease  

PubMed Central

Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders.

Barbosa, Cristina; Peixeiro, Isabel; Romao, Luisa

2013-01-01

201

Catalytic Ignition and Upstream Reaction Propagation in a Platinum Tube  

NASA Technical Reports Server (NTRS)

A challenge for catalytic combustion in monolithic reactors at elevated temperatures is the start-up or "light-off" from a cold initial condition. In this work, we demonstrate a concept called "back-end catalytic ignition that potentially can be utilized in the light-off of catalytic monoliths. An external downstream flame or Joule heating raises the temperature of a small portion of the catalyst near the outlet initiating a localized catalytic reaction that propagates upstream heating the entire channel. This work uses a transient numerical model to demonstrate "back-end" ignition within a single channel which can characterize the overall performance of a monolith. The paper presents comparisons to an experiment using a single non-adiabatic channel but the concept can be extended to the adiabatic monolith case. In the model, the time scales associated with solid heat-up are typically several orders of magnitude larger than the gas-phase and chemical kinetic time-scales. Therefore, the model assumes a quasi-steady gas-phase with respect to a transient solid. The gas phase is one-dimensional. Appropriate correlations, however, account for heat and mass transfer in a direction perpendicular to the flow. The thermally-thin solid includes axial conduction. The gas phase, however, does not include axial conduction due to the high Peclet number flows. The model includes both detailed gas-phase and catalytic surface reactions. The experiment utilizes a pure platinum circular channel oriented horizontally though which a CO/O2 mixture (equivalence ratios ranging from 0.6 to 0.9) flows at 2 m/s.

Struk, P. M.; Dietrich, D. L.; Mellish, B. P.; Miller, F. J.; T'ien, J. S.

2007-01-01

202

PHEV Cold Start Emissions Management.  

National Technical Information Service (NTIS)

Plug-in hybrid electric vehicles (PHEV) operate predominantly as electric vehicles (EV) with intermittent assist from the engine. As a consequence, the engine can be subjected to multiple cold start events. These cold start events have a significant impac...

2013-01-01

203

Increased Upstream Ionization due to Formation of a Double Layer  

SciTech Connect

We report observations that confirm a theoretical prediction that formation of a current-free double layer in a plasma expanding into a chamber of larger diameter is accompanied by an increase in ionization upstream of the double layer. The theoretical model argues that the increased ionization is needed to balance the difference in diffusive losses upstream and downstream of the expansion region. In our expanding helicon source experiments, we find that the upstream plasma density increases sharply at the same antenna frequency at which the double layer appears.

Thakur, S. Chakraborty; Harvey, Z.; Biloiu, I. A.; Hansen, A.; Hardin, R. A.; Przybysz, W. S.; Scime, E. E. [Department of Physics, West Virginia University, Morgantown, West Virginia 26506-6315 (United States)

2009-01-23

204

High codon adaptation in citrus tristeza virus to its citrus host  

PubMed Central

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

2012-01-01

205

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

PubMed

The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENc values are below it. ENc-plot suggested that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally and we propose that codons containing A or U at third position are used preferentially in nemertean species, regardless of whether corresponding tRNAs are encoded in the mitochondrial DNA. Context-dependent analysis indicated that the nucleotide at the second codon position slightly affects synonymous codon choices. These results suggested that mutational and selection forces are probably acting to codon usage bias in nemertean mitochondrial genomes. PMID:24454907

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

2014-01-01

206

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

PubMed

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

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

2013-01-01

207

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

PubMed Central

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

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

2012-01-01

208

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

PubMed Central

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

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

2014-01-01

209

The unfolded protein response affects readthrough of premature termination codons.  

PubMed

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

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

2014-05-01

210

The unfolded protein response affects readthrough of premature termination codons  

PubMed Central

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

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

2014-01-01

211

Suppression of premature termination codons as a therapeutic approach.  

PubMed

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

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

2012-09-01

212

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

PubMed

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

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

2014-01-01

213

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

214

Far upstream element binding protein 1: a commander of transcription, translation and beyond.  

PubMed

The far upstream binding protein 1 (FBP1) was first identified as a DNA-binding protein that regulates c-Myc gene transcription through binding to the far upstream element (FUSE) in the promoter region 1.5?kb upstream of the transcription start site. FBP1 collaborates with TFIIH and additional transcription factors for optimal transcription of the c-Myc gene. In recent years, mounting evidence suggests that FBP1 acts as an RNA-binding protein and regulates mRNA translation or stability of genes, such as GAP43, p27(Kip) and nucleophosmin. During retroviral infection, FBP1 binds to and mediates replication of RNA from Hepatitis C and Enterovirus 71. As a nuclear protein, FBP1 may translocate to the cytoplasm in apoptotic cells. The interaction of FBP1 with p38/JTV-1 results in FBP1 ubiquitination and degradation by the proteasomes. Transcriptional and post-transcriptional regulations by FBP1 contribute to cell proliferation, migration or cell death. FBP1 association with carcinogenesis has been reported in c-Myc dependent or independent manner. This review summarizes biochemical features of FBP1, its mechanism of action, FBP family members and the involvement of FBP1 in carcinogenesis. PMID:22926519

Zhang, J; Chen, Q M

2013-06-13

215

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

PubMed Central

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

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

1987-01-01

216

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

PubMed Central

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

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

2010-01-01

217

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

Microsoft Academic Search

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

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

2007-01-01

218

23. Upstream view of buttress and arch form work and ...  

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

23. Upstream view of buttress and arch form work and construction. Photographer unknown, 1927. Source: MWD. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

219

41. Upstream end of emergency spillway excavation. Photographer unknown, 1929. ...  

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

41. Upstream end of emergency spillway excavation. Photographer unknown, 1929. Source: Arizona Department of Water Resources (ADWR). - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

220

30. Upstream face of construction effort. Photographer unknown, January 29, ...  

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

30. Upstream face of construction effort. Photographer unknown, January 29, 1927. Source: Fritz Seifritz. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

221

56. Upstream face of diversion dam looking east. Headgates are ...  

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

56. Upstream face of diversion dam looking east. Headgates are partially visible at far left. Photographer Mark Durben, 1986. Source: Salt River Project. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

222

2. General view of Mormon Flat looking upstream. Construction activity ...  

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

2. General view of Mormon Flat looking upstream. Construction activity is visible at center right. Photographer unknown, September 30, 1923. Source: Salt River Project. - Mormon Flat Dam, On Salt River, Eastern Maricopa County, east of Phoenix, Phoenix, Maricopa County, AZ

223

19. Upstream face of arches and buttresses at west end. ...  

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

19. Upstream face of arches and buttresses at west end. Photographer unknown, January 29, 1927. Source: MWD. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

224

1. Site of Mormon Flat Dam looking upstream. Photographer unknown, ...  

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

1. Site of Mormon Flat Dam looking upstream. Photographer unknown, 1923. Source: Salt River Project. - Mormon Flat Dam, On Salt River, Eastern Maricopa County, east of Phoenix, Phoenix, Maricopa County, AZ

225

50. Upstream face of Humbug Creek Diversion Dam showing sluice ...  

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

50. Upstream face of Humbug Creek Diversion Dam showing sluice opening. Photographer James Eastwood, 1986. Source: Salt River Project. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

226

4. View to westsouthwest. Oblique view of upstream side of ...  

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

4. View to west-southwest. Oblique view of upstream side of bridge from approximately deck level. (90mm lens) - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

227

9. View to northeast. Oblique view of upstream side of ...  

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

9. View to northeast. Oblique view of upstream side of bridge from approximately deck level. (90mm lens) - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

228

45. VIEW OF STAGE RECORDER AT END OF UPSTREAM GUIDEWALL, ...  

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

45. VIEW OF STAGE RECORDER AT END OF UPSTREAM GUIDEWALL, LOOKING NORTH - Upper Mississippi River 9-Foot Channel, Lock & Dam No. 8, On Mississippi River near Houston County, MN, Genoa, Vernon County, WI

229

94. VIEW SHOWING STEEL ERECTION TO DATE, LOOKING NORTHNORTHEAST (UPSTREAM), ...  

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

94. VIEW SHOWING STEEL ERECTION TO DATE, LOOKING NORTH-NORTHEAST (UPSTREAM), June 28, 1935. (Steamer Delta King is moored at River Lines Terminal.) - Sacramento River Bridge, Spanning Sacramento River at California State Highway 275, Sacramento, Sacramento County, CA

230

11. DETAIL OF UPSTREAM FACE OF SLUICE GATE CONTROLS FROM ...  

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

11. DETAIL OF UPSTREAM FACE OF SLUICE GATE CONTROLS FROM CATWALK, SHOWING GATE LIFTING GEARS (TOP) AND GEAR SHAFTS (BOTTOM). VIEW TO SOUTHWEST. - Boise Project, Boise River Diversion Dam, Across Boise River, Boise, Ada County, ID

231

10. DETAIL OF UPSTREAM FACE OF NEW YORK CANAL HEADWORKS, ...  

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

10. DETAIL OF UPSTREAM FACE OF NEW YORK CANAL HEADWORKS, SHOWING GATE LIFTING GEARS (TOP), WORM GEAR SHAFTS (CENTER) AND SLIDE GATES (BOTTOM). VIEW TO NORTHWEST. - Boise Project, Boise River Diversion Dam, Across Boise River, Boise, Ada County, ID

232

UPSTREAM LOCK GATE DETAIL AND DOG HOUSE. NOTE ARM AND ...  

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

UPSTREAM LOCK GATE DETAIL AND DOG HOUSE. NOTE ARM AND GEARING FOR CONTROLLING LOCK GATE. LOOKING WEST SOUTHWEST. - Illinois Waterway, Brandon Road Lock and Dam , 1100 Brandon Road, Joliet, Will County, IL

233

DOG HOUSE AT UPSTREAM LOCK GATE. ALSO SEEN AT LEFT ...  

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

DOG HOUSE AT UPSTREAM LOCK GATE. ALSO SEEN AT LEFT IN PHOTO NO. IL-164-A-23. - Illinois Waterway, La Grange Lock and Dam, 3/4 mile south of Country 795N at Illinois River, Versailles, Brown County, IL

234

65. VIEW LOOKING UPSTREAM FROM FLUME SUBSTRUCTURE, SHOWING COLUMBIA IMPROVEMENT ...  

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

65. VIEW LOOKING UPSTREAM FROM FLUME SUBSTRUCTURE, SHOWING COLUMBIA IMPROVEMENT COMPANY'S NEISSON CREEK SAWMILL. Print No. 177, November 1903 - Electron Hydroelectric Project, Along Puyallup River, Electron, Pierce County, WA

235

18. VIEW OF SETTLING BASIN FROM UPSTREAM TRESTLE, SHOWING BULKHEAD ...  

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

18. VIEW OF SETTLING BASIN FROM UPSTREAM TRESTLE, SHOWING BULKHEAD ON RIGHT AND SAND BANK ON LEFT, LOOKING NORTHWEST - Electron Hydroelectric Project, Along Puyallup River, Electron, Pierce County, WA

236

View of Lake Sabrina Dam upstream face from ridge showing ...  

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

View of Lake Sabrina Dam upstream face from ridge showing spillway at lower right of photo, view southwest - Bishop Creek Hydroelectric System, Plant 2, Lake Sabrina Dam, Bishop Creek, Bishop, Inyo County, CA

237

9. Upstream view showing diversion flume at lower left and ...  

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

9. Upstream view showing diversion flume at lower left and mixing plant at left center. Photographer unknown, June 9, 1924. Source: Salt River Project. - Mormon Flat Dam, On Salt River, Eastern Maricopa County, east of Phoenix, Phoenix, Maricopa County, AZ

238

23. UPSTREAM DETAIL OF PIER NO. 2 AND THROUGH AND ...  

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

23. UPSTREAM DETAIL OF PIER NO. 2 AND THROUGH AND DECK TRUSS END PANELS. VIEW TO SOUTHEAST. - MacArthur Bridge, Spanning Mississippi River on Highway 34 between IA & IL, Burlington, Des Moines County, IA

239

15. OVERALL VIEW OF UPSTREAM FACE OF LIFT GATE SECTION ...  

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

15. OVERALL VIEW OF UPSTREAM FACE OF LIFT GATE SECTION WITH TAINTER GATE SECTION OF SPILLWAY TO THE LEFT. VIEW TO SOUTHWEST. - Starved Rock Locks & Dam, Illinois Waterway River mile 231, Peru, La Salle County, IL

240

10. UPSTREAM SIDE OF UPPER MITER GATES SHOWING STOWED LEFT ...  

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

10. UPSTREAM SIDE OF UPPER MITER GATES SHOWING STOWED LEFT WING OF UPPER GUARD GATE (FAR LEFT). VIEW TO NORTHWEST. - Starved Rock Locks & Dam, Illinois Waterway River mile 231, Peru, La Salle County, IL

241

1. OVERALL VIEW OF UPSTREAM FACE OF DAM; SPILLWAY IN ...  

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

1. OVERALL VIEW OF UPSTREAM FACE OF DAM; SPILLWAY IN FOREGROUND, LOCK IN BACKGROUND ON NORTH RIVER BANK. VIEW TO NORTH. - Starved Rock Locks & Dam, Illinois Waterway River mile 231, Peru, La Salle County, IL

242

29. VIEW OF TWIN FALLS MAIN CANAL BRIDGE FROM UPSTREAM ...  

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

29. VIEW OF TWIN FALLS MAIN CANAL BRIDGE FROM UPSTREAM LOOKING DOWNSTREAM. - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

243

45. VIEW UPSTREAM AT FOREBAY, INLET GATES, PIT GATES AND ...  

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

45. VIEW UPSTREAM AT FOREBAY, INLET GATES, PIT GATES AND TRASH RACKS. Taken by Jet Lowe, HAER staff photographer, September 1980 - Dam No. 5 Hydroelectric Plant, On Potomac River, Hedgesville, Berkeley County, WV

244

10. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: MISCELLANEOUS METAL DETAILS. ...  

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

10. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: MISCELLANEOUS METAL DETAILS. Sheet A-22, November, 1940. File no. SA 342/31. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

245

2. UPSTREAM SIDE OF DIVERSION DAM ON THE SNAKE RIVER, ...  

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

2. UPSTREAM SIDE OF DIVERSION DAM ON THE SNAKE RIVER, LOOKING SOUTH-SOUTHWEST. NOTE BANK REINFORCEMENT ON LEFT AND SPILLWAY ON RIGHT. - Snake River Ditch, Headgate on north bank of Snake River, Dillon, Summit County, CO

246

5. Contextual oblique view to northwest showing upstream (east) side ...  

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

5. Contextual oblique view to northwest showing upstream (east) side of bridge in setting, with Jacob Meyer Park at right. - Stanislaus River Bridge, Atchison, Topeka & Santa Fe Railway at Stanislaus River, Riverbank, Stanislaus County, CA

247

20. VIEW OF LE CLAIRE LOCK (19211925), SHOWING UPSTREAM GATES, ...  

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

20. VIEW OF LE CLAIRE LOCK (1921-1925), SHOWING UPSTREAM GATES, DOWNSTREAM SIDE AND SOUTH LOCKWALL - Mississippi River 9-Foot Channel, Lock & Dam No. 14, Upper Mississippi River, Le Claire, Scott County, IA

248

23. VIEW LOOKING UPSTREAM FROM WEST BANK OF HEADRACE SHOWING ...  

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

23. VIEW LOOKING UPSTREAM FROM WEST BANK OF HEAD-RACE SHOWING RECONSTRUCTED MAIN AND DIVERSION DAMS; HEAD-RACE IS JUST OUT OF PICTURE AT LEFT. - Forge Creek Dam-John Cable Mill, Townsend, Blount County, TN

249

24. VIEW FROM EAST BANK, LOOKING UPSTREAM, SHOWING RECONSTRUCTED MAIN ...  

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

24. VIEW FROM EAST BANK, LOOKING UPSTREAM, SHOWING RECONSTRUCTED MAIN AND DIVERSION DAMS IN BACKGROUND WITH WATER-GATE AND BEGINNING OF HEAD-RACE IN LEFT FOREGROUND. - Forge Creek Dam-John Cable Mill, Townsend, Blount County, TN

250

1. UPSTREAM VIEW OF THE SOUTH CHANNEL DAM, LOOKING EAST. ...  

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

1. UPSTREAM VIEW OF THE SOUTH CHANNEL DAM, LOOKING EAST. - Washington Water Power Company Post Falls Power Plant, South Channel Dam, West of intersection of Spokane & Fourth Streets, Post Falls, Kootenai County, ID

251

EVALUATING THE EFFECT OF UPSTREAM WATERSHED ACTIVITIES TO DOWNSTREAM STREAMFLOW  

EPA Science Inventory

Linking the impacts of upstream activities such as urban development to changes in downstream streamflow is critical to achieving a balance between economic development and environmental protection as a basis for sustainable watershed development. This paper presents a modeling a...

252

7. Detail view of reinforced concrete archrings comprising dam's upstream ...  

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

7. Detail view of reinforced concrete arch-rings comprising dam's upstream face. Impressions of the wooden formwork used in construction are visible in the concrete. - Little Rock Creek Dam, Little Rock Creek, Littlerock, Los Angeles County, CA

253

The electron distribution function upstream from the earth's bow shock  

NASA Astrophysics Data System (ADS)

A general analytic theory for the distribution function of particles backstreaming from an arbitrary shock in a magnetized plasma is presented. Particle motions are shown to be restricted to two-dimensional planes. A general form for the source term describing upstreaming particles accelerated at the shock is presented along with explicit source terms for planar and parabolic shocks. The origin and form of the escape velocity cutoff for a shock in a magnetized plasma are discussed. The distribution function upstream of a finite planar shock and a parabolic shock in two dimensions is calculated, and an analytic approximation of the cutoff velocity at points in the upstream region is derived. The theory is then applied to the earth's bow shock, calculating distribution functions and the nature and spatial variation of the cutoff velocity. The theory for the particle distribution upstream of the bow shock is compared with the model of Filbert and Kellogg (1979).

Cairns, Iver H.

1987-03-01

254

The electron distribution function upstream from the earth's bow shock  

NASA Technical Reports Server (NTRS)

A general analytic theory for the distribution function of particles backstreaming from an arbitrary shock in a magnetized plasma is presented. Particle motions are shown to be restricted to two-dimensional planes. A general form for the source term describing upstreaming particles accelerated at the shock is presented along with explicit source terms for planar and parabolic shocks. The origin and form of the escape velocity cutoff for a shock in a magnetized plasma are discussed. The distribution function upstream of a finite planar shock and a parabolic shock in two dimensions is calculated, and an analytic approximation of the cutoff velocity at points in the upstream region is derived. The theory is then applied to the earth's bow shock, calculating distribution functions and the nature and spatial variation of the cutoff velocity. The theory for the particle distribution upstream of the bow shock is compared with the model of Filbert and Kellogg (1979).

Cairns, Iver H.

1987-01-01

255

6. CREST ROAD ON UPPER EMBANKMENT, SHOWING MASONRY UPSTREAM PARAPET ...  

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

6. CREST ROAD ON UPPER EMBANKMENT, SHOWING MASONRY UPSTREAM PARAPET WALL (LEFT) AND ENTRANCE TO DEER FLAT NAMPA CANAL HEADWORKS (ALSO LEFT). VIEW TO WEST. - Boise Project, Deer Flat Embankments, Lake Lowell, Nampa, Canyon County, ID

256

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

PubMed Central

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

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

1981-01-01

257

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

PubMed

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

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

2014-01-01

258

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

PubMed Central

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

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

2013-01-01

259

Pushing the limits of the scanning mechanism for initiation of translation  

Microsoft Academic Search

Selection of the translational initiation site in most eukaryotic mRNAs appears to occur via a scanning mechanism which predicts that proximity to the 5? end plays a dominant role in identifying the start codon. This ‘position effect’ is seen in cases where a mutation creates an AUG codon upstream from the normal start site and translation shifts to the upstream

Marilyn Kozak

2002-01-01

260

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

PubMed Central

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

2014-01-01

261

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

PubMed

Protein domains can fold into stable tertiary structures while they are synthesized by the ribosome in a process known as cotranslational folding. If a protein does not fold cotranslationally, however, it has the opportunity to do so post-translationally, that is, after the nascent chain has been fully synthesized and released from the ribosome. The rate at which a ribosome adds an amino acid encoded by a particular codon to the elongating nascent chain can vary significantly and is called the codon translation rate. Recent experiments have illustrated the profound impact that codon translation rates can have on the cotranslational folding process and the acquisition of function by nascent proteins. Synonymous codon mutations in an mRNA molecule change the chemical identity of a codon and its translation rate without changing the sequence of the synthesized protein. This change in codon translation rate can, however, cause a nascent protein to malfunction as a result of cotranslational misfolding. In some situations, such dysfunction can have profound implications; for example, it can alter the substrate specificity of an ABC transporter protein, resulting in patients who are nonresponsive to chemotherapy treatment. Thus, codon translation rates are crucial in coordinating protein folding in a cellular environment and can affect downstream cellular processes that depend on the proper functioning of newly synthesized proteins. As the importance of codon translation rates makes clear, a necessary aspect of fully understanding cotranslational folding lies in considering the kinetics of the process in addition to its thermodynamics. In this Account, we examine the contributions that have been made to elucidating the mechanisms of cotranslational folding by using the theoretical and computational tools of chemical kinetics, molecular simulations, and systems biology. These efforts have extended our ability to understand, model, and predict the influence of codon translation rates on cotranslational protein folding and misfolding. The application of such approaches to this important problem is creating a framework for making quantitative predictions of the impact of synonymous codon substitutions on cotranslational folding that has led to a novel hypothesis regarding the role of fast-translating codons in coordinating cotranslational folding. In addition, it is providing new insights into proteome-wide cotranslational folding behavior and making it possible to identify potential molecular mechanisms by which molecular chaperones can influence such behavior during protein synthesis. As we discuss in this Account, bringing together these theoretical developments with experimental approaches is increasingly helping answer fundamental questions about the nature of nascent protein folding on the ribosome. PMID:24784899

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

2014-05-20

262

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

Microsoft Academic Search

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

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

2010-01-01

263

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

Microsoft Academic Search

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

Brian R. Morton

1998-01-01

264

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

PubMed Central

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

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

2008-01-01

265

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

Microsoft Academic Search

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

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

2010-01-01

266

Barriers impede upstream spawning migration of flathead chub  

USGS Publications Warehouse

Many native cyprinids are declining throughout the North American Great Plains. Some of these species require long reaches of contiguous, flowing riverine habitat for drifting eggs or larvae to develop, and their declining populations have been attributed to habitat fragmentation or barriers (e.g., dams, dewatered channels, and reservoirs) that restrict fish movement. Upstream dispersal is also needed to maintain populations of species with passively drifting eggs or larvae, and prior researchers have suggested that these fishes migrate upstream to spawn. To test this hypothesis, we conducted a mark–recapture study of Flathead Chub Platygobio gracilis within a 91-km reach of continuous riverine habitat in Fountain Creek, Colorado. We measured CPUE, spawning readiness (percent of Flathead Chub expressing milt), and fish movement relative to a channel-spanning dam. Multiple lines of evidence indicate that Flathead Chub migrate upstream to spawn during summer. The CPUE was much higher at the base of the dam than at downstream sites; the seasonal increases in CPUE at the dam closely tracked seasonal increases in spawning readiness, and marked fish moved upstream as far as 33 km during the spawning run. The upstream migration was effectively blocked by the dam. The CPUE of Flathead Chub was much lower upstream of the OHDD than at downstream sites, and <0.2% of fish marked at the dam were recaptured upstream. This study provides the first direct evidence of spawning migration for Flathead Chub and supports the general hypothesis that barriers limit adult dispersal of these and other plains fishes.

Walters, David M.; Zuellig, Robert E.; Crockett, Harry J.; Bruce, James F.; Lukacs, Paul M.; Fitzpatrick, Ryan M.

2014-01-01

267

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

PubMed Central

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

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

1995-01-01

268

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

PubMed

The standard classification scheme of the genetic code is organized for alphabetic ordering of nucleotides. Here we introduce the new, "ideal" classification scheme in compact form, for the first time generated by codon sextets encoding Ser, Arg and Leu amino acids. The new scheme creates the known purine/pyrimidine, codon-anticodon, and amino/keto type symmetries and a novel A+U rich/C+G rich symmetry. This scheme is built from "leading" and "nonleading" groups of 32 codons each. In the ensuing 4×16 scheme, based on trinucleotide quadruplets, Ser has a central role as initial generator. Six codons encoding Ser and six encoding Arg extend continuously along a linear array in the "leading" group, and together with four of six Leu codons uniquely define construction of the "leading" group. The remaining two Leu codons enable construction of the "nonleading" group. The "ideal" genetic code suggests the evolution of genetic code with serine as an initiator. PMID:24709107

Rosandi?, Marija; Paar, Vladimir

2014-06-10

269

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

PubMed

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

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

2014-02-01

270

Transcription start site evolution in Drosophila.  

PubMed

Transcription start site (TSS) evolution remains largely undescribed in Drosophila, likely due to limited annotations in non-melanogaster species. In this study, we introduce a concise new method that selectively sequences from the 5'-end of mRNA and used it to identify TSS in four Drosophila species, including Drosophila melanogaster, D. simulans, D. sechellia, and D. pseudoobscura. For verification, we compared our results in D. melanogaster with known annotations, published 5'-rapid amplification of cDNA ends data, and with RNAseq from the same mRNA pool. Then, we paired 2,849 D. melanogaster TSS with its closest equivalent TSS in each species (likely to be its true ortholog) using the available multiple sequence alignments. Most of the D. melanogaster TSSs were successfully paired with an ortholog in each species (83%, 86%, and 55% for D. simulans, D. sechellia, and D. pseudoobscura, respectively). On the basis of the number and distribution of reads mapped at each TSS, we also estimated promoter-specific expression (PSE) and TSS peak shape, respectively. Among paired TSS orthologs, the location and promoter activity were largely conserved. TSS location appears important as PSE, and TSS peak shape was more frequently divergent among TSS that had moved. Unpaired TSS were surprisingly common in D. pseudoobscura. An increased mutation rate upstream of TSS might explain this pattern. We found an enrichment of ribosomal protein genes among diverged TSS, suggesting that TSS evolution is not uniform across the genome. PMID:23649539

Main, Bradley J; Smith, Andrew D; Jang, Hyosik; Nuzhdin, Sergey V

2013-08-01

271

Kansas: Early Head Start Initiative  

ERIC Educational Resources Information Center

Kansas Early Head Start (KEHS) provides comprehensive services following federal Head Start Program Performance Standards for pregnant women and eligible families with children from birth to age 4. KEHS was implemented in 1998 using Child Care and Development Block Grant (CCDBG) quality set-aside dollars augmented by a transfer of federal…

Center for Law and Social Policy, Inc. (CLASP), 2012

2012-01-01

272

An alternative transcription start site yields estrogen-unresponsive kiss1 mRNA transcripts in the hypothalamus of prepubertal female rats.  

PubMed

The importance of the Kiss1 gene in the control of reproductive development is well documented. However, much less is known about the transcriptional regulation of Kiss1 expression in the hypothalamus. Critical for these studies is an accurate identification of the site(s) where Kiss1 transcription is initiated. Employing 5'-RACE PCR, we detected a transcription start site (TSS1) used by the hypothalamus of rats, mice, nonhuman primates and humans to initiate Kiss1 transcription. In rodents, an exon 1 encoding 5'-untranslated sequences is followed by an alternatively spliced second exon, which encodes 5'-untranslated regions of two different lengths and contains the translation initiation codon (ATG). In nonhuman primates and humans, exon 2 is not alternatively spliced. Surprisingly, in rat mediobasal hypothalamus (MBH), but not preoptic area (POA), an additional TSS (TSS2) located upstream from TSS1 generates an exon 1 longer (377 bp) than the TSS1-derived exon 1 (98 bp). The content of TSS1-derived transcripts increased at puberty in the POA and MBH of female rats. It also increased in the MBH after ovariectomy, and this change was prevented by estrogen. In contrast, no such changes in TSS2-derived transcript abundance were detected. Promoter assays showed that the proximal TSS1 promoter is much more active than the putative TSS2 promoter, and that only the TSS1 promoter is regulated by estrogen. These differences appear to be related to the presence of a TATA box and binding sites for transcription factors activating transcription and interacting with estrogen receptor-? in the TSS1, but not TSS2, promoter. © 2014 S. Karger AG, Basel. PMID:24686008

Castellano, Juan Manuel; Wright, Hollis; Ojeda, Sergio R; Lomniczi, Alejandro

2014-01-01

273

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

PubMed Central

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

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

1990-01-01

274

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

PubMed

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

Kapoor, Suman; Samhita, Laasya; Varshney, Umesh

2011-07-01

275

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

PubMed

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

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

2012-06-01

276

MESSENGER Observations of Upstream Whistler Waves in Mercury's Foreshock Region  

NASA Astrophysics Data System (ADS)

The region upstream from a planetary bow shock is a natural plasma laboratory containing a variety of wave particle phenomena. The study of foreshocks other than the Earth's is important for extending our understanding of collisionless shocks and foreshock physics since the bow shock strength varies with heliocentric distance from the Sun, and the sizes of the bow shocks are different at different planets. The Mercury's bow shock is unique in our solar system as it is produced by low Mach number and low plasma beta solar wind blowing over a small magnetized body with a predominately radial interplanetary magnetic field. Previous observations of Mercury upstream ultra-low frequency (ULF) waves came exclusively from two Mercury flybys of Mariner 10. The MESSENGER orbiter data enable us to study upstream waves in the Mercury's foreshock in depth. This paper reports an overview of upstream ULF waves in the Mercury's foreshock using high-time resolution magnetic field data, 20 samples per second, from the MESSENGER spacecraft. A preliminary study has shown the existence of at least three types of upstream waves: 1) whistler waves at frequencies near 2 Hz, similar to 1-Hz waves at the Earth; 2) waves with frequencies ~ 0.1 Hz, similar to the large-amplitude 30-s waves at the Earth; 3) fluctuations with broad spectral peaks centered at ~ 0.6 Hz. Unlike the Earth's foreshock where the most prominent upstream wave phenomenon is locally generated large-amplitude 30-s waves, the most common foreshock waves are whistler waves generated at the bow shock, with properties similar to the 1-Hz waves in the Earth's foreshock. These "one-Hz" waves are present in both the flyby data and in every orbit of the orbital data we have surveyed. We will discuss their properties, spatial variations, and propagation and occurrence characteristics in this paper.

Le, G.; Chi, P. J.; Blanco-Cano, X.; Boardsen, S. A.; Slavin, J. A.; Anderson, B. J.; Korth, H.

2012-12-01

277

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

PubMed Central

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

2014-01-01

278

Internal Impedance of Starting Batteries.  

National Technical Information Service (NTIS)

Starting batteries of the lead accumulator type have an internal impedance which varies with, among other things, the load conditions, working temperature and measurement frequency. The impedance lies between 3 and 30 mohm with frequencies between 20 and ...

R. Andersson

1971-01-01

279

Head Start Dental Health Curriculum.  

National Technical Information Service (NTIS)

There are many ways to provide meaningful learning experiences about dental health that can help Head Start children develop good attitudes and habits. Learning about good dental health care at an early age can help children throughout their lives. Dental...

1997-01-01

280

Novel group of virulence activators within the AraC family that are not restricted to upstream binding sites.  

PubMed

Several regulators within the AraC family control the expression of genes known or thought to be required for virulence of bacterial pathogens. One of these, Rns, activates transcription from an unprecedented variety of binding-site locations. Although nearly all prokaryotic activators bind within a small region upstream and adjacent to the promoter that they regulate, Rns does not bind within this region to activate its own promoter, Prns. Instead, to activate Prns, Rns requires one binding site 224.5 bp upstream and one downstream of the transcription start site. We show in this study that several other AraC family activators recognize the same binding sites as Rns and share with it the ability to utilize a downstream binding site. Like Rns, other members of this group of activators positively regulate the expression of virulence factors in pathogenic bacteria. These regulators are also able to activate transcription from promoter-proximal upstream binding sites since they are able to substitute for Rns at Pcoo, a promoter with only upstream binding sites. Thus, Rns is the prototype for a group of regulators, which include CfaR, VirF, AggR, and CsvR and which activate transcription from locations that are more diverse than those of any other known activator. PMID:11119505

Munson, G P; Holcomb, L G; Scott, J R

2001-01-01

281

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

Microsoft Academic Search

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

Jean-Claude Perez

2010-01-01

282

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

PubMed Central

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

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

2013-01-01

283

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

PubMed Central

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

Ahn, Insung; Bae, Se-Eun

2011-01-01

284

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

PubMed Central

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

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

2013-01-01

285

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

PubMed

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

Anisimova, Maria; Kosiol, Carolin

2009-02-01

286

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

PubMed

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

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

2012-12-01

287

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

PubMed

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

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

2009-05-01

288

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

PubMed

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

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

2013-10-01

289

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

PubMed Central

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

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

2008-01-01

290

Two-codon T-box riboswitch binding two tRNAs  

PubMed Central

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

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

2013-01-01

291

Evidence of abundant stop codon readthrough in Drosophila and other metazoa  

PubMed Central

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

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

2011-01-01

292

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

PubMed

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

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

1992-01-01

293

STARTing Again: What Happens After START I Expires?  

SciTech Connect

The Strategic Arms Reduction Treaty (START I), a seminal arms control agreement that substantially reduced the levels of deployed strategic nuclear arms in the United States and Russia, will expire in December 2009. At this time, it is unclear what—if anything—will replace it. While the treaty remains relevant, more than a simple extension is appropriate. Instead the authors advocate for a successor regime that builds on the START I legacy but does not rely on the traditional tools of arms control. This paper examines the strategic context in which a successor regime would be developed and proposes several recommendations for future action.

Mladineo, Stephen V.; Durbin, Karyn R.; Eastman, Christina M.

2007-08-01

294

8. Upstream face of Mormon Flat, both concrete placement tower ...  

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

8. Upstream face of Mormon Flat, both concrete placement tower and 105 foot derrick are visible. Photographer unknown, June 8, 1924. Source: Salt River Project. - Mormon Flat Dam, On Salt River, Eastern Maricopa County, east of Phoenix, Phoenix, Maricopa County, AZ

295

63. Upstream face of Waddell Dam as viewed from the ...  

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

63. Upstream face of Waddell Dam as viewed from the west abutment. Crane at center is used to service the penstock intake. Photographer Mark Durben. Source: Salt River Project. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

296

18. Upstream face of arches, concrete placing tower is at ...  

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

18. Upstream face of arches, concrete placing tower is at far right. Tower at center was used to convey material. Photographer unknown, January 29, 1927. Source: MWD. - Waddell Dam, On Agua Fria River, 35 miles northwest of Phoenix, Phoenix, Maricopa County, AZ

297

Upstream oil and gas facility energy efficiency tools  

Microsoft Academic Search

Optimizing the energy consumption of Upstream Oil & Gas (UOG) facilities offers opportunities to reduce operating costs, increase revenues and address greenhouse gas emissions, all with cost-effective actions. All of these objectives have been achieved through the application of performance benchmarking, auditing and simulation tools to oil and gas production facilities in the Western Canadian Sedimentary Basin.Combining the experience of

D. G. Colley; B. R. Young; W. Y. Svrcek

2009-01-01

298

8. GENERAL EXTERIOR VIEW LOOKING NORTHWEST TOWARD UPSTREAM END OF ...  

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

8. GENERAL EXTERIOR VIEW LOOKING NORTHWEST TOWARD UPSTREAM END OF NAVIGATION LOCK #1; SOUTH END OF POWERHOUSE #1 IS VISIBLE ON RIGHT; BRADFORD SLOUGH IS VISIBLE IN FOREGROUND. - Bonneville Project, Navigation Lock No. 1, Oregon shore of Columbia River near first Powerhouse, Bonneville, Multnomah County, OR

299

42. VIEW OF STAGE RECORDER AT END OF UPSTREAM GUIDE ...  

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

42. VIEW OF STAGE RECORDER AT END OF UPSTREAM GUIDE WALL, LOOKING NORTHEAST. (Several hours after this view was taken, the stage recorder was hit a~d heavily damaged by a grain barge.) - Upper Mississippi River 9-Foot Channel, Lock & Dam No. 9, Lynxville, Crawford County, WI

300

25. TWIN FALLS MAIN CANAL HEADWORKS FROM UPSTREAM LOOKING TOWARD ...  

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

25. TWIN FALLS MAIN CANAL HEADWORKS FROM UPSTREAM LOOKING TOWARD THE WEST (DAM-TENDER RICHARD CARL ADJUSTING THE GATES TO ALLOW 3400 CFS THROUGH). - Milner Dam & Main Canal: Twin Falls Canal Company, On Snake River, 11 miles West of city of Burley, Idaho, Twin Falls, Twin Falls County, ID

301

PHOTO OF THE BOAT HOUSE, GATE HOUSE, UPSTREAM SIDE OF ...  

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

PHOTO OF THE BOAT HOUSE, GATE HOUSE, UPSTREAM SIDE OF SPILLWAYS LOOKING EAST; WATER INTAKE AND LOG BOOMS ARE SEEN ON RESERVOIR. PHOTO BY JET LOWE, HAER, 1995. - Elwha River Hydroelectric System, Glines Hydroelectric Dam & Plant, Port Angeles, Clallam County, WA

302

18. View to southwest. Detail, bearing shoe, upstream side of ...  

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

18. View to southwest. Detail, bearing shoe, upstream side of east pier. Copy negative made from 35mm color transparency made with with 135mm lens by John Snyder, due to lack of sufficiently long lens for 4x5 camera. - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

303

On the Characteristics of the Upstream Bedrock Erosion in Taiwan  

NASA Astrophysics Data System (ADS)

Taiwan is located in a region with frequent natural hazards and active tectonic activities; moreover, the significant surface displacement caused by the 1999 Chi-Chi Earthquake resulted in a huge impact on riverbed erosion. Over the past years, hazards to the mid- and up-stream slopes have been increasing, which is closely related to bedrock erosion and the channel instability due to the erosion. This study investigate the behavior of upstream bedrock erosion of the Ba-chang River and the Chou-Shuei River in Central Taiwan through a modified stream-power erosion model. The data collected from the field measurement of erosion nails and the change in riverbed elevation from the multi-timescale digital elevation were applied in the analyses. In addition, the slope of the slope unit as well as the sub-watershed was derived from the digital elevation model, and to the upstream discharge was obtained from the rainfall distributions and the elevation model. Additionally, to consider the influence of landslides in the upstream, the landslide ratio was also considered and included in the modified erosion model. The influence of the riverbed concavity index of the longitudinal river profile was compared for the regression results of the models with and without modification. The results show that the modified erosion model has better regression results and correlates significantly to the riverbed concavity index.

Shou, K.-J.; Lee, Y.-Y.

2012-04-01

304

9. Detail, typical bearing, upstream side of west end of ...  

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

9. Detail, typical bearing, upstream side of west end of Bridge Number 301.85, view to east, 210mm lens with electronic flash fill. - Southern Pacific Railroad Shasta Route, Bridge No. 301.85, Milepost 301.85, Pollard Flat, Shasta County, CA

305

2. VIEW SHOWING UPSTREAM FACE OF DAM, WITH UPRIGHT (INOPERABLE) ...  

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

2. VIEW SHOWING UPSTREAM FACE OF DAM, WITH UPRIGHT (INOPERABLE) OUTLET GATE, LOOKING WEST - High Mountain Dams in Upalco Unit, Water Lily Lake Dam, Ashley National Forest, 1.1 miles Northeast of Swift Creek Campground, Mountain Home, Duchesne County, UT

306

3. VIEW SHOWING UPSTREAM FACE OF DAM, WITH UPRIGHT (INOPERABLE) ...  

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

3. VIEW SHOWING UPSTREAM FACE OF DAM, WITH UPRIGHT (INOPERABLE) OUTLET GATE, LOOKING EAST - High Mountain Dams in Upalco Unit, Water Lily Lake Dam, Ashley National Forest, 1.1 miles Northeast of Swift Creek Campground, Mountain Home, Duchesne County, UT

307

1. OVERALL VIEW OF WATER LILY LAKE AND UPSTREAM FACE ...  

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

1. OVERALL VIEW OF WATER LILY LAKE AND UPSTREAM FACE OF DAM, SHOWING UPRIGHT (INOPERABLE) OUTLET GATE, LOOKING NORTH - High Mountain Dams in Upalco Unit, Water Lily Lake Dam, Ashley National Forest, 1.1 miles Northeast of Swift Creek Campground, Mountain Home, Duchesne County, UT

308

1. VIEW NORTH FROM UPSTREAM WITH IMPOUNDED LAKE AND (LEFT ...  

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

1. VIEW NORTH FROM UPSTREAM WITH IMPOUNDED LAKE AND (LEFT TO RIGHT): EARTHEN DIKE, HYDROELECTRIC GENERATING FACILITY, AND DAM - Middle Creek Hydroelectric Dam, On Middle Creek, West of U.S. Route 15, 3 miles South of Selinsgrove, Selinsgrove, Snyder County, PA

309

2. UPSTREAM SIDE OF DAM AND BRIDGE WITH ABANDONED SAN ...  

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

2. UPSTREAM SIDE OF DAM AND BRIDGE WITH ABANDONED SAN TAN FLOOD-WATER HEADGATE IN FOREGROUND. TAKEN FROM NORTH END OF DAM - San Carlos Irrigation Project, Sacaton Dam & Bridge, Gila River, T4S R6E S12/13, Coolidge, Pinal County, AZ

310

Impulse noise identification for the HFC upstream channel  

Microsoft Academic Search

An algorithm is described that identifies the shape of the impulse within the impulse noise component of the HFC upstream channel. The cross-correlation function (CCF) is used to align samples of the impulse waveforms in time. The singular value decomposition (SVD) finds the dominant basis waveforms that represent the collection of samples. We find that two frequency-modulated basis waveforms sufficiently

Kuo-Hui Li; Arden Huang; Mary Ann Ingram; Daniel Howard

1998-01-01

311

2. VIEW OF UPSTREAM SIDE OF HISTORIC OUTLET WORKS TAKEN ...  

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

2. VIEW OF UPSTREAM SIDE OF HISTORIC OUTLET WORKS TAKEN FROM CENTER OF THE CHANNEL FROM TWIN LAKES. VIEW LOOKING EAST. - Twin Lakes Dam & Outlet Works, Beneath Twin Lakes Reservoir, T11S, R80W, S22, Twin Lakes, Lake County, CO

312

10. VIEW UPSTREAM OF PIPELINE SECTION AT JUNCTION OF HUME ...  

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

10. VIEW UPSTREAM OF PIPELINE SECTION AT JUNCTION OF HUME CEMENT PIPE AND CAST-IRON (460'). NOTE CYLINDRICAL COLLAR OF CEMENT SECTIONS AND BELL JUNCTIONS OF IRON PIPE. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI

313

12. Upstream view showing thelower log pond log chute in ...  

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

12. Upstream view showing thelower log pond log chute in the main channel of the Hudson River. The log chute in the dam can be seen in the background. Facing southwest. - Glens Falls Dam, 100' to 450' West of U.S. Route 9 Bridge Spanning Hudson River, Glens Falls, Warren County, NY

314

Upstream processes in antibody production: Evaluation of critical parameters  

Microsoft Academic Search

The demand for monoclonal antibody for therapeutic and diagnostic applications is rising constantly which puts up a need to bring down the cost of its production. In this context it becomes a prerequisite to improve the efficiency of the existing processes used for monoclonal antibody production. This review describes various upstream processes used for monoclonal antibody production and evaluates critical

Era Jain; Ashok Kumar

2008-01-01

315

4. AERATOR AT 525, CONSTRUCTED 19371938, VIEW FROM UPSTREAM (TRASH ...  

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

4. AERATOR AT 525, CONSTRUCTED 1937-1938, VIEW FROM UPSTREAM (TRASH SCREEN REMOVED FOR CLARITY), WATER FROM INTAKE FLOWS THROUGH FLUME, THEN DAMS, AND SPILLS OVER STEPS TO MIX WITH OXYGEN, THUS REDUCING ACIDITY LEVELS. ACID INDUCES FASTER CORROSION OF PIPES AND SPOILS TASTE. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI

316

9. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: REINFORCEMENT DETAILS OF ...  

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

9. UPSTREAM EXTENSION TO 60' INFILTRATION PIPE: REINFORCEMENT DETAILS OF VALVE CONTROL STRUCTURE. Sheet A-20, July, 1939. File no. SA 342/29. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

317

10. View to west from Jacob Meyer Park, showing upstream ...  

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

10. View to west from Jacob Meyer Park, showing upstream (east) side of truss span. Bend is visible in lower portion of damaged vertical compression member third from right. - Stanislaus River Bridge, Atchison, Topeka & Santa Fe Railway at Stanislaus River, Riverbank, Stanislaus County, CA

318

Innovation and performance: The case of the upstream petroleum sector  

Microsoft Academic Search

This thesis investigates innovation in the upstream crude oil and natural gas sector, a strategic part of the Canadian economy and a vital industry for North American energy trade and security. Significant interest exists in understanding innovation in this sector from a private and public policy perspective. Interest in the sector has intensified recently due to concerns about world oil

A. C. Jai Persaud

2007-01-01

319

View of upstream face of the forebay dam of Grand ...  

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

View of upstream face of the forebay dam of Grand Coulee Dam, looking southwest. Note the trash racks at the entrance to the penstocks. - Columbia Basin Project, Grand Coulee Dam & Franklin D. Roosevelt Lake, Across Columbia River, Southeast of Town of Grand Coulee, Grand Coulee, Grant County, WA

320

5. UPSTREAM VIEW OF THE TRASH RAKES, GATES AND GATELIFTING ...  

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

5. UPSTREAM VIEW OF THE TRASH RAKES, GATES AND GATE-LIFTING MECHANISMS FOR THE POST FALLS DAM AND POWERHOUSE, LOOKING NORTHWEST. - Washington Water Power Company Post Falls Power Plant, Middle Channel Powerhouse & Dam, West of intersection of Spokane & Fourth Streets, Post Falls, Kootenai County, ID

321

6. UPSTREAM VIEW OF THE SPILLWAY OF THE POST FALLS ...  

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

6. UPSTREAM VIEW OF THE SPILLWAY OF THE POST FALLS POWERHOUSE, WITH A PARTIAL VIEW OF THE MODERN TRANSFORMER IN THE FOREGROUND, AND THE OLD SWITCHING BUILDING IN THE LEFT BACKGROUND, LOOKING SOUTHEAST. - Washington Water Power Company Post Falls Power Plant, Middle Channel Powerhouse & Dam, West of intersection of Spokane & Fourth Streets, Post Falls, Kootenai County, ID

322

68. VIEW, LOOKING NORTH (UPSTREAM) FROM LOWER ARM OF COFFERDAM, ...  

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

68. VIEW, LOOKING NORTH (UPSTREAM) FROM LOWER ARM OF COFFERDAM, SHOWING STATUS OF CONSTRUCTION. NOTE CONCRETE FORMS IN DISTANCE, TIMBER PILES FOR INTERMEDIATE WALL IN CENTER, AND CONCRETE MIXING PLANT ON RIGHT. Taken September 4, 1934. - Upper Mississippi River 9-Foot Channel, Lock & Dam No. 10, Guttenberg, Clayton County, IA

323

13. Detail, upper chord connection point on upstream side of ...  

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

13. Detail, upper chord connection point on upstream side of truss, showing connection of upper chord, laced vertical compression member, knee-braced strut, counters, and laterals. - Red Bank Creek Bridge, Spanning Red Bank Creek at Rawson Road, Red Bluff, Tehama County, CA

324

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

PubMed Central

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

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

2008-01-01

325

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

PubMed

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

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

2002-02-01

326

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

PubMed Central

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

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

2002-01-01

327

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

PubMed Central

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

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

1989-01-01

328

Streptococcus pyogenes type 12 M protein gene regulation by upstream sequences.  

PubMed Central

A partial nucleotide sequence that included 1,693 base pairs of the M12 (emm12) gene of group A streptococci (strain CS24) and adjacent upstream DNA was determined. Type 12 M protein-specific mRNA of strain CS24 is transcribed from two promoters (P1 and P3) separated by 30 bases. The transcription start sites of the emm12 gene were located more than 400 bases downstream of a deletion that causes decreased M-protein gene transcription in strain CS64. Deletion analysis of M protein-expressing plasmids indicated that an upstream region greater than 1 kilobase is required for M-protein gene expression. The M-protein gene transcriptional unit appears to be monocistronic. Analysis of the emm12 DNA sequence revealed three major repeat regions. Two copies of each repeat, A and B, existed within the variable 5' end of the gene; repeat C demarcated the 5' end of the constant region shared by emm12 and emm6. Images

Robbins, J C; Spanier, J G; Jones, S J; Simpson, W J; Cleary, P P

1987-01-01

329

Mean velocities and Reynolds stresses upstream of a simulated wing-fuselage juncture  

NASA Technical Reports Server (NTRS)

Values of three mean velocity components and six turbulence stresses measured in a turbulent shear layer upstream of a simulated wing-fuselage juncture and immediately downstream of the start of the juncture are presented nd discussed. Two single-sensor hot-wire probes were used in the measurements. The separated region just upstream of the wing contains an area of reversed flow near the fuselage surface where the turbulence level is high. Outside of this area the flow skews as it passes around the body, and in this skewed region the magnitude and distribution of the turbulent normal and shear stresses within the shear layer are modified slightly by the skewing and deceleration of the flow. A short distance downstream of the wing leading edge the secondary flow vortext is tightly rolled up and redistributes both mean flow and turbulence in the juncture. The data acquisition technique employed here allows a hot wire to be used in a reversed flow region to indicate flow direction.

Mcmahon, H.; Hubbartt, J.; Kubendran, L. R.

1983-01-01

330

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

331

Mutation analysis of the GALT gene in Czech and Slovak galactosemia populations: identification of six novel mutations, including a stop codon mutation (X380R).  

PubMed

A study of the galactose-1-phosphate uridyltransferase (GALT) gene from 37 unrelated galactosemia families is reported here. A total of 16 sequence variations in eleven mutated alleles was found. The two most common molecular defects were the mutations Q188R (46.0%) and K285N (25.7%). Six novel mutations in the GALT gene, X380R, Y209S, E340K, L74fsdelCT, Q169K and L256/P257delGCC, were detected. Three mutations, V151A, L195P and R204X that were previously described in other populations, were also found. The mutation X380R, which breaks the stop codon of the GALT gene, causes elongation of the GALT enzyme's protein chain. A deletion of four nucleotides in the 5' promoter region, in a position 116 - 119 nucleotides upstream from the initiate codon (5'UTR-119delGTCA), was revealed in Duarte (D2) alleles, in addition to N314D, IVS4nt-27g-->c, IVS5nt+62g-->a, and IVS5nt-24g-->a. An unusual molecular genotype was observed on 2 types of classical galactosemia alleles, with six variations from the normal nucleotide sequence presented in cis (mutation V151A or E340K plus five Duarte (D2) characteristic variations). In summary, galactosemia is a heterogeneous disorder at the molecular level, and mutation N314D, appears to be an ancient genetic variant of the GALT gene. Hum Mutat 15:206, 2000. PMID:10649501

Kozák, L; Francová, H; Fajkusová, L; Pijácková, A; Macku, J; Stastná, S; Peskovová, K; Martincová, O; Krijt, J; Bzdúch, V

2000-02-01

332

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

PubMed Central

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

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

2005-01-01

333

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

PubMed Central

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

Plotkin, Joshua B.; Kudla, Grzegorz

2010-01-01

334

The density of cometary protons upstream of Comet Halley's bow shock  

NASA Technical Reports Server (NTRS)

Cometary protons picked up by the solar wind were detected by the high energy range spectrometer of the Giotto ion mass spectrometer starting at a cometocentric distance of about 12 million km. On the average, the density of cometary protons varied approximately as the inverse square of the cometocentric distance, reaching a value of 0.11/cu cm just outside the bow shock. The data can be successfully fit to models that include substantial amounts of both slow (1 km/s) and fast (8 km/s or greater) H atoms beyond the bow shock. Large local variations in the density of picked-up protons can be explained on the basis of variations in the direction of the interplanetary magnetic field in upstream regions where pitch angle scattering was weak.

Neugebauer, M.; Goldstein, B. E.; Balsiger, H.; Neubauer, F. M.; Schwenn, R.

1989-01-01

335

The density of cometary protons upstream of comet Halley's bow shock  

SciTech Connect

Cometary protons picked up by the solar wind were detected by the high energy range spectrometer of the Giotto ion mass spectrometer starting at a cometocentric distance of {approximately}12 {times} 10{sup 6} km. On the average, the density of cometary protons varied approximately as the inverse square of the cometocentric distance, reaching a value of 0.11 cm{sup {minus}3} just outside the bow shock. The data can be successfully fit to models that include substantial amounts of both slow ({approximately}1 km/s) and fast ({ge} 8 km/s) H atoms beyond the bow shock. Large local variations in the density of picked-up protons can be explained on the basis of variations in the direction of the interplanetary magnetic field in upstream regions where pitch angle scattering was weak.

Neugebauer, M.; Goldstein, B.E. (California Institute of Technology, Pasadena (USA)); Balsiger, H. (Univ. of Bern (Switzerland)); Neubauer, F.M. (Univ. of Cologne (West Germany)); Schwenn, R. (Max-Planck-Institut fuer Aeronomie, Katlenburg-Lindau (West Germany)); Shelley, E.G. (Lockheed Palo Alto Research Lab., CA (USA))

1989-02-01

336

Upstream Erosion and Sedimentation in small reservoirs in Burkina Faso  

NASA Astrophysics Data System (ADS)

The Hydroagricultural management of small reservoirs, of which there exist very many in Burkina Faso, can be considered as either "upstream", or "downstream" installations. Installation downstream is often preferred by designers because it makes it possible to carry out the collective irrigation by gravity. Otherwise, installations upstream often correspond to the spontaneous use by the farmers, of limited surfaces close to non man-made reservoirs. Designers often emphasize that an irrigation installation upstream, from its nature and its situation, would worsen the erosion process of the catch basin area, and thus hasten the premature filling of reserves. However, these installations upstream represent very little total surface of the land irrigated, and the methods typically used by the farmers to water these lands , reduce largely the possibilities of erosion. The annual silting of reserves, such as reported in the research studies, corresponds in volume to 0,1 to 0,5 % per year of the capacity of the reservoir. Thus one can deduce, that the time estimated for filling these reservoirs with silting, lies between 200 and 1000 years. The relatively small angle of the ground slopes, the nature of the rocks and the groundcover, do not encourage erosion and especially not the transport of the products of erosion, even if the cultivated part of the catch basin would happen, in some cases, to undergo a considerable erosion. There exist in Burkina some very old reservoirs which are still functional, as well as the many reservoirs created in the 1960's, which do not appear to have appreciable filling. That would not been possible to observe had there been significant silting over the years. Existing measurements as well as the observation of the numerous reservoirs and the general conditions of the sites, make it possible to estimate that the time alloted for the eventual filling by erosion of these reservoirs remains generally within acceptable values . It also appears that the number of irrigation installations upstream from reservoirs is, generally speaking, most probably sufficiently small to be acceptable. For these reasons, it would be thus regrettable to refuse this type of installation (Installations Upstream), controlled well by the farmers themselves and enabling them to transform their availability into a productive labour investment.

de Boissezon, J.

2003-04-01

337

Off to a Good Start.  

ERIC Educational Resources Information Center

Caring Start is a mobile-clinic program that provides prenatal care, well-baby clinics, childhood immunizations, counseling services, and contraceptives to rural poor families in northwest Pennsylvania. Before the mobile clinic, many rural women (mostly teenagers) went without prenatal health care due to lack of transportation. (LP)

Hoffman, Carl

1994-01-01

338

Head Start Center Design Guide.  

ERIC Educational Resources Information Center

This guide contains suggested criteria for planning, designing, and renovating Head Start centers so that they are safe, child-oriented, developmentally appropriate, beautiful, environmentally sensitive, and functional. The content is based on the U.S. General Services Administration's Child Care Center Design Guide, PBS-P140, which was intended…

Administration for Children, Youth, and Families (DHHS), Washington, DC. Head Start Bureau.

339

Rigor Made Easy: Getting Started  

ERIC Educational Resources Information Center

Bestselling author and noted rigor expert Barbara Blackburn shares the secrets to getting started, maintaining momentum, and reaching your goals. Learn what rigor looks like in the classroom, understand what it means for your students, and get the keys to successful implementation. Learn how to use rigor to raise expectations, provide appropriate…

Blackburn, Barbara R.

2012-01-01

340

Starting School: A Community Endeavor  

ERIC Educational Resources Information Center

Much of the current debate about children's transition to school focuses on children's readiness for school. Indeed, Boethel (2004, p. 17) describes transition as the "focal point of readiness." Typically, this focus extends to considering children's competencies--particularly their skills and abilities--at the time of starting school. This…

Dockett, Sue; Perry, Bob

2008-01-01

341

Whitepaper: Starting a New Program  

NSDL National Science Digital Library

This is a white paper on starting a geospatial educational program. The paper covers the growth of geospatial technology and introduces a model for creating a program in the field. Useful logic model templates are included to help educators going through the process. This paper would be a useful resource for educators and administrators creating a program from scratch at their institution.

Johnson, Ann B.; Lewis, Chris

2011-08-08

342

Chicken ovalbumin upstream promoter transcription factor II regulates uncoupling protein 3 gene transcription in Phodopus sungorus  

PubMed Central

Background Ucp3 is an integral protein of the inner mitochondrial membrane with a role in lipid metabolism preventing deleterious effects of fatty acids in states of high lipid oxidation. Ucp3 is expressed in brown adipose tissue and skeletal muscle and controlled by a transcription factor complex including PPARalpha, MyoD and the histone acetyltransferase p300. Several studies have demonstrated interaction of these factors with chicken ovalbumin upstream promoter transcription factor II (Coup-TFII). This nuclear receptor is involved in organogenesis and other developmental processes including skeletal muscle development, but also co-regulates a number of metabolic genes. In this study we in silico analyzed the upstream region of Ucp3 of the Djungarian hamster Phodopus sungorus and identified several putative response elements for Coup-TFII. We therefore investigated whether Coup-TFII is a further player in the transcriptional control of the Ucp3 gene in rodents. Results By quantitative PCR we demonstrated a positive correlation of Coup-TFII and Ucp3 mRNA expression in skeletal muscle and brown adipose tissue in response to food deprivation and cold exposure, respectively. In reporter gene assays Coup-TFII enhanced transactivation of the Ucp3 promoter conveyed by MyoD, PPARalpha, RXRalpha and/or p300. Using deletions and mutated constructs, we identified a Coup-TFII enhancer element 816–840 bp upstream of the transcriptional start site. Binding of Coup-TFII to this upstream enhancer was confirmed in electrophoretic mobility shift and supershift assays. Conclusion Transcriptional regulation of the Coup-TFII gene in response to starvation and cold exposure seems to be the regulatory mechanism of Ucp3 mRNA expression in brown adipose and skeletal muscle tissue determining the final appropriate rate of transcript synthesis. These findings add a crucial component to the complex transcriptional machinery controlling expression of Ucp3. Given the substantial evidence for a function of Ucp3 in lipid metabolism, Coup-TFII may not only be a negative regulator of glucose responsive genes but also transactivate genes involved in lipid metabolism.

Fromme, Tobias; Reichwald, Kathrin; Platzer, Matthias; Li, Xing-Sheng; Klingenspor, Martin

2007-01-01

343

Vaccine production: upstream processing with adherent or suspension cell lines.  

PubMed

The production of viral vaccines in cell culture can be accomplished with primary, diploid, or continuous (transformed) cell lines. Each cell line, each virus type, and each vaccine preparation require the specific design of upstream and downstream processing. Media have to be selected as well as production vessels, cultivation conditions, and modes of operation. Many viruses only replicate to high titers in adherently growing cells, but similar to processes established for recombinant protein production, an increasing number of suspension cell lines is being evaluated for future use. Here, we describe key issues to be considered for the establishment of large-scale virus production in bioreactors. As an example upstream processing of cell culture-derived influenza virus production is described in more detail for adherently growing and for suspension cells. In particular, use of serum-containing, serum-free, and chemically defined media as well as choice of cultivation vessel are considered. PMID:24297427

Genzel, Yvonne; Rödig, Jana; Rapp, Erdmann; Reichl, Udo

2014-01-01

344

Translation of the human erythropoietin transcript is regulated by an upstream open reading frame in response to hypoxia.  

PubMed

Erythropoietin (EPO) is a key mediator hormone for hypoxic induction of erythropoiesis that also plays important nonhematopoietic functions. It has been shown that EPO gene expression regulation occurs at different levels, including transcription and mRNA stabilization. In this report, we show that expression of EPO is also regulated at the translational level by an upstream open reading frame (uORF) of 14 codons. As judged by comparisons of protein and mRNA levels, the uORF acts as a cis-acting element that represses translation of the main EPO ORF in unstressed HEK293, HepG2, and HeLa cells. However, in response to hypoxia, this repression is significantly released, specifically in HeLa cells, through a mechanism that involves processive scanning of ribosomes from the 5' end of the EPO transcript and enhanced ribosome bypass of the uORF. In addition, we demonstrate that in HeLa cells, hypoxia induces the phosphorylation of eukaryotic translation initiation factor 2? (eIF2?) concomitantly with a significant increase of EPO protein synthesis. These findings provide a framework for understanding that production of high levels of EPO induced by hypoxia also involves regulation at the translational level. PMID:24647661

Barbosa, Cristina; Romão, Luísa

2014-05-01

345

12. Detail, lower chord connection point on upstream side of ...  

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

12. Detail, lower chord connection point on upstream side of truss, showing pinned connection of lower chord eye bars, laced vertical compression member, diagonal eye bar tension members, turnbuckled diagonal counters, and floor beam. Note also timber floor stringers supported by floor beam, and exposed ends of timber deck members visible at left above lower chord eye bar. View to northwest. - Red Bank Creek Bridge, Spanning Red Bank Creek at Rawson Road, Red Bluff, Tehama County, CA

346

Vertical Fence Wake Manipulation Using Periodic Variation of Upstream Flow  

NASA Astrophysics Data System (ADS)

The effect of periodic variation of upstream flow on the separated shear flows behind the vertical fence was experimentally investigated. Upstream flow was modified using small obstacles and this device made the periodic change of streamwise velocities in front of the fence. The experiments were performed in a circulating water channel. The Reynolds number based on the height of fence and freestream velocity was varied from 2000 to 6000. The vertical fence was submerged in the turbulent boundary layer. Stereoscopic-PIV method was used to measure the instantaneous velocity fields around a vertical fence. 800 instantaneous velocity fields were acquired in each experimental condition and the mean properties were calculated using the ensemble average method. The obtained results were compared with those of uncontrolled fence flow. The results showed the vertical fence under the upstream flow change has the local downwash flow behind the fence and this flow suppressed the separation bubble and made the smaller recirculation region compared with uncontrolled fence wake.

Lee, Seung-Hwan; Tu, Xin Cheng; Kim, Hyoung-Woo; Kim, Hyoung-Bum

2011-11-01

347

Microgravity induced selective lesions in immunosignaling: Upstream targets in lymphocytes  

NASA Astrophysics Data System (ADS)

Microgravity is a novel milieu for cells where re-ordering of forces induces different responses. Human lymphocytes undergo a suppression of activation and locomotion in space and modeled microgravity. Based on recovery of activation and locomotion with the phorbol ester PMA, the lesion induced by microgravity is presumed up- stream of the level of PKC signaling. Lymphocytes cultured in ground-based microgravity analog conditions display depressed calcium independent PKC isoforms. Upstream signaling molecules such as Phospholipase C gamma were not sufficiently activated in modeled microgravity. Immunoblotting revealed LAT, which is an adaptor protein crucial for Phospholipase C gamma recruitment in T cell activation, was down regulated in lymphocytes cultured at 72 and 96 hours in modeled microgravity. Also, ZAP 70 kinase, which is a LAT activator, down- regulated (>2 fold) at 96 hours modeled microgravity culture. Microarray analysis of lymphocytes cultured in 1g and modeled microgravity revealed significant down- regulation in upstream T cell activation molecules such as Diacylglycerol kinase, serine/threonine kinases, and tyrosine kinases. All up-stream targets in T cell activation are negatively affected in microgravity. Optimal immune function is critical in the ISS era where long term space travel is inevitable. Elucidation of the key mechanisms affected by microgravity lays the foundation for development of treatments that can counter these deleterious effects.

Sundaresan, A.; Pellis, N.

348

Interaction of upstream flow distortions with high Mach number cascades  

NASA Technical Reports Server (NTRS)

Features of the interaction of flow distortions, such as gusts and wakes with blade rows of advance type fans and compressors having high tip Mach numbers are modeled. A typical disturbance was assumed to have harmonic time dependence and was described, at a far upstream location, in three orthogonal spatial coordinates by a double Fourier series. It was convected at supersonic relative to a linear cascade described as an unrolled annulus. Conditions were selected so that the component of this velocity parallel to the axis of the turbomachine was subsonic, permitting interaction between blades through the upstream as well as downstream flow media. A strong, nearly normal shock was considered in the blade passages which was allowed curvature and displacement. The flows before and after the shock were linearized relative to uniform mean velocities in their respective regions. Solution of the descriptive equations was by adaption of the Wiener-Hopf technique, enabling a determination of distortion patterns through and downstream of the cascade as well as pressure distributions on the blade and surfaces. Details of interaction of the disturbance with the in-passage shock were discussed. Infuences of amplitude, wave length, and phase of the disturbance on lifts and moments of cascade configurations are presented. Numerical results are clarified by reference to an especially orderly pattern of upstream vertical motion in relation to the cascade parameters.

Englert, G. W.

1981-01-01

349

Catalytic Ignition and Upstream Reaction Propagation in Monolith Reactors  

NASA Technical Reports Server (NTRS)

Using numerical simulations, this work demonstrates a concept called back-end ignition for lighting-off and pre-heating a catalytic monolith in a power generation system. In this concept, a downstream heat source (e.g. a flame) or resistive heating in the downstream portion of the monolith initiates a localized catalytic reaction which subsequently propagates upstream and heats the entire monolith. The simulations used a transient numerical model of a single catalytic channel which characterizes the behavior of the entire monolith. The model treats both the gas and solid phases and includes detailed homogeneous and heterogeneous reactions. An important parameter in the model for back-end ignition is upstream heat conduction along the solid. The simulations used both dry and wet CO chemistry as a model fuel for the proof-of-concept calculations; the presence of water vapor can trigger homogenous reactions, provided that gas-phase temperatures are adequately high and there is sufficient fuel remaining after surface reactions. With sufficiently high inlet equivalence ratio, back-end ignition occurs using the thermophysical properties of both a ceramic and metal monolith (coated with platinum in both cases), with the heat-up times significantly faster for the metal monolith. For lower equivalence ratios, back-end ignition occurs without upstream propagation. Once light-off and propagation occur, the inlet equivalence ratio could be reduced significantly while still maintaining an ignited monolith as demonstrated by calculations using complete monolith heating.

Struk, Peter M.; Dietrich, Daniel L.; Miller, Fletcher J.; T'ien, James S.

2007-01-01

350

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

Microsoft Academic Search

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

Andrew J. Doig

1997-01-01

351

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

Microsoft Academic Search

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

Marilyn Kozak

1995-01-01

352

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

PubMed Central

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

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

2012-01-01

353

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

Microsoft Academic Search

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

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

2010-01-01

354

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

PubMed Central

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

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

355

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

PubMed

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

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

2004-01-01

356

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

Microsoft Academic Search

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

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

2008-01-01

357

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

PubMed

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

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

2010-08-01

358

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

359

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

PubMed Central

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

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

2007-01-01

360

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

Microsoft Academic Search

BACKGROUND: Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. One factor known to affect translational power is biased use of synonymous codons. The correlation within an organism between expression level

Les Dethlefsen; Thomas M. Schmidt

2005-01-01

361

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

PubMed Central

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

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

2013-01-01

362

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

PubMed

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

Li, Sen; Yang, Jie

2014-08-21

363

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

364

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

Microsoft Academic Search

BACKGROUND: Out-of-frame stop codons (OSCs) occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated with frameshift events can be reduced. Given such a functional significance, we expect statistically overrepresented OSCs in coding sequences as a result of a widespread selection. Accordingly, we examined

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

2010-01-01

365

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

Microsoft Academic Search

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

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

2003-01-01

366

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

PubMed

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

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

2013-08-01

367

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

Microsoft Academic Search

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

Avril Coghlan; Kenneth H. Wolfe

2000-01-01

368

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

Microsoft Academic Search

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

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

2003-01-01

369

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

370

Head Start Impact Study: First Year Findings  

ERIC Educational Resources Information Center

The Congressionally-mandated Head Start Impact Study is being conducted across 84 nationally representative grantee/delegate agencies. Approximately 5,000 newly entering 3- and 4-year-old children applying for Head Start were randomly assigned to either a Head Start group that had access to Head Start program services or to a non-Head Start group…

Puma, Michael; Bell, Stephen; Cook, Ronna; Heid, Camilla; Lopez, Michael

2005-01-01

371

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

PubMed Central

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

Miyazawa, Sanzo

2011-01-01

372

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

PubMed

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

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

2014-01-01

373

Meeting Report: Moving Upstream--Evaluating Adverse Upstream End Points for Improved Risk Assessment and Decision-Making  

PubMed Central

Background Assessing adverse effects from environmental chemical exposure is integral to public health policies. Toxicology assays identifying early biological changes from chemical exposure are increasing our ability to evaluate links between early biological disturbances and subsequent overt downstream effects. A workshop was held to consider how the resulting data inform consideration of an “adverse effect” in the context of hazard identification and risk assessment. Objectives Our objective here is to review what is known about the relationships between chemical exposure, early biological effects (upstream events), and later overt effects (downstream events) through three case studies (thyroid hormone disruption, antiandrogen effects, immune system disruption) and to consider how to evaluate hazard and risk when early biological effect data are available. Discussion Each case study presents data on the toxicity pathways linking early biological perturbations with downstream overt effects. Case studies also emphasize several factors that can influence risk of overt disease as a result from early biological perturbations, including background chemical exposures, underlying individual biological processes, and disease susceptibility. Certain effects resulting from exposure during periods of sensitivity may be irreversible. A chemical can act through multiple modes of action, resulting in similar or different overt effects. Conclusions For certain classes of early perturbations, sufficient information on the disease process is known, so hazard and quantitative risk assessment can proceed using information on upstream biological perturbations. Upstream data will support improved approaches for considering developmental stage, background exposures, disease status, and other factors important to assessing hazard and risk for the whole population.

Woodruff, Tracey J.; Zeise, Lauren; Axelrad, Daniel A.; Guyton, Kathryn Z.; Janssen, Sarah; Miller, Mark; Miller, Gregory G.; Schwartz, Jackie M.; Alexeeff, George; Anderson, Henry; Birnbaum, Linda; Bois, Frederic; Cogliano, Vincent James; Crofton, Kevin; Euling, Susan Y.; Foster, Paul M.D.; Germolec, Dori R.; Gray, Earl; Hattis, Dale B.; Kyle, Amy D.; Luebke, Robert W.; Luster, Michael I.; Portier, Chris; Rice, Deborah C.; Solomon, Gina; Vandenberg, John; Zoeller, R. Thomas

2008-01-01

374

An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators  

SciTech Connect

The R/B genes of maize encode a family of basic helix-loop-helix proteins that determine where and when the anthocyanin-pigment pathway will be expressed in the plant. Previous studies showed that allelic diversity among family members reflects differences in gene expression, specifically in transcription initiation. The authors present evidence that the R gene Lc is under translational control. They demonstrate that the 235-nt transcript leader of Lc represses expression 25- to 30-fold in an in vivo assay. Repression is mediated by the presence in cis of a 38-codon upstream open reading frame. Furthermore, the coding capacity of the upstream open reading frame influences the magnitude of repression. It is proposed that translational control does not contribute to tissue specificity but prevents overexpression of the Lc protein. The diversity of promoter and 5' untranslated leader sequences among the R/B genes provides an opportunity to study the coevolution of transcriptional and translational mechanisms of gene regulation. 36 refs., 5 figs.

Damiani, R.D. Jr.; Wessler, S.R. (Univ. of Georgia, Athens, GA (United States))

1993-09-01

375

Identification of an upstream activation sequence and other cis-acting elements required for transcription of COX6 from Saccharomyces cerevisiae.  

PubMed Central

Transcription of Saccharomyces cerevisiae COX6, the nuclear gene for subunit VI of cytochrome c oxidase, is activated in heme-proficient cells, requires the HAP2 gene, and is subject to glucose repression. In this study, by deletion mutagenesis of the COX6 promoter, we identified two regions that are important for transcription. The first was an upstream activation site, UAS6. It was found to be contained within an 84-base-pair (bp) sequence, between bp -256 and -340 of the COX6 translational initiation codon, and to contain sequences required for activation by heme and HAP2 and for release from glucose repression. When located upstream of a CYC1-lacZ fusion gene, deleted for both of its UASs, this segment functioned as a UAS element. Although UAS6 could promote expression in either orientation, it showed a marked orientation dependence in its response to HAP2 and the carbon source. The second region lay between bp -255 and -91. It contained two of the three major 5' termini of COX6 mRNAs and a putative TATA box. Deletion analysis of this region demonstrated that the putative TATA box is not required for transcription and that this region is separable into two redundant domains.

Trawick, J D; Rogness, C; Poyton, R O

1989-01-01

376

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

PubMed

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

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

2008-01-01

377

Starting a High School newspaper  

NSDL National Science Digital Library

This Website will provide some resources to help you create a high school newspaper. You will see the connection of education and news, see some methods for creation and be able to see available resources i n helping you out Newspapers are very important part of everyday life. Although there are many new forms of media around, newspapers continue to stand the test of time. They can also be very important in the classroom. On this page you will find some valuable resources to help you start a campus paper or ...

Dart, Greg

2007-10-19

378

Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins  

PubMed Central

A-repeats are the simplest form of tandem repeats and are found ubiquitously throughout genomes. These mononucleotide repeats have been widely believed to be non-functional ‘junk’ DNA. However, studies in yeasts suggest that A-repeats play crucial biological functions, and their role in humans remains largely unknown. Here, we showed a non-random pattern of distribution of sense A- and T-repeats within 20 kb around transcription start sites (TSSs) in the human genome. Different distributions of these repeats are observed upstream and downstream of TSSs. Sense A-repeats are enriched upstream, whereas sense T-repeats are enriched downstream of TSSs. This enrichment directly correlates with repeat size. Genes with different functions contain different lengths of repeats. In humans, tissue-specific genes are enriched for short repeats of <10 bp, whereas housekeeping genes are enriched for long repeats of ?10 bp. We demonstrated that DICER1 and Argonaute proteins are required for the cis-regulatory role of A-repeats. Moreover, in the presence of a synthetic polymer that mimics an A-repeat, protein binding to A-repeats was blocked, resulting in a dramatic change in the expression of genes containing upstream A-repeats. Our findings suggest a length-dependent cis-regulatory function of A-repeats and that Argonaute proteins serve as trans-acting factors, binding to A-repeats.

Aporntewan, Chatchawit; Pin-on, Piyapat; Chaiyaratana, Nachol; Pongpanich, Monnat; Boonyaratanakornkit, Viroj; Mutirangura, Apiwat

2013-01-01

379

A segment of Myxococcus xanthus ops DNA functions as an upstream activation site for tps gene transcription.  

PubMed Central

A segment of DNA located between 131 and 311 base pairs (bp) upstream from the transcriptional start of the Myxococcus xanthus ops gene (-131 to -311) was shown to function as an upstream activation site (UAS) for developmentally regulated transcription from the tps gene promoter region. The activation of early developmental transcription by the ops UAS was independent of orientation and could be increased by the addition of a second copy of the UAS. The ops UAS segment continued to function when placed 1.5 kbp upstream from the transcription initiation site. DNA from the tps promoter region was required for transcriptional activation by the ops UAS, and a specific requirement for the sequence of tps DNA between -34 and -66 was demonstrated. Several specific ops UAS DNA-protein complexes were observed after incubation of this DNA segment with an extract of early developmental M. xanthus cells. Extracts of vegetative cells contained much less ops UAS-specific DNA-binding activity. When the distance between the tps and ops genes was increased from 2 to 15 kbp by insertion of a transduced segment of DNA, the amount of developmentally induced tps RNA was found to be about one-third that found in wild-type M. xanthus. Our observations suggest that the regulatory region of the ops gene functions not only to control ops gene expression but also to increase early developmental expression of the tps gene located about 2 kbp downstream on the M. xanthus chromosome. Images

Kil, K S; Brown, G L; Downard, J S

1990-01-01

380

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

PubMed

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

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

2004-04-30

381

Upstream Mixing Cavity Coupled with a Downstream Flameholding Cavity Behavior in Supersonic Flow (Postprint).  

National Technical Information Service (NTIS)

Experimental investigations of the flowfield associated with three upstream direct injection acoustic resonance cavities coupled with a previously designed downstream combustion cavity in a non-reacting flow are described. All of the upstream mixing cavit...

A. Quick C. D. Carter K. Hsu M. R. Gruber P. I. King

2005-01-01

382

Rapid starting methanol reactor system  

DOEpatents

The invention relates to a methanol-to-hydrogen cracking reactor for use with a fuel cell vehicular power plant. The system is particularly designed for rapid start-up of the catalytic methanol cracking reactor after an extended shut-down period, i.e., after the vehicular fuel cell power plant has been inoperative overnight. Rapid system start-up is accomplished by a combination of direct and indirect heating of the cracking catalyst. Initially, liquid methanol is burned with a stoichiometric or slightly lean air mixture in the combustion chamber of the reactor assembly. The hot combustion gas travels down a flue gas chamber in heat exchange relationship with the catalytic cracking chamber transferring heat across the catalyst chamber wall to heat the catalyst indirectly. The combustion gas is then diverted back through the catalyst bed to heat the catalyst pellets directly. When the cracking reactor temperature reaches operating temperature, methanol combustion is stopped and a hot gas valve is switched to route the flue gas overboard, with methanol being fed directly to the catalytic cracking reactor. Thereafter, the burner operates on excess hydrogen from the fuel cells.

Chludzinski, Paul J. (38 Berkshire St., Swampscott, MA 01907); Dantowitz, Philip (39 Nancy Ave., Peabody, MA 01960); McElroy, James F. (12 Old Cart Rd., Hamilton, MA 01936)

1984-01-01

383

Upstream processes in antibody production: evaluation of critical parameters.  

PubMed

The demand for monoclonal antibody for therapeutic and diagnostic applications is rising constantly which puts up a need to bring down the cost of its production. In this context it becomes a prerequisite to improve the efficiency of the existing processes used for monoclonal antibody production. This review describes various upstream processes used for monoclonal antibody production and evaluates critical parameters and efforts which are being made to enhance the efficiency of the process. The upstream technology has tremendously been upgraded from host cells used for manufacturing to bioreactors type and capacity. The host cells used range from microbial, mammalian to plant cells with mammalian cells dominating the scenario. Disposable bioreactors are being promoted for small scale production due to easy adaptation to process validation and flexibility, though they are limited by the scale of production. In this respect Wave bioreactors for suspension culture have been introduced recently. A novel bioreactor for immobilized cells is described which permits an economical and easy alternative to hollow fiber bioreactor at lab scale production. Modification of the cellular machinery to alter their metabolic characteristics has further added to robustness of cells and perks up cell specific productivity. The process parameters including feeding strategies and environmental parameters are being improved and efforts to validate them to get reproducible results are becoming a trend. Online monitoring of the process and product characterization is increasingly gaining importance. In total the advancement of upstream processes have led to the increase in volumetric productivity by 100-fold over last decade and make the monoclonal antibody production more economical and realistic option for therapeutic applications. PMID:17920803

Jain, Era; Kumar, Ashok

2008-01-01

384

Increased risk of oesophageal adenocarcinoma among upstream petroleum workers  

PubMed Central

Objectives To investigate cancer risk, particularly oesophageal cancer, among male upstream petroleum workers offshore potentially exposed to various carcinogenic agents. Methods Using the Norwegian Registry of Employers and Employees, 24 765 male offshore workers registered from 1981 to 2003 was compared with 283 002 male referents from the general working population matched by age and community of residence. The historical cohort was linked to the Cancer Registry of Norway and the Norwegian Cause of Death Registry. Results Male offshore workers had excess risk of oesophageal cancer (RR 2.6, 95% CI 1.4 to 4.8) compared with the reference population. Only the adenocarcinoma type had a significantly increased risk (RR 2.7, 95% CI 1.0 to 7.0), mainly because of an increased risk among upstream operators (RR 4.3, 95% CI 1.3 to 14.5). Upstream operators did not have significant excess of respiratory system or colon cancer or mortality from any other lifestyle-related diseases investigated. Conclusion We found a fourfold excess risk of oesophageal adenocarcinoma among male workers assumed to have had the most extensive contact with crude oil. Due to the small number of cases, and a lack of detailed data on occupational exposure and lifestyle factors associated with oesophageal adenocarcinoma, the results must be interpreted with caution. Nevertheless, given the low risk of lifestyle-related cancers and causes of death in this working group, the results add to the observations in other low-powered studies on oesophageal cancer, further suggesting that factors related to the petroleum stream or carcinogenic agents used in the production process might be associated with risk of oesophageal adenocarcinoma.

Kirkeleit, Jorunn; Riise, Trond; Bj?rge, Tone; Moen, Bente E; Bratveit, Magne; Christiani, David C

2013-01-01

385

Discrete wave packets upstream from the earth and comets  

NASA Astrophysics Data System (ADS)

Discrete wave packets are nearly monochromatic waves lasting several wave cycles which are frequently found on the leading edge of steepened low-frequency waves or shocklets upstream from the earth's bow shock. They apparently are whistler-mode waves which are generated as the shocklets steepen. These shocklets are blown back across the spacecraft so that the structure is observed in reverse order. Similarly appearing waves are present at comet Giacobini-Zinner. To determine if these waves are the same as those observed at earth a detailed comparison of the properties of the two sets of waves was undertaken. The waves have very similar amplitudes, durations, and directions of propagation.

Le, G.; Russell, C. T.; Smith, E. J.

386

Energetic Ions and Magnetic Fields Upstream From the Kronian Magnetosphere  

NASA Astrophysics Data System (ADS)

The existence of energetic particle events to ~200 Rs upstream and ~1300 Rs downstream of Saturn was established during the Voyager 1, 2 flybys in 1980 and 1981, respectively. The origin of the events could not be determined with certainty because of lack of particle charge state and species measurements at lower (<300 keV) energies, which dominate the spectra. High sensitivity observations of energetic ion directional intensities, energy spectra, and ion composition were obtained by the Ion and Neutral Camera (INCA) of the MIMI instrument complement with a geometry factor of ~2.5 cm2 sr and some capability of separating light (H, He) and heavier (C, N, O) ion groups (henceforth referred to as "hydrogen" and "oxygen" respectively). Charge state information was provided where possible by the Charge-Energy-Mass-Spectrometer (CHEMS) over the range ~3 to 220 keV per charge, and magnetic field (IMF) data by the MAG instrument on Cassini. The observations revealed the presence of distinct upstream bursts of energetic hydrogen and oxygen ions whenever the IMF connected the spacecraft to the planetary bow shock, up to distances of 135 RS. The events exhibited the following characteristics: (1) Hydrogen ion bursts are observed in the energy range 3 to 220 keV (and occasionally to E > 220 keV) and oxygen ion bursts in the energy range 32 to -300 keV. (2) Particle onsets are nearly field-aligned, but the distribution tends to isotropize as the event progresses in time. (3) The duration of the ion bursts is several minutes up to 4 hrs. (4) The events are of varying composition, with some exhibiting significant fluxes of oxygen. (5) The bursts have a filamentary structure with some exhibiting distinct signatures of "velocity- filtering effects" at the edges of convecting IMF filaments. (6) Some ion bursts are accompanied by distinct diamagnetic field depressions and exhibit wave structures consistent with ion cyclotron waves for H+, and O+. Given the repeated magnetic field configuration during the detection of the events and that energetic ions trapped within the magnetosphere of Saturn are mostly H+ and O+ we conclude that O+-rich upstream events must be particles leaking from Saturn's magnetosphere under favorable IMF conditions. The spectral evolution of the upstream events and their anisotropy characteristics will be presented and discussed in the context of current models.

Krimigis, S. M.; Sarris, E.; Sergis, N.; Dialynas, K.; Mitchell, D. G.; Hamilton, D. C.; Dougherty, M.

2008-12-01

387

Electron plasma oscillations upstream of the solar wind termination shock.  

PubMed

Electron plasma oscillations have been detected upstream of the solar wind termination shock by the plasma wave instrument on the Voyager 1 spacecraft. These waves were first observed on 11 February 2004, at a heliocentric radial distance of 91.0 astronomical units, and continued sporadically with a gradually increasing occurrence rate for nearly a year. The last event occurred on 15 December 2004, at 94.1 astronomical units, just before the spacecraft crossed the termination shock. Since then, no further electron plasma oscillations have been observed, consistent with the spacecraft having crossed the termination shock into the heliosheath. PMID:16179470

Gurnett, D A; Kurth, W S

2005-09-23

388

Hybrid simulation codes with application to shocks and upstream waves  

SciTech Connect

Hybrid codes in which part of the plasma is represented as particles and the rest as fluid are discussed. In the past few years such codes with particle ions and massless, fluid electrons have been applied to space plasmas, especially to collisionless shocks. All of these simulation codes are one-dimensional and similar in structure, except for how the field equation are solved. We describe in detail the various approaches that are used (resistive Ohm's law, predictor-corrector, Hamiltonian) and compare results from the various codes with examples taken from collisionless shocks and low frequency wave phenomena upstream of shocks.

Winske, D.

1985-02-03

389

Hybrid simulation codes with application to shocks and upstream waves  

NASA Technical Reports Server (NTRS)

Hybrid codes in which part of the plasma is represented as particles and the rest as a fluid are discussed. In the past few years such codes with particle ions and massless, fluid electrons have been applied to space plasmas, especially to collisionless shocks. All of these simulation codes are one-dimensional and similar in structure, except for how the field equations are solved. The various approaches that are used (resistive Ohm's law, predictor-corrector, Hamiltonian) are described in detail and results from the various codes are compared with examples taken from collisionless shocks and low frequency wave phenomena upstream of shocks.

Winske, D.

1985-01-01

390

The conserved upstream region of lscB/C determines expression of different levansucrase genes in plant pathogen Pseudomonas syringae  

PubMed Central

Background Pseudomonas syringae pv. glycinea PG4180 is an opportunistic plant pathogen which causes bacterial blight of soybean plants. It produces the exopolysaccharide levan by the enzyme levansucrase. Levansucrase has three gene copies in PG4180, two of which, lscB and lscC, are expressed while the third, lscA, is cryptic. Previously, nucleotide sequence alignments of lscB/C variants in various P. syringae showed that a ~450-bp phage-associated promoter element (PAPE) including the first 48 nucleotides of the ORF is absent in lscA. Results Herein, we tested whether this upstream region is responsible for the expression of lscB/C and lscA. Initially, the transcriptional start site for lscB/C was determined. A fusion of the PAPE with the ORF of lscA (lscB UpN A) was generated and introduced to a levan-negative mutant of PG4180. Additionally, fusions comprising of the non-coding part of the upstream region of lscB with lscA (lscB Up A) or the upstream region of lscA with lscB (lscA Up B) were generated. Transformants harboring the lscB UpN A or the lscB Up A fusion, respectively, showed levan formation while the transformant carrying lscA Up B did not. qRT-PCR and Western blot analyses showed that lscB UpN A had an expression similar to lscB while lscB Up A had a lower expression. Accuracy of protein fusions was confirmed by MALDI-TOF peptide fingerprinting. Conclusions Our data suggested that the upstream sequence of lscB is essential for expression of levansucrase while the N-terminus of LscB mediates an enhanced expression. In contrast, the upstream region of lscA does not lead to expression of lscB. We propose that lscA might be an ancestral levansucrase variant upstream of which the PAPE got inserted by potentially phage-mediated transposition events leading to expression of levansucrase in P. syringae.

2014-01-01

391

Modified diffusion model of pseudo-shock waves considering upstream boundary layers  

Microsoft Academic Search

Experiments were performed to investigate the effects of the upstream boundary layer on pseudo-shock waves, by varying the Mach number and boundary layer thickness upstream of the pseudo-shock. A new flow model is presented in which both the effects of the upstream boundary layer and wall friction are taken into account. The configuration and axial static pressure distribution of the

T. Ikui; K. Matsuo; K. Sasaguchi

1981-01-01

392

The `upstream wake' of swimming and flying animals and its correlation with propulsive efficiency  

Microsoft Academic Search

SUMMARY The interaction between swimming and flying animals and their fluid environments generates downstream wake structures such as vortices. In most studies, the upstream flow in front of the animal is neglected. In this study, we demonstrate the existence of upstream fluid structures even though the upstream flow is quiescent or possesses a uniform incoming velocity. Using a computational model,

Jifeng Peng; John O. Dabiri

2008-01-01

393

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

PubMed

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

Pluhar, Wolfgang

2006-12-01

394

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

PubMed

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

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

2014-02-15

395

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

Microsoft Academic Search

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

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

2007-01-01

396

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

PubMed Central

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

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

2005-01-01

397

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

PubMed Central

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

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

2013-01-01

398

How to Start Interventional Radiology  

PubMed Central

Interventional techniques aim to find safer and better ways to treat vascular diseases even in many instances, the interventional radiology solutions has been considered the only treatment option for the patients. Interventional radiologists are specialists who perform minimally invasive procedures instead of surgery or other treatments. These procedures apply various imaging and catheterization procedures in order to diagnose and treat diseases. In each country, interventional radiology practice establishment of varies according to local factors, but following a standard strategy seems better to set up this facility. According to above mentioned points, we decided to establish this specialty in our hospital since 2001 as the pioneer center in Iran. In this presentation we will discuss about our experience for start interventional radiology.

Ghanaati, Hossein; Firouznia, Kavous; Jalali, Amir Hossein; Shakiba, Madjid

2013-01-01

399

How to start interventional radiology.  

PubMed

Interventional techniques aim to find safer and better ways to treat vascular diseases even in many instances, the interventional radiology solutions has been considered the only treatment option for the patients. Interventional radiologists are specialists who perform minimally invasive procedures instead of surgery or other treatments. These procedures apply various imaging and catheterization procedures in order to diagnose and treat diseases. In each country, interventional radiology practice establishment of varies according to local factors, but following a standard strategy seems better to set up this facility. According to above mentioned points, we decided to establish this specialty in our hospital since 2001 as the pioneer center in Iran. In this presentation we will discuss about our experience for start interventional radiology. PMID:24693402

Ghanaati, Hossein; Firouznia, Kavous; Jalali, Amir Hossein; Shakiba, Madjid

2013-12-01

400

A Large Eddy Simulation Study for upstream wind energy conditioning  

NASA Astrophysics Data System (ADS)

The wind energy industry is increasingly focusing on optimal power extraction strategies based on layout design of wind farms and yaw alignment algorithms. Recent field studies by Mikkelsen et al. (Wind Energy, 2013) have explored the possibility of using wind lidar technology installed at hub height to anticipate incoming wind direction and strength for optimizing yaw alignment. In this work we study the benefits of using remote sensing technology for predicting the incoming flow by using large eddy simulations of a wind farm. The wind turbines are modeled using the classic actuator disk concept with rotation, together with a new algorithm that permits the turbines to adapt to varying flow directions. This allows for simulations of a more realistic atmospheric boundary layer driven by a time-varying geostrophic wind. Various simulations are performed to investigate possible improvement in power generation by utilizing upstream data. Specifically, yaw-correction of the wind-turbine is based on spatio-temporally averaged wind values at selected upstream locations. Velocity and turbulence intensity are also considered at those locations. A base case scenario with the yaw alignment varying according to wind data measured at the wind turbine's hub is also used for comparison. This reproduces the present state of the art where wind vanes and cup anemometers installed behind the rotor blades are used for alignment control.

Sharma, V.; Calaf, M.; Parlange, M. B.

2013-12-01

401

Delay at signal-controlled intersection with bus stop upstream  

SciTech Connect

Because of the tight constraints on many streets in urban areas, it is not uncommon to situate a bus stop upstream of a signal-controlled intersection without the provision of a proper bus bay or setback. For a single-lane approach, where the overtaking of a stopped bus at the bus stop is prohibited, the setup of such a bus stop would significantly affect the delay incurred by road users. It is believed that the delay in such situations depends on a number of factors, such as the distance between bus stop and stop line, traffic and bus flows, dwell time of buses and signal settings. In this paper, a simulation model for estimating the delay on an approach to a signal-controlled intersection with a bus stop upstream is developed. To test the reliability of the model, field surveys were conducted to validate the simulation model. A good agreement between the observed and simulation results was obtained. When the simulation model was used, a new delay formula was established and calibrated for use in the design of a signal-controlled intersection.

Wong, S.C.; Yeung, W.S.A.; Cheuk, S.L.; Lo, M.K. [Univ. of Hong Kong (Hong Kong). Dept. of Civil and Structural Engineering; Yang, H. [Hong Kong Univ. of Science and Technology, Clear Water Bay (Hong Kong)

1998-05-01

402

Flow directs surface-attached bacteria to twitch upstream.  

PubMed

Bacteria inhabit a wide variety of environments in which fluid flow is present, including healthcare and food processing settings and the vasculature of animals and plants. The motility of bacteria on surfaces in the presence of flow has not been well characterized. Here we focus on Pseudomonas aeruginosa, an opportunistic human pathogen that thrives in flow conditions such as in catheters and respiratory tracts. We investigate the effects of flow on P. aeruginosa cells and describe a mechanism in which surface shear stress orients surface-attached P. aeruginosa cells along the flow direction, causing cells to migrate against the flow direction while pivoting in a zig-zag motion. This upstream movement is due to the retraction of type IV pili by the ATPase motors PilT and PilU and results from the effects of flow on the polar localization of type IV pili. This directed upstream motility could be beneficial in environments where flow is present, allowing bacteria to colonize environments that cannot be reached by other surface-attached bacteria. PMID:22828341

Shen, Yi; Siryaporn, Albert; Lecuyer, Sigolene; Gitai, Zemer; Stone, Howard A

2012-07-01

403

Upstream Photon Veto Studies for the GlueX Project  

NASA Astrophysics Data System (ADS)

The Upstream Photon Veto (UPV), being developed at Florida State University, is a sampling electromagnetic calorimeter that will become part of the GlueX project. The detector will be placed upstream of the photon beam. The main goal of this detector is to veto photons in the backwards direction of the target. This study looks to optimize the detector configuration for resolution and efficiency. To do this, we've modeled the detector in the Geant4 simulation toolkit. Past studies have shown that the optimal configuration is 12 layers of lead-scintillator followed by 6 layers of double the thickness of lead, and scintillator. In this study, we test how the resolution and efficiency respond to changing the number of layers with a fixed total volume, by changing the sizes of the layers overall, and the addition of a pre-radiator. The results have shown that we can most effectively increase our resolution and efficiency by doubling the thickness of the scintillator, or by doubling the number of layers, but keeping the same overall volume.

Custer, James

2006-10-01

404

A light- and developmentally-regulated DNA-binding interaction is common to the upstream sequences of the wheat Calvin cycle bisphosphatase genes  

Microsoft Academic Search

We have characterised a DNA-binding interaction common to the upstream sequences of the wheat fructose-1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) genes. The recognition site for this sequence-specific binding activity, designated wheat FBPase factor (WF-1), is located within 125 bp of the transcription start site of each gene. Within these regions there are no sequence motifs similar to those shown to be

Alison J. Miles; Susan C. Potts; Nicola M. Willingham; Christine A. Raines; Julie C. Lloyd

1993-01-01

405

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

PubMed

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

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

2009-01-01

406

Fundamental role of start/stop regulators in whole DNA and new trinucleotide classification.  

PubMed

The origin and logic of genetic code are two of greatest mysteries of life sciences. Analyzing DNA sequences we showed that the start/stop trinucleotides have broader importance than just marking start and stop of exons in coding DNA. On this basis, here we introduced new classification of trinucleotides and showed that all A+T rich trinucleotides consisting of three different nucleotides arise from start-ATG, stop-TGA and stop-TAG using their complement, reverse complement and reverse transformations. Due to the same transformations during generations of crossing-over they can switch from one form to the other. By direct process the start-ATG and stop-TAG can irreversibly transform into stop-TAA. By transformation into A+T rich trinucleotides and 16/32 C+G rich they can lose the start/stop function and take the role of a sense codon in reversible way. The remaining 16 C+G trinucleotides cannot directly transform into start/stop trinucleotides and thus remain a firm skeleton for structuring the C+G rich DNA. We showed that start/stops strongly enrich the A+T rich noncoding DNA through frequently extended forms. From the evolutionary viewpoint the start/stops are chief creators of prevailing A+T rich noncoding DNA, and of more stable coding DNA. We propose that start/stops have basic role as "seeds" in trinucleotide evolution of noncoding and coding sequences and lead to asymmetry between A+T and C+G rich DNA. By dynamical transformations during evolution they enabled pronounced phylogenetic broadness, keeping the regulator function. PMID:24042127

Rosandi?, Marija; Paar, Vladimir; Glun?i?, Matko

2013-12-01

407

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

PubMed

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

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

2010-01-01

408

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

PubMed

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

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

2005-04-11

409

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

PubMed Central

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

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

1982-01-01

410

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

PubMed Central

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

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

1977-01-01

411

The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences.  

PubMed Central

Paramutation is an interaction between alleles that leads to a heritable change in the expression of one allele. In B'/B-I plants, B-I (high transcription) always changes to B' (low transcription). The new B' allele retains the low expression state in the next generation and paramutates B-I at a frequency of 100%. Comparisons of the structure and expression of B' with that of a closely related allele that does not participate in paramutation demonstrated that transcription from the same promoter-proximal sequences is not sufficient for paramutation. Fine-structure recombination mapping localized sequences required for B' expression and paramutation. The entire 110 kb upstream of the B' transcription start site was cloned and sequenced and the recombination breakpoints were determined for 12 recombinant alleles. Sequences required for expression and paramutation mapped to distinct regions, 8.5-49 kb and 93-106 kb upstream of the B' transcription start site, respectively. Sequencing and DNA blot analyses indicate that the B' region required for paramutation is mostly unique or low copy in the maize genome. These results represent the first example of long-distance regulatory elements in plants and demonstrate that paramutation is mediated by long-distance cis and trans interactions.

Stam, Maike; Belele, Christiane; Ramakrishna, Wusirika; Dorweiler, Jane E; Bennetzen, Jeffrey L; Chandler, Vicki L

2002-01-01

412

Analysis of synonymous codon usage bias in 09H1N1  

Microsoft Academic Search

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

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

2010-01-01

413

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

PubMed

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

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

2013-09-01

414

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

Microsoft Academic Search

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

Gerard A. Kennedy

415

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

Microsoft Academic Search

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

Douglas N. Robinson; Lynn Cooley

416

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

PubMed

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

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

2013-01-01

417

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

PubMed

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

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

2013-07-01

418

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

PubMed

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

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

2004-01-01

419

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

PubMed Central

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

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

2014-01-01

420

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

PubMed

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

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

2012-04-26

421

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

PubMed

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

Lee, Yuh Chwen G; Reinhardt, Josephine A

2012-01-01

422

Environmental shaping of codon usage and functional adaptation across microbial communities  

PubMed Central

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

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

2013-01-01

423

When to start antiretroviral therapy.  

PubMed

The question of when to initiate antiretroviral therapy has been a central controversy in HIV management for more than 15 years, yet there are limited data from randomized controlled trials addressing it. A major obstacle to performing such a study is the need for large numbers of asymptomatic, antiretroviral therapy-naive individuals observed over many years beginning from when their CD4+ cell counts are above 500/mm3. Observational cohort studies with substantial person-years of follow-up have informed this debate in the absence of randomized trials. Emerging evidence regarding the damage caused by untreated HIV infection-related inflammation and immune activation at all stages of disease, and the benefits of modern antiretroviral therapy in preventing both AIDS- and non-AIDS-related morbidity and mortality has supported a return to starting treatment early. The NA-ACCORD (North American AIDS Cohort Collaboration on Research and Design) study compared long-term outcomes of immediate versus deferred therapy at 2 CD4+ cell count thresholds. Results showed a 94% increased risk of all-cause mortality when antiretroviral therapy was deferred at CD4+ cell counts greater than 500/mm3. This article summarizes presentations made by Mari M. Kitahata, MD, MPH, at the International AIDS Society-USA continuing medical education programs held in November 2009 in New York City and May 2010 in San Francisco. The original presentations are available as Webcasts at www.iasusa.org. PMID:20921578

Kitahata, Mari M

2010-01-01

424

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

PubMed Central

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

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

2010-01-01

425

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

PubMed

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

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

2013-01-01

426

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

PubMed Central

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

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

1996-01-01

427

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

PubMed Central

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

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

2012-01-01

428

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

PubMed Central

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

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

2013-01-01

429

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

PubMed

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

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

2011-01-01

430

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

PubMed Central

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

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

2011-01-01

431

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

PubMed Central

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

2009-01-01

432

Titan’s induced magnetosphere under variable upstream conditions  

NASA Astrophysics Data System (ADS)

Over the last 5 years, Cassini magnetic field and plasma observations in the vicinity of Titan have revealed that the properties of the moon’s plasma environment are strongly influenced by the dynamics of Saturn’s equatorial magnetodisk. As the magnetodisk flaps past Titan’s orbit in response to changes in solar wind dynamic pressure and Saturn kilometric radiation phase, the pressure inventory of the flow ahead of the moon varies with implications on its atmopsheric escape. In this work we identify some basic properties of Titan’s induced magnetosphere (size, shape) and, in sectors where upstream conditions are less variable, we compare the importance of the different pressure terms (magnetic, dynamic, thermal) at different altitudes to study the pressure balance.

Bertucci, C.; Sillampaa, I.; Sittler, E. C.; Sergis, N.; Modolo, R.; Rymer, A.; Tokar, R. L.; Dougherty, M. K.; Young, D. T.; Krimigis, S. M.; Kurth, W. S.

2009-12-01

433

Numerical analysis of supersonic combustion ramjet with upstream fuel injection  

NASA Astrophysics Data System (ADS)

This paper describes possible fuel injection scheme for airbreathing engines that use hydrocarbon fuels. The basic idea is to inject fuel at the spike tip of the supersonic inlet to achieve mixing and combustion efficiency with a limited length combustion chamber. A numerical code, able to solve the full Navier-Stokes equations in turbulent and reacting flows, is employed to obtain numerical simulations of the thermo-fluidynamic fields at different scramjet flight conditions, at Mach numbers of M=6.5 and 8. The feasibility of the idea of the upstream injection is checked for a simple axisymmetric configuration and relatively small size. The results are discussed in connection with the potential benefits deriving from the use of new ultra high temperature ceramics (UHTC).

Savino, Raffaele; Pezzella, Giuseppe

2003-09-01

434

5. Looking west upstream, towards the location of the erstwhile ...  

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

5. Looking west upstream, towards the location of the erstwhile intake flume into canal from the upper reaches of the Potomac River above the Great Falls, on the old Potowmack Canal built by George Washington. The plan contemplated canal navigation around the Great Falls of the Potomac River, located on the Virginia side of the Potomac, about 15 miles above Washington, D.C. The Company was organized in 1785, and by 1802, this and three or four smaller canals were substantially completed and raft-like boats began operation with materials from the west to the city of Georgetown. 'Although the canals and locks of the Potomac Canal were considered a great engineering accomplishment, the improvements to the river channel were inadequate. Disappointment ... - Potowmack Company: Great Falls Canal & Locks, Great Falls, Fairfax County, VA

435

Multilateral drilling, seismic acquisition top upstream technology needs  

SciTech Connect

High-impact technology needs for the US upstream oil industry include advanced seismic acquisition, high-resolution depth imaging, cementing, and multilateral drilling. The Department of Energy and the national labs have shown a definite willingness to work on oil and gas research projects, providing the research and development could not be accomplished by private industry alone. Advanced seismic acquisition was identified as a high need for independent operators, and horizontal well technology was the highest ranking need for service companies. The highest areas of impact identified by majors, other integrated companies, and independents were high-resolution depth imaging and improved well productivity. Technology will be a critical component to discovery and utilization of new oil and gas resources. The paper discusses the technology needed to advance exploration, drilling and completion, and resource development in Arctic regions.

Rappold, K..

1995-10-30

436

Upstream Structures and Their Effects on the Magnetosphere  

NASA Technical Reports Server (NTRS)

Kinetic processes within the Earth's foreshock generate a profusion of plasma and magnetic field structures with sizes and durations ranging from the microscale (e.g. SLAMs, solitons, and density holes) to the mesoscale (e.g. foreshock cavities or boundaries, hot flow anomalies, and bubbles). Swept into the bow shock by the solar wind flow, the perturbations associated with these features batter the magnetosphere, driving a wide variety of magnetospheric effects, including large amplitude magnetopause motion, bursty reconnection and the generation of flux transfer events, enhanced pulsation activity within the magnetosphere, diffusion and energization of radiation belt particles, enhanced particle precipitation resulting in dayside aurora and riometer absorption, and the generation of field-aligned currents and magnetic impulse events in high-latitude ground magnetometers. This talk revie