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1

Upstream start codon in segment 4 of North American H2 avian influenza A viruses.  

PubMed

H2N2 influenza A virus was the cause of the 1957 pandemic. Due to its constant presence in birds, the H2 subtype remains a topic of interest. In this work, comparison of H2 leader sequences of influenza A segment 4 revealed the presence of an upstream in-frame start codon in a majority of North American avian strains. This AUG is located seven codons upstream of the conventional start codon and is in a good Kozak context. In vivo experiments, using a luciferase reporter gene fused to leader sequences derived from North American avian H2 strains, support the efficient use of the upstream start codon. These results were corroborated by in vitro translation data using full-length segment 4 mRNA. Phylogenic analyses indicate that the upstream AUG, first detected in 1976, is stably nested in the North American avian lineage of H2 strains nowadays. The possible consequences of the upstream AUG are discussed. PMID:21232632

Girard, Geneviève; Gultyaev, Alexander P; Olsthoorn, René C L

2011-01-11

2

The psbC start codon in Synechocystis sp. PCC 6803.  

PubMed

The translation start codon for psbC, the gene encoding CP43, a chlorophyll-binding protein of photosystem II, has been identified for the cyanobacterium Synechosystis sp. PCC 6803 using site-directed mutagenesis. An AUG codon, about 50 bases upstream from the end of psbD-I had previously been assumed to be the translation start site of psbC. However, the fact that the AUG codon is not present in psbC from several other organisms, whereas a GUG codon 14 bases upstream from the end of psbD-I is strictly conserved suggests that CP43 translation starts at the latter codon. Mutation of GUG, but not of AUG, led to a loss of CP43 and photoautotrophic growth, indicating that the GUG codon is the sole initiation site for translation of the CP43 protein in Synechocystis sp. PCC 6803. PMID:2105233

Carpenter, S D; Charite, J; Eggers, B; Vermaas, W F

1990-01-15

3

Translation initiation in Drosophila melanogaster is reduced by mutations upstream of the AUG initiator codon  

SciTech Connect

The importance to in vivo translation of sequences immediately upstream of the Drosophila alcohol dehydrogenase (Adh) start codon was examined at two developmental stages. Mutations were introduced into the Adh gene in vitro, and the mutant gene was inserted into the genome via germ line transformation. An A-to-T substitution at the [minus]3 position did not affect relative translation of ADH at the adult stage. A second mutant gene, containing five mutations in the region [minus]1 to [minus]9, was designed to completely block translation initiation. However, transformant lines bearing these mutations still exhibit detectable ADH, albeit at substantially reduced levels. The average fold reduction at the second-instar larval stage was 5.9, while at the adult stage a 12.5-fold reduction was observed.

Feng, Yue; Gunter, L.E.; Organ, E.L.; Cavener, D.R. (Vanderbilt University, Nashville, TN (United States))

1991-04-01

4

A non-canonical start codon in the Drosophila fragile X gene yields two functional isoforms  

PubMed Central

Fragile X syndrome is caused by the loss of expression of the fragile X mental retardation protein (FMRP). As a RNA binding protein, FMRP functions in translational regulation, localization, and stability of its neuronal target transcripts. The Drosophila homologue, dFMR1, is well conserved in sequence and function with respect to human FMRP. Although dFMR1 is known to express two main isoforms, the mechanism behind production of the second, more slowly migrating isoform has remained elusive. Furthermore, it remains unknown whether the two isoforms may also contribute differentially to dFMR1 function. We have found that this second dFMR1 isoform is generated through an alternative translational start site in the dfmr1 5’UTR. This 5'UTR coding sequence is well conserved in the melanogaster group. Translation of the predominant, smaller form of dFMR1 (dFMR1-SN) begins at a canonical start codon (ATG), whereas translation of the minor, larger form (dFMR1-LN) begins upstream at a non-canonical start codon (CTG). To assess the contribution of the N-terminal extension toward dFMR1 activity, we generated transgenic flies that exclusively express either dFMR1-SN or dFMR1-LN. Expression analyses throughout development revealed that dFMR1-SN is required for normal dFMR1-LN expression levels in adult brains. In situ expression analyses showed that either dFMR1-SN or dFMR1-LN is individually sufficient for proper dFMR1 localization in the nervous system. Functional studies demonstrated that both dFMR1-SN and dFMR1-LN can function independently to rescue dfmr1 null defects in synaptogenesis and axon guidance. Thus, dfmr1 encodes two functional isoforms with respect to expression and activity throughout neuronal development.

Beerman, Rebecca W.; Jongens, Thomas A.

2011-01-01

5

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes  

PubMed Central

Summary: The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5? end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNAiMet) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an “open” conformation of the 40S subunit with Met-tRNAiMet bound in a low-affinity state conducive to scanning and in triggering rearrangement into a “closed” conformation incompatible with scanning, which features Met-tRNAiMet more tightly bound to the “P” site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded “landing pad” for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site.

Hinnebusch, Alan G.

2011-01-01

6

Genetic diversity of mango cultivars estimated using Start Codon Targeted (SCoT) markers  

Technology Transfer Automated Retrieval System (TEKTRAN)

Diversity and genetic relationships among 23 mango germplasm accessions, collected from different locations in Guangxi province in China, were analyzed by using a novel and simple gene targeted DNA marker: Start Codon Targeted (SCoT) markers. This technique uses a single, 18-mer primer PCR amplifica...

7

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

8

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

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. PMID:22863195

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

2012-08-02

9

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

2012-09-28

10

Comprehensive analysis of transcript start sites in ly49 genes reveals an unexpected relationship with gene function and a lack of upstream promoters.  

PubMed

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. PMID:21483805

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

2011-03-31

11

Start codon targeted polymorphism for evaluation of functional genetic variation and relationships in cultivated peanut ( Arachis hypogaea L.) genotypes  

Microsoft Academic Search

Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the\\u000a use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting\\u000a cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic\\u000a diversity and relatedness among 20 accessions of four major botanical

Faqian Xiong; Ruichun Zhong; Zhuqiang Han; Jing Jiang; Liangqiong He; Weijian Zhuang; Ronghua Tang

2011-01-01

12

Vitamin D receptor start codon polymorphism and colorectal cancer risk: effect modification by dietary calcium and fat in Singapore Chinese  

Microsoft Academic Search

Vitamin D has been implicated as a protective agent against colorectal cancer. We hypothesized that a func- tional start codon polymorphism in the vitamin D receptor (VDR) influences the risk of colorectal carcinoma. We conducted a case-control study nested within a large cohort of Singapore Chinese. VDR genotypes, determined by FokI restriction endonuclease digestion of PCR-amplified DNA, were performed on

Hui-Lee Wong; Adeline Seow; Kazuko Arakawa; Hin-Peng Lee; Mimi C. Yu; Sue A. Ingles

13

GTP hydrolysis controls stringent selection of the AUG start codon during translation initiation in Saccharomyces?cerevisiae  

PubMed Central

We have isolated and characterized two suppressor genes, SUI4 and SUI5, that can initiate translation in the absence of an AUG start codon at the HIS4 locus in Saccharomyces cerevisiae. Both suppressor genes are dominant in diploid cells and lethal in haploid cells. The SUI4 suppressor gene is identical to the GCD11 gene, which encodes the ? subunit of the eIF-2 complex and contains a mutation in the G2 motif, one of the four signature motifs that characterizes this subunit to be a G-protein. The SUI5 suppressor gene is identical to the TIF5 gene that encodes eIF-5, a translation initiation factor known to stimulate the hydrolysis of GTP bound to eIF-2 as part of the 43S preinitiation complex. Purified mutant eIF-5 is more active in stimulating GTP hydrolysis in vitro than wild-type eIF-5, suggesting that an alteration of the hydrolysis rate of GTP bound to the 43S preinitiation complex during ribosomal scanning allows translation initiation at a non-AUG codon. Purified mutant eIF-2? complex is defective in ternary complex formation and this defect correlates with a higher rate of dissociation from charged initiator-tRNA in the absence of GTP hydrolysis. Biochemical characterization of SUI3 suppressor alleles that encode mutant forms of the ? subunit of eIF-2 revealed that these mutant eIF-2 complexes have a higher intrinsic rate of GTP hydrolysis, which is eIF-5 independent. All of these biochemical defects result in initiation at a UUG codon at the his4 gene in yeast. These studies in light of other analyses indicate that GTP hydrolysis that leads to dissociation of eIF-2???GDP from the initiator-tRNA in the 43S preinitiation complex serves as a checkpoint for a 3-bp codon/anticodon interaction between the AUG start codon and the initiator-tRNA during the ribosomal scanning process.

Huang, Han-kuei; Yoon, Heejeong; Hannig, Ernest M.; Donahue, Thomas F.

1997-01-01

14

SBP, SECIS binding protein, binds to the RNA fragment upstream of the Sec UGA codon in glutathione peroxidase mRNA  

Microsoft Academic Search

In mammals, most of the selenium contained in the body is present as an unusual amino acid, selenocysteine (Sec), whose codon is UGA. Because the UGA codon is typically recognized as a translation stop signal, it is intriguing how a cell recognizes and distinguishes a UGA Sec codon from a UGA stop codon. For eukaryotic selenoprotein mRNAs, it has been

Takaharu Mizutani; Toshinobu Fujiwara

2000-01-01

15

The C-terminal domain of eukaryotic initiation factor 5 promotes start codon recognition by its dynamic interplay with eIF1 and eIF2?.  

PubMed

Recognition of the proper start codon on mRNAs is essential for protein synthesis, which requires scanning and involves eukaryotic initiation factors (eIFs) eIF1, eIF1A, eIF2, and eIF5. The carboxyl terminal domain (CTD) of eIF5 stimulates 43S preinitiation complex (PIC) assembly; however, its precise role in scanning and start codon selection has remained unknown. Using nuclear magnetic resonance (NMR) spectroscopy, we identified the binding sites of eIF1 and eIF2? on eIF5-CTD and found that they partially overlapped. Mutating select eIF5 residues in the common interface specifically disrupts interaction with both factors. Genetic and biochemical evidence indicates that these eIF5-CTD mutations impair start codon recognition and impede eIF1 release from the PIC by abrogating eIF5-CTD binding to eIF2?. This study provides mechanistic insight into the role of eIF5-CTD's dynamic interplay with eIF1 and eIF2? in switching PICs from an open to a closed state at start codons. PMID:22813744

Luna, Rafael E; Arthanari, Haribabu; Hiraishi, Hiroyuki; Nanda, Jagpreet; Martin-Marcos, Pilar; Markus, Michelle A; Akabayov, Barak; Milbradt, Alexander G; Luna, Lunet E; Seo, Hee-Chan; Hyberts, Sven G; Fahmy, Amr; Reibarkh, Mikhail; Miles, David; Hagner, Patrick R; O'Day, Elizabeth M; Yi, Tingfang; Marintchev, Assen; Hinnebusch, Alan G; Lorsch, Jon R; Asano, Katsura; Wagner, Gerhard

2012-05-24

16

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

17

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

18

The suil suppressor locus in Saccharomyces cerevisiae encodes a translation factor that functions during tRNA(iMet) recognition of the start codon.  

PubMed Central

We initiated a genetic reversion analysis at the HIS4 locus to identify components of the translation initiation complex that are important for ribosomal recognition of an initiator codon. Three unlinked suppressor loci, suil, sui2, and SUI3, that restore expression of both HIS4 and HIS4-lacZ in the absence of an AUG initiator codon were identified. In previous studies, it was demonstrated that the sui2 and SUI3 genes encode mutated forms of the alpha and beta subunits, respectively, of eukaryotic translation initiation factor 2 (eIF-2). In this report, we describe the molecular and biochemical characterizations of the sui1 suppressor locus. The DNA sequence of the SUI1+ gene shows that it encodes a protein of 108 amino acids with a calculated Mr of 12,300. The sui1 suppressor genes all contain single base pair changes that alter a single amino acid within this 108-amino-acid sequence. sui1 suppressor strains that are temperature sensitive for growth on enriched medium have altered polysome profiles at the restrictive temperature typical of those caused by alteration of a protein that functions during the translation initiation process. Gene disruption experiments showed that the SUI1+ gene encodes an essential protein, and antibodies directed against the SUI1+ coding region identified a protein with the predicted Mr in a ribosomal salt wash fraction. As observed for sui2 and SUI3 suppression events, protein sequence analysis of His4-beta-galactosidase fusion proteins produced by sui1 suppression events indicated that a UUG codon is used as the site of translation initiation in the absence of an AUG start codon in HIS4. Changing the penultimate proline codon 3' to UUG at his4 to a Phe codon (UUC) blocks aminopeptidase cleavage of the amino-terminal amino acid of the His4-beta-galactosidase protein, as noted by the appearance of Met in the first cycle of the Edman degradation reaction. The appearance of Met in the first cycle, as noted, in either a sui1 or a SUI3 suppressor strain showed that the mechanism of suppression is the same for both suppressor genes and allows the initiator tRNA to mismatch base pair with the UUG codon. This suggests that the Sui1 gene product performs a function similar to that of the beta subunit of eIF-2 as encoded by the SUI3 gene. However, the Sui1 gene product does not appear to be a required subunit of eIF-2 on the basis of purification schemes designed to identify the GTP-dependent binding activity of eIF-2 for the initiator tRNA. In addition, suppressor mutations in the sui1 gene, in contrast to suppressor mutations in the sui2 or SUI3 gene, do not alter the GTP-dependent binding activity of the eIF-2. The simplest interpretation of these studies is that the sui1 suppressor gene defines an additional factor that functions in concert with eIF-2 to enable tRNAiMet to establish ribosomal recognition of an AUG initiator codon. Images

Yoon, H J; Donahue, T F

1992-01-01

19

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

20

Start codon targeted (SCoT) polymorphism in toxic and non-toxic accessions of Jatropha curcas L. and development of a codominant SCAR marker.  

PubMed

Thirty six start codon targeted (SCoT) primers were used for characterization of 48 accessions of Jatropha curcas from different countries and include material with genetic variation for levels of phorbol esters, yield, seed oil content, test weight and plant type. SCoT analysis revealed high polymorphism and 74% of the primers generated polymorphic profiles. The SCoT6 primer discriminated edible and toxic accessions in a single reaction while the SCoT26 and 27 primers produced amplicons specific to toxic and non-toxic accessions, respectively. The polymorphic SCoT markers obtained with these three primers were converted to sequence characterized amplicon regions (SCARs) which resulted in codominant SCARs with SCoT6 primer and dominant SCARs with SCoT 26 and 27 primers. The codominant nature of SCoT6 primer and the resultant SCAR6 primer were validated on intraspecific hybrids derived from a cross between non-toxic and toxic accessions. The accession JP38 from Madagascar was found to be distinct and showed accession specific bands with 9 different SCoT primers. Sequence analysis of polymorphic amplicons obtained with SCoT6 primer showed a 65 bp deletion in accessions with low/zero phorbol esters. Diversity analysis separated the toxic and non-toxic accessions into two groups and the accessions JP29 and JP48 from Mexico formed a third cluster. PMID:23602106

Mulpuri, Sujatha; Muddanuru, Tarakeswari; Francis, George

2013-03-04

21

Common genetic mutations in the start codon of the SDH subunit D gene among Chinese families with familial head and neck paragangliomas.  

PubMed

Head and neck paragangliomas (HNPGLs) are rare, and frequently associated with germline mutations of the succinate dehydrogenase (SDH) genes, especially for familial cases. The purpose of the study is to explore SDH mutations in Chinese families with familial HNPGLs in Taiwan. Four unrelated families with familial HNPGLs were screened for germline mutations in the SDHB, SDHC and SDHD genes by direct sequencing. One hundred healthy subjects without a diagnosis or family history of HNPGLs were screened as normal controls. Immunohistochemistry with SDHB antibody was performed for a carotid body tumor. Two allele variants were identified, including p.Met1Val (c.1A>G) in the SDHD gene in one family and p.Met1Ile (c.3G>C) in the SDHD gene in the other three families. Both variants are considered pathogenic because of the absence of these variants in 100 normal controls, 100% evolutionary conservation of the p.Met1 residue, co-segregation of the variants with the phenotype of HNPGL in pedigrees, and predicted abolishment of the translation start site. The tumor cells obtained from one proband harboring c.3G>C mis-sense mutation were weak diffuse staining in the cytoplasm of tumors cells. This study demonstrates that two mis-sense mutations at the start codon of the SDHD gene, including p.Met1Val (c.1A>G) and p.Met1Ile (c.3G>C), might be mutation hotspots in Chinese patients with familial HNPGLs. PMID:21945342

Wang, Cheng-Ping; Chen, Tseng-Cheng; Chang, Yih-Leong; Ko, Jenq-Yuh; Yang, Tsung-Lin; Lo, Fei-Yun; Hu, Ya-Ling; Chen, Pei-Lung; Wu, Chen-Chi; Lou, Pei-Jen

2011-09-25

22

The in vivo TRPV6 protein starts at a non-AUG triplet, decoded as methionine, upstream of canonical initiation at AUG.  

PubMed

TRPV6 channels function as epithelial Ca(2+) 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 Ca(2+) entry to prevent deleterious Ca(2+) overload. PMID:23612980

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

2013-04-23

23

Small, synthetic, GC-rich mRNA stem-loop modules 5? proximal to the AUG start-codon predictably tune gene expression in yeast  

PubMed Central

Background A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5? UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Results Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5? UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (?G = ?15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (?G = ?4.4 kcal/mol) inhibited Cdr1p expression by ~50%. Conclusion We have developed a simple cloning strategy to fine-tune protein expression levels in yeast that has many potential applications in metabolic engineering and the optimization of protein expression in yeast. This study also highlights the importance of considering the use of multiple cloning-sites carefully to preclude unwanted effects on gene expression.

2013-01-01

24

Hidden coding potential of eukaryotic genomes: nonAUG started ORFs.  

PubMed

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 AUG codons in a weak nucleotide context could make an important contribution to eukaryotic proteomes. However, accurate prediction of alternative start codons demands detailed investigation of mRNA features influencing their recognition by eukaryotic ribosomes. In this work, we present the results of computational analysis of characteristics of yeast and mammalian mRNAs potentially involved in the recognition of nonAUG start codons. It was found that sequence features of nonAUG started Saccharomyces cerevisiae upstream ORFs (uORFs) were adjusted for efficient translation and these uORFs could frequently encode functional polypeptides. In particular, our initial studies revealed that predicted tertiary structures downstream of nonAUG start sites in mammalian mRNAs were energetically more stable than those predicted for AUG start sites with strong Kozak context. We hypothesize that presence of such stable tertiary structure downstream of nonAUG start sites could be an important factor for the ribosome to recognize noncanonical start codons. PMID:22804099

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

2012-07-18

25

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

26

Codon usage in Pseudomonas aeruginosa.  

PubMed Central

We have generated a codon usage table for Pseudomonas aeruginosa. Codon usage in P. aeruginosa is extremely biased. In contrast to E. coli and yeast, P. aeruginosa preferentially uses those codons within a synonymous codon group with the strongest predicted codon-anticodon interaction. We were unable to correlate a particular codon usage pattern with predicted levels of mRNA expressivity. The choice of a third base reflects the high guanine plus cytosine content of the P. aeruginosa genome (67.2%) and cytosine is the preferred nucleotide for the third codon position.

West, S E; Iglewski, B H

1988-01-01

27

The initiation codon determines the efficiency but not the site of translation initiation in Chlamydomonas chloroplasts.  

PubMed Central

To study translation initiation in Chlamydomonas chloroplasts, we mutated the initiation codon AUG to AUU, ACG, ACC, ACU, and UUC in the chloroplast petA gene, which encodes cytochrome f of the cytochrome b6/f complex. Cytochrome f accumulated to detectable levels in all mutant strains except the one with a UUC codon, but only the mutant with an AUU codon grew well at 24 degrees C under conditions that require photosynthesis. Because no cytochrome f was detectable in the UUC mutant and because each mutant that accumulated cytochrome f did so at a different level, we concluded that any residual translation probably initiates at the mutant codon. As a further demonstration that alternative initiation sites are not used in vivo, we introduced in-frame UAA stop codons immediately downstream or upstream or in place of the initiation codon. Stop codons at or downstream of the initiation codon prevented accumulation of cytochrome f, whereas the one immediately upstream of the initiation codon had no effect on the accumulation of cytochrome f. These results suggest that an AUG codon is not required to specify the site of translation initiation in chloroplasts but that the efficiency of translation initiation depends on the identity of the initiation codon.

Chen, X; Kindle, K L; Stern, D B

1995-01-01

28

Problem-Solving Test: The Effect of Synonymous Codons on Gene Expression  

ERIC Educational Resources Information Center

|Terms to be familiar with before you start to solve the test: the genetic code, codon, degenerate codons, protein synthesis, aminoacyl-tRNA, anticodon, antiparallel orientation, wobble, unambiguous codons, ribosomes, initiation, elongation and termination of translation, peptidyl transferase, translocation, degenerate oligonucleotides, green…

Szeberenyi, Jozsef

2009-01-01

29

Tandem Stop Codons in Ciliates That Reassign Stop Codons  

Microsoft Academic Search

Tandem stop codons are extra stop codons hypothesized to be present downstream of genes to act as a backup in case of read-through\\u000a of the real stop codon. Although seemingly absent from Escherichia coli, recent studies have confirmed the presence of such codons in yeast. In this paper we will analyze the genomes of two ciliate\\u000a species—Paramecium tetraurelia and Tetrahymena

Marie Adachi; Andre R. O. Cavalcanti

2009-01-01

30

FoxA2, Nkx2.2, and PDX-1 regulate islet beta-cell-specific mafA expression through conserved sequences located between base pairs -8118 and -7750 upstream from the transcription start site.  

PubMed

The MafA transcription factor is both critical to islet beta-cell function and has a unique pancreatic cell-type-specific expression pattern. To localize the potential transcriptional regulatory region(s) involved in directing expression to the beta cell, areas of identity within the 5' flanking region of the mouse, human, and rat mafA genes were found between nucleotides -9389 and -9194, -8426 and -8293, -8118 and -7750, -6622 and -6441, -6217 and -6031, and -250 and +56 relative to the transcription start site. The identity between species was greater than 75%, with the highest found between bp -8118 and -7750 ( approximately 94%, termed region 3). Region 3 was the only upstream mammalian conserved region found in chicken mafA (88% identity). In addition, region 3 uniquely displayed beta-cell-specific activity in cell-line-based reporter assays. Important regulators of beta-cell formation and function, PDX-1, FoxA2, and Nkx2.2, were shown to specifically bind to region 3 in vivo using the chromatin immunoprecipitation assay. Mutational and functional analyses demonstrated that FoxA2 (bp -7943 to -7910), Nkx2.2 (bp -7771 to -7746), and PDX-1 (bp -8087 to -8063) mediated region 3 activation. Consistent with a role in transcription, small interfering RNA-mediated knockdown of PDX-1 led to decreased mafA mRNA production in INS-1-derived beta-cell lines (832/13 and 832/3), while MafA expression was undetected in the pancreatic epithelium of Nkx2.2 null animals. These results suggest that beta-cell-type-specific mafA transcription is principally controlled by region 3-acting transcription factors that are essential in the formation of functional beta cells. PMID:16847327

Raum, Jeffrey C; Gerrish, Kevin; Artner, Isabella; Henderson, Eva; Guo, Min; Sussel, Lori; Schisler, Jonathan C; Newgard, Christopher B; Stein, Roland

2006-08-01

31

Tuning gene expression with synthetic upstream open reading frames.  

PubMed

We engineered short ORFs and used them to control the expression level of recombinant proteins. These short ORFs, encoding a two-amino acid peptide, were placed upstream of an ORF encoding a protein of interest. Insertion of these upstream ORFs (uORFs) resulted in suppression of protein expression. By varying the base sequence preceding the uORF, we sought to vary the translation initiation rate of the uORF and subsequently control the degree of this suppression. Using this strategy, we generated a library of RNA sequence elements that can specify protein expression over a broad range of levels. By also using multiple uORFs in series and non-AUG start codons, we were able to generate particularly low expression levels, allowing us to achieve expression levels spanning three orders of magnitude. Modeling supported a mechanism where uORFs shunt the flow of ribosomes away from the downstream protein-coding ORF. With a lower translation initiation rate at the uORF, more ribosomes "leak" past the uORF; consequently, more ribosomes are able to reach and translate the downstream ORF. We report expression control by engineering uORFs and translation initiation to be robust, predictable, and reproducible across all cell types tested. We propose control of translation initiation as a primary method of choice for tuning expression in mammalian systems. PMID:23798422

Ferreira, Joshua P; Overton, K Wesley; Wang, Clifford L

2013-06-24

32

Profitability analysis of upstream petroleum projects.  

National Technical Information Service (NTIS)

This report discusses theoretical and practical aspects of valuation of exploration and development ventures in the upstream petroleum industry. The report starts with a discussion of the methodology for valuation and risk assessment. The next sections de...

K. Ingeberg E. Magnus

1993-01-01

33

Regulation of Tomato golden mosaic virus AL2 and AL3 gene expression by a conserved upstream open reading frame.  

PubMed

A translational regulatory mechanism for Tomato golden mosaic virus (TGMV) complementary-sense gene expression has been characterized. TGMV transcribes two mRNAs, AL-1935 and AL-1629 transcripts, both of which contain the AL2 and AL3 open reading frames. However, AL2 is only expressed from AL-1629 whereas AL3 is expressed from both. Three AUG translation initiation codons are located upstream of both the AL2 and AL3 coding regions, within the 5'-untranslated region (UTR) of the AL-1935 transcript. Translation can initiate at the first AUG, specifying the C-terminal 122 amino acids of the AL1 protein (cAL1). Initiation of translation at this AUG is inhibitory for the downstream expression of both AL2 and AL3. This is most likely due to the terminator codon of cAL1 being positioned after the AUG initiation codon for the AL2 ORF. The mechanism by which AL3 is expressed from AL-1935 is currently unknown but a gap between the cAL1 termination codon and the start of AL3 suggests that it may involve reinitiation and/or internal initiation. In contrast, expression of AL3 from AL-1629 most likely occurs via leaky ribosome scanning since the AL3 initiation codon occurs before the terminator codon of AL2. Mutation of the AUG encoding cAL1 in the curtovirus, Spinach curly top virus, leads to increased infectivity as measured by a shorter latent period. Together this suggests that geminiviruses use a post-translational regulatory mechanism to regulate the synthesis of viral proteins important for replication and suppression of host defenses. PMID:19012941

Shung, Chia-Yi; Sunter, Garry

2008-11-14

34

Codon usage in plant genes.  

PubMed Central

We have examined codon bias in 207 plant gene sequences collected from Genbank and the literature. When this sample was further divided into 53 monocot and 154 dicot genes, the pattern of relative use of synonymous codons was shown to differ between these taxonomic groups, primarily in the use of G + C in the degenerate third base. Maize and soybean codon bias were examined separately and followed the monocot and dicot codon usage patterns respectively. Codon preference in ribulose 1,5 bisphosphate and chlorophyll a/b binding protein, two of the most abundant proteins in leaves was investigated. These highly expressed are more restricted in their codon usage than plant genes in general.

Murray, E E; Lotzer, J; Eberle, M

1989-01-01

35

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

2011-06-16

36

Codon Usage Domains over Bacterial  

Microsoft Academic Search

The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of

Antoine Danchin; Mudassar Iqbal; Matteo Marsili; Massimo Vergassola

37

The C-terminal region of eukaryotic translation initiation factor 3a (eIF3a) promotes mRNA recruitment, scanning, and, together with eIF3j and the eIF3b RNA recognition motif, selection of AUG start codons.  

PubMed

The C-terminal domain (CTD) of the a/Tif32 subunit of budding yeast eukaryotic translation initiation factor 3 (eIF3) interacts with eIF3 subunits j/Hcr1 and b/Prt1 and can bind helices 16 to 18 of 18S rRNA, suggesting proximity to the mRNA entry channel of the 40S subunit. We have identified substitutions in the conserved Lys-Glu-Arg-Arg (KERR) motif and in residues of the nearby box6 element of the a/Tif32 CTD that impair mRNA recruitment by 43S preinitiation complexes (PICs) and confer phenotypes indicating defects in scanning and start codon recognition. The normally dispensable CTD of j/Hcr1 is required for its binding to a/Tif32 and to mitigate the growth defects of these a/Tif32 mutants, indicating physical and functional interactions between these two domains. The a/Tif32 CTD and the j/Hcr1 N-terminal domain (NTD) also interact with the RNA recognition motif (RRM) in b/Prt1, and mutations in both subunits that disrupt their interactions with the RRM increase leaky scanning of an AUG codon. These results, and our demonstration that the extreme CTD of a/Tif32 binds to Rps2 and Rps3, lead us to propose that the a/Tif32 CTD directly stabilizes 43S subunit-mRNA interaction and that the b/Prt1-RRM-j/Hcr1-a/Tif32-CTD module binds near the mRNA entry channel and regulates the transition between scanning-conducive and initiation-competent conformations of the PIC. PMID:20584985

Chiu, Wen-Ling; Wagner, Susan; Herrmannová, Anna; Burela, Laxminarayana; Zhang, Fan; Saini, Adesh K; Valásek, Leos; Hinnebusch, Alan G

2010-06-28

38

The Trimethylamine Methyltransferase Gene and Multiple Dimethylamine Methyltransferase Genes of Methanosarcina barkeri Contain In-Frame and Read-Through Amber Codons  

PubMed Central

Three different methyltransferases initiate methanogenesis from trimethylamine (TMA), dimethylamine (DMA) or monomethylamine (MMA) by methylating different cognate corrinoid proteins that are subsequently used to methylate coenzyme M (CoM). Here, genes encoding the DMA and TMA methyltransferases are characterized for the first time. A single copy of mttB, the TMA methyltransferase gene, was cotranscribed with a copy of the DMA methyltransferase gene, mtbB1. However, two other nearly identical copies of mtbB1, designated mtbB2 and mtbB3, were also found in the genome. A 6.8-kb transcript was detected with probes to mttB and mtbB1, as well as to mtbC and mttC, encoding the cognate corrinoid proteins for DMA:CoM and TMA:CoM methyl transfer, respectively, and with probes to mttP, encoding a putative membrane protein which might function as a methylamine permease. These results indicate that these genes, found on the chromosome in the order mtbC, mttB, mttC, mttP, and mtbB1, form a single transcriptional unit. A transcriptional start site was detected 303 or 304 bp upstream of the translational start of mtbC. The MMA, DMA, and TMA methyltransferases are not homologs; however, like the MMA methyltransferase gene, the genes encoding the DMA and TMA methyltransferases each contain a single in-frame amber codon. Each of the three DMA methyltransferase gene copies from Methanosarcina barkeri contained an amber codon at the same position, followed by a downstream UAA or UGA codon. The C-terminal residues of DMA methyltransferase purified from TMA-grown cells matched the residues predicted for the gene products of mtbB1, mtbB2, or mtbB3 if termination occurred at the UAA or UGA codon rather than the in-frame amber codon. The mttB gene from Methanosarcina thermophila contained a UAG codon at the same position as the M. barkeri mttB gene. The UAG codon is also present in mttB transcripts. Thus, the genes encoding the three types of methyltransferases that initiate methanogenesis from methylamine contain in-frame amber codons that are suppressed during expression of the characterized methyltransferases.

Paul, Ligi; Ferguson, Donald J.; Krzycki, Joseph A.

2000-01-01

39

The sequence context of the initiation codon in the encephalomyocarditis virus leader modulates efficiency of internal translation initiation.  

PubMed Central

Translation initiation on poliovirus and encephalomyocarditis virus (EMCV) mRNAs occurs by a cap-independent mechanism utilizing an internal ribosomal entry site (IRES). However, no unifying mechanism for AUG initiation site selection has been proposed. Analysis of initiation of mRNAs translated in vitro has suggested that initiation of poliovirus mRNA translation likely involves both internal binding of ribosomes and scanning to the first AUG which is in a favorable context for initiation. In contrast, internal initiation on EMCV mRNA may not utilize scanning, since ribosomes bind directly or very close to the initiation codon AUG-11. We have studied in vivo the sequence requirements for internal initiation around the EMCV initiation codon, both in monocistronic and in dicistronic mRNAs. Our studies show that the upstream AUG-10 is normally not used and that there is no specific sequence requirement for nucleotides between AUG-10 and AUG-11. However, the sequence context of AUG-11 does influence the efficiency of initiation at AUG-11. Efficient IRES-mediated internal initiation at AUG-11 exhibits a requirement for an adenine in the -3 position, similar to cap-dependent initiation. These results support a model for internal initiation on EMCV mRNA in which scanning starts at or near AUG-11. Although initiation primarily occurs at AUG-11, initiation at multiple downstream AUG codons can be detected. In addition, a poor sequence context around AUG-11 results in increased initiation at one or more downstream AUG codons, indicative of leaky scanning or jumping by the ribosome from AUG-11 mediated by the EMCV IRES. Images

Davies, M V; Kaufman, R J

1992-01-01

40

Codon preference in Dictyostelium discoideum.  

PubMed Central

Dictyostelium discoideum is of increasing interest as a model eukaryotic cell because its many attributes have recently been expanded to include improved genetic and biochemical manipulability. The ability to transform Dictyostelium using drug resistance as a selectable marker (1) and to gene target by high frequency homologous integration (2) makes this organism particularly useful for molecular genetic approaches to cell structure and function. Given this background, it becomes important to analyze the codon preference used in this organism. Dictyostelium displays a strong and unique overall codon preference. This preference varies between different coding regions and even varies between coding regions from the same gene family. The degree of codon preference may be correlated with expression levels but not with the developmental time of expression of the gene product. The strong codon preference can be applied to identify coding regions in Dictyostelium DNA and aid in the design of oligonucleotide probes for cloning Dictyostelium genes.

Warrick, H M; Spudich, J A

1988-01-01

41

Transcription of the chicken myb proto-oncogene starts within a CpG island.  

PubMed Central

The nucleotide sequence of an 8.2-kb DNA fragment from the 5' proximal part of the chicken myb proto-oncogene spanning 1761 nucleotides upstream and 6436 nucleotides downstream from a presumed c-myb initiation codon was determined. A 3.3-kb G + C-rich region found in this sequence had also other features characterizing CpG islands, i.e. no CpG underrepresentation and lack of CpG methylation. In haematopoietic tissues c-myb mRNA synthesis starts in two major regions of the CpG island, namely 98 to 108 and 143 to 145 nucleotides upstream from the c-myb initiation codon. These two regions are in or close to the 124-bp evolutionarily conserved element located in the middle part of the CpG island. No alternative splicing of the 5' end of c-myb mRNA suggested earlier (1,2) was observed. The c-myb promoter contains neither TATA nor CAAT box-like structures at the usual positions. Instead, numerous potential Sp1 factor binding sites were found both upstream and downstream from the transcription initiation sites. Moreover, consensus v-myb protein DNA-binding sites were revealed in the promoter region and in sequences downstream from it. Images

Dvorak, M; Urbanek, P; Bartunek, P; Paces, V; Vlach, J; Pecenka, V; Arnold, L; Travnicek, M; Riman, J

1989-01-01

42

Expected frequencies of codon use as a function of mutation rates and codon fitnesses  

Microsoft Academic Search

Summary A method is shown to determine the expected pattern of codon use for any given set of mutation rates between nucleotides and any set of fitnesses for the codons. If it is assumed that mutations to stop codons are lethal then those codons which can mutate in one step to a stop codon tend to be used less frequently.

G. B. Golding; C. Strobeck

1982-01-01

43

Low-usage codons and rare codons of Escherichia coli Mini Review  

Microsoft Academic Search

Summary In Escherichia coli (E. coli), a low-usage codon is defined as a codon that is used rarely or infrequently in the genome with usage frequency lower than the smallest value (or frequency cut-off) among the usage frequencies of non-degenerate codons (Met codon AUG and Trp codon UGG) and the optimal codons for amino acids Leu, Ile, Val, Ser, Pro,

Dequan Chen; Donald E. Texada

44

Variegated Expression from the Murine Band 3 (AE1) Promoter in Transgenic Mice Is Associated with mRNA Transcript Initiation at Upstream Start Sites and Can Be Suppressed by the Addition of the Chicken ?-Globin 5? HS4 Insulator Element  

PubMed Central

The anion exchanger protein 1 (AE1; band 3) is an abundant erythrocyte transmembrane protein that regulates chloride-bicarbonate exchange and provides an attachment site for the erythrocyte membrane skeleton on the cytoplasmic domain. We analyzed the function of the erythroid AE1 gene promoter by using run-on transcription, RNase protection, transient transfection, and transgenic mouse assays. AE1 mRNA was transcribed at a higher level and maintained at a higher steady-state level than either ankyrin or ?-spectrin in mouse fetal liver cells. When linked to a human ?-globin gene, two different AE1 promoters directed erythroid-specific expression of ?-globin mRNA in 18 of 18 lines of transgenic mice. However, variegated expression of ?-globin was observed in 14 of 18 lines. While there was a significant correlation between transgene copy number and the amount of ?-globin mRNA in all 18 lines, the transgene mRNAs initiated upstream of the start site of the endogenous AE1 mRNA. Addition of the insulator element from 5?HS4 of the chicken ?-globin cluster to the AE1/?-globin transgene allowed position-independent, copy-number-dependent expression at levels similar to the AE1 transcription rate in six of six lines of transgenic mice. The mRNA from the insulated AE1/?-globin transgene mapped to the start site of the endogenous AE1 mRNA, and ?-globin protein was expressed in 100% of erythrocytes in all lines. We conclude that the chicken ?-globin 5?HS4 element is necessary for full function of the AE1 promoter and that position effect variegation is associated with RNA transcription from the upstream start sites.

Frazar, Tiffany F.; Weisbein, Jessica L.; Anderson, Stacie M.; Cline, Amanda P.; Garrett, Lisa J.; Felsenfeld, Gary; Gallagher, Patrick G.; Bodine, David M.

2003-01-01

45

Rare codons regulate KRas oncogenesis.  

PubMed

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

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

2012-12-13

46

Upstream waves at Uranus  

Microsoft Academic Search

Since the Mach number of the solar wind increases with increasing heliocentric distance, the ratio of thermal to magnetic pressure, or beta, of the Uranian magnetosheath is expected to be much higher than in the terrestrial magnetosheath. Consistent with this expectation the magnetosheath is observed to be extremely turbulent, and one may expect many particles to leak back upstream into

C.T. Russell; R. P. Lepping; C. W. Smith

1990-01-01

47

Upstream waves at Uranus  

SciTech Connect

Since the Mach number of the solar wind increases with increasing heliocentric distance, the ratio of thermal to magnetic pressure, or beta, of the Uranian magnetosheath is expected to be much higher than in the terrestrial magnetosheath. Consistent with this expectation the magnetosheath is observed to be extremely turbulent, and one may expect many particles to leak back upstream into the solar wind and/or be scattered from the bow shock. In accord with the expected presence of backstreaming particles, waves of the type associated with terrestrial backstreaming particles are seen outbound along the trajectory of Voyager in the pre-shock solar wind with frequencies close to 10{sup {minus}3} Hz. The wave frequency is close to that expected for upstream waves based on measurements closer to the Sun. Upstream from the bow shock the magnetic field was found to be much weaker than expected from observations in the inner solar system. The cause of this depression is unlikely to be the upstream particles; rather the cause is probably intrinsic to the solar wind such as reconnection across the heliospheric current sheet.

Russell, C.T. (Univ. of California, Los Angeles (United States)); Lepping, R.P. (NASA Goddard Space Flight Center, Greenbelt, MD (United States)); Smith, C.W. (Univ. of Delaware, Newark (United States))

1990-03-01

48

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

49

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

50

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

51

Accumulation of a mRNA decay intermediate by ribosomal pausing at a stop codon.  

PubMed Central

A RNA fragment which is protected from degradation by ribosome pausing at a stop codon has been identified in growing Escherichia coli. The fragment is 261 nt long and corresponds to the 3'-end of the mRNA expressed from a semi-synthetic model gene. The 5'-end of the RNA fragment, denoted rpRNA (ribosomal pause RNA), is located 13 bases upstream of the stop codon. In vivo decay of the complete mRNA and accumulation of rpRNA are dependent on the nature of the stop codon and its codon context. The data indicate that the rpRNA fragment arises from interrupted decay of the S3A'mRNA in the 5'-->m3'direction, in connection with a ribosomal pause at the stop codon. RF-2 decoding of UGA is less efficient than RF-1 decoding of UAG in identical codon contexts, as judged from rpRNA steady-state levels. The half-life of UGA-containing rpRNAs is at least 5 min, indicating that ribosomal pausing can be a major factor in stabilising downstream regions of messenger RNAs.

Bjornsson, A; Isaksson, L A

1996-01-01

52

Site-Specific Codon Bias in Bacteria  

PubMed Central

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.

Smith, J. M.; Smith, N. H.

1996-01-01

53

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

54

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

Microsoft Academic Search

BACKGROUND: Codon bias is believed to play an important role in the control of gene expression. In Escherichia coli, some rare codons, which can limit the expression level of exogenous protein, have been defined by gene engineering operations. Previous studies have confirmed the existence of codon pair's preference in many genomes, but the underlying cause of this bias has not

Xianming Wu; Songfeng Wu; Dong Li; Jiyang Zhang; Lin Hou; Jie Ma; Wanlin Liu; Daming Ren; Yunping Zhu; Fuchu He

2010-01-01

55

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

56

Factors affecting codon usage in Yersinia pestis.  

PubMed

The complete genome of Yersinia pestis which was the causative agent of the systemic invasive infectious disease classically referred as plague, had been recently sequenced. In order to have a further insight into the synonymous codon usage evolution, factors shaping synonymous codon usage pattern of Yersinia pestis were analyzed in this paper. The coding sequences larger than or equal to 300 bp were used in codon usage analysis. Though "G"+"C" content in Y. pestis genome was slightly lower (47.64%), the highly expressed genes tended to use "C" or "G" at synonymous sites compared with lowly expressed genes. Conversely, lowly expressed genes tended to prefer "A" or "T" at synonymous positions. Gene expression level was strongly correlated with the first axis of the correspondence analysis (COA) (R=0.63, P<0.0001). By the analyses of the codon usage pattern of highly and lowly expressed genes, it was confirmed that gene expression level was partially responsible for the codon usage bias. GC-skew analysis showed that codon usage suffered replication-transcriptional selection. Codon adaptation index (CAI), frequency of "C"+"G" at the synonymous third position of codon (GC3s) and the effective number of codons (Nc) values showed some differences among different gene length groups. "G"+"C" content of genes was strongly correlated with the first axis of the COA (R=0.72, P<0.0001). It could be concluded that gene expressivity, replication-transcriptional selection, gene length and gene composition constraints were the main affecting factors of codon usage variation in Y. pestis. PMID:12796821

Hou, Zhuo-Cheng; Yang, Ning

2003-06-01

57

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

58

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

59

The Start of Head Start  

ERIC Educational Resources Information Center

|The creation of the Head Start program occurred at break-neck speed with many dramatic turns and many colorful players. No one tells the story better than Edward Zigler in "Head Start: The Inside Story of America's Most Successful Educational Experiment"--a detailed and personal, behind the scenes look at the program's inception. From this…

Neugebauer, Roger

2010-01-01

60

The imprint of codons on protein structure.  

PubMed

The "central dogma" of biology outlines the unidirectional flow of interpretable data from genetic sequence to protein sequence. This has led to the idea that a protein's structure is dependent only on its amino acid sequence and not its genetic sequence. Recently, however, a more than transient link between the coding genetic sequence and the protein structure has become apparent. The two interact at the ribosome via the process of co-translational protein folding. Evidence for co-translational folding is growing rapidly, but the influence of codons on the protein structure attained is still highly contentious. It is theorised that the speed of codon translation modulates the time available for protein folding and hence the protein structure. Here, past and present research regarding synonymous codons and codon translation speed are reviewed within the context of protein structure attainment. PMID:21567957

Deane, Charlotte M; Saunders, Rhodri

2011-05-13

61

Combinatorial codon-based amino acid substitutions  

PubMed Central

Twenty Fmoc-protected trinucleotide phosphoramidites representing a complete set of codons for the natural amino acids were chemically synthesized for the first time. A pool of these reagents was incorporated into oligonucleotides at substoichiometric levels to generate two libraries of variants that randomly carry either few or many codon replacements on a region encoding nine amino acids of the bacterial enzyme TEM-1 ?-lactamase. Assembly of the libraries was performed in a completely automated mode through a simple modification of ordinary protocols. This technology eliminates codon redundancy, stop codons and enables complete exploration of sequence space for single, double and triple mutations throughout a protein region spanning several residues. Sequence analysis of many non-selected clones revealed a good incorporation of the trinucleotides, producing combinations of mutations quite different from those obtained using conventional degenerate oligonucleotides. Ceftazidime-selection experiments yielded several never before reported variants containing novel amino acid combinations in the ?-lactamase omega loop region.

Yanez, Jorge; Arguello, Martha; Osuna, Joel; Soberon, Xavier; Gaytan, Paul

2004-01-01

62

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

63

Codon Preference Optimization Increases Heterologous PEDF Expression  

Microsoft Academic Search

Pigment epithelium-derived factor (PEDF) is widely known for its neurotrophic and antiangiogenic functions. Efficacy studies of PEDF in animal models are limited because of poor heterologous protein yields. Here, we redesigned the human PEDF gene to preferentially match codon frequencies of E coli without altering the amino acid sequence. Following de novo synthesis, codon optimized PEDF (coPEDF) and the wtPEDF

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

2010-01-01

64

Universal function-specificity of codon usage  

PubMed Central

Synonymous codon usage has long been known as a factor that affects average expression level of proteins in fast-growing microorganisms, but neither its role in dynamic changes of expression in response to environmental changes nor selective factors shaping it in the genomes of higher eukaryotes have been fully understood. Here, we propose that codon usage is ubiquitously selected to synchronize the translation efficiency with the dynamic alteration of protein expression in response to environmental and physiological changes. Our analysis reveals that codon usage is universally correlated with gene function, suggesting its potential contribution to synchronized regulation of genes with similar functions. We directly show that coexpressed genes have similar synonymous codon usages within the genomes of human, yeast, Caenorhabditis elegans and Escherichia coli. We also demonstrate that perturbing the codon usage directly affects the level or even direction of changes in protein expression in response to environmental stimuli. Perturbing tRNA composition also has tangible phenotypic effects on the cell. By showing that codon usage is universally function-specific, our results expand, to almost all organisms, the notion that cells may need to dynamically alter their intracellular tRNA composition in order to adapt to their new environment or physiological role.

Najafabadi, Hamed Shateri; Goodarzi, Hani; Salavati, Reza

2009-01-01

65

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 (${{\\rm tRNA}{{{\\rm Pyl}\\hfill \\atop {\\rm CCG}\\hfill}}}$), and the genes for pyrrolysine biosynthesis. Here we show that ${{\\rm tRNA}{{{\\rm Pyl}\\hfill \\atop {\\rm CCG}\\hfill}}}$ is efficiently recognized by the endogenous arginyl-tRNA synthetase, presumably at the anticodon. Mass spectrometry revealed that in the presence of ${{\\rm tRNA}{{{\\rm Pyl}\\hfill \\atop {\\rm CCG}\\hfill}}}$, 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

2013-09-02

66

Recoding elements located adjacent to a subset of eukaryal selenocysteine-specifying UGA codons  

PubMed Central

Incorporation of the 21st amino acid, selenocysteine, into proteins is specified in all three domains of life by dynamic translational redefinition of UGA codons. In eukarya and archaea, selenocysteine insertion requires a cis-acting selenocysteine insertion sequence (SECIS) usually located in the 3?UTR of selenoprotein mRNAs. Here we present comparative sequence analysis and experimental data supporting the presence of a second stop codon redefinition element located adjacent to a selenocysteine-encoding UGA codon in the eukaryal gene, SEPN1. This element is sufficient to stimulate high-level (6%) translational redefinition of the SEPN1 UGA codon in human cells. Readthrough levels further increased to 12% when tested in the presence of the SEPN1 3?UTR SECIS. Directed mutagenesis and phylogeny of the sequence context strongly supports the importance of a stem loop starting six nucleotides 3? of the UGA codon. Sequences capable of forming strong RNA structures were also identified 3? adjacent to, or near, selenocysteine-encoding UGA codons in the Sps2, SelH, SelO, and SelT selenoprotein genes.

Howard, Michael T; Aggarwal, Gaurav; Anderson, Christine B; Khatri, Shikha; Flanigan, Kevin M; Atkins, John F

2005-01-01

67

The usage of codons which are similar to stop codons in the genomes of Xylella fastidiosa and Xanthomonas citri.  

PubMed

During the evolution of living organisms, a natural selection event occurs toward the optimization of their genomes regarding the usage of codons. During this process which is known as codon bias, a set of preferred codons is naturally defined in the genome of a given organism, since there are 61 possible codons (plus 3 stop codons) to 20 amino acids. Such event leads to optimization of metabolic cellular processes such as translational efficiency, RNA stability and energy saving. Although we know why, we do not know how exactly a set of preferred codons for each amino acid is defined for a given genome considering that the usage frequency of each synonymous codons is peculiar to each organism. In order to help answering this question, we analyzed the usage frequency of codons which are similar to stop codons, since a minor mutation on these codons may lead to a stop codon into the open reading frame compromising the protein expression as a result. We found a reduced use of those codons in Xanthomomas axonopodis pv. citri which presents an optimized genome regarding codon usage. On the other hand, such codons are more often used in Xylella fastidiosa, which does not seem to have established codon preferences as previously shown. Our results support that a set of preferred codons is not randomly selected and propose new ideas to the field warranting further experiments in this regard. PMID:21046398

Galves-dos-Santos, Dilermando P; Martins-de-Souza, Daniel

2010-11-04

68

Hand gesture recognition by analysis of codons  

NASA Astrophysics Data System (ADS)

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

Ramachandra, Poornima; Shrikhande, Neelima

2007-09-01

69

Start Young!  

NSDL National Science Digital Library

A person, place, or thing is what usually sparks those first memorable childhood impressions. Of course, we often do not study our newfound interests from the time of our personal enlightenment to adulthood, but early childhood interests are strong and they can have a powerful hold on us. Children usually show interest in many areas, though one interest usually resurfaces as they get older. Often, it seems this interest--usually one from childhood--is the one that leads to a profession. This free selection from Start Young! Early Childhood Science Activities also includes a Contents, Introduction, and Index section, along with a Quick Reference Chart.

Rubin, Penni

2006-01-01

70

Analysis of synonymous codon usage patterns in the genus Rhizobium.  

PubMed

The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearman's rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium. PMID:23653263

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

2013-05-08

71

Blepharisma Uses UAA as a termination codon  

Microsoft Academic Search

It has generally been assumed that all ciliates deviate from the universal genetic code by translating UAA and UAG as glutamine and using UGA as the sole termination codon. This assumption was based on sequence analyses of genes in four genera: Paramecium [1], Tetrahymena [2], Stylonychia [3], and Oxytrieha [4]. Recently, this view was challenged by the finding that in

A. Liang; K. Heckmann

1993-01-01

72

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

73

Alternative splicing within the elk-1 5' untranslated region serves to modulate initiation events downstream of the highly conserved upstream open reading frame 2.  

PubMed

The 5' untranslated region (UTR) plays a central role in the regulation of mammalian translation initiation. Key components include RNA structure, upstream AUGs (uAUGs), upstream open reading frames (uORFs), and internal ribosome entry site elements that can interact to modulate the readout. We previously reported the characterization of two alternatively spliced 5' UTR isoforms of the human elk-1 gene. Both contain two uAUGs and a stable RNA stem-loop, but the long form (5' UTR(L)) was more repressive than the short form (5' UTR(S)) for initiation at the ELK-1 AUG. We now demonstrate that ELK-1 expression arises by a combination of leaky scanning and reinitiation, with the latter mediated by the small uORF2 conserved in both spliced isoforms. In HEK293T cells, a considerable fraction of ribosomes scans beyond the ELK-1 AUG in a reinitiation mode. These are sequestered by a series of out-of-frame AUG codons that serve to prevent access to a second in-frame AUG start site used to express short ELK-1 (sELK-1), an N-terminally truncated form of ELK-1 that has been observed only in neuronal cells. We present evidence that all these events are fine-tuned by the nature of the 5' UTR and the activity of the ? subunit of eukaryotic initiation factor 2 and provide insights into the neuronal specificity of sELK-1 expression. PMID:22354998

Rahim, Gwendoline; Araud, Tanguy; Jaquier-Gubler, Pascale; Curran, Joseph

2012-02-21

74

Codon usage in Entamoeba histolytica, E. dispar and E. invadens  

Microsoft Academic Search

We analyzed the frequencies of genetic codon usage of 68 non-redundant protein coding genes from the human-pathogenic E. histolytica (28 117 codons), 6 from the non-pathogenic E. dispar (1744 codons), and 4 from the reptilian E. invadens (933 codons). The A + U contents of the protein coding sequences from E. histolytica, E. dispar, and E. invadens were 67%, 66%,

Tomoyoshi Nozaki; Takashi Asai; Tsutomu Takeuchi

1997-01-01

75

Codon preference optimization increases heterologous PEDF expression.  

PubMed

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

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

2010-11-30

76

Codon Preference Optimization Increases Heterologous PEDF Expression  

PubMed Central

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

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

2010-01-01

77

A common periodic table of codons and amino acids  

Microsoft Academic Search

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

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

2003-01-01

78

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids  

PubMed Central

Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation.

Wald, Naama; Alroy, Maya; Botzman, Maya; Margalit, Hanah

2012-01-01

79

Rare codon content affects the solubility of recombinant proteins in a codon bias-adjusted Escherichia coli strain  

Microsoft Academic Search

BACKGROUND: The expression of heterologous proteins in Escherichia coli is strongly affected by codon bias. This phenomenon occurs when the codon usage of the mRNA coding for the foreign protein differs from that of the bacterium. The ribosome pauses upon encountering a rare codon and may detach from the mRNA, thereby the yield of protein expression is reduced. Several bacterial

Germán L Rosano; Eduardo A Ceccarelli

2009-01-01

80

Synonymous codon usage in Zea mays L. nuclear genes is varied by levels of C and G-ending codons.  

PubMed Central

A multivariate statistical method called correspondence analysis was used to examine the codon usage of one-hundred-and-one nuclear genes of maize (Zea mays L.). Forty percent of the variation in codon usage was due to bias toward G or C-ending versus A or U-ending codons. Differences in levels of G-ending codons showed the weakest correlation with the major codon usage bias. The bias toward C or U versus A or G in the silent third nucleotide position of synonymous codons accounted for approximately 10% of the variation in codon usage. The G+C content of the silent third nucleotide position of coding regions was not strongly correlated with G+C content of introns. Codon usage was strongly biased toward codons ending in G or C for a number of highly expressed genes including most light-regulated chloroplast proteins, ABA-induced proteins, histones, and anthocyanin biosynthetic enzymes. Codon usage of genes encoding storage proteins and regulatory proteins, such as transposases, kinases, phosphatases and transcription factors, was more random than that of genes encoding cytosolic enzymes with similar bias toward G or C-ending codons. Codon usage in maize may reflect both regional bias on nucleotide composition and selection on the silent third nucleotide position.

Fennoy, S L; Bailey-Serres, J

1993-01-01

81

P53 codon 72 Arg/Pro polymorphism and glioma risk: an updated meta-analysis.  

PubMed

P53 codon 72 Arg/Pro is a C/G variation upstream of the p53 gene on human chromosome 17p13. Many case-control studies have investigated the association between p53 codon 72 Arg/Pro polymorphism and glioma risk but provided inconsistent findings. To better understand the pathogenesis of glioma, we performed the current meta-analysis by pooling data from all available individual studies. According to the inclusion criteria, ten independent publications with 11 case-control studies were included into this meta-analysis. The pooled odds ratio (OR) with 95 % confidence interval (95 % CI) was calculated to estimate the effect of p53 codon 72 Arg/Pro variant on the development of glioma. Overall, no appreciable correlation was observed among the total studies in all gene models (ORPro allele vs. Arg allele?=?1.04, 95 % CI?=?0.90-1.20, P OR?=?0.581; ORPro/Pro vs. Arg/Arg?=?0.95, 95 % CI?=?0.80-1.14, P OR?=?0.614; ORPro/Arg vs. Arg/Arg?=?1.01, 95 % CI?=?0.79-1.29, P OR?=?0.993; ORPro/Arg + Pro/Pro vs. Arg/Arg?=?1.03, 95 % CI?=?0.82-1.29, P OR?=?0.799; ORPro/Pro vs. Arg/Arg + Pro/Arg?=?1.02, 95 % CI?=?0.86-1.22, P OR?=?0.785). In stratified analyses by ethnicity, source of controls, and glioma subtypes, the p53 codon 72 Arg/Pro polymorphism did not alter the risk for glioma in population-based, hospital-based, astrocytoma, and oligodendroglioma studies among Caucasian. Interestingly, the Pro/Pro genotype seemed to be negatively associated with the glioma risk among patients with glioblastoma (ORPro/Pro vs. Arg/Arg?=?0.68, 95 % CI?=?0.48-0.95, P OR?=?0.026). Our study suggests that the polymorphism of p53 codon 72 Arg/Pro may play a protective role in the development of glioblastoma. The relationship of p53 codon 72 Arg/Pro polymorphism with the susceptibility to glioma needs further estimation by more individual studies with high quality across ethnicities. PMID:23860773

He, Fang; Xia, Yi; Liu, Huafeng; Li, Jin; Wang, Chao

2013-07-17

82

Selective pressure dominates the synonymous codon usage in parvoviridae.  

PubMed

Parvoviridae is a family of small non-enveloped viruses and divided into two subfamilies. The family members infect a wide range of organisms from insects to humans and some of the members (e.g., nonpathogenic adeno-associated viruses) are effective gene therapy delivery vectors. We detailed the synonymous codon usage pattern of Parvoviridae family from the available 58 sequenced genomes through multivariate statistical methods. Our results revealed that nine viruses showed some degree of strong codon bias, and the others possessed a general weak trend of codon bias. ENc-plot and neutrality plot results showed that selective pressure dominated over mutation in shapes coding sequence's composition. The overall GC content and GC content at the third synonymous codon position were the principal determinants behind the variations within the codon usage patterns, as they both significantly correlated with the first axis of correspondence analysis. In addition, gene length had no direct influence on the codon usage pattern. Densovirinae subfamily and Parvovirinae subfamily possessed nine identical preferred codons, though most of the two subfamilies codon usage frequencies were significantly different. The result of cluster analysis based on synonymous codon usage was discordant with that of taxonomic classification. Adeno-associated viruses formed a separated clade far from other Parvoviridae members in the dendrogram. Thus, we concluded that natural selection rather than mutation pressure accounts for the main factor that affects the codon bias in Parvoviridae family. PMID:22996735

Shi, Sheng-Lin; Jiang, Yi-Ren; Liu, Yan-Qun; Xia, Run-Xi; Qin, Li

2012-09-21

83

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

2013-01-23

84

TrimerDimer: an oligonucleotide-based saturation mutagenesis approach that removes redundant and stop codons  

PubMed Central

9-fluorenylmethoxycarbonyl (Fmoc) and 4,4?-dimethoxytrityl (DMTr) are orthogonal hydroxyl protecting groups that have been used in conjunction to assemble oligonucleotide libraries whose variants contain wild-type and mutant codons randomly interspersed throughout a focused DNA region. Fmoc is labile to organic bases and stable to weak acids, whereas DMTr behaves oppositely. Based on these chemical characteristics, we have now devised TrimerDimer, a novel codon-based saturation mutagenesis approach that removes redundant and stop codons during the assembly of degenerate oligonucleotides. In this approach, five DMTr-protected trinucleotide phosphoramidites (dTGG, dATG, dTTT, dTAT and dTGC) and five Fmoc-protected dinucleotide phosphoramidites (dAA, dTT, dAT, dGC and dCG) react simultaneously with a starting oligonucleotide growing on a solid support. The Fmoc group is then removed and the incorporated dimers react with a mixture of three DMTr-protected monomer phosphoramidites (dC, dA and dG) to produce 15 trinucleotides: dCAA, dAAA, dGAA, dCTT, dATT, dGTT, dCAT, dAAT, dGAT, dCGC, dAGC, dGGC, dCCG, dACG and dGCG. After one mutagenic cycle, 20 codons are generated encoding the 20 natural amino acids. TrimerDimer was tested by randomizing the four contiguous codons that encode amino acids L64–G67 of an engineered, nonfluorescent GFP protein. Sequencing of 89 nonfluorescent mutant clones and isolation of two fluorescent mutants confirmed the principle.

Gaytan, Paul; Contreras-Zambrano, Casandra; Ortiz-Alvarado, Monica; Morales-Pablos, Alfredo; Yanez, Jorge

2009-01-01

85

TrimerDimer: an oligonucleotide-based saturation mutagenesis approach that removes redundant and stop codons.  

PubMed

9-fluorenylmethoxycarbonyl (Fmoc) and 4,4'-dimethoxytrityl (DMTr) are orthogonal hydroxyl protecting groups that have been used in conjunction to assemble oligonucleotide libraries whose variants contain wild-type and mutant codons randomly interspersed throughout a focused DNA region. Fmoc is labile to organic bases and stable to weak acids, whereas DMTr behaves oppositely. Based on these chemical characteristics, we have now devised TrimerDimer, a novel codon-based saturation mutagenesis approach that removes redundant and stop codons during the assembly of degenerate oligonucleotides. In this approach, five DMTr-protected trinucleotide phosphoramidites (dTGG, dATG, dTTT, dTAT and dTGC) and five Fmoc-protected dinucleotide phosphoramidites (dAA, dTT, dAT, dGC and dCG) react simultaneously with a starting oligonucleotide growing on a solid support. The Fmoc group is then removed and the incorporated dimers react with a mixture of three DMTr-protected monomer phosphoramidites (dC, dA and dG) to produce 15 trinucleotides: dCAA, dAAA, dGAA, dCTT, dATT, dGTT, dCAT, dAAT, dGAT, dCGC, dAGC, dGGC, dCCG, dACG and dGCG. After one mutagenic cycle, 20 codons are generated encoding the 20 natural amino acids. TrimerDimer was tested by randomizing the four contiguous codons that encode amino acids L64-G67 of an engineered, nonfluorescent GFP protein. Sequencing of 89 nonfluorescent mutant clones and isolation of two fluorescent mutants confirmed the principle. PMID:19783828

Gaytán, Paul; Contreras-Zambrano, Casandra; Ortiz-Alvarado, Mónica; Morales-Pablos, Alfredo; Yáñez, Jorge

2009-09-25

86

Gender-specific selection on codon usage in plant genomes  

PubMed Central

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

2007-01-01

87

Intercodon dinucleotides affect codon choice in plant genes.  

PubMed

In this work, 710 CDSs corresponding to over 290 000 codons equally distributed between Brassica napus, Arabidopsis thaliana, Lycopersicon esculentum, Nicotiana tabacum, Pisum sativum, Glycine max, Oryza sativa, Triticum aestivum, Hordeum vulgare and Zea mays were considered. For each amino acid, synonymous codon choice was determined in the presence of A, G, C or T as the initial nucleotide of the subsequent triplet; data were statistically analysed under the hypothesis of an independent assortment of codons. In 33.4% of cases, a frequency significantly (P: = 0.01) different from that expected was recorded. This was mainly due to a pervasive intercodon TpA and CpG deficiency. As a general rule, intercodon TpAs and CpGs were preferably replaced by CpAs and TpGs, respectively. In several instances, codon frequencies were also modified to avoid homotetramer and homotrimer formation, to reduce intercodon ApCs downstream (1,2) GG or AG dinucleotides, as well as to increase GpA or ApG intercodons under certain contexts. Since TpA, CpG and homotetra(tri)mer deficiency directly or indirectly accounted for 77% of significant variation in the codon frequency, it can be concluded that codon usage mirrors precise needs at the DNA structure level. Plant species exhibited a phylogenetically-related adaptation to structural constraints. Codon usage flexibility was reflected in strikingly different arrays of optimum codons for probe design. PMID:10954603

De Amicis, F; Marchetti, S

2000-09-01

88

Selection, Mutations and Codon Usage in Bacterial Model  

Microsoft Academic Search

We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to mutation process and the improvement of the translation phase due to natural selection. We develop a thermodynamical description of the asymptotic state

Franco Bagnoli; Pietro Lio

1998-01-01

89

Selection, mutations and codon usage in a bacterial model  

Microsoft Academic Search

We present a statistical model of bacterial evolution based on the coupling between codon usage and tRNA abundance. Such a model interprets this aspect of the evolutionary process as a balance between the codon homogenization effect due to mutation process and the improvement of the translation phase due to natural selection. We develop a thermodynamical description of the asymptotic state

Franco Bagnoli

1995-01-01

90

P-value based visualization of codon usage data  

Microsoft Academic Search

Two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. Both problems can be addressed by multivariate analysis of codon usage data. In particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. We here propose

Peter Meinicke; Thomas Brodag; Wolfgang Florian Fricke; Stephan Waack

2006-01-01

91

Measure of synonymous codon usage diversity among genes in bacteria  

Microsoft Academic Search

BACKGROUND: In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synonymous codon usage among all genes within a genome. RESULTS: The application of Dmean to

Haruo Suzuki; Rintaro Saito; Masaru Tomita

2009-01-01

92

Analysis of Synonymous Codon Usage Bias in Chlamydia  

Microsoft Academic Search

Abstract , Chlamydiae,are obligate intracellular bacterial pathogens that cause ocular and sexually transmitted diseases, and are associated with cardiovascular diseases. The analysis of codon usage may improve our understanding of the evolution and pathogenesis of Chlamydiaand allow reengineering of target genes to improve their expression for gene therapy. Here, we analyzed the codon usage of C. muridarum, C. trachomatis(here indicating

H. Lu; Wei-ming Zhao; Yan Zheng; Hong Wang; Mei Qi; Xiu-ping Yu

2005-01-01

93

Selected codon usage bias in members of the class Mollicutes.  

PubMed

Mollicutes are parasitic microorganisms mainly characterized by small cell sizes, reduced genomes and great A and T mutational bias. We analyzed the codon usage patterns of the completely sequenced genomes of bacteria that belong to this class. We found that for many organisms not only mutational bias but also selection has a major effect on codon usage. Through a comparative perspective and based on three widely used criteria we were able to classify Mollicutes according to the effect of selection on codon usage. We found conserved optimal codons in many species and study the tRNA gene pool in each genome. Previous results are reinforced by the fact that, when selection is operative, the putative optimal codons found match the respective cognate tRNA. Finally, we trace selection effect backwards to the common ancestor of the class and estimate the phylogenetic inertia associated with this character. We discuss the possible scenarios that explain the observed evolutionary patterns. PMID:21147204

Iriarte, Andrés; Baraibar, Juan Diego; Romero, Héctor; Musto, Héctor

2010-12-13

94

Quantitative analysis of in vivo ribosomal events at UGA and UAG stop codons.  

PubMed Central

An in vivo translation assay system has been designed to measure, in one and the same assay, the three alternatives for a ribosome poised at a stop codon (termination, read-through and frameshift). A quantitative analysis of the competition has been done in the presence and absence of release factor (RF) mutants, nonsense suppressors and an upstream Shine-Dalgarno-like sequence. The ribosomal +1 frameshift product is measurable when the stop codon is decoded by wild-type or mutant RF (prf A1 or prf B2) and also in the presence of competing suppressor tRNAs. Frameshift frequency appears to be influenced by RF activity. The amount of frameshift product decreases in the presence of competing suppressor tRNAs, however, this decrease is not in proportion to the corresponding increase in the suppression product. Instead, there is an increase in the total amount of protein expressed from the gene, perhaps due to the purging of queued ribosomes. Mutated RFs reduce the total output of the reporter gene by reducing the amount of all three protein products. The nascent peptide has earlier been shown to influence the translation termination process by interacting with the RFs. At 42 degrees C in a temperature-sensitive RF mutant strain, protein measurements indicate that the nascent peptide seems to influence the binding efficiencies of the RFs.

Mottagui-Tabar, S

1998-01-01

95

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

96

kinA mRNA is missing a stop codon in the undomesticated Bacillus subtilis strain ATCC 6051.  

PubMed

Several features distinguish laboratory and undomesticated strains of Bacillus subtilis. For example, unlike the laboratory strain 168, the undomesticated strain ATCC 6051 is deficient in sporulation in a rich sporulation medium, 2x SG. ATCC 6051 cannot induce transcription of the spoIIG operon, suggesting that this strain has a defect in initiation of sporulation. To determine the genetic difference between 168 and ATCC 6051, the DNA region responsible for the Spo(-) phenotype was transferred to strain 168. Genetic mapping and DNA sequencing analysis revealed that a stop codon (TAA) for kinA in 168 is replaced with Lys (TAT) in ATCC 6051, making the kinA open reading frame 201 bp longer in the undomesticated strain ATCC 6051. Introduction of kinA from strain 168 restored sporulation in ATCC 6051, indicating that the difference in kinA is responsible for the Spo(-) phenotype of ATCC 6051. A potential rho-independent terminator is located upstream of a stop codon for the extended kinA open reading frame in ATCC 6051. Northern blot analysis showed that transcription of kinA terminated at this terminator, and kinA mRNA is missing a stop codon in ATCC 6051. Moreover, deletion of tmRNA suppresses the sporulation defect in ATCC 6051. These observations indicate that in ATCC 6051 the absence of a stop codon in kinA mRNA affects sporulation, probably by leading to rapid degradation of KinA via the trans-translation process. In ATCC 6051, the kinA mutation affects sporulation but not other Spo0A-dependent phenomena such as biofilm formation, which can be activated by a low level of Spo0A approximately P. This is due to the fact that KinA activity is kept low during the exponential phase via transcriptional and post-translational regulation. Thus, the stop-codon-less kinA probably affects only sporulation. DNA sequencing of 30 B. subtilis strains revealed that another strain also produces stop-codon-less kinA mRNA. This observation suggests that the lack of a stop codon for kinA mRNA may give rise to a selective advantage under certain conditions. PMID:18174125

Kobayashi, Kazuo; Kuwana, Ritsuko; Takamatsu, Hiromu

2008-01-01

97

Slow fitness recovery in a codon-modified viral genome.  

PubMed

Extensive synonymous codon modification of viral genomes appears to be an effective way of attenuating strains for use as live vaccines. An assumption of this method is that codon changes have individually small effects, such that codon-attenuated viruses will be slow to evolve back to high fitness (and thus to high virulence). The major capsid gene of the bacterial virus T7 was modified to have varying levels of suboptimal synonymous codons in different constructs, and fitnesses declined linearly with the number of changes. Adaptation of the most extreme design, with 182 codon changes, resulted in a slow fitness recovery by standards of previous experimental evolution with this virus, although fitness effects of substitutions were higher than expected from the average effect of an engineered codon modification. Molecular evolution during recovery was modest, and changes evolved both within the modified gene and outside it. Some changes within the modified gene evolved in parallel across replicates, but with no obvious explanation. Overall, the study supports the premise that codon-modified viruses recover fitness slowly, although the evolution is substantially more rapid than expected from the design principle. PMID:22532576

Bull, J J; Molineux, I J; Wilke, C O

2012-04-24

98

Synonymous codon usage in chloroplast genome of Coffea arabica  

PubMed Central

Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A3, T3, G3, C3, GC3) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC3 plot grouped majority of the analyzed genes on or just below the left side of the expected GC3 curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica.

Nair, Rahul R; Nandhini, Manivasagam B; Monalisha, Elango; Murugan, Kavitha; Sethuraman, Thilaga; Nagarajan, Sangeetha; Rao, Nayani Surya Prakash; Ganesh, Doss

2012-01-01

99

Synonymous codon usage in chloroplast genome of Coffea arabica.  

PubMed

Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz., leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A(3), T(3), G(3), C(3), GC(3)) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast genome. ENC Vs GC(3) plot grouped majority of the analyzed genes on or just below the left side of the expected GC(3) curve indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents. Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica. PMID:23251044

Nair, Rahul R; Nandhini, Manivasagam B; Monalisha, Elango; Murugan, Kavitha; Sethuraman, Thilaga; Nagarajan, Sangeetha; Rao, Nayani Surya Prakash; Ganesh, Doss

2012-11-13

100

Trends in the codon usage patterns of Chromohalobacter salexigens genes  

PubMed Central

Chromohalobacter salexigens, a Gammaproteobacterium belonging to the family Halomonadaceae, shows a broad salinity range for growth. In order to reveal the factors influencing architecture of protein coding genes in C. salexigens, pattern of synonymous codon usage bias has been investigated. Overall codon usage analysis of the microorganism revealed that C and G ending codons are predominantly used in all the genes which are indicative of mutational bias. Multivariate statistical analysis showed that the genes are separated along the first major explanatory axis according to their expression levels and their genomic GC content at the synonymous third positions of the codons. Both NC plot and correspondence analysis on Relative Synonymous Codon Usage (RSCU) indicates that the variation in codon usage among the genes may be due to mutational bias at the DNA level and natural selection acting at the level of mRNA translation. Gene length and the hydrophobicity of the encoded protein also influence the codon usage variation of genes to some extent. A comparison of the relative synonymous codon usage between 10% each of highly and lowly expressed genes determines 23 optimal codons, which are statistically over represented in the former group of genes and may provide useful information for salt-stressed gene prediction and gene-transformation. Furthermore, genes for regulatory functions; mobile and extrachromosomal element functions; and cell envelope are observed to be highly expressed. The study could provide insight into the gene expression response of halophilic bacteria and facilitate establishment of effective strategies to develop salt-tolerant crops of agronomic value.

Sanjukta, Rajkumari; Farooqi, Mohammad Samir; Sharma, Naveen; Rai, Anil; Mishra, Dwijesh Chandra; Singh, Dhananjaya P

2012-01-01

101

Saccharomyces cerevisiae PHO5 promoter region: location and function of the upstream activation site.  

PubMed Central

Saccharomyces cerevisiae repressible acid phosphatase (PHO5) is induced when inorganic phosphate in the culture medium is depleted. To study the mechanism of this regulation, we constructed various deletions in the 5'-flanking region of the PHO5 gene. Two elements were revealed by this analysis: an upstream activation site (UAS) and a downstream element, both playing parts in the expression of this gene. The UAS is located between -384 and -292 upstream of the initiation codon and activates expression of the gene when inorganic phosphate is depleted. It consists of two homologous regions (UAS I and UAS II) that contain CTGCACAAATG and an adenine-plus-thymine-rich sequence, either one of which suffices for the effect. The downstream element includes a putative TATA box at -100 from the ATG codon and is necessary for efficient transcription and expression of the normal-sized PHO5 transcript. The distance between the UAS and the downstream element can be altered without causing loss of expression efficiency, and the action of the UAS is not affected by its orientation. These results are consistent with a model wherein UAS acts as a site of activation for transcription by interaction with a protein factor(s) that becomes active when inorganic phosphate is depleted from the culture medium. Images

Nakao, J; Miyanohara, A; Toh-e, A; Matsubara, K

1986-01-01

102

A novel mutation in the upstream open reading frame of the CDKN1B gene causes a MEN4 phenotype.  

PubMed

The CDKN1B gene encodes the cyclin-dependent kinase inhibitor p27(KIP1), an atypical tumor suppressor playing a key role in cell cycle regulation, cell proliferation, and differentiation. Impaired p27(KIP1) expression and/or localization are often observed in tumor cells, further confirming its central role in regulating the cell cycle. Recently, germline mutations in CDKN1B have been associated with the inherited multiple endocrine neoplasia syndrome type 4, an autosomal dominant syndrome characterized by varying combinations of tumors affecting at least two endocrine organs. In this study we identified a 4-bp deletion in a highly conserved regulatory upstream ORF (uORF) in the 5'UTR of the CDKN1B gene in a patient with a pituitary adenoma and a well-differentiated pancreatic neoplasm. This deletion causes the shift of the uORF termination codon with the consequent lengthening of the uORF-encoded peptide and the drastic shortening of the intercistronic space. Our data on the immunohistochemical analysis of the patient's pancreatic lesion, functional studies based on dual-luciferase assays, site-directed mutagenesis, and on polysome profiling show a negative influence of this deletion on the translation reinitiation at the CDKN1B starting site, with a consequent reduction in p27(KIP1) expression. Our findings demonstrate that, in addition to the previously described mechanisms leading to reduced p27(KIP1) activity, such as degradation via the ubiquitin/proteasome pathway or non-covalent sequestration, p27(KIP1) activity can also be modulated by an uORF and mutations affecting uORF could change p27(KIP1) expression. This study adds the CDKN1B gene to the short list of genes for which mutations that either create, delete, or severely modify their regulatory uORFs have been associated with human diseases. PMID:23555276

Occhi, Gianluca; Regazzo, Daniela; Trivellin, Giampaolo; Boaretto, Francesca; Ciato, Denis; Bobisse, Sara; Ferasin, Sergio; Cetani, Filomena; Pardi, Elena; Korbonits, Márta; Pellegata, Natalia S; Sidarovich, Viktoryia; Quattrone, Alessandro; Opocher, Giuseppe; Mantero, Franco; Scaroni, Carla

2013-03-21

103

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

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

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

104

Selective constraint on the upstream open reading frames that overlap with coding sequences in animals.  

PubMed

Upstream open reading frames (uORFs) are translational regulatory elements located in 5' untranslated regions. They can significantly repress the translation of the downstream coding sequences (CDS), and participate in the spatio-temporal regulations of protein translation. Notwithstanding this biological significance, the selective constraint on uORFs remains underexplored. Particularly, the uORFs that partially overlap with CDS with a different reading frame (overlapping uORFs, or "VuORFs") may lead to strong translational inhibition or N-terminal truncation of the peptides encoded by the affected CDS. By analyzing VuORF-containing transcripts (designated as "VuORF transcripts") in human, mouse, and fruit fly, we demonstrate that VuORFs are in general slightly deleterious--the proportion of genes that encode at least one VuORF transcript is significantly smaller than expected in all of the three examined species. In addition, this proportion is significantly smaller in fruit fly than in mammals, indicating a higher efficiency of removing VuORFs in the former species because of its larger effective population size. Furthermore, the deleterious effect of a VuORF depends on the sequence context of its start codon (VuAUG). VuORFs with an optimal VuAUG context are more strongly disfavored than those with a suboptimal context in all of the three examined species. And the propensity to remove optimal-context VuAUGs is stronger in fruit fly than in mammals. Intriguingly, however, the currently observable optimal-context VuAUGs (but not suboptimal-context VuAUGs) are more conserved than expected. These observations suggest that the regulatory functions of VuORFs may have been gained fortuitously in organisms with a small effective population size because the slightly deleterious effect of these elements can be better tolerated in these organisms, thus allowing opportunities for the development of novel biological functions. Nevertheless, once the functions of VuORFs were established, they became subject to negative selection. PMID:23133632

Hsu, Ming-Kung; Chen, Feng-Chi

2012-11-01

105

Trends in Codon and Amino Acid Usage in Thermotoga maritima  

Microsoft Academic Search

.   The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium\\u000a Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon\\u000a usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino

Alejandro Zavala; Hugo Naya; Héctor Romero; Héctor Musto

2002-01-01

106

Tracing Specific Synonymous Codon–Secondary Structure Correlations Through Evolution  

Microsoft Academic Search

  Abstract\\u000a \\u000a We previously showed that GAU codons are preferred (relative to synonymous GAC codons) for encoding aspartates specifically\\u000a at the N-termini of ?-helices in human, but not in E. coli, proteins. To test if this difference reflected a general difference between eucaryotes and procaryotes, we now extended\\u000a the analysis to include the proteins and coding sequences of mammals, vertebrates, S.

Matej Oreši?; Michael H. H. Dehn; Daniel H. H. Korenblum; David H. H. Shalloway

2003-01-01

107

Evolutionary Lability of Context-Dependent Codon Bias in Bacteria  

Microsoft Academic Search

.   In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent\\u000a biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we\\u000a consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In\\u000a particular, we focus on two contextual biases previously identified in

Gilean A. T. McVean; Gregory D. D. Hurst

2000-01-01

108

Direct upstream motility in Escherichia coli.  

PubMed

We provide an experimental demonstration of positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface. This hydrodynamic phenomenon is dominant below a critical shear rate and robust against Brownian motion and cell tumbling. We deduce that individual bacteria entering a flow system can rapidly migrate upstream (>20 ?m/s) much faster than a gradually advancing biofilm. Given a bacterial population with a distribution of sizes and swim speeds, local shear rate near the surface determines the dominant hydrodynamic mode for motility, i.e., circular or random trajectories for low shear rates, positive rheotaxis for moderate flow, and sideways swimming at higher shear rates. Faster swimmers can move upstream more rapidly and at higher shear rates, as expected. Interestingly, we also find on average that both swim speed and upstream motility are independent of cell aspect ratio. PMID:22500751

Kaya, Tolga; Koser, Hur

2012-04-03

109

Direct Upstream Motility in Escherichia coli  

PubMed Central

We provide an experimental demonstration of positive rheotaxis (rapid and continuous upstream motility) in wild-type Escherichia coli freely swimming over a surface. This hydrodynamic phenomenon is dominant below a critical shear rate and robust against Brownian motion and cell tumbling. We deduce that individual bacteria entering a flow system can rapidly migrate upstream (>20 ?m/s) much faster than a gradually advancing biofilm. Given a bacterial population with a distribution of sizes and swim speeds, local shear rate near the surface determines the dominant hydrodynamic mode for motility, i.e., circular or random trajectories for low shear rates, positive rheotaxis for moderate flow, and sideways swimming at higher shear rates. Faster swimmers can move upstream more rapidly and at higher shear rates, as expected. Interestingly, we also find on average that both swim speed and upstream motility are independent of cell aspect ratio.

Kaya, Tolga; Koser, Hur

2012-01-01

110

UPSTREAM MOTIONS IN STRATIFIED FLOW (JOURNAL VERSION)  

EPA Science Inventory

In the paper experimental measurements of the time-dependent velocity and density perturbations upstream of obstacles in linearly stratified flow are presented. Attention is concentrated on obstacles which generate turbulent separated wakes at Froude numbers, based on velocity an...

111

Suprathermal ions upstream from interplanetary shocks  

Microsoft Academic Search

Suprathermal ions with energies between solar wind thermal energies and approx.29 keV are occasionally observed ahead of outward propagating interplanetary shocks with the Los Alamos\\/Garching fast plasma experiment on ISEE 1 and 2. Compared with suprathermal ion velocity distributions observed upstream from the earth's bow shock, the upstream interplanetary shock ion velocity distributions are relatively structureless, and the particle fluxes

J. T. Gosling; S. J. Bame; W. C. Feldman; G. Paschmann; N. Sckopke; C.T. Russell

1984-01-01

112

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

113

INCA: synonymous codon usage analysis and clustering by means of self-organizing map  

Microsoft Academic Search

Summary: INteractive Codon usage Analysis (INCA) provides an array of features useful in analysis of synonymous codon usage in whole genomes. In addition to computing codon fre- quencies and several usage indices, such as 'codon bias', effective Nc and CAI, the primary strength of INCA has numer- ous options for the interactive graphical display of calculated values, thus allowing visual

Fran Supek; Kristian Vlahovicek

2004-01-01

114

Relationships Among Stop Codon Usage Bias, Its Context, Isochores, and Gene Expression Level in Various Eukaryotes  

Microsoft Academic Search

It is well known that stop codons play a critical role in the process of protein synthesis. However, little effort has been made to investigate whether stop codon usage exhibits biases, such as widely seen for synonymous codon usage. Here we systematically investigate stop codon usage bias in various eukaryotes as well as its relationships with its context, GC3 content,

Jingchun Sun; Ming Chen; Jinlin Xu; Jianhua Luo

2005-01-01

115

Role for gene sequence, codon bias and mRNA folding energy in modulating structural symmetry of proteins.  

PubMed

Structural symmetry in proteins is commonly observed in the majority of fundamental protein folds. Meanwhile, nascent polypeptide chains of proteins have the potential to start the co-translational folding process and this process can have drastic effects on protein structure. Thus we are interested in understanding mechanisms that gene adopts in specifying structural symmetry in proteins. In the present paper, we reveal that for two representative symmetric proteins from (a?)8-barrel fold and beta-trefoil fold, intragenic symmetry is detected in the corresponding gene sequences. Codon bias and mRNA folding energy might be involved in mediating translation speed for the formation of structural symmetry: at least one major decrease in both codon bias and mRNA folding energy can be observed in the connecting region of the symmetric substructures along the codon sequence. Results suggest that gene duplication and fusion is responsible for structural symmetry in these proteins, and the usage of rare codons or higher order of secondary structure near the boundaries of symmetric substructures might be selected in order to slow down translation speed for effectively co-translational folding process of symmetric proteins. PMID:24109757

Shen, Xiaojuan; Chen, Shixiong; Li, Guanglin

2013-07-01

116

The Head Start Debates  

ERIC Educational Resources Information Center

The future of Head Start depends on how well people learn from and apply the lessons from its past. That's why everyone involved in early education needs this timely, forward-thinking book from the leader of Head Start. The first book to capture the Head Start debates in all their complexity and diversity, this landmark volume brings together the…

Zigler, Edward, Ed.; Styfco, Sally J., Ed.

2004-01-01

117

Head Start Facilities Manual.  

ERIC Educational Resources Information Center

|A quality Head Start facility should provide a physical environment responsive both to the needs of the children and families served and to the needs of staff, volunteers, and community agencies that share space with Head Start. This manual is a tool for Head Start grantees and delegate agencies for assessing existing facilities, making…

Research Assessment Management, Inc., Silver Spring, MD.

118

Sprint start instrumentation  

Microsoft Academic Search

A prototype instrument has been developed to measure the forces generated on the starting blocks and the speed of a sprinter at the start of a sprint event. The starting block forces can be resolved into horizontal and vertical components for each foot, or the various combinations of these four forces can be calculated and displayed along with the resultant

R. E. Gander; J. D. McClements; L. K. Sanderson; B. A. Rostad; K. E. Josephson; A. J. Pratt

1994-01-01

119

The Head Start Debates  

ERIC Educational Resources Information Center

|The future of Head Start depends on how well people learn from and apply the lessons from its past. That's why everyone involved in early education needs this timely, forward-thinking book from the leader of Head Start. The first book to capture the Head Start debates in all their complexity and diversity, this landmark volume brings together the…

Zigler, Edward, Ed.; Styfco, Sally J., Ed.

2004-01-01

120

Nevada Head Start, 2002.  

ERIC Educational Resources Information Center

This pamphlet describes the current services of the Nevada Head Start program. Information is provided on program eligibility requirements, the number of children and families served during the 2001-2002 program year, the counties served by Head Start programs, health services provided, demographic characteristics of families served by Head Start,…

Biagi, Kathy

121

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

122

Identification of stop codon readthrough genes in Saccharomyces cerevisiae  

PubMed Central

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.

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

2003-01-01

123

Dual functions of codons in the genetic code  

PubMed Central

The discovery of the genetic code provided one of the basic foundations of modern molecular biology. Most organisms use the same genetic language, but there are also well-documented variations representing codon reassignments within specific groups of organisms (such as ciliates and yeast) or organelles (such as plastids and mitochondria). In addition, duality in codon function is known in the use of AUG in translation initiation and methionine insertion into internal protein positions as well as in the case of selenocysteine and pyrrolysine insertion (encoded by UGA and UAG, respectively) in competition with translation termination. Ambiguous meaning of CUG in coding for serine and leucine is also known. However, a recent study revealed that codons in any position within the open reading frame can serve a dual function and that a change in codon meaning can be achieved by availability of a specific type of RNA stem-loop structure in the 3’-untranslated region. Thus, duality of codon function is a more widely used feature of the genetic code than previously known, and this observation raises the possibility that additional recoding events and additional novel features have evolved in the genetic code.

Lobanov, Alexey V.; Turanov, Anton A.; Hatfield, Dolph L.; Gladyshev, Vadim N.

2011-01-01

124

An expanded genetic code with a functional quadruplet codon  

PubMed Central

With few exceptions the genetic codes of all known organisms encode the same 20 amino acids, yet all that is required to add a new building block are a unique tRNA/aminoacyl-tRNA synthetase pair, a source of the amino acid, and a unique codon that specifies the amino acid. For example, the amber nonsense codon, TAG, together with orthogonal Methanococcus jannaschii or Escherichia coli tRNA/synthetase pairs have been used to genetically encode a variety of unnatural amino acids in E. coli and yeast, respectively. However, the availability of noncoding triplet codons ultimately limits the number of amino acids encoded by any organism. Here, we report the design and generation of an orthogonal synthetase/tRNA pair derived from archaeal tRNALys sequences that efficiently and selectively incorporates an unnatural amino acid into proteins in response to the quadruplet codon, AGGA. Frameshift suppression with l-homoglutamine (hGln) does not significantly affect protein yields or cell growth rates and is mutually orthogonal with amber suppression, permitting the simultaneous incorporation of two unnatural amino acids, hGln and O-methyl-l-tyrosine, at distinct positions within myoglobin. This work suggests that neither the number of available triplet codons nor the translational machinery itself represents a significant barrier to further expansion of the genetic code.

Anderson, J. Christopher; Wu, Ning; Santoro, Stephen W.; Lakshman, Vishva; King, David S.; Schultz, Peter G.

2004-01-01

125

The association of p53 mutations and p53 codon 72, Her 2 codon 655 and MTHFR C677T polymorphisms with breast cancer in Northern Greece  

Microsoft Academic Search

The aim of this study was to explore a possible association between p53 codon 72, Her 2 codon 655 and MTHFR C677T polymorphisms and breast cancer in Northern Greece. We examined 42 women with breast cancer and 51 controls. A total of 42 women with breast cancer as well as healthy controls were investigated and results showed that p53 codon

Theodora G. Kalemi; Alexandros F. Lambropoulos; Maria Gueorguiev; Sofia Chrisafi; Konstantinos T. Papazisis; Alexandros Kotsis

2005-01-01

126

STARTING EXCAVATION PIER 2. This view is roughly northeast, with ...  

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

STARTING EXCAVATION PIER 2. This view is roughly northeast, with Pier 2 on the Trinity County end of the bridge. The old suspension bridge, at upper right, was upstream of new bridge - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

127

Model for Codon Position Bias in RNA Editing  

NASA Astrophysics Data System (ADS)

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

Liu, Tsunglin; Bundschuh, Ralf

2005-08-01

128

A model for codon position bias in RNA editing  

NASA Astrophysics Data System (ADS)

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

Bundschuh, Ralf; Liu, Tsunglin

2006-03-01

129

Codon reassignment in the Escherichia coli genetic code  

PubMed Central

Most organisms, from Escherichia coli to humans, use the ‘universal’ genetic code, which have been unchanged or ‘frozen’ for billions of years. It has been argued that codon reassignment causes mistranslation of genetic information, and must be lethal. In this study, we successfully reassigned the UAG triplet from a stop to a sense codon in the E. coli genome, by eliminating the UAG-recognizing release factor, an essential cellular component, from the bacterium. Only a few genetic modifications of E. coli were needed to circumvent the lethality of codon reassignment; erasing all UAG triplets from the genome was unnecessary. Thus, UAG was assigned unambiguously to a natural or non-natural amino acid, according to the specificity of the UAG-decoding tRNA. The result reveals the unexpected flexibility of the genetic code.

Mukai, Takahito; Hayashi, Akiko; Iraha, Fumie; Sato, Aya; Ohtake, Kazumasa; Yokoyama, Shigeyuki; Sakamoto, Kensaku

2010-01-01

130

Estimating selection on synonymous codon usage from noisy experimental data.  

PubMed

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. PMID:23493257

Wallace, Edward W J; Airoldi, Edoardo M; Drummond, D Allan

2013-03-14

131

Modular innovations in upstream fish passage  

SciTech Connect

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 feasibility and economic viability with the object of providing alternative means of meeting the biological requirements of an upstream fish passage in a more cost-effective manner than strictly traditional methods. An overview is presented of the fish passage design process in a project formation flowchart and design data checklist. The design features, materials and equipment specifically considered in this study are described with information on the characteristics, advantages, and applicability of each item.

Truebe, J.; Drooker, M.

1980-01-01

132

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

133

Starting School in August  

ERIC Educational Resources Information Center

|In this article, the author discusses the controversial decision of the school board from the Broward County, Florida to start the school year on August 9. School boards across the country that are grappling with the idea of starting school earlier in the year are increasingly running up against strong opposition from parents. In many districts,…

Chmelynski, Carol

2006-01-01

134

Head Start. Fact Sheet.  

ERIC Educational Resources Information Center

Head Start is a national program that provides comprehensive developmental services for preschool children (ages 3 to 5) from low-income families and social services for their families. Approximately 1,400 community-based nonprofit organizations and school systems develop programs to meet specific needs. Head Start began in 1965 in the Office of…

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

135

Smart Start News, 1999.  

ERIC Educational Resources Information Center

|Smart Start is a comprehensive public-private initiative to help all North Carolina children enter school healthy and ready to succeed, and provides children from birth to age five access to high-quality and affordable child care, health care, and other critical services. This document comprises the first two issues of "Smart Start News," a…

Harris, Monica, Ed.

1999-01-01

136

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

137

Starting School in August  

ERIC Educational Resources Information Center

In this article, the author discusses the controversial decision of the school board from the Broward County, Florida to start the school year on August 9. School boards across the country that are grappling with the idea of starting school earlier in the year are increasingly running up against strong opposition from parents. In many districts,…

Chmelynski, Carol

2006-01-01

138

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

139

An upstream alternative to personal carbon trading  

Microsoft Academic Search

An upstream trading scheme is described that could operate alongside the EU Emissions Trading Scheme (EU ETS). In this proposed scheme, fossil fuel producers (or suppliers) surrender allowances for the carbon contained in their fuel sales. Since the administrative costs are relatively low, such a scheme could provide a simpler, cheaper and more practical alternative to personal carbon trading, while

STEVE SORRELL

2010-01-01

140

BUTANOL FERMENTATION RESEARCH: UPSTREAM AND DOWNSTREAM MANIPULATIONS  

Technology Transfer Automated Retrieval System (TEKTRAN)

An overview of advances in acetone-butanol fermentation research is presented with specific reference to the history of acetone-butanol fermentation, genetic manipulation of the butanol-producing Clostridium beijerinckii NCIMB 8052, as well as upstream and downstream processing. Butanol is a superi...

141

Effect of upstream ponds on stream temperature  

Microsoft Academic Search

Many tributaries feeding streams are connected to ponds that heat up during summer months; however, the influence of these ponds on receiving stream temperature was not known. Stream temperature affects microfauna and fish habitats in aquatic ecosystems. Three tributaries with headwater ponds exposed to sunlight and one tributary unassociated with a large, upstream pond were selected for study within the

J. Ham; L. Toran; J. Cruz

2006-01-01

142

Russian upstream joint ventures logging progress  

SciTech Connect

This paper reports that Occidental Petroleum Corp. has begun exporting oil from Russia as part of an enhanced recovery joint venture in western Siberia. Oxy holds a 50% interest in the joint venture company, Vanyoganneft, and will market the oil. In other activity, two Canadian companies are marking progress with Russian upstream joint ventures.

Not Available

1992-11-02

143

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

PubMed Central

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

2010-01-01

144

Can simple codon pair usage predict protein-protein interaction?  

PubMed

Deciphering functional interactions between proteins is one of the great challenges in biology. Sequence-based homology-free encoding schemes have been increasingly applied to develop promising protein-protein interaction (PPI) predictors by means of statistical or machine learning methods. Here we analyze the relationship between codon pair usage and PPIs in yeast. We show that codon pair usage of interacting protein pairs differs significantly from randomly expected. This motivates the development of a novel approach for predicting PPIs, with codon pair frequency difference as input to a Support Vector Machine predictor, termed as CCPPI. 10-fold cross-validation tests based on yeast PPI datasets with balanced positive-to-negative ratios indicate that CCPPI performs better than other sequence-based encoding schemes. Moreover, it ranks the best when tested on an unbalanced large-scale dataset. Although CCPPI is subjected to high false positive rates like many PPI predictors, statistical analyses of the predicted true positives confirm that the success of CCPPI is partly ascribed to its capability to capture proteomic co-expression and functional similarities between interacting protein pairs. Our findings suggest that codon pairs of interacting protein pairs evolve in a coordinated manner and consequently they provide additional information beyond amino acids-based encoding schemes. CCPPI has been made freely available at: http://protein.cau.edu.cn/ccppi. PMID:22392100

Zhou, Yuan; Zhou, Ying-Si; He, Fei; Song, Jiangning; Zhang, Ziding

2012-03-05

145

Translational selection on codon usage in the genus Aspergillus.  

PubMed

Aspergillus is a genus of mold fungi that includes more than 200 described species. Many members of the group are relevant pathogens and other species are economically important. Only one species has been analyzed for codon usage, and this was performed with a small number of genes. In this paper, we report the codon usage patterns of eight completely sequenced genomes which belong to this genus. The results suggest that selection for translational efficiency and accuracy are the major factors shaping codon usage in all of the species studied so far, and therefore they were active in the last common ancestor of the group. Composition and molecular distances analyses show that highly expressed genes evolve slower at synonymous sites. We identified a conserved core of translationally optimal codons and study the tRNA gene pool in each genome. We found that the great majority of preferred triplets match the respective cognate tRNA with more copies in the respective genome. We discuss the possible scenarios that can explain the observed differences among the species analyzed. Finally we highlight the biotechnological application of this research regarding heterologous protein expression. PMID:22742978

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

2012-06-26

146

Evolution of optimal codon choices in the family Enterobacteriaceae.  

PubMed

The Enterobacteriaceae are a large family of Proteobacteria that include many well-known prokaryotic genera, such as Escherichia, Yersinia and Salmonella. The main ideas of synonymous codon usage (CU) evolution and translational selection have been deeply influenced by studies with these bacterial groups. In this work we report the analysis of the CU pattern of completely sequenced bacterial genomes that belong to the Enterobacteriaceae. The effect of selection in translation acting at the levels of speed and accuracy, and phylogenetic trends within this group are described. Preferred (optimal) codons were identified. The evolutionary dynamics of these codons were studied and following a Bayesian approach these preferences were traced back to the common ancestor of the family. We found that there is some level of variation in selection among the analysed micro-organisms that is probably associated with lineage-specific trends. The codon bias was largely conserved across the evolutionary time of the family in highly expressed genes and protein conserved regions, suggesting a major role of negative selection. In this sense, the results support the idea that the extant CU bias is finely tuned over the ancestral well-conserved pool of tRNAs. PMID:23288542

Iriarte, Andrés; Baraibar, Juan Diego; Romero, Héctor; Castro-Sowinski, Susana; Musto, Héctor

2013-01-03

147

Electric starting apparatus  

SciTech Connect

An electric starting system is described for cranking an engine comprising, a source of voltage, an electric starter comprising an electric cranking motor and a solenoid having pull-in and hold-in coils and a shiftable plunger, a pinion that is shifted by movement of the plunger that is adapted to mesh with the ring gear of the engine, switch means having first and second contacts that are at times electrically connected by a contactor shiftable by movement of the plunger, a manually operable start switch, means connecting the start switch and the hold-in coil in series and across the voltage source whereby the hold-in coil is energized when the start switch is closed and is deenergized when the start switch is opened, means connecting one side of the voltage source to the first contact, means connecting an opposite side of the voltage source to one side of the cranking motor, a circuit connecting the first contact to an opposite side of the cranking motor comprising in a series connection the pull-in coil and the current carrying electrodes of a semiconductor switch, a circuit connecting the second contact to the opposite side of the cranking motor, and means connecting a control electrode of the semiconductor switch to the start switch such that the semiconductor switch is biased conductive between its current carrying electrodes to energize the pull-in coil when the start switch is closed.

Raver, L.J.

1986-05-06

148

An AP2-type transcription factor, WRINKLED1, of Arabidopsis thaliana binds to the AW-box sequence conserved among proximal upstream regions of genes involved in fatty acid synthesis.  

PubMed

Although an APETALA2 (AP2)-type transcription factor, WRINKLED1 (WRI1), has been shown to be required for accumulation of triacylglycerols (TAGs) in Arabidopsis seeds, its direct target genes have not been established. Overexpression of WRI1 up-regulated a set of genes involved in fatty acid (FA) synthesis in plastids, including genes for a subunit of pyruvate kinase (Pl-PKbeta1), acetyl-CoA carboxylase (BCCP2), acyl carrier protein (ACP1), and ketoacyl-acyl carrier protein synthase (KAS1), while expression of these genes is reduced in mutants with reduced WRI1 expression. Transient expression of LUC reporter genes with the proximal sequences upstream from the ATG codon of Pl-PKbeta1, BCCP2, and KAS1 in protoplasts was activated by co-expression of WRI1, and recombinant WRI1 bound to these upstream sequences in vitro. The seven WRI1 binding sites shared a sequence [CnTnG](n)(7)[CG], where n is any nucleotide designated as the AW-box, and mutations in AW-boxes near the transcription start site and in the 5'-untranslated region of Pl-PKbeta1 abolished activation by WRI1 in protoplasts and expression during seed maturation. Although expression of genes for the synthesis of TAGs and packaging into oil bodies in the endoplasmic reticulum in developing seeds required WRI1, their expression was not up-regulated by WRI1 overexpression. Thus, WRI1 promotes the flow of carbon to oil during seed maturation by directly activating genes involved in FA synthesis and controlling genes for assembly and storage of TAG. PMID:19594710

Maeo, Kenichiro; Tokuda, Tsuyoshi; Ayame, Atsuko; Mitsui, Naoko; Kawai, Tsutae; Tsukagoshi, Hironaka; Ishiguro, Sumie; Nakamura, Kenzo

2009-07-06

149

The CLAS Start Counter  

SciTech Connect

The design, construction, and performance of a hexagonal-nose-cone shaped plastic scintillation counter system is described. This ''Start Counter'' is used as part of the trigger and to measure event start times for photon beam running with CLAS in Hall B at the Thomas Jefferson National Accelerator Facility. The Start Counter is constructed of three 3-mm thick coupled paddle scintillators and achieves a software-corrected time resolution of 260 ps. Each coupled-paddle scintillator operated without appreciable sagging up to {approx}1.2 MHz rate.

S. Taylor; S. Ahmad; J. Distelbrink; G. S. Mutchler; E. Smith; T. Smith

2001-08-01

150

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

151

Bow Shock and Upstream Phenomena at Mars  

NASA Astrophysics Data System (ADS)

Mars Global Surveyor is the sixth spacecraft to return measurements of the Martian bow shock. The earlier missions were Mariner 4 (1964), Mars 2 and 3 (1972), Mars 5 (1975) and Phobos 2 (1989) (see reviews by Gringauz, 1981; Slavin and Holzer, 1982; Russell, 1985; Vaisberg, 1992a,b; Zakharov, 1992). Previous investigations of planetary bow shocks have established that their position, shape and jump conditions are functions of the upstream flow parameters and the nature of the solar wind — planet interaction (Spreiter and Stahara, 1980; Slavin et al., 1983; Russell, 1985). At Mars, however, the exact nature of the solar wind interaction was elusive due to the lack of low altitude plasma and magnetic field measurements (e.g., Axford, 1991). In fact our knowledge of the nature of the interaction of Mars with the solar wind was incomplete until the arrival of MGS and the acquisition of close-in magnetic field data (Acuña et al., 1998). As detailed by a series of review papers in this monograph, the Mars Global Surveyor (MGS) mission has now shown that the Mars environment is very complex with strong, highly structured crustal magnetic remnants in the southern hemisphere, while the northern hemisphere experiences the direct impingement of solar wind plasma. This review paper first presents a survey of the observations on the Martian bow shock and the upstream phenomena in the light of results from all the missions to date. It also discusses the kinetic properties of the Martian bow shock compared to the predictions of simulations studies. Then it examines the current status of understanding of these phenomena, including the possible sources of upstream low-frequency waves and the interpretations of localized disturbances in the upstream solar wind around Mars. Finally, it briefly discusses the open issues and questions that require further study.

Mazelle, C.; Winterhalter, D.; Sauer, K.; Trotignon, J. G.; Acuña, M. H.; Baumgärtel, K.; Bertucci, C.; Brain, D. A.; Brecht, S. H.; Delva, M.; Dubinin, E.; Øieroset, M.; Slavin, J.

2004-03-01

152

A new ?-thalassemia deletion mutation [codon 36 (-C)] observed in a Chinese woman.  

PubMed

In this study we present the first report of the detection of a new ?-thalassemia (?-thal) mutation at codon 36 (-C) in the Chinese population. This frameshift mutation generates a TGA stop codon at position 60, resulting in a thalassemia phenotype. This is the first example of a premature stop codon at position 60 because of codon 36. The characterization of uncommon mutations is useful for the screening of ?-thal carriers, genetic counseling and prenatal diagnosis. PMID:21077770

Huang, Hailong; Xu, Liangpu; Lin, Na; Xu, Jinbang; He, Deqin; Li, Ying; Zheng, Lin; Liu, Hekun; Lin, Yuan

2010-01-01

153

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

Microsoft Academic Search

All living organisms encode the 20 natural amino acid units of polypeptides using a universal scheme of triplet nucleotide\\u000a “codons”. Disparate features of this codon scheme are potentially informative of early molecular evolution: (i) the absence\\u000a of any codons for d-amino acids; (ii) the odd combination of alternate codon patterns for some amino acids; (iii) the confinement of synonymous\\u000a positions

Albert Erives

154

Waves which travel upstream in boundary layers  

NASA Astrophysics Data System (ADS)

Upstream propagation and diffusion of vorticity in a boundary layer is described by a numerical solution of the Orr-Sommerfeld equation. This traveling wave grows very rapidly in the downstream direction. The growth rate is approximately exp(+ R (sub delta)x) where R sub delta is the Reynolds number based on the characteristic boundary layer thickness, and x is the streamwise coordinate nondimensionalized against delta. Far from the boundary layer, the solution oscillates neutrally in the Y-direction. Analyses reveal high frequency wave which oscillates and decays in the y-direction approximately as exp(-i R(sub delta) y - omega Y) where omega is the frequency. This high frequency wave can survive into the freestream. Numerical solutions of the Orr-Sommerfeld equation with a Blasius layer are obtained by a series expansion of Chebyshev polynomials. Since the y-wavenumber of the oscillations increases with increasing Reynolds number, the calculations have been restricted to low Reynolds numbers. In the boundary-value problem, this solution appears as a branch line in Laplace space. It is one of the possible solutions in a mathematically complete description of the spatial evolution of fluctuations. This traveling wave represents one of the upstream influences of a boundary in a calculational domain. Another mechanism of upstream influence is the growing standing wave.

Rogler, H. L.

1985-07-01

155

Investigating protein-coding sequence evolution with probabilistic codon substitution models  

Microsoft Academic Search

Abstract 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

Maria Anisimova; Carolin Kosiol

2008-01-01

156

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles  

PubMed Central

Background It is widely acknowledged that synonymous codons are used unevenly among genes in a genome. In organisms under translational selection, genes encoding highly expressed proteins are enriched with specific codons. This phenomenon, termed codon usage bias, is common to many organisms and has been recognized as influencing cellular fitness. This suggests that the global extent of codon usage bias of an organism might be associated with its phenotypic traits. Results To test this hypothesis we used a simple measure for assessing the extent of codon bias of an organism, and applied it to hundreds of sequenced prokaryotes. Our analysis revealed a large variability in this measure: there are organisms showing very high degrees of codon usage bias and organisms exhibiting almost no differential use of synonymous codons among different genes. Remarkably, we found that the extent of codon usage bias corresponds to the lifestyle of the organism. Especially, organisms able to live in a wide range of habitats exhibit high extents of codon usage bias, consistent with their need to adapt efficiently to different environments. Pathogenic prokaryotes also demonstrate higher extents of codon usage bias than non-pathogenic prokaryotes, in accord with the multiple environments that many pathogens occupy. Our results show that the previously observed correlation between growth rate and metabolic variability is attributed to their individual associations with codon usage bias. Conclusions Our results suggest that the extent of codon usage bias of an organism plays a role in the adaptation of prokaryotes to their environments.

2011-01-01

157

The extent of codon usage bias in human RNA viruses and its evolutionary origin  

Microsoft Academic Search

Revealing the determinants of codon usage bias is central to the understanding of factors governing viral evolution. Herein, we report the results of a survey of codon usage bias in a wide range of genetically and ecologically diverse human RNA viruses. This analysis showed that the overall extent of codon usage bias in RNA viruses is low and that there

Gareth M Jenkins; Edward C Holmes

2003-01-01

158

Selection on Codon Usage for Error Minimization at the Protein Level  

Microsoft Academic Search

Given the structure of the genetic code, synonymous codons differ in their capacity to minimize the effects of errors due to mutation or mistranslation. I suggest that this may lead, in protein-coding genes, to a preference for codons that minimize the impact of errors at the protein level. I develop a theoretical measure of error minimization for each codon, based

Marco Archetti

2004-01-01

159

A General Model of Codon Bias Due to GC Mutational Bias  

Microsoft Academic Search

BackgroundIn spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias of a genome or genomic region is highly correlated with GC3, a

Gareth A. Palidwor; Theodore J. Perkins; Xuhua Xia; Dov Joseph Stekel

2010-01-01

160

HER-2 codon 655 polymorphism in cervical carcinogenesis.  

PubMed

HER-2 codon 655 polymorphism together with human papillomavirus (HPV) types were examined in a total of 279 cervical smear samples. Forty-nine patients with high-grade squamous intraepithelial lesion had higher frequency of high-risk HPV than 167 patients with low-grade squamous intraepithelial lesion and 63 controls. There was no statistical difference in the frequencies of HER-2 Ile/Ile, Ile/Val, and Val/Val genotypes between squamous intraepithelial lesions (SILs) and controls. When the Ile/Ile genotype was compared to the Ile/Val + Val/Val genotypes, there was also no statistical difference in the genotype prevalence between SILs and controls either in 91 or 188 patients with or without high-risk HPV, respectively. These results suggest that the HER-2 polymorphism at codon 655 in cervical cell samples is unlikely to be associated with HPV status and the onset of cervical cancer in a Japanese population. PMID:16445653

Ueda, M; Hung, Y-C; Terai, Y; Saito, J; Nunobiki, O; Noda, S; Ueki, M

161

KRAS codon 12 mutations occur very frequently in pancreatic adenocarcinomas  

Microsoft Academic Search

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

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

1988-01-01

162

The influence of codon context on genetic code translation  

Microsoft Academic Search

A class of mutations that increase the efficiency of a suppressor tRNA in translating a particular amber codon has been characterized. The increased efficiency is due to a mutation resulting in a change in the mRNA that affects the nucleotide adjacent to the 3' side of the UAG triplet. Thus the interaction of tRNA with mRNA is influenced by mRNA

Lionello Bossi; John R. Roth

1980-01-01

163

Codon-anticodon interaction and the genetic code evolution.  

PubMed

The evolution of the genetic code, with 20 amino acids encoded from the beginning, is analyzed from the viewpoint of codon-anticodon interaction. Imposing a minimum principle for the interaction, in the framework of the so called crystal basis model of the genetic code, we determine the structure of the anticodons in the ancient, archetypal and early genetic codes, that are all reconciled in a unique frame. Most of our results agree with the generally accepted scheme. PMID:23438637

Sciarrino, A; Sorba, P

2013-02-21

164

Codon usage patterns among genes for lepidopteran hemolymph proteins  

Microsoft Academic Search

Patterns in codon usage were examined for the coding regions of the 23 known lepidopteran hemolymph proteins. Coding triplets\\u000a are GC rich at the third position and a significant linear relationship between GC content of silent and nonsilent (replacement)\\u000a sites was demonstrated. Intron GC content was significantly lower than in coding regions and no relationship between intron\\u000a GC content and

Donald R. Frohlich; Michael A. Wells

1994-01-01

165

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

166

Developmental Stage and Level of Codon Usage Bias in Drosophila  

PubMed Central

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

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

2008-01-01

167

A Synthetic Approach to Stop-Codon Scanning Mutagenesis  

PubMed Central

A general combinatorial mutagenesis strategy using common DMT-protected mononucleotide phosphoramidites and a single orthogonally-protected trinucleotide phosphoramidite (Fmoc-TAG) was developed to scan a gene with the TAG amber stop codon with complete synthetic control. In combination with stop-codon suppressors that insert natural (e.g., alanine) or unnatural (e.g., p-benzoylphenylalanine or Bpa) amino acids, a single DNA library can be used to incorporate different amino acids for diverse purposes. Here, we scanned TAG codons through part of the gene for a model four-helix bundle protein, Rop, which regulates the copy number of ColE1 plasmids. Alanine was incorporated into Rop for mapping its binding site using an in vivo activity screen, and subtle but important differences from in vitro gel-shift studies of Rop function are evident. As a test, Bpa was incorporated using a Phe14 amber mutant isolated from the scanning library. Surprisingly, Phe14Bpa Rop is weakly active, despite the critical role of Phe14 in Rop activity. Bpa is a photoaffinity label unnatural amino acid that can form covalent bonds with adjacent molecules upon UV irradiation. Irradiation of Phe14Bpa-Rop, which is a dimer in solution like wild-type Rop, results in covalent dimers, trimers and tetramers. This suggests that Phe14Bpa Rop weakly associates as a tetramer in solution and highlights the use of Bpa crosslinking as a means of trapping weak and transient interactions.

Nie, Lihua; Lavinder, Jason J.; Sarkar, Mohosin; Stephany, Kimberly; Magliery, Thomas J.

2011-01-01

168

Translational redefinition of UGA codons is regulated by selenium availability.  

PubMed

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. PMID:23696641

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

2013-05-21

169

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

170

Starting Trees from Cuttings.  

ERIC Educational Resources Information Center

|Describes a procedure for starting tree cuttings from woody plants, explaining "lag time," recommending materials, and giving step-by-step instructions for rooting and planting. Points out species which are likely candidates for cuttings and provides tips for teachers for developing a unit. (JM)|

Kramer, David C.

1983-01-01

171

Head Start Curriculum Guide.  

ERIC Educational Resources Information Center

|One of a series of guides for preschool teachers and aides, the book offers a Head Start curriculum guide to help achieve goals regarding social behavior, general attitudes, academic skills, health, and parent development. Information on curriculum is divided into areas of bloc time outline, classroom arrangement, building concepts (such as…

Smith, Clare Coe; And Others

172

Start a Rock Collection  

NSDL National Science Digital Library

Learners follow a three-step process to start their own rock collection. Learners will collect rocks, record information about each rock on a Rock Chart, observe and sort their rocks, and create a rock display. This activity also includes a book list with resources for rock classification.

History, American M.

2012-06-26

173

Electric starting apparatus  

Microsoft Academic Search

An electric starting system is described for cranking an engine comprising, a source of voltage, an electric starter comprising an electric cranking motor and a solenoid having pull-in and hold-in coils and a shiftable plunger, a pinion that is shifted by movement of the plunger that is adapted to mesh with the ring gear of the engine, switch means having

Raver

1986-01-01

174

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

175

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

176

"New Start at 45."  

ERIC Educational Resources Information Center

New Start at 45, operated by Fujitsu Ltd. in Japan, is a management development course for 45-year-old adults in management or supervisory positions. Two components are a 6-week liberal arts curriculum and a 2-week, intensive course in either international management, sales management, or subsidiaries management. Benefits include increased…

Greenstein, Pearl

1989-01-01

177

Project Right Start.  

ERIC Educational Resources Information Center

|The University-Urban Interface Program (UUIP) is a federally-funded project to study an urban university's community relations efforts and innovations, their successes and failures. This is a study of one of the UUIP areas of priority, Project Right Start, a plan for creating a facility for the detection and treatment of psychological problems in…

Jameson, Barbara B.

178

Hydraulic type starting clutch  

Microsoft Academic Search

This patent describes a hydraulic type starting clutch comprising: an input shaft; an input rotating member arranged for rotation in unison with the input shaft; an output shaft; an output rotating member arranged for rotation in unison with the output shaft; friction plates interposed between the input rotating member and the output rotating member for engagement to transmit torque from

K. Ohzono; K. Hayashi; M. Saito; M. Kato; Y. Yoshida

1987-01-01

179

Corporation-induced Diseases, Upstream Epidemiologic Surveillance, and Urban Health  

PubMed Central

Corporation-induced diseases are defined as diseases of consumers, workers, or community residents who have been exposed to disease agents contained in corporate products. To study the epidemiology and to guide expanded surveillance of these diseases, a new analytical framework is proposed. This framework is based on the agent–host–environment model and the upstream multilevel epidemiologic approach and posits an epidemiologic cascade starting with government-sanctioned corporate profit making and ending in a social cost, i.e., harm to population health. Each of the framework’s levels addresses a specific level of analysis, including government, corporations, corporate conduits, the environment of the host, and the host. The explained variable at one level is also the explanatory variable at the next lower level. In this way, a causal chain can be followed along the epidemiologic cascade from the site of societal power down to the host. The framework thus describes the pathways by which corporate decisions filter down to disease production in the host and identifies opportunities for epidemiologic surveillance. Since the environment of city dwellers is strongly shaped by corporations that are far upstream and several levels away, the framework has relevance for the study of urban health. Corporations that influence the health of urban populations include developers and financial corporations that determine growth or decay of urban neighborhoods, as well as companies that use strategies based on neighborhood characteristics to sell products that harm consumer health. Epidemiological inquiry and surveillance are necessary at all levels to provide the knowledge needed for action to protect the health of the population. To achieve optimal inquiry and surveillance at the uppermost levels, epidemiologists will have to work with political scientists and other social scientists and to utilize novel sources of information.

2008-01-01

180

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

Microsoft Academic Search

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

R. Medori; H. J. Tritschler

1993-01-01

181

Manufacturing Technician-Upstream: John Condosta  

NSDL National Science Digital Library

This online video in Windows Media (wmv) format is a brief lecture from a biopharmaceutical manufacturing operator about his job experience. John Condosta was a microbiology major in college and now enjoys working 12-hour days in upstream processing. He gives advice about job searching, resumes, and how to interview before taking questions from the audience. He describes his typical day working with fermentation or purification. Everyday is a new learning experience for him due to new products and new processes. This video would be useful for college or technical students who are interested in hearing a firsthand account of the work-life in the field of biopharmaceutics and bio-manufacturing.

2009-09-24

182

Causes and effects of N-terminal codon bias in bacterial genes.  

PubMed

Most amino acids are encoded by multiple codons, and codon choice has strong effects on protein expression. Rare codons are enriched at the N terminus of genes in most organisms, although the causes and effects of this bias are unclear. Here, we measure expression from >14,000 synthetic reporters in Escherichia coli and show that using N-terminal rare codons instead of common ones increases expression by ~14-fold (median 4-fold). We quantify how individual N-terminal codons affect expression and show that these effects shape the sequence of natural genes. Finally, we demonstrate that reduced RNA structure and not codon rarity itself is responsible for expression increases. Our observations resolve controversies over the roles of N-terminal codon bias and suggest a straightforward method for optimizing heterologous gene expression in bacteria. PMID:24072823

Goodman, Daniel B; Church, George M; Kosuri, Sriram

2013-09-26

183

Synonymous Codon Ordering: A Subtle but Prevalent Strategy of Bacteria to Improve Translational Efficiency  

PubMed Central

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

Shao, Zhu-Qing; Zhang, Yan-Mei; Feng, Xue-Ying; Wang, Bin; Chen, Jian-Qun

2012-01-01

184

Pickup Ions Upstream and Downstream of Shocks  

NASA Astrophysics Data System (ADS)

The evolution of differential energy spectra and distribution functions of H+, He+ and He++ across shock boundaries is examined to gain insight into the acceleration of solar wind and pickup ions by various types of shocks. Data from the SWICS and HISCALE instruments on Ulysses are combined in order to span the wide energy range from ~0.6 keV/e to almost 5 MeV. We study two different types of shock crossings, the reverse shock of a Corotating Interaction Region, and the Jovian bow shock. Upstream ion velocity distributions are found to have hard suprathermal tails extending to high energies. Downstream ion distributions have higher particle densities in the tails, especially at energies corresponding to a few times the solar wind speed. At velocities greater than about ten times the solar wind speed the density increase from upstream to downstream is relatively small in the case of Jupiter's bow shock. The presence of preexisting suprathermal tails provides particles with sufficiently high speeds to be readily injected into the shock acceleration mechanism.

Gloeckler, G.; Fisk, L. A.; Lanzerotti, L. J.

2005-08-01

185

Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions.  

PubMed

The genetic code of nuclear genes in some ciliates was found to differ from that of other organisms in the assignment of UGA, UAG, and UAA codons, which are normally assigned as stop codons. In some ciliate species, the universal stop codons UAA and UAG instead encode glutamine. In some other ciliates, the universal stop codon UGA appears to be translated as cysteine or tryptophan. Eukaryotic release factor 1 (eRF1) is a key protein in stop codon recognition, thus, the protein is believed to play an important role in the stop codon reassignment in ciliates. We have cloned, sequenced, and analyzed the cDNA of eRF1 from four ciliate species of three different classes: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Phylogenetic analysis of these eRF1s supports the hypothesis that the genetic code in ciliates has deviated independently several times from the universal genetic code, and that different ciliate eRF1s may have undergone different processes to change the codon specificity. Using computational methods, we have also suggested areas on the surface of eRF1s that are important for stop codon recognition in ciliate eRF1s. PMID:15716103

Kim, Oanh Thi Phuong; Yura, Kei; Go, Nobuhiro; Harumoto, Terue

2005-01-04

186

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

Microsoft Academic Search

The effective number of codons (Nc) used in a gene is one of the most commonly used measures of synonymous codon usage bias, owing much of its popularity to the fact that it is species independent and that simulation studies have shown that it is less dependent of gene length than other measures. In this paper I provide a clear

Anders Fuglsang

2008-01-01

187

INFLUENCE OF UPSTREAM WIND SHEAR AND TURBULENCE ON THE WIND PATTERN AND POLLUTANT CONCENTRATING WITHIN STREET CANYONS: A NUMERICAL STUDY  

EPA Science Inventory

This study serves as a start of future research on the subject. his study shows that the canyon geometry and the upstream boundary conditions have significant influences on the flow and concentration fields in the vicinity of urban street canyons. ollutants emitted within a canyo...

188

Modulation of Poliovirus Replicative Fitness in HeLa Cells by Deoptimization of Synonymous Codon Usage in the Capsid Region  

Microsoft Academic Search

We replaced degenerate codons for nine amino acids within the capsid region of the Sabin type 2 oral poliovirus vaccine strain with corresponding nonpreferred synonymous codons. Codon replacements were introduced into four contiguous intervals spanning 97% of the capsid region. In the capsid region of the most highly modified virus construct, the effective number of codons used (NC) fell from

Cara Carthel Burns; Jing Shaw; Ray Campagnoli; Jaume Jorba; Annelet Vincent; Jacqueline Quay; Olen Kew

2006-01-01

189

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

Microsoft Academic Search

Codon use in the three sequenced chloroplast genomes (Marchantia, Oryza, and Nicotiana) is examined. The chloroplast has a bias in that codons NNA and NNT are favored over synonymous NNC and NNG codons. This appears to be a consequence of an overall high A + T content of the genome. This pattern of codon use is not followed by the

Brian R. Morton

1993-01-01

190

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

Microsoft Academic Search

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

Carles Rentero; Pere Puigdomènech

2006-01-01

191

Analysis of Synonymous Codon Usage Patterns in Seven Different Citrus Species  

PubMed Central

We used large samples of expressed sequence tags to characterize the patterns of codon usage bias (CUB) in seven different Citrus species and to analyze their evolutionary effect on selection and base composition. We found that A- and T-ending codons are predominant in Citrus species. Next, we identified 21 codons for 18 different amino acids that were considered preferred codons in all seven species. We then performed correspondence analysis and constructed plots for the effective number of codons (ENCs) to analyze synonymous codon usage. Multiple regression analysis showed that gene expression in each species had a constant influence on the frequency of optional codons (FOP). Base composition differences between the proportions were large. Finally, positive selection was detected during the evolutionary process of the different Citrus species. Overall, our results suggest that codon usages were the result of positive selection. Codon usage variation among Citrus genes is influenced by translational selection, mutational bias, and gene length. CUB is strongly affected by selection pressure at the translational level, and gene length plays only a minor role. One possible explanation for this is that the selection-mediated codon bias is consistently strong in Citrus, which is one of the most widely cultivated fruit trees.

Xu, Chen; Dong, Jing; Tong, Chunfa; Gong, Xindong; Wen, Qiang; Zhuge, Qiang

2013-01-01

192

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

PubMed Central

Background Variations in codon usage between species are one of the major causes affecting recombinant protein expression levels, with a significant impact on the economy of industrial enzyme production processes. The use of codon-optimized genes may overcome this problem. However, designing a gene for optimal expression requires choosing from a vast number of possible DNA sequences and different codon optimization methods have been used in the past decade. Here, a comparative study of the two most common methods is presented using calf prochymosin as a model. Results Seven sequences encoding calf prochymosin have been designed, two using the "one amino acid-one codon" method and five using a "codon randomization" strategy. When expressed in Escherichia coli, the variants optimized by the codon randomization approach produced significantly more proteins than the native sequence including one gene that produced an increase of 70% in the amount of prochymosin accumulated. On the other hand, no significant improvement in protein expression was observed for the variants designed with the one amino acid-one codon method. The use of codon-optimized sequences did not affect the quality of the recovered inclusion bodies. Conclusions The results obtained in this study indicate that the codon randomization method is a superior strategy for codon optimization. A significant improvement in protein expression was obtained for the largely established process of chymosin production, showing the power of this strategy to reduce production costs of industrial enzymes in microbial hosts.

2011-01-01

193

Distinct Paths To Stop Codon Reassignment by the Variant-Code Organisms Tetrahymena and Euplotes  

PubMed Central

The reassignment of stop codons is common among many ciliate species. For example, Tetrahymena species recognize only UGA as a stop codon, while Euplotes species recognize only UAA and UAG as stop codons. Recent studies have shown that domain 1 of the translation termination factor eRF1 mediates stop codon recognition. While it is commonly assumed that changes in domain 1 of ciliate eRF1s are responsible for altered stop codon recognition, this has never been demonstrated in vivo. To carry out such an analysis, we made hybrid proteins that contained eRF1 domain 1 from either Tetrahymena thermophila or Euplotes octocarinatus fused to eRF1 domains 2 and 3 from Saccharomyces cerevisiae. We found that the Tetrahymena hybrid eRF1 efficiently terminated at all three stop codons when expressed in yeast cells, indicating that domain 1 is not the sole determinant of stop codon recognition in Tetrahymena species. In contrast, the Euplotes hybrid facilitated efficient translation termination at UAA and UAG codons but not at the UGA codon. Together, these results indicate that while domain 1 facilitates stop codon recognition, other factors can influence this process. Our findings also indicate that these two ciliate species used distinct approaches to diverge from the universal genetic code.

Salas-Marco, Joe; Fan-Minogue, Hua; Kallmeyer, Adam K.; Klobutcher, Lawrence A.; Farabaugh, Philip J.; Bedwell, David M.

2006-01-01

194

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

195

Induction of Myelin Protein Zero by Early Growth Response 2 through Upstream and Intragenic Elements*  

PubMed Central

The Mpz (myelin protein zero) gene codes for the principal component of myelin in the peripheral nervous system, and mutations in this gene cause human peripheral myelinopathies. Expression of the Mpz gene is controlled by two major transactivators that coordinate Schwann cell development: Egr2/Krox20 and Sox10. Our in vivo ChIP-chip analysis in myelinating peripheral nerve identified major sites of Egr2 interaction within the first intron of the Mpz gene and ?5 kb upstream of the transcription start site. In addition, the sites of Egr2 binding display many of the hallmarks associated with enhancer elements. Interestingly, the upstream Egr2 binding sites lie proximal to the divergently transcribed succinate dehydrogenase C gene, but Sdhc expression was not affected by the massive induction of Mpz mediated by Egr2. Mpz induction was greatly enhanced in the presence of the Egr2 binding sites, and removal of them markedly diminished transgenic expression of a construct derived from the Mpz locus. Sox10 was also found to be associated with the upstream region, and its binding was required for Egr2-mediated activation in this distal regulatory region. Our findings highlight that peripheral nerve-specific expression of Mpz is primarily regulated by both upstream and intron-associated regulatory elements. Overall, these results provide a locus-wide analysis of the role and activity of Egr2 in regulation of the Mpz gene within its native chromosomal context.

Jang, Sung-Wook; Svaren, John

2009-01-01

196

p53 codon 72 polymorphism and risk of cervical cancer.  

PubMed

Storey et al. (1998) implicated the proline/argine polymorphism of the codon 72 of the tumor-suppressor gene p53 in the development of cervical cancer (CC) with the observation that the p53 protein is more efficiently inactivated by the E6 oncoprotein of human papillomavirus in p53 arginine as compared with its proline isoform. These authors further noted that in the United Kingdom, individuals homozygous for the arginine allele were several times more susceptible to HPV-associated tumorigenesis that proline/arginine heterozygotes. Subsequent studies in different countries failed to unanimously confirm this association. Motivated by the high incidence of CC in Chile, we undertook a case control study obtaining the following frequencies for genotypes PP, AP and AA in 60 ICC cases and 53 carefully selected controls: 0.067, 0.250, 0.683 and 0.075, 0.453, 0.472 respectively. A significant difference (X2 = 3.19 p < 0.02) and an odds ratio of 2.62 supported Storey et al (1998)'s results. In addition, rejecting previous hypotheses about the world distribution of the p53 codon 72 polymorphism, we conclude that this distribution most likely represents ancient human dispersal routes. Several methodological and biological explanations for the results obtained in previous negative association studies are briefly discussed. PMID:14513722

Ojeda, José M; Ampuero, Sandra; Rojas, Patricio; Prado, Rodrigo; Allende, Jorge E; Barton, Sara A; Chakraborty, Ranajit; Rothhammer, Francisco

2003-01-01

197

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

PubMed Central

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

Morton, B R

2001-01-01

198

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

Microsoft Academic Search

In-frame stop codons normally signal termination during mRNA translation, but they can be read as 'sense' (readthrough) depending on their context, comprising the 6 nt preceding and following the stop codon. To identify novel contexts directing read- through, under-represented 50 and 30 stop codon con- texts from Saccharomyces cerevisiae were identified by genome-wide survey in silico. In contrast with the

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

2004-01-01

199

Evolutionary Patterns of Codon Usage in the Chloroplast Gene rbc L  

Microsoft Academic Search

In this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL using a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chloroplast genomic nucleotide content, as an attempt to limit plausible explanations for patterns of codon bias evolution to selection- or drift-based processes. This measure uses maximum

Dennis P. Wall; Joshua T. Herbeck

2003-01-01

200

Evolutionary Patterns of Codon Usage in the Chloroplast Gene rbc L  

Microsoft Academic Search

In this study we reconstruct the evolution of codon usage bias in the chloroplast gene rbcL us- ing a phylogeny of 92 green-plant taxa. We employ a measure of codon usage bias that accounts for chlo- roplast genomic nucleotide content, as an attempt to limit plausible explanations for patterns of codon bias evolution to selection- or drift-based processes. This measure

Dennis P. Wall; Joshua T. Herbeck

2003-01-01

201

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

PubMed Central

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

Parisien, Marc; Yi, Chengqi; Pan, Tao

2012-01-01

202

Effect of allelic variation at the NACP-Rep1 repeat upstream of the ?-synuclein gene (SNCA) on transcription in a cell culture luciferase reporter system  

Microsoft Academic Search

Mutations in the ?-synuclein gene (SNCA) have been implicated in familial Parkinson's disease (PD) while certain polymorphic alleles at a microsatellite repeat, NACP-Rep1, located ?10 kb upstream of the gene, have been associated with sporadic PD. In order to study the regulation of the human ?-synuclein gene, we performed a deletion analysis of 10.7 kb upstream of the translational start

Ornit Chiba-Falek; Robert L. Nussbaum

2001-01-01

203

3. Credit JTL Long distance view looking upstream towards New ...  

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

3. Credit JTL Long distance view looking upstream towards New Hampshire; commercial structures in foreground. - Bellows Falls Arch Bridge, Spanning Connecticut River, North Walpole, Cheshire County, NH

204

The factors shaping synonymous codon usage in the genome of Burkholderia mallei.  

PubMed

Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as 'optimal codons' might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders. PMID:17498635

Zhao, Sheng; Zhang, Qin; Chen, Zhihua; Zhao, Yixin; Zhong, Jincheng

2007-04-01

205

Are stop codons recognized by base triplets in the large ribosomal RNA subunit?  

PubMed Central

The precise mechanism of stop codon recognition in translation termination is still unclear. A previously published study by Ivanov and colleagues proposed a new model for stop codon recognition in which 3-nucleotide Ter-anticodons within the loops of hairpin helices 69 (domain IV) and 89 (domain V) in large ribosomal subunit (LSU) rRNA recognize stop codons to terminate protein translation in eubacteria and certain organelles. We evaluated this model by extensive bioinformatic analysis of stop codons and their putative corresponding Ter-anticodons across a much wider range of species, and found many cases for which it cannot explain the stop codon usage without requiring the involvement of one or more of the eight possible noncomplementary base pairs. Involvement of such base pairs may not be structurally or thermodynamically damaging to the model. However, if, according to the model, Ter-anticodon interaction with stop codons occurs within the ribosomal A-site, the structural stringency which that site imposes on sense codon·tRNA anticodon interaction should also extend to stop codon·Ter-anticodon interactions. Moreover, with Ter-tRNA in place of an aminoacyl-tRNA, for each of the various Ter-anticodons there is a sense codon that can interact with it preferentially by complementary and wobble base-pairing. Both these considerations considerably weaken the arguments put forth previously.

LIANG, HAN; LANDWEBER, LAURA F.; FRESCO, JACQUES R.

2005-01-01

206

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

207

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

208

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

209

Negatively buoyant starting jets  

NASA Astrophysics Data System (ADS)

The initial development of negatively buoyant jets has been investigated experimentally and numerically, focusing on the role played by gravity in the evolution of the leading vortex ring. Under the experimental conditions considered in this work, the densimetric Froude number, Fr=?jUj2/[(?0-?j)gD], which represents the ratio between the jet momentum and the buoyancy forces, emerges as the most relevant parameter characterizing the dynamics of the flow. Two different flow regimes have been observed depending on the Froude number: for sufficiently small Fr, the vortex ring generated initially is pushed radially away by gravity forces before it has time to detach from the shear layer originating at the orifice. On the other hand, when the Froude number is larger than a critical value, Fr>Frc~1, the vortex ring detaches from the injection orifice and propagates downstream into the stagnant ambient followed by a trailing jet until it eventually reaches a maximum penetration depth. In order to clarify the mechanisms leading to the transition between the two regimes, and to gain physical understanding of the formation dynamics of negatively buoyant starting jets, the total and the vortex circulation, as well as the trajectory of the vortex center, have been measured and compared to the case of neutrally buoyant jets. Finally, based on the experimental measurements and on the results of the numerical computations, a kinematic model that successfully describes the evolution of both total circulation and vortex trajectory is proposed.

Marugán-Cruz, C.; Rodríguez-Rodríguez, J.; Martínez-Bazán, C.

2009-11-01

210

From Head Start to Sure Start: Reflections on Policy Transfer  

ERIC Educational Resources Information Center

|This article uses the history of debates over the US Head Start programme (1965), Early Head Start (1994) and the UK Sure Start initiative (1998), as a window on to policy transfer. In all the three, the aim was that early intervention could offer a means of boosting children's educational attainment and of countering the wider effects of poverty…

Welshman, John

2010-01-01

211

Manual for Head Start Administrators. Volume I: Head Start Requirements.  

ERIC Educational Resources Information Center

|Head Start Administrators must be fully knowledgeable of all applicable Federal requirements and skilled in applying these requirements in the daily operation of their program, whether starting a new program or striving to maintain a high quality program. This manual provides Head Start administrators with a compilation of the program…

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

212

A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV.  

PubMed

The synonymous codon usage pattern of African swine fever virus (ASFV), the similarity degree of the synonymous codon usage between this virus and some organisms and the synonymous codon usage bias for the translation initiation region of viral functional genes in the whole genome of ASFV have been investigated by some simply statistical analyses. Although both GC12% (the GC content at the first and second codon positions) and GC3% (the GC content at the third codon position) of viral functional genes have a large fluctuation, the significant correlations between GC12 and GC3% and between GC3% and the first principal axis of principle component analysis on the relative synonymous codon usage of the viral functional genes imply that mutation pressure of ASFV plays an important role in the synonymous codon usage pattern. Turning to the synonymous codon usage of this virus, the codons with U/A end predominate in the synonymous codon family for the same amino acid and a weak codon usage bias in both leading and lagging strands suggests that strand compositional asymmetry does not take part in the formation of codon usage in ASFV. The interaction between the absolute codon usage bias and GC3% suggests that other selections take part in the formation of codon usage, except for the mutation pressure. It is noted that the similarity degree of codon usage between ASFV and soft tick is higher than that between the virus and the pig, suggesting that the soft tick plays a more important role than the pig in the codon usage pattern of ASFV. The translational initiation region of the viral functional genes generally have a strong tendency to select some synonymous codons with low GC content, suggesting that the synonymous codon usage bias caused by translation selection from the host takes part in modulating the translation initiation efficiency of ASFV functional genes. PMID:23161403

Zhou, Jian-Hua; Gao, Zong-Liang; Sun, Dong-Jie; Ding, Yao-Zhong; Zhang, Jie; Stipkovits, Laszlo; Szathmary, Susan; Pejsak, Zygmunt; Liu, Yong-Sheng

2012-11-16

213

Rapid detection of ethambutol-resistant Mycobacterium tuberculosis strains by PCR-RFLP targeting embB codons 306 and 497 and iniA codon 501 mutations  

Microsoft Academic Search

Mutations at embB gene codons 306 and 497 and iniA gene codon 501 occur frequently in ethambutol (EMB)-resistant Mycobacterium tuberculosis strains worldwide. The identification of these mutations in resistant strains has been achieved by labor-intensive DNA sequencing or by tedious amplification protocols followed by restriction endonuclease digestion. In this report, we describe PCR-restriction fragment length polymorphism (RFLP)-based methods for determining

S Ahmad; E Mokaddas; A.-A Jaber

2004-01-01

214

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

215

Too Smart to Start: Families  

MedlinePLUS

... e-Cards Push Play Resources Did You Know? Families Welcome to Too Smart To Start, your Web ... help young people be too smart to start. Families While many teens drink alcohol, underage alcohol use ...

216

Butanol fermentation research: upstream and downstream manipulations.  

PubMed

An overview of advances in acetone-butanol fermentation research is presented with specific reference to the history of acetone-butanol fermentation, genetic manipulation of the butanol-producing Clostridium beijerinckii NCIMB 8052, as well as upstream and downstream processing. Specific reference is made to the development of the hyperamylolytic, hyper-"butanolagenic" C. beijerinckii BA101 strain. Amylolytic enzyme production by C. beijerinckii BA101 was 1.8- and 2.5-fold greater than that of the C. beijerinckii NCIMB 8052 strain grown in starch and glucose, respectively. We confirmed the presence of a phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) associated with cell extracts of C. beijerinckii BA101 by glucose phosphorylation by PEP and ATP-dependent glucose phosphorylation. It was found that C. beijerinckii BA101 was defective in PTS activity and that it compensates for this defect with enhanced glucokinase activity, resulting in an ability to transport and utilize glucose during the solventogenic stage. The principal problem associated with acetone-butanol fermentation by C. beijerinckii or C. acetobutylicum is butanol toxicity/inhibition to the culture. To solve this problem, we have attempted various alternative in situ/online techniques of butanol removal including membrane-based systems such as pervaporation, liquid-liquid extraction, and gas stripping. We found that gas stripping and pervaporation appear to be the most promising of the in situ acetone-butanol fermentation and recovery techniques but, in terms of cost-effective industrial applications, gas stripping appears to be the most promising. PMID:15543610

Ezeji, Thaddeus C; Qureshi, Nasib; Blaschek, Hans P

2004-01-01

217

Variation in the strength of selected codon usage bias among bacteria  

Microsoft Academic Search

Among bacteria, many species have synonymous codon usage patterns that have been influenced by natural selection for those codons that are translated more accurately and\\/or efficiently. However, in other species selection appears to have been ineffective. Here, we introduce a population genetics-based model for quantifying the extent to which selection has been effective. The approach is applied to 80 phylogenetically

Paul M. Sharp; Elizabeth Bailes; Russell J. Grocock; John F. Peden; R. Elizabeth Sockett

2005-01-01

218

An Empirical Examination of the Utility of Codon-Substitution Models in Phylogeny Reconstruction  

Microsoft Academic Search

Models of codon substitution have been commonly used to compare protein-coding DNA sequences and are particularly effective in detecting signals of natural selection acting on the protein. Their utility in reconstructing molecular phylogenies and in dating species divergences has not been explored. Codon models naturally accommodate synonymous and nonsynonymous substitutions, which occur at very different rates and may be informative

Fengrong Ren; Hiroshi Tanaka; Ziheng Yang

2005-01-01

219

Impact of translational selection on codon usage bias in the archaeon Methanococcus maripaludis  

PubMed Central

Patterns of codon usage have been extensively studied among Bacteria and Eukaryotes, but there has been little investigation of species from the third domain of life, the Archaea. Here, we examine the nature of codon usage bias in a methanogenic archaeon, Methanococcus maripaludis. Genome-wide patterns of codon usage are dominated by a strong A + T bias, presumably largely reflecting mutation patterns. Nevertheless, there is variation among genes in the use of a subset of putatively translationally optimal codons, which is strongly correlated with gene expression level. In comparison with Bacteria such as Escherichia coli, the strength of selected codon usage bias in highly expressed genes in M. maripaludis seems surprisingly high given its moderate growth rate. However, the pattern of selected codon usage differs between M. maripaludis and E. coli: in the archaeon, strongly selected codon usage bias is largely restricted to twofold degenerate amino acids (AAs). Weaker bias among the codons for fourfold degenerate AAs is consistent with the small number of tRNA genes in the M. maripaludis genome.

Emery, Laura R.; Sharp, Paul M.

2011-01-01

220

The codon preference plot: graphic analysis of protein coding sequences and prediction of gene expression.  

PubMed Central

The codon preference plot is useful for locating genes in sequenced DNA, predicting the relative level of their expression and for detecting DNA sequencing errors resulting in the insertion or deletion of bases within a coding sequence. The three possible reading frames are displayed in parallel along with the open reading frames and plots of the location of rare codons in each reading frame.

Gribskov, M; Devereux, J; Burgess, R R

1984-01-01

221

[Analysis of codon use features of CBF gene in Camellia sinensis].  

PubMed

CBF (C-repeat-binding factor) transcription factor exists widely in all kinds of plants. It is an important regulative factor in the process of plant resistance adversity. In this paper, Camellia sinensis CBF1 gene sequence was analyzed by Codon W, CHIPS, and CUSP programs online, and then compared with C. sinensis genes, genomes in other species, and CBF genes from 39 plant species. It is important to identify the codon usage of CsCBF1 gene and select appropriate expression systems. The results showed that CsCBF1 gene and selected 70 C. sinensis genes had distinct usage differences. CsCBF1 gene was bias toward the synonymous codons with G and C at the third codon position, but 70 C. sinensis genes were bias toward the synonymous codons with A and T. The differences in codon usage frequency between CsCBF1 gene and dicotyledons such as Arabidopsis thaliana and Nicotiana tobacum were less than monocotyledons such as wheat (Triticum aestivum) and corn (Zea mays). Therefore, A. thaliana and N. tobacum expression systems may be more suitable for the expression of CsCBF1 gene. The analysis results of CBF genes from 40 plant species also showed that most of the CBF genes were bias toward the synonymous codons with G and C at the third codon position. The reason of this phenomenon is possible due to special functions of these genes. PMID:23262110

Guo, Xiu-Li; Wang, Yu; Yang, Lu-Cheng; Ding, Zhao-Tang

2012-12-01

222

Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias  

Microsoft Academic Search

Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates, their distribution across the genetic code and the resulting implications have received little attention. In general, studies of codon usage bias (CUB) assume that codons with higher tRNA abundance have lower missense error rates. Using a model of protein translation based on

Premal Shah; Michael A. Gilchrist

2010-01-01

223

The translational stop signal: Codon with a context, or extended factor recognition element?  

Microsoft Academic Search

Wide ranging studies of the readthrough of translational stop codons within the last 25 years have suggested that the stop codon might be only part of the molecular signature for recognition of the termination signal. Such studies do not distinguish between effects on suppression and effects on termination, and so we have used a number of different approaches to deduce

W. P. Tate; E. S. Poole; M. E. Dalphin; L. L. Major; D. J. G. Crawford; S. A. Mannering

1996-01-01

224

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

Microsoft Academic Search

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

HARITHA VALLABHANENI; HUA FAN-MINOGUE; DAVID M. BEDWELL; PHILIP J. FARABAUGH

2009-01-01

225

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

Microsoft Academic Search

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 to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses

Grzegorz Kudla; Joshua B. Plotkin

2010-01-01

226

Toward the experimental codon reassignment in vivo: protein building with an expanded amino acid repertoire  

Microsoft Academic Search

The high precision and fidelity of the genetic message transmission are ensured by numer- ous proofreading steps, from DNA replication and transcription to protein translation. The key event for translational fidelity is the proper codon assignment for 20 canonical amino acids. An experimental codon reassignment is possible for noncanonical amino ac- ids in vivo using artificially constructed expression hosts under

NEDILJKO BUDISA; CAROLINE MINKS; STEFAN ALEFELDER; WALTRAUD WENGER; FUMIN DONG; LUIS MORODER; ROBERT HUBER

227

Adaptation to Different Human Populations by HIV1 Revealed by Codon-Based Analyses  

Microsoft Academic Search

Several codon-based methods are available for detecting adaptive evolution in protein-coding sequences, but to date none specifically identify sites that are selected differentially in two populations, although such comparisons between populations have been historically useful in identifying the action of natural selection. We have developed two fixed effects maximum likelihood methods: one for identifying codon positions showing selection patterns that

Sergei L. Kosakovsky Pond; Simon D. W. Frost; Zehava Grossman; Michael B. Gravenor; Douglas D. Richman; Andrew J. Leigh Brown

2006-01-01

228

The Relation of Codon Bias to Tissue-Specific Gene Expression in Arabidopsis thaliana  

PubMed Central

The codon composition of coding sequences plays an important role in the regulation of gene expression. Herein, we report systematic differences in the usage of synonymous codons among Arabidopsis thaliana genes that are expressed specifically in distinct tissues. Although we observed that both regionally and transcriptionally associated mutational biases were associated significantly with codon bias, they could not explain the observed differences fully. Similarly, given that transcript abundances did not account for the differences in codon usage, it is unlikely that selection for translational efficiency can account exclusively for the observed codon bias. Thus, we considered the possible evolution of codon bias as an adaptive response to the different abundances of tRNAs in different tissues. Our analysis demonstrated that in some cases, codon usage in genes that were expressed in a broad range of tissues was influenced primarily by the tissue in which the gene was expressed maximally. On the basis of this finding we propose that genes that are expressed in certain tissues might show a tissue-specific compositional signature in relation to codon usage. These findings might have implications for the design of transgenes in relation to optimizing their expression.

Camiolo, Salvatore; Farina, Lorenzo; Porceddu, Andrea

2012-01-01

229

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

Microsoft Academic Search

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

Yasukazu Nakamura; Takashi Gojobori; Toshimichi Ikemura

2000-01-01

230

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

PubMed Central

Background Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. One factor known to affect translational power is biased use of synonymous codons. The correlation within an organism between expression level and degree of codon bias among genes of Escherichia coli and other bacteria capable of rapid growth is commonly attributed to selection for high translational power. Conversely, the absence of such a correlation in some slowly growing microbes has been interpreted as the absence of selection for translational power. Because codon bias caused by translational selection varies between rapidly growing and slowly growing microbes, we investigated whether observed differences in translational power among microbes could be explained entirely by differences in the degree of codon bias. Although the data are not available to estimate the effect of codon bias in other species, we developed an empirically-based mathematical model to compare the translation rate of E. coli to the translation rate of a hypothetical strain which differs from E. coli only by lacking codon bias. Results Our reanalysis of data from the scientific literature suggests that translational power can differ by a factor of 5 or more between E. coli and slowly growing microbial species. Using empirical codon-specific in vivo translation rates for 29 codons, and several scenarios for extrapolating from these data to estimates over all codons, we find that codon bias cannot account for more than a doubling of the translation rate in E. coli, even with unrealistic simplifying assumptions that exaggerate the effect of codon bias. With more realistic assumptions, our best estimate is that codon bias accelerates translation in E. coli by no more than 60% in comparison to microbes with very little codon bias. Conclusions While codon bias confers a substantial benefit of faster translation and hence greater translational power, the magnitude of this effect is insufficient to explain observed differences in translational power among bacterial and archaeal species, particularly the differences between slowly growing and rapidly growing species. Hence, large differences in translational power suggest that the translational apparatus itself differs among microbes in ways that influence translational performance.

Dethlefsen, Les; Schmidt, Thomas M

2005-01-01

231

Evolutionary conservation of codon optimality reveals hidden signatures of co-translational folding  

PubMed Central

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

Pechmann, Sebastian; Frydman, Judith

2012-01-01

232

Identification of amino acids responsible for stop codon recognition for polypeptide chain release factor.  

PubMed

One factor involved in eukaryotic translation termination is class 1 release factor in eukaryotes (eRF1), which functions to decode stop codons. Variant code species, such as ciliates, frequently exhibit altered stop codon recognition. Studies revealed that some class-specific residues in the eRF1 N-terminal domain are responsible for stop codon reassignment in ciliates. Here, we investigated the effects on stop codon recognition of chimeric eRF1s containing the N-terminal domain of Euplotes octocarinatus and Blepharisma japonicum eRF1 fused to Saccharomyces cerevisiae M and C domains using dual luciferase read-through assays. Mutation of class-specific residues in different eRF1 classes was also studied to identify key residues and motifs involved in stop codon decoding. As expected, our results demonstrate that 3 pockets within the eRF1 N-terminal domain were involved in decoding stop codon nucleotides. However, allocation of residues to each pocket was revalued. Our data suggest that hydrophobic and class-specific surface residues participate in different functions: modulation of pocket conformation and interaction with stop codon nucleotides, respectively. Residues conserved across all eRF1s determine the relative orientation of the 3 pockets according to stop codon nucleotides. However, quantitative analysis of variant ciliate and yeast eRF1 point mutants did not reveal any correlation between evolutionary conservation of class-specific residues and termination-related functional specificity and was limited in elucidating a detailed mechanism for ciliate stop codon reassignment. Thus, based on isolation of suppressor tRNAs from Euplotes and Tetrahymena, we propose that stop codon reassignment in ciliates may be controlled by cooperation between eRF1 and suppressor tRNAs. PMID:23668788

Xu, Lijun; Hao, Yanrong; Li, Cui; Shen, Quan; Chai, Baofeng; Wang, Wei; Liang, Aihua

2013-05-07

233

Evaluating Sure Start, Head Start, and Early Head Start: Finding Their Signals Amidst Methodological Static  

ERIC Educational Resources Information Center

|Evaluations of three national early childhood programs--Sure Start in England and Head Start and Early Head Start in the United States--are examined to determine what their respective methodological strengths and weaknesses are and to detect impacts or signals common to all of these evaluations. These shared signals include improved family…

Allen, Benjamin L.

2008-01-01

234

Evaluating Sure Start, Head Start, and Early Head Start: Finding Their Signals Amidst Methodological Static  

Microsoft Academic Search

Evaluations of three national early childhood programs–Sure Start in England and Head Start and Early Head Start in the United States–are examined to determine what their respective methodological strengths and weaknesses are and to detect impacts or signals common to all of these evaluations. These shared signals include improved family functioning and parenting practices and strong signs of parental and

Benjamin L. Allen

2008-01-01

235

Evaluating Sure Start, Head Start, and Early Head Start: Finding Their Signals Amidst Methodological Static  

ERIC Educational Resources Information Center

Evaluations of three national early childhood programs--Sure Start in England and Head Start and Early Head Start in the United States--are examined to determine what their respective methodological strengths and weaknesses are and to detect impacts or signals common to all of these evaluations. These shared signals include improved family…

Allen, Benjamin L.

2008-01-01

236

Cold-start vs. warm-start miss ratios  

Microsoft Academic Search

In a two-level computer storage hierarchy, miss ratio measurements are often made from a “cold start”, that is, made with the first-level store initially empty. For large capacities the effect on the measured miss ratio of the misses incurred while filling the first-level store can be significant, even for long reference strings. Use of “warm-start” rather than “cold-start” miss ratios

Malcolm C. Easton; Ronald Fagin

1978-01-01

237

Nicotinic ?5 receptor subunit mRNA expression is associated with distant 5? upstream polymorphisms  

PubMed Central

CHRNA5, encoding the nicotinic ?5 subunit, is implicated in multiple disorders, including nicotine addiction and lung cancer. Previous studies demonstrate significant associations between promoter polymorphisms and CHRNA5 mRNA expression, but the responsible sequence variants remain uncertain. To search for cis-regulatory variants, we measured allele-specific mRNA expression of CHRNA5 in human prefrontal cortex autopsy tissues and scanned the CHRNA5 locus for regulatory variants. A cluster of six frequent single-nucleotide polymorphisms (rs1979905, rs1979906, rs1979907, rs880395, rs905740, and rs7164030), in complete linkage disequilibrium (LD), fully account for a >2.5-fold allelic expression difference and a fourfold increase in overall CHRNA5 mRNA expression. This proposed enhancer region resides more than 13 kilobases upstream of the CHRNA5 transcription start site. The same upstream variants failed to affect CHRNA5 mRNA expression in peripheral blood lymphocytes, indicating tissue-specific gene regulation. Other promoter polymorphisms were also correlated with overall CHRNA5 mRNA expression in the brain, but were inconsistent with allelic mRNA expression ratios, a robust and proximate measure of cis-regulatory variants. The enhancer region and the nonsynonymous polymorphism rs16969968 generate three main haplotypes that alter the risk of developing nicotine dependence. Ethnic differences in LD across the CHRNA5 locus require consideration of upstream enhancer variants when testing clinical associations.

Smith, Ryan M; Alachkar, Houda; Papp, Audrey C; Wang, Danxin; Mash, Deborah C; Wang, Jen-Chyong; Bierut, Laura J; Sadee, Wolfgang

2011-01-01

238

The 17 Nucleotides Downstream from the env Gene Stop Codon Are Important for Murine Leukemia Virus Packaging  

PubMed Central

We have identified a previously unknown nucleotide sequence important for the packaging of murine leukemia virus. This nucleotide sequence is located downstream from the stop codon of the env gene but does not overlap the polypurine tract. Deletion of 17 bp from this region resulted in a more than 10-fold decrease in viral titer. Consistent with this result, the deletion mutant showed a 20- to 30-fold drop in the amount of virion RNA in the culture supernatant. The total amount of virion protein in the culture supernatant was comparable for the deletion mutant and the parental virus, suggesting that the mutant construct could release the empty viral particles. These results suggested that the packaging signal sequence might be present at the two extreme sites of the viral genome, one in the region around the splice donor sequence downstream from the 5? long terminal repeat (LTR) and the other immediately upstream from the 3? LTR. Implications for gene therapy, especially in regard to construction of retroviral vectors and packaging constructs, are discussed.

Shin Yu, Seung; Kim, Jong-Mook; Kim, Sunyoung

2000-01-01

239

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

240

Suprathermal ions observed upstream of the Venus bow shock  

NASA Astrophysics Data System (ADS)

Suprathermal ions with arrival directions quite distinct from those of the solar wind have been detected upstream of the Venus bow shock. The possibility that these events could be caused by instrumental or spacecraft effects or that they could be either solar wind disturbances, planetary pickup ions, or suprethermal ions upstream of the Venus bow shock is examined. It is concluded that they are consistent with upstream suprathermal ions associated with the bow shock that are observed downstream from the points of intersection of their extrapolated trajectories with the shock.

Moore, K. R.; McComas, D. J.; Russell, C. T.; Mihalov, J. D.

1989-04-01

241

Upstream power equalization in a gigabit passive optical network.  

PubMed

We propose a technique for achieving equalized power in upstream traffic in the gigabit passive optical network (G-PON). A simple power equalizer based on a Fabry-Perot laser diode (FP-LD) is proposed and demonstrated experimentally. By the proposed scheme, the different upstream powers can be equalized. As a result, a 20 dB dynamic upstream power range from -5 to -25 dBm, having a 1.7 dB maximal power variation, is attained. Moreover, the performance of the proposed configuration is also discussed. PMID:19532770

Yeh, Chien-Hung; Hsu, Dar-Zu; Chi, Sien

2007-04-16

242

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

243

Glutathione peroxidase codon 198 polymorphism variant increases lung cancer risk.  

PubMed

Human cellular glutathione peroxidase 1 (hGPX1) is a selenium-dependent enzyme that participates in the detoxification of hydrogen peroxide and a wide range of organic peroxides. We conducted a case-control study nested within the alpha-Tocopherol, beta-Carotene Cancer Prevention Study cohort to evaluate the association between the proline to leucine polymorphism at codon 198 of hGPX1 and lung cancer risk. Cases (n = 315) were matched to controls on age (+/-5 years), intervention group, and study clinic using incidence density sampling in a 1:1 ratio. The prevalence of the hGPX1 Pro198Leu variant allele was 58% for controls and 71% for cases (P < 0.001). Using conditional logistic regression, we found a significant association between hGPX1 genotype and lung cancer risk. The odds ratio for heterozygotes was 1.8 (95% confidence interval, 1.2-2.8) and 2.3 (95% confidence interval, 1.3-3.8) for homozygous variants compared to wild-type individuals. Due to its high prevalence, the hGPX1 variant may contribute significantly to lung cancer risk among Caucasians but not among ethnic Chinese who do not exhibit this polymorphism. PMID:11103801

Ratnasinghe, D; Tangrea, J A; Andersen, M R; Barrett, M J; Virtamo, J; Taylor, P R; Albanes, D

2000-11-15

244

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

245

Synonymous codon usage in forty staphylococcal phages identifies the factors controlling codon usage variation and the phages suitable for phage therapy.  

PubMed

The immergence and dissemination of multidrug-resistant strains of Staphylococcus aureus in recent years have expedited the research on the discovery of novel anti-staphylococcal agents promptly. Bacteriophages have long been showing tremendous potentialities in curing the infections caused by various pathogenic bacteria including S. aureus. Thus far, only a few virulent bacteriophages, which do not carry any toxin-encoding gene but are capable of eradicating staphylococcal infections, were reported. Based on the codon usage analysis of sixteen S. aureus phages, previously three phages were suggested to be useful as the anti-staphylococcal agents. To search for additional S. aureus phages suitable for phage therapy, relative synonymous codon usage bias has been investigated in the protein-coding genes of forty new staphylococcal phages. All phages appeared to carry A and T ending codons. Several factors such as mutational pressure, translational selection and gene length seemed to be responsible for the codon usage variation in the phages. Codon usage indeed varied phage to phage. Of the phages, phages G1, Twort, 66 and Sap-2 may be extremely lytic in nature as majority of their genes possess high translational efficiency, indicating that these phages may be employed in curing staphylococcal infections. PMID:23275718

Bishal, Arghya Kamal; Saha, Soumya; Sau, Keya

2012-12-08

246

Significance of codon usage and irregularities of rare codon distribution in genes for expression of BspLU11III methyltransferases.  

PubMed

Genes of adenine-specific DNA-methyltransferase M.BspLU11IIIa and cytosine-specific DNA-methyltransferase M.BspLU11IIIb of the type IIG BspLU11III restriction-modification system from the thermophilic strain Bacillus sp. LU11 were expressed in E. coli. They contain a large number of codons that are rare in E. coli and are characterized by equal values of codon adaptation index (CAI) and expression level measure (E(g)). Rare codons are either diffused (M.BspLU11IIIa) or located in clusters (M.BspLU11IIIb). The expression level of the cytosine-specific DNA-methyltransferase was increased by a factor of 7.3 and that of adenine-specific DNA only by a factor of 1.25 after introduction of the plasmid pRARE supplying tRNA genes for six rare codons in E. coli. It can be assumed that the plasmid supplying minor tRNAs can strongly increase the expression level of only genes with cluster distribution of rare codons. Using heparin-Sepharose and phosphocellulose chromatography and gel filtration on Sephadex G-75 both DNA-methyltransferases were isolated as electrophoretically homogeneous proteins (according to the results of SDS-PAGE). PMID:15193127

Kirienko, N V; Lepikhov, K A; Zheleznaya, L A; Matvienko, N I

2004-05-01

247

Particles and waves Upstream of ICME Driven Interplanetary Shocks  

NASA Astrophysics Data System (ADS)

We use STEREO data to study interplanetary shocks driven by coronal mass ejections. We have found ultra-low frequency (ULF, f ~ 0.01 - 0.2 Hz) waves and high-frequency (HF, f ~ 1 Hz) fluctuations in regions upstream and downstream of these shocks. Some of the upstream HF fluctuations were classified as whistler waves. In the past whistler origin has been explained in terms of shock generation. The variety of waves found in the studied regions suggests that some of them may be generated by particle populations (electrons, ions) that can be unstable to different types of instabilities. In this work we study ions and electrons in regions immediately upstream of ten IP shocks of our sample. We use the STEREO SWEA data for electrons and STEREO PLASTIC data for ions. We study particle distributions in different points upstream of the shocks (anisotropies, temperatures, etc.) and investigate which of the observed waves can be generated by backstreaming particles.

Kajdic, P.; Blanco-Cano, X.; Aguilar-Rodriguez, E.; Russell, C. T.; Jian, L.; Opitz, A.; Luhmann, J. G.; Galvin, A. B.

2011-12-01

248

1. View from the northwest of the bridge's northwest (upstream) ...  

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

1. View from the northwest of the bridge's northwest (upstream) elevation - Big Cottonwood River Bridge No. 246, Spanning Big Cottonwood River at Cottonwood Street (City Road No. 165), New Ulm, Brown County, MN

249

2. View from the north of the bridge's northwest (upstream) ...  

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

2. View from the north of the bridge's northwest (upstream) elevation - Big Cottonwood River Bridge No. 246, Spanning Big Cottonwood River at Cottonwood Street (City Road No. 165), New Ulm, Brown County, MN

250

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

251

4. UPSTREAM ELEVATION VIEW OF BIG TUJUNGA DAM SHOWING THE ...  

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

4. UPSTREAM ELEVATION VIEW OF BIG TUJUNGA DAM SHOWING THE CONTROL HOUSE AND THE SPILLWAY BRIDGE AT THE ENDS OF THE DAM FACING WEST. - Big Tujunga Dam, 809 West Big Tujunga Road, Sunland, Los Angeles County, CA

252

7. DETAIL CENTRAL PIER (SKEWBACK) WITH BREAKWATER, UPSTREAM (EAST) SIDE. ...  

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

7. DETAIL CENTRAL PIER (SKEWBACK) WITH BREAKWATER, UPSTREAM (EAST) SIDE. NOTE FRACTURES ALONG BARREL ARCH EXTRADOS. - Roaring Creek Bridge, State Road 2005 spanning Roaring Creek in Locust Township, Slabtown, Columbia County, PA

253

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

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

14. Detail, upper chord connection point on upstream side of truss, showing connection of upper chord, laced vertical compression member, strut, counters, and laterals. - Dry Creek Bridge, Spanning Dry Creek at Cook Road, Ione, Amador County, CA

254

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

255

View of upstream face of Lake Sabrina Dam showing redwood ...  

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

View of upstream face of Lake Sabrina Dam showing redwood planks and boulders in Lake Sabrina Basin, view north - Bishop Creek Hydroelectric System, Plant 2, Lake Sabrina Dam, Bishop Creek, Bishop, Inyo County, CA

256

View of upstream face of Lake Sabrina Dam showing the ...  

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

View of upstream face of Lake Sabrina Dam showing the redwood planks and base of dam from Lake Sabrina Basin, view north - Bishop Creek Hydroelectric System, Plant 2, Lake Sabrina Dam, Bishop Creek, Bishop, Inyo County, CA

257

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

258

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

259

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

260

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

261

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

262

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

263

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

264

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

265

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

266

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

267

51. VIEW, LOOKING UPSTREAM, SHOWING THE REINFORCING FOR APRON BELOW ...  

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

51. VIEW, LOOKING UPSTREAM, SHOWING THE REINFORCING FOR APRON BELOW MAIN LOCK Photograph No. 1856. December 22, 1936 - Upper Mississippi River Nine-Foot Channel Project, Lock & Dam No. 25, Cap au Gris, Lincoln County, MO

268

10. VIEW OF MINIMUM FLOW CONTROL GATE STRUCTURE INSTALLED UPSTREAM ...  

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

10. VIEW OF MINIMUM FLOW CONTROL GATE STRUCTURE INSTALLED UPSTREAM FACE OF DAM 357 IN MID-1960s, LOOKING NORTHWEST - J. Clark Salyer National Wildlife Refuge, Dam 357, Along Lower Souris River, Kramer, Bottineau County, ND

269

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

270

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

271

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

272

OVERALL VIEW OF CASCADE CANAL COMPANY CRIB DAM, LOOKING UPSTREAM ...  

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

OVERALL VIEW OF CASCADE CANAL COMPANY CRIB DAM, LOOKING UPSTREAM FROM DIRECTION OF KACHESS DAM. VIEW TO NORTH - Kachess Dam, 1904 Cascade Canal Company Crib Dam, Kachess River, 1.5 miles north of Interstate 90 , Easton, Kittitas County, WA

273

1. Rockwork approximately 6 of a mile upstream from Keystone ...  

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

1. Rockwork approximately 6 of a mile upstream from Keystone Bridge. View looking south from a distance of 50 feet. - Denver & Rio Grande Rockwork, East of South Platte, Waterton, Jefferson County, CO

274

Detail of upstream fender system from subdeck pier cap. View ...  

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

Detail of upstream fender system from subdeck pier cap. View northwest - New York, New Haven & Hartford Railroad, Fort Point Channel Rolling Lift Bridge, Spanning Fort Point Channel, Boston, Suffolk County, MA

275

2. VIEW OF MAIN STORAGE RESERVOIR, SHOWING UPSTREAM SIDE OF ...  

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

2. VIEW OF MAIN STORAGE RESERVOIR, SHOWING UPSTREAM SIDE OF DAM AND DISCHARGE GATE (LEFT), LOOKING SOUTHWEST (October 1991) - Bonanza Hydraulic Mining Site, Main Storage Reservoir, Swamp Gulch, Salmon, Lemhi County, ID

276

4. VIEW SHOWING UPSTREAM FACE OF DAM, LOOKING NORTHEAST ...  

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

4. VIEW SHOWING UPSTREAM FACE OF DAM, LOOKING NORTHEAST - High Mountain Dams in Upalco Unit, Kidney Lake Dam, Ashley National Forest, 4.7 miles North of Miners Gulch Campground, Mountain Home, Duchesne County, UT

277

3. OVERALL VIEW OF DAM, SHOWING UPSTREAM FACE, LOOKING EAST ...  

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

3. OVERALL VIEW OF DAM, SHOWING UPSTREAM FACE, LOOKING EAST - High Mountain Dams in Upalco Unit, Kidney Lake Dam, Ashley National Forest, 4.7 miles North of Miners Gulch Campground, Mountain Home, Duchesne County, UT

278

7. Chandler Falls, looking upstream (from north). Golf tee of ...  

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

7. Chandler Falls, looking upstream (from north). Golf tee of the Mesa Country Club on right. Photographer: Mark Durben, February 1989. Source: SRPA - Tempe Canal, South Side Salt River in Tempe, Mesa & Phoenix, Tempe, Maricopa County, AZ

279

63. INTERIOR VIEW OF UPSTREAM LOCKKEEPER'S HOUSE, SHOWING FIRST FLOOR ...  

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

63. INTERIOR VIEW OF UPSTREAM LOCKKEEPER'S HOUSE, SHOWING FIRST FLOOR DINING ROOM, WITH ENTRY FRENCH DOORS IN RIGHT FOREGROUND, LOOKING NORTH - Upper Mississippi River 9-Foot Channel, Lock & Dam No. 10, Guttenberg, Clayton County, IA

280

29. Upstream face of spillway superstructure at left and HEFU ...  

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

29. Upstream face of spillway superstructure at left and HEFU service tower at right. Photographer Mark Durben, 1988. Source: Salt River Project. - Mormon Flat Dam, On Salt River, Eastern Maricopa County, east of Phoenix, Phoenix, Maricopa County, AZ

281

6. View northeast and upstream, west end of spillway to ...  

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

6. View northeast and upstream, west end of spillway to left, east end of spillway and east abutment to right - Sewall's Falls Hydroelectric Facility, East end of Second Street spanning Merrimack River, Concord, Merrimack County, NH

282

Transcription Start Site Evolution in Drosophila  

PubMed Central

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.

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

2013-01-01

283

Orographic Flow Response to Variations in Upstream Humidity  

Microsoft Academic Search

The effects of upstream relative humidity (RH) on low-level wind and precipitation patterns for low- speed, statically stable flows over a mountain are investigated using idealized two- and three-dimensional numerical-simulation experiments in which RH is increased from 0% to 100%. For RH less than some critical threshold, the flow upstream becomes less decelerated as RH is increased; for RH greater

Heather Dawn Reeves; Richard Rotunno

2008-01-01

284

A phycocyanin-deficient mutant of synechocystis PCC 6714 with a single-base substitution upstream of the cpc operon.  

PubMed

The structure and expression of the cpc operon encoding phycocyanin subunits and linker polypeptides in a phycocyanin-deficient mutant (PD-1) and the wild-type of Synechocystis PCC 6714 were analyzed. The results of sequence and Northern blot analyses of the wild type indicate that the cpc operon consists of cpcB, cpcA, cpcC1, cpcC2 and cpcD, in that order. The levels of the transcripts in PD-1 were one-tenth to one-sixth as high as those in the wild type. In the PD-1 genome, a single-base substitution of C for T has occurred at base 259 upstream of the translational initiation codon of cpcB (at three bases downstream of the putative -10 region). To evaluate the in vivo transcription activities of these promoters in a cyanobacterium, we constructed vectors for the transformation of Synechococcus PCC7942, pANY1 and pANY2, which contain the upstream region of cpcB of the wild type (pANY1) or PD-1 (pANY2) and the promoter-less luxAB fusion. The bioluminescence of the transformants with pANY2 was one-tenth to one-sixth as high as that with pANY1. The coincidence of the results of Northern analysis and the promoter assay shows that the phycocyanin deficiency of PD-1 is due to the single-base substitution in the upstream region of the cpc operon. PMID:11577194

Nakajima, Y; Fujiwara, S; Sawai, H; Imashimizu, M; Tsuzuki, M

2001-09-01

285

Nonlinear Evolution of the Upstream Edge of the Density Holes in the Solar Wind Upstream of the Bow Shock  

Microsoft Academic Search

In this study we present new observations of the nonlinear evolution of the upstream edge of the density hole into a shock-like structure. In 2003 the Cluster constellation was largely elongated in the Sun-Earth direction, with the maximum separation of ~1.5 RE. In this configuration the Cluster have observed the temporal evolution of the upstream edge of the density holes

E. Lee; G. K. Parks; M. Wilber; N. Lin; F. Mozer; E. Lucek; I. Dandouras; H. Reme

2006-01-01

286

Pyrrolysine is not hardwired for cotranslational insertion at UAG codons.  

PubMed

Pyrrolysine (Pyl), the 22nd naturally encoded amino acid, gets acylated to its distinctive UAG suppressor tRNA(Pyl) by the cognate pyrrolysyl-tRNA synthetase (PylRS). Here we determine the RNA elements required for recognition and aminoacylation of tRNA(Pyl) in vivo by using the Pyl analog N-epsilon-cyclopentyloxycarbonyl-l-lysine. Forty-two Methanosarcina barkeri tRNA(Pyl) variants were tested in Escherichia coli for suppression of the lac amber A24 mutation; then relevant tRNA(Pyl) mutants were selected to determine in vivo binding to M. barkeri PylRS in a yeast three-hybrid system and to measure in vitro tRNA(Pyl) aminoacylation. tRNA(Pyl) identity elements include the discriminator base, the first base pair of the acceptor stem, the T-stem base pair G51:C63, and the anticodon flanking nucleotides U33 and A37. Transplantation of the tRNA(Pyl) identity elements into the mitochondrial bovine tRNA(Ser) scaffold yielded chimeric tRNAs active both in vitro and in vivo. Because the anticodon is not important for PylRS recognition, a tRNA(Pyl) variant could be constructed that efficiently suppressed the lac opal U4 mutation in E. coli. These data suggest that tRNA(Pyl) variants may decode numerous codons and that tRNA(Pyl):PylRS is a fine orthogonal tRNA:synthetase pair that facilitated the late addition of Pyl to the genetic code. PMID:17360621

Ambrogelly, Alexandre; Gundllapalli, Sarath; Herring, Stephanie; Polycarpo, Carla; Frauer, Carina; Söll, Dieter

2007-02-20

287

Identification of a pH-responsive DNA region upstream of the transcription start site of human NBCe1-B  

PubMed Central

In rodent incisors two distinct stages of enamel formation can be identified visually based on cell morphology: the secretory stage and the maturation stage. The expression profiles of many genes characterize both stages, including the bicarbonate transport protein NBCe1. Bicarbonate is a requirement for the mineralizing enamel matrix to buffer excessive protons that form as a consequence of hydroxyapatite formation. NBCe1-B mRNA is up-regulated during the maturation stage of amelogenesis, where hydroxyapatite formation predominates. In this study, a presumed 572-bp NBCe1-B promoter region was subcloned into a reporter construct, and within this 572-bp region of DNA we characterized a 285-bp segment that shows an increase of ~ 2.3-fold in gene-transcription activity when transfected into ameloblast-like cells and cultured in medium maintained at pH 6.8 (vs. pH 7.4). A presumed pH-responsive transcriptional factor-binding domain(s) thus resides in the 285-bp NBCe1-B promoter region where candidate domains include the nuclear factor of kappa light polypeptide gene enhancer in B-cells1(NFKB1), jun proto-oncogene (JUN), and tumor protein p53(TP53)-binding sites. Mutagenesis studies identify that both the NFKB1- and TP53-binding sites are responsive to changes in the extracellular pH. These data help to explain how ameloblasts respond to the altered extracellular milieu of protons by changing their gene-expression profile throughout the stages of amelogenesis.

Snead, Christian M.; Smith, Susan M.; Sadeghein, Negar; Lacruz, Rodrigo S.; Hu, Ping; Kurtz, Ira; Paine, Michael L.

2012-01-01

288

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

PubMed Central

Although the surface proteins of human influenza A virus evolve rapidly and continually produce antigenic variants, the internal viral genes acquire mutations very gradually. In this paper, we analyze the sequence evolution of three influenza A genes over the past two decades. We study codon usage as a discriminating signature of gene- and even residue-specific diversifying and purifying selection. Nonrandom codon choice can increase or decrease the effective local substitution rate. We demonstrate that the codons of hemagglutinin, particularly those in the antibody-combining regions, are significantly biased toward substitutional point mutations relative to the codons of other influenza virus genes. We discuss the evolutionary interpretation and implications of these biases for hemagglutinin's antigenic evolution. We also introduce information-theoretic methods that use sequence data to detect regions of recent positive selection and potential protein conformational changes.

Plotkin, Joshua B.; Dushoff, Jonathan

2003-01-01

289

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

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

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

290

Good Codons, Bad Transcript: Large Reductions in Gene Expression and Fitness Arising from Synonymous Mutations in a Key Enzyme  

PubMed Central

Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely encoded by a specific subset of possible codons. Within individual genes, codon bias is stronger at evolutionarily conserved residues, favoring codons recognized by abundant tRNAs. Although this observation suggests an overall pattern of selection for translation speed and/or accuracy, other work indicates that transcript structure or binding motifs drive codon usage. However, our understanding of codon bias evolution is constrained by limited experimental data on the fitness effects of altering codons in functional genes. To bridge this gap, we generated synonymous variants of a key enzyme-coding gene in Methylobacterium extorquens. We found that mutant gene expression, enzyme production, enzyme activity, and fitness were all significantly lower than wild-type. Surprisingly, encoding the gene using only rare codons decreased fitness by 40%, whereas an allele coded entirely by frequent codons decreased fitness by more than 90%. Increasing gene expression restored mutant fitness to varying degrees, demonstrating that the fitness disadvantage of synonymous mutants arose from a lack of beneficial protein rather than costs of protein production. Protein production was negatively correlated with the frequency of motifs with high affinity for the anti-Shine-Dalgarno sequence, suggesting ribosome pausing as the dominant cause of low mutant fitness. Together, our data support the idea that, although a particular set of codons are favored on average across a genome, in an individual gene selection can either act for or against codons depending on their local context.

Agashe, Deepa; Martinez-Gomez, N. Cecilia; Drummond, D. Allan; Marx, Christopher J.

2013-01-01

291

INFLUENCE OF UPSTREAM WIND SHEAR AND TURBULENCE ON THE WIND PATTERN AND POLLUTANT CONCENTRATIONS WITHIN STREET CANYONS: A NUMERICAL SIMULATION STUDY  

EPA Science Inventory

This study serves as a start of future research on the subject. his study shows that the canyon geometry and the upstream boundary conditions have significant influences on the flow and concentration fields in the vicinity of urban street canyons. ollutants emitted within a canyo...

292

Characterizing the native codon usages of a genome: an axis projection approach.  

PubMed

Codon usage can provide insights into the nature of the genes in a genome. Genes that are "native" to a genome (have not been recently acquired by horizontal transfer) range in codon usage from a low-bias "typical" usage to a more biased "high-expression" usage characteristic of genes encoding abundant proteins. Genes that differ from these native codon usages are candidates for foreign genes that have been recently acquired by horizontal gene transfer. In this study, we present a method for characterizing the codon usages of native genes--both typical and highly expressed--within a genome. Each gene is evaluated relative to a half line (or axis) in a 59D space of codon usage. The axis begins at the modal codon usage, the usage that matches the largest number of genes in the genome, and it passes through a point representing the codon usage of a set of genes with expression-related bias. A gene whose codon usage matches (does not significantly differ from) a point on this axis is a candidate native gene, and the location of its projection onto the axis provides a general estimate of its expression level. A gene that differs significantly from all points on the axis is a candidate foreign gene. This automated approach offers significant improvements over existing methods. We illustrate this by analyzing the genomes of Pseudomonas aeruginosa PAO1 and Bacillus anthracis A0248, which can be difficult to analyze with commonly used methods due to their biased base compositions. Finally, we use this approach to measure the proportion of candidate foreign genes in 923 bacterial and archaeal genomes. The organisms with the most homogeneous genomes (containing the fewest candidate foreign genes) are mostly endosymbionts and parasites, though with exceptions that include Pelagibacter ubique and Beutenbergia cavernae. The organisms with the most heterogeneous genomes (containing the most candidate foreign genes) include members of the genera Bacteroides, Corynebacterium, Desulfotalea, Neisseria, Xylella, and Thermobaculum. PMID:20679093

Davis, James J; Olsen, Gary J

2010-08-02

293

Leakiness of termination codons in mitochondrial mutants of the yeast Saccharomyces cerevisiae  

Microsoft Academic Search

Seven mutants in exon 1 of the mitochondrial cob gene in yeast are described with respect to their translation products, RNA pattern, and deoxyribonucleotide sequence alteration(s). Sequence analysis of the mutations, which previously were shown to cause premature termination of apocytochrome b, revealed that two of them directly transform sense codons to chain-termination codons, whereas the other four are frame-shift

Brigitte Weiss-Brummer; Alexander Hiittenhofer; Fritz Kaudewitz

1984-01-01

294

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

Microsoft Academic Search

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

Brendan P. Cormack; Kevin Struhl

1993-01-01

295

Doublet frequencies and codon weighting in the DNA of Escherichia coli and its phages  

Microsoft Academic Search

Summary A compilation of nucleic acid sequences fromE.coli and its phages has been analysed for the frequency of occurrence of nearest neighbour base doublets and codons. Several statistically significant deviations from random are found in both doublet and codon frequencies. The deviations inE.coli also appear to occur in ? and in the coat protein gene of MS2, whereas T4 and

R. A. Elton; G. J. Russell; J. H. Subak-Sharpe

1976-01-01

296

tRNA properties help shape codon pair preferences in open reading frames  

Microsoft Academic Search

Translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of tRNAs in the ribosomal A- and P-sites. Here, we sought evidence of A- and P-site tRNA interaction by examining bias in codon pair choice within open reading frames from a range of genomes. Three dis- tinct and marked effects were revealed once codon and dipeptide biases had

J. Ross Buchan; Lorna S. Aucott; Ian Stansfield

2006-01-01

297

tRNA proper ties help shape codon pair preferences in open reading frames  

Microsoft Academic Search

Translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of tRNAs in the ribosomal A- and P-sites. Here, we sought evidence of A- and P-site tRNA interaction by examining bias in codon pair choice within open reading frames from a range of genomes. Three dis- tinct and marked effects were revealed once codon and dipeptide biases had

J. Ross Buchan; Lorna S. Aucott; Ian Stansfield

298

Relationship Between p53 Codon 72 Polymorphism and Susceptibility to Sunburn and Skin Cancer  

Microsoft Academic Search

Upregulation of p53 protein induces either growth arrest or apoptosis in response to cellular injury This is signaled from a highly conserved p53 domain between codons 64 and 92, where a functional polymorphism results in either a proline (p53-72P) or an arginine (p53-72R) at codon 72. Preliminary studies suggest that p53-72R may be a risk factor for cervical cancer and,

Jane M. McGregor; Catherine A. Harwood; Louise Brooks; Sheila A. Fisher; Deirdre A. Kelly; Jenny O'nions; Antony R. Young; Thiru Surentheran; Judith Breuer; Thomas P. Millard; Cathryn M. Lewis; Irene M. Leigh; Alan Storey; Timothy Crook

2002-01-01

299

764. RNA and Codon Optimized HIV Candidate Vaccines - from Bench to Clinical Trials  

Microsoft Academic Search

As recently demonstrated, extensive codon-usage modifications increased the overall GC content of late HIV transcripts by almost 30%, enhanced the nuclear stability of viral RNAs and resulted in a constitutive export of these RNAs into the cytoplasm. Besides, codon-usage modifications tremendously supported Rev-independent viral gene expression and significantly increased the safety of related vaccine constructs by reducing the risk for

Ralf Wagner; Petra Mooij; Sunita Balla; Jens Wild; Kurt Bieler; Hans Wolf; Frank Notka; Jonathan Heeney; Giuseppe Pantaleo

2005-01-01

300

Codon reassignment and amino acid composition in hemichordate mitochondria (Balanoglossus carnosusycodon captureygenetic code changeyneutral theoryyprotein evolution)  

Microsoft Academic Search

In the mitochondrial genome of the hemi- chordate Balanoglossus carnosus, the codon AAA, which is assigned to lysine in most metazoans but to asparagine in echinoderms, is absent. Furthermore, the lysine tRNA gene carries an anticodon substitution that renders its gene prod- uct unable to decode AAA codons, whereas the asparagine tRNA gene has not changed to encode a tRNA

JOSE CASTRESANA; GERTRAUD FELDMAIER-FUCHS; SVANTE PAABO

301

Codon usage and G+C content in Bradyrhizobium japonicum genes are not uniform  

Microsoft Academic Search

To date, the sequences of 45 Bradyrhizobium japonicum genes are known. This provides sufficient information to determine their codon usage and G+C content. Surprisingly, B. japonicum nodulation and NifA-regulated genes were found to have a less biased codon usage and a lower G+C content than genes not belonging to these two groups. Thus, the coding regions of nodulation genes and

Tom M. Ramseier; Michael Giittfert

1991-01-01

302

Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum  

Microsoft Academic Search

Here, the codon usage patterns of two Clostridium species (Clostridium perfringens and Clostridium acetobutylicum) are reported. These prokaryotes are characterized by a strong mutational bias towards A+T, a striking excess of coding sequences and purine-rich leading strands of replication, strong GC-skews and a high frequency of genomic rearrangements. As expected, it was found that the mutational bias dominates codon usage

Hector Musto; Hector Romero; Alejandro Zavala

2003-01-01

303

Two-nucleotide codon change in a hemoglobin polymorphism of the Celebes black ape (Macaca nigra).  

PubMed

A hemoglobin polymorphism involving variant beta-chains was demonstrated in the Celebes black ape, Macaca nigra. Fingerprinting and amino acid analysis of the tryptic peptides from the two chain types have shown that they differ by a single amino acid substitution, between lysine and aspartic acid, which requires a two-nucleotide change in the corresponding codon. Another substitution in the same codon is found as a species between the black ape and that of other macaques. PMID:816351

Murata, M; Thompson, P E

1976-02-01

304

Genetic Polymorphism in p53 Codon 72 and Skin Cancer in Southwestern Taiwan  

Microsoft Academic Search

The Pro\\/Pro polymorphism of p53 codon 72 has been reported to be related to bladder and lung cancer, but its relationship with skin cancer is unclear. We assessed the hypothesis that there is a relationship between the p53 codon 72, Pro\\/Pro polymorphism, cumulative arsenic exposure, and the risk of skin cancer in a hospital-based case–control study in southwestern Taiwan. From

Yen-Ching Chen; Lilian Xu; Yu-Liang Leon Guo; Huey-Jen Jenny Su; Yu-Mei Hsueh; Thomas J. Smith; Louise M. Ryan; Meei-Shyuan Lee; Sheau-Chiou Chaor; Julia Yu-Yun Lee; David C. Christiani

2003-01-01

305

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

PubMed

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

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

2013-10-10

306

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

PubMed Central

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

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

2013-01-01

307

Too Smart to Start: Teens  

MedlinePLUS

... Smart To Start, your Web site on avoiding underage alcohol use and its consequences. We’re glad that ... affects your body and your behavior. Facts About Underage Drinking : Learn about alcohol facts, myths, consequences, and more. ...

308

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

309

Design of the START experiment  

SciTech Connect

The START experiment (Small Tight Aspect Ratio Tokamak) is a low-budget device under construction that is specifically intended to investigate MHD behavior at extremely tight aspect ratios (as low as R/a-1.2) as well as the effectiveness of a major radius compression technique to produce high toroidal current in such plasmas. The main components of the START assembly are described along with the mode of operation.

Smith, R.T.C. [UKAEA Fusion, Culham UK; Peng, Yueng Kay Martin [ORNL

1989-01-01

310

Experimental Measurements of Starting Loads and Model Behaviors in the Indraft Supersonic Wind Tunnel  

NASA Astrophysics Data System (ADS)

Measurements of starting load in the indraft supersonic wind tunnel of Muroran Institute of Technology were conducted for Mach 2, 3 and 4 conditions with the AGARD-B model. The high-speed photographs covering the behaviors of the wind tunnel model from the start to end of the operation were taken. Those photographs make clear that the oscillations of the model coincide with the measured starting load oscillation and starting loads were caused by two shock waves. The first shock wave is the reflection shock, generated at the nozzle throat by expansion wave reflection. The second wave is comprised asymmetric oblique shock waves (AOS) coming from upstream. AOS can generate asymmetric conical shock (ACS) around the nose cone of the model, which would have directly caused the starting loads on the wind tunnel model. Based on these observations, propose a conical shock theory, as an alternative starting load prediction theory instead of the normal shock theory.

Minato, Ryojiro; Mizobata, Kazuhide; Kuwata, Komei

311

Mechanism of controlling supersonic cavity oscillations using upstream mass injection  

NASA Astrophysics Data System (ADS)

The mechanism of controlling supersonic cavity oscillations using upstream mass injection is investigated by implicit large-eddy simulations of a turbulent flow (M? = 2.0, ReD = 105) past a rectangular cavity with a length-to-depth ratio of 2. The mass injection is simulated by specifying a vertical velocity profile of a jet ejecting steadily through a slot placed at the upstream of the cavity leading edge. The results show that the steady upstream mass injection produces significant attenuation of the cavity oscillations, and two primary mechanisms are demonstrated to be directly responsible for the noise suppression: lifting up of the cavity shear layer, and damping of the shear-layer instability. It is found that the case of low mass flow injection investigated is more effective in stabilizing the cavity shear layer than the high mass flow injection. A transition stage might exist between two well-developed oscillating modes, but ``mode-switching'' is not observed.

Li, Weipeng; Nonomura, Taku; Fujii, Kozo

2013-08-01

312

Effects of shock parameters on upstream energetic electron burst events  

NASA Astrophysics Data System (ADS)

Recent simulation results have revealed that energetic electron bursts are produced cyclically at the shock reformation period upstream of reforming shocks and are qualitatively very different from the continuous beam expected from time-stationary shocks (Yuan et al., 2007a). This paper extends our previous studies by numerically investigating the dependence of electron burst events on shock parameters (the upstream plasma ? and Mach number MA). The test particle approximation is made for electrons, and the electron trajectories are traced exactly in the time-dependent electromagnetic field profiles, generated by one-dimensional hybrid simulation code. Simulation results indicate that the upstream incoming electrons can be reflected nonuniformly or continuously depending on the shock parameters. Bursty energetic electron events take place when the plasma beta is low (? ? 0.4) and the shock Mach number is high (MA ? 6). Time-varying loss cone, beam, and ring beam features are observed in the upstream electron distribution functions. The beam density, speed, average kinetic energy, and speed spread cyclically change with time by factor of ˜2-4. In contrast, continuously reflected electrons are observed for low beta (? ? 0.4), low Mach number (MA ? 4) shocks, even when the shock is reforming because the changes in shock fields are relative small. The electron burst events disappear and the observed upstream electron distribution function contours are steady state. A continuous electron beam is formed, which is qualitative the same as the beam from steady-state shocks. Increasing the plasma beta (providing the shock is still reforming) has minor effects on the upstream electron beam features.

Yuan, Xingqiu; Cairns, Iver H.; Trichtchenko, Larisa; Rankin, Robert

2008-09-01

313

Functional Significance of an Evolutionarily Conserved Alanine (GCA) Resume Codon in tmRNA in Escherichia coli?  

PubMed Central

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.

Kapoor, Suman; Samhita, Laasya; Varshney, Umesh

2011-01-01

314

A mammalian sequence-dependent upstream open reading frame mediates polyamine-regulated translation in yeast.  

PubMed Central

In mammals, control of S-adenosylmethionine decarboxylase (AdoMetDC) translation is one component of a feedback network that regulates intracellular levels of the polyamines, spermidine, and spermine. AdoMetDC mRNA from mammals contains a highly conserved upstream open reading frame (uORF) within its leader sequence that confers polyamine-regulated suppression of translation on the associated downstream cistron. This regulation is mediated through an interaction that depends on the amino acid sequence of the uORF-encoded hexapeptide. It remains to be shown whether polyamines participate directly in this interaction or indirectly through a specialized signal transduction pathway. We show that Saccharomyces cerevisiae does not have a uORF associated with its AdoMetDC gene (SPE2) and that ribosome loading on the SPE2 mRNA is not positively influenced by polyamine depletion, as it is in mammalian cells. Nevertheless, the mammalian AdoMetDC uORF, when introduced into a polyamine auxotroph of yeast, conferred polyamine regulation of both translational efficiency and ribosome loading on the associated mRNA. This regulatory activity depended on the amino acid sequence encoded by the fourth and fifth codons of the uORF, as in mammalian cells. The fact that the regulatory properties of this mammalian translational control element are quite similar in both mammalian and yeast cells suggests that a specialized signal transduction pathway is not required. Rather, it seems likely that polyamines may be directly participating in an interaction between the uORF-encoded peptide and a constitutive component of the translation machinery, which leads to inhibition of ribosome activity.

Mize, G J; Morris, D R

2001-01-01

315

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

PubMed Central

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.

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

2012-01-01

316

Stiffness and leakage in spiral groove upstream pumping mechanical seals  

NASA Astrophysics Data System (ADS)

A numerical analysis of the lubricating film in spiral groove upstream pumping mechanical seals, accounting for the occurrence of cavitation, has been performed. Axial stiffness and leakage rate have been determined as functions of the operating conditions and design parameters. Results indicate that properly designed spiral groove upstream pumping seals will perform well in a double seal arrangement, with good stiffness characteristics and negative leakage of the buffer fluid. However, results also suggest that such seals will operate poorly as single seals, due to negative stiffness resulting from excessive cavitation.

Salant, Richard F.; Homiller, Stephen J.

1993-01-01

317

Identification of cis-acting regulatory regions upstream of the rRNA operons of Rhodobacter sphaeroides.  

PubMed Central

The promoter region(s) for the rRNA operons of Rhodobacter sphaeroides was identified. By utilizing both in vivo and in vitro techniques, the transcriptional start sites of all three operons were identified. Upstream of the transcriptional start, -10 and -35 promoter regions that bear little similarity to typical Escherichia coli promoter sequences were identified. In addition to the promoter sequences, probable Fis protein-binding sites were identified upstream of all three rRNA operons. Transcriptional fusions of the promoter regions from rrnA and rrnB were constructed by utilizing the reporter molecule encoded by xylE and analyzed under various growth conditions, in both a wild-type background and an rrnBC mutant background. Production of the xylE gene product (catechol 2,3-dioxygenase) was always greatest under photosynthetic growth conditions. However, the upstream region of rrnB, when fused with xylE, produced significantly more catechol 2,3-dioxygenase than did analogous regions of rrnA, suggesting that the promoters of the rrn operons differ in strength. These results were further confirmed by the study of mutant strains altered for the rrn operons either singly or in combination. Little or no expression of the xylE gene was manifest in E. coli when directed by rDNA sequences derived from R. sphaeroides. Images

Dryden, S C; Kaplan, S

1993-01-01

318

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality  

PubMed Central

Circadian rhythms are oscillations in biological processes that function as a key adaptation to the daily rhythms of most environments. In the model cyanobacterial circadian clock system, the core oscillator proteins are encoded by the gene cluster kaiABC1. Genes with high expression and functional importance like the kai genes are usually encoded by optimal codons, yet the codon usage bias of the kaiBC genes is not optimized for translational efficiency. We discovered a relationship between codon usage and a general property of circadian rhythms called conditionality; namely, that endogenous rhythmicity is robustly expressed under some environmental conditions but not under others2. Despite the generality of circadian conditionality, however, its molecular basis is unknown for any system. Here we show that non-optimal codon usage was selected as a post-transcriptional mechanism to switch between circadian and non-circadian regulation of gene expression as an adaptive response to environmental conditions. When the kaiBC sequence was experimentally optimized to enhance expression of the KaiB and KaiC proteins, intrinsic rhythmicity was enhanced at cool temperatures that are experienced by this organism in its natural habitat. However, fitness at those temperatures was highest in cells whose endogenous rhythms were suppressed at cool temperatures as compared with cells exhibiting high-amplitude rhythmicity. These results indicate natural selection against circadian systems in cyanobacteria that are intrinsically robust at cool temperatures. Modulation of circadian amplitude is therefore critical to its adaptive significance3. Moreover, these results show the direct effects of codon usage on a complex phenotype and organismal fitness. Our work also challenges the long-standing view of directional selection towards optimal codons4–7, and provides a key example of natural selection against optimal codon to achieve adaptive responses to environmental changes.

Xu, Yao; Ma, Peijun; Shah, Premal; Rokas, Antonis; Liu, Yi; Johnson, Carl Hirschie

2013-01-01

319

Parents Should Start Talking Before They Start Drinking  

Microsoft Academic Search

Most Oakland County youth who drink alcohol usually began drinking in the seventh, eighth or ninth grades. When youth drink alcohol at such young ages, serious harm begins. More children are killed by alcohol than all illegal drugs combined. In addition, children who begin drinking alcohol before the age of 15 are 5 times more likely than those who start

Donnis Reese

320

A synonymous codon variant in two patients with autosomal recessive bestrophinopathy alters in vitro splicing of BEST1  

PubMed Central

Purpose Autosomal recessive bestrophinopathy (ARB) is a newly defined retinal dystrophy caused by biallelic mutations in bestrophin-1 (BEST1) and is hypothesized to represent the null bestrophin-1 phenotype in humans. The aim was to determine whether a synonymous BEST1 variant, c.102C>T, identified in two unrelated ARB patients, alters pre-mRNA splicing of the gene. Additionally a detailed phenotypic characterization of this distinctive condition is presented for both patients. Methods BEST1 was analyzed by direct sequencing. Patients underwent standard ophthalmic assessment. In silico and in vitro analysis using a minigene system was performed to assess whether a synonymous variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing of BEST1. Results Both ARB patients harbored either proven (patient 1; c.102C>T p.Gly34Gly and c.572T>C p.Leu191Pro) or presumed (patient 2; c.102C>T p.Gly34Gly and c.1470_1471delCA, p.His490GlnfsX24) biallelic mutations in BEST1 and were found to have phenotypes consistent with ARB. In vitro analysis of the synonymous variant, c.102C>T p.Gly34Gly, demonstrated it to introduce a cryptic splice donor site 52 nucleotides upstream of the actual splice donor site. Conclusions The novel BEST1 variant identified, c.102C>T p.Gly34Gly, alters pre-mRNA splicing in vitro and is potentially pathogenic. In vivo this splicing variant is predicted to lead to the production of an mRNA transcript with a premature termination codon (p.Glu35TrpfsX11) that is predicted to be degraded by NMD.

Davidson, Alice E.; Sergouniotis, Panagiotis I.; Burgess-Mullan, Rosemary; Hart-Holden, Nichola; Low, Sancy; Foster, Paul J.; Manson, Forbes D.C.; Black, Graeme C.M.

2010-01-01

321

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

322

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

PubMed Central

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

Carlini, David B; Stephan, Wolfgang

2003-01-01

323

Non-universal decoding of the leucine codon CUG in several Candida species.  

PubMed Central

It has been reported that CUG, a universal leucine codon, is read as serine in an asporogenic yeast, Candida cylindracea. The distribution of this non-universal genetic code in various yeast species was studied using an in vitro translation assay system with a synthetic messenger RNA containing CUG codons in-frame. It was found that CUG is used as a serine codon in six out of the fourteen species examined, while it is used for leucine in the remaining eight. The tRNA species responsible for the translation of codon CUG as serine was detected in all the six species in which CUG is translated as serine. The grouping according to the CUG codon assignments in these yeast species shows a good correlation with physiological classification by the chain lengths of the isoprenoid moiety of ubiquinone and the cell-wall sugar contained in the yeasts. The six Candida species examined in which CUG is used as serine belong to one distinct group in Hemiascomycetes.

Ohama, T; Suzuki, T; Mori, M; Osawa, S; Ueda, T; Watanabe, K; Nakase, T

1993-01-01

324

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

PubMed Central

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.

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

2009-01-01

325

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

326

Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data  

PubMed Central

We have analyzed synonymous codon usage in the genome of A. tamarense CCMP 1598 for protein-coding sequences from 10865 expressed sequence tags (ESTs). We reconstructed a total of 4284 unigenes, including 74 ribosomal protein and 40 plastid-related genes, from ESTs using FrameDP, an open reading frame (ORF) prediction program. Correspondence analysis of A. tamarense genes based on codon usage showed that the GC content at the third base of synonymous codons (GC3s) was strongly correlated with the first axis (r = 0.93 with P < .001). On the other hand, the second axis discriminated between presumed highly and low expressed genes, with expression levels being confirmed by the analysis of EST frequencies (r = ?0.89 with P < .001). Our results suggest that mutational bias is the major factor in shaping codon usage in A. tamarense genome, but other factors, namely, translational selection, hydropathy, and aromaticity, also appear to influence the selection of codon usage in this species.

Hsiao, Yi-Yuong; Lin, Chorng-Horng; Liu, Jong-Kang; Wong, Tit-Yee; Kuo, Jimmy

2010-01-01

327

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

328

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

329

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

330

VIEW OF UPSTREAM (EAST) SIDES OF UPPER (EAST) END OF ...  

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

VIEW OF UPSTREAM (EAST) SIDES OF UPPER (EAST) END OF LOCK, SOUTHEAST AND NORTHEAST CONTROL HOUSES, LOCK UNDER REPAIR, BUILDING NOS. 51, 52 AND SOUTHWEST CONTROL HOUSE IN BACKGROUND, VIEW TOWARDS WEST-NORTHWEST - Ortona Lock, Lock No. 2, Machinery and Control Houses, Caloosahatchee River, Cross-State Canal, Okeechobee Intracoastal Waterway, Ortona, Glades County, FL

331

Multilateral drilling, seismic acquisition top upstream technology needs  

Microsoft Academic Search

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

Rappold

1995-01-01

332

Capital is in short supply for upstream operations  

SciTech Connect

National oil companies are struggling to earn revenue needed to fund additional upstream development that could boost their sagging earnings. This vicious circle has exacerbated economic chaos in several nations, resulting in civil strife and political unrest that further impact these companies' performance.

Muller, H. (Argentina Correspondent, Buenos Aires (AR))

1989-08-01

333

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

334

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

335

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

336

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

337

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

338

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

339

1. View looking upstream (southwest) at diversion dam. Water enters ...  

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

1. View looking upstream (southwest) at diversion dam. Water enters half-round flume on right. Break in diversion structure provides a view of water flow in flume during the high water runoff in June. - Rock Creek Hydroelectric Project, Rock Creek, Baker County, OR

340

9. Oblique view to southsouthwest of upstream (east) side of ...  

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

9. Oblique view to south-southwest of upstream (east) side of bridge from near north abutment in Jacob Meyer Park. Note cutwaters on piers, distinctive appearance of boxed, repaired vertical compression members as compared to original, laced compression members. - Stanislaus River Bridge, Atchison, Topeka & Santa Fe Railway at Stanislaus River, Riverbank, Stanislaus County, CA

341

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters  

Microsoft Academic Search

Studies have shown that the bulk of eukaryotic genomes is transcribed. Transcriptome maps are frequently updated, but low-abundant transcripts have probably gone unnoticed. To eliminate RNA degradation, we depleted the exonucleolytic RNA exosome from human cells and then subjected the RNA to tiling microarray analysis. This revealed a class of short, polyadenylated and highly unstable RNAs. These promoter upstream transcripts

Pascal Preker; Jesper Nielsen; Susanne Kammler; Søren Lykke-Andersen; Marianne S. Christensen; Christophe K. Mapendano; Mikkel H. Schierup; Torben Heick Jensen

2008-01-01

342

15. UPSTREAM VIEW (PHOTOGRAPHER UNKNOWN) SHOWING BIG DALTON DAM NEAR ...  

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

15. UPSTREAM VIEW (PHOTOGRAPHER UNKNOWN) SHOWING BIG DALTON DAM NEAR FULL CAPACITY AFTER CONSTRUCTION. PICTURE WAS DEVELOPED FROM COPY NEGATIVES WHICH WERE TAKEN ON 2-15-1973 BY PHOTOGRAPHER D. MEIER OF L.A. COUNTY PUBLIC WORKS. - Big Dalton Dam, 2600 Big Dalton Canyon Road, Glendora, Los Angeles County, CA

343

14. VIEW OF THE UPSTREAM ELEVATION SHOWING CONSTRUCTION OF THE ...  

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

14. VIEW OF THE UPSTREAM ELEVATION SHOWING CONSTRUCTION OF THE ARCHES NEAR THE TOP OF THE DAM TAKEN IN 1928-1929 (PHOTOGRAPHER UNKNOWN). PICTURE WAS DEVELOPED FROM COPY NEGATIVES WHICH WERE TAKEN ON 2-15-1973 BY PHOTOGRAPHER D. MEIER OF L.A. COUNTY PUBLIC WORKS. - Big Dalton Dam, 2600 Big Dalton Canyon Road, Glendora, Los Angeles County, CA

344

12. VIEW OF UPSTREAM ELEVATION SHOWING CONSTRUCTION OF THE ARCHES ...  

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

12. VIEW OF UPSTREAM ELEVATION SHOWING CONSTRUCTION OF THE ARCHES TAKEN ON NOVEMBER 21, 1928 (PHOTOGRAPHER UNKNOWN). PICTURE WAS DEVELOPED FROM COPY NEGATIVES WHICH WERE TAKEN ON 6/5/1973 BY PHOTOGRAPHER GATSON OF L.A. COUNTY PUBLIC WORKS. - Big Dalton Dam, 2600 Big Dalton Canyon Road, Glendora, Los Angeles County, CA

345

UPSTREAM (WEST) VIEW SHOWING SOUTH EMBANKMENT BERM AND CONCRETE COREWALL ...  

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

UPSTREAM (WEST) VIEW SHOWING SOUTH EMBANKMENT BERM AND CONCRETE COREWALL AT CENTER, WITH COOKE DAM POND AT LEFT AND POWERHOUSE (MI-98-C) AND SPILLWAY (MI-98-B) IN BACKGROUND. VIEW TO NORTHEAST - Cooke Hydroelectric Plant, South Embankment, Cook Dam Road at Au Sable River, Oscoda, Iosco County, MI

346

COOKE DAM POND AND UPSTREAM (WEST) SIDE OF (LR) NORTH ...  

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

COOKE DAM POND AND UPSTREAM (WEST) SIDE OF (L-R) NORTH EMBANKMENT (MI-98-A), SPILLWAY (MI-98-B), PENSTOCK ENTRANCES, POWERHOUSE (MI-98-C), AND SOUTH EMBANKMENT (MI-98-E). VIEW TO NORTHEAST - Cooke Hydroelectric Plant, Cook Dam Road at Au Sable River, Oscoda, Iosco County, MI

347

The Management of Flexibility in the Upstream Petroleum Industry  

Microsoft Academic Search

This paper is the third in a series that describes how Modern Asset Pricing (MAP) may be used for project evaluation in the upstream petroleum industry. It demonstrates how MAP can be applied to projects where policies for the management of future flexibility must be considered within the context of the valuation. We illustrate this use of MAP by looking

David Laughton

1998-01-01

348

View of Stehr Lake from FS 502 looking upstream (northeast). ...  

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

View of Stehr Lake from FS 502 looking upstream (northeast). Vehicle at right center is parked on earthen Upper Stehr Lake Dam. - Childs-Irving Hydroelectric Project, Childs System, Stehr Lake & Dams, Forest Service Road 708/502, Camp Verde, Yavapai County, AZ

349

DESCHUTES PROJECT ? WICKIUP DAM ? VIEW OF UPSTREAM FACE ...  

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

DESCHUTES PROJECT ? WICKIUP DAM ? VIEW OF UPSTREAM FACE FROM RIGHT ABUTMENT. CPS CREW PLACING RIPRAP. Photocopy of historic photographs (original photograph on file at National Archives, Rocky Mountain Region, Denver, CO). Unknown USBR Photographer, July 26, 1944 - Wickiup Dam, Deschutes River, La Pine, Deschutes County, OR

350

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 west. Construction of the forebay dam, which replaced the eastern end of the original Grand Coulee Dam, was completed in 1974. - Columbia Basin Project, Grand Coulee Dam & Franklin D. Roosevelt Lake, Across Columbia River, Southeast of Town of Grand Coulee, Grand Coulee, Grant County, WA

351

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

352

32. AERIAL VIEW OF TIETON DAM, UPSTREAM FACE OF DAM ...  

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

32. AERIAL VIEW OF TIETON DAM, UPSTREAM FACE OF DAM (Trashrack-structure for outlet at lower left in reservoir, spillway at upper left. Reservoir nearly empty due to drought.) - Tieton Dam, South & East of State Highway 12, Naches, Yakima County, WA

353

Compaction of Upstream Construction Tailings Dam Beaches Using Dozers  

Microsoft Academic Search

Upstream construction tailings dams in the oilsands mining industry rely on a compacted shell and beaches of non- liquefiable sand to contain the pond and internal loose beach deposits. Compaction energy to densify the sand in the shell is provided by dozers which densify the sand through the vibration of trafficking repeatedly across the sand surface, together with the downward

Scott Martens; Tyler Lappin

354

UPSTREAM EFFECTS OF GENERIC ADVERTISING: THE CASE OF CATFISH  

Microsoft Academic Search

Muth's model is adapted to determine the effects of generic advertising on upstream factor markets in a competitive industry where funds for promotion are raised through a feed tax. Optimality conditions indicate that a feed tax is an inferior funding mechanism. That is, the resulting promotion budget, in general, is too small to maximize producer surplus at the farm level.

Henry W. Kinnucan; Laxmi Paudel

2001-01-01

355

Therapeutic anti-cancer targets upstream of the proteasome  

Microsoft Academic Search

Polyubiquitination of a protein is generally the first step in its degradation. This article discusses how altered protein destruction pathways impact the cell cycle and allow for abnormal cell proliferation, and explores how this process can be utilized in anticancer therapy. There are several levels of possible therapeutic intervention in ubiquitin-dependent proteolysis pathways upstream of the proteasome. In principle, targeting

Grzegorz Nalepa; J Wade Harper

2003-01-01

356

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

357

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.

358

Head Start Center Design Guide.  

National Technical Information Service (NTIS)

This design guide contains suggested criteria for planning, designing, and renovating Head Start centers. The centent is based on the U.S. Gneral Services Administration's Child Care Center Design Guide, PBS-P140, which was intended for use in developing ...

2000-01-01

359

Head Start Dental Health Curriculum.  

ERIC Educational Resources Information Center

|This curriculum for Head Start programs provides preschool learning experiences that teach about dental health. The majority of the curriculum guide is devoted to the following lesson plans: (1) "Introduction of 'Smiley the Super Pup'," an optional puppet character which may be used to review the concepts covered in each lesson; (2) "Visiting the…

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

360

HANDBOOK FOR PROJECT HEAD START.  

ERIC Educational Resources Information Center

THIS BOOKLET WAS DESIGNED TO MEET SOME IMMEDIATE NEEDS FOR THE FIRST SUMMER SESSION OF PROJECT HEAD START. IT CONTAINS SOME OF THE MOST WORKABLE AND PROMISING TEACHING METHODS IN THE ENTIRE FIELD OF COMPENSATORY EDUCATIONS, METHODS THAT HAVE BEEN USED IN PRIVATELY SPONSORED CENTERS AND HAVE PROVED VALUABLE IN COPING WITH PROBLEMS ENCOUNTERED IN…

GRAHAM, JORY

361

Commentary on project head start  

Microsoft Academic Search

Conclusion Head Start is in a position to evaluate its successes and failures of the last 20 years, to assess the needs of low-income children and their families in the eighties and nineties, and to plan ahead for another 20 years of successful operation. We must take this challenge seriously, because if we don't our program will not meet the

Francis Wardle

1986-01-01

362

Running Start Research and Discussion.  

ERIC Educational Resources Information Center

|This report discusses several studies of Running Start, a dual-enrollment program for high school juniors and seniors in Washington. The program was created in 1990 by the Washington State Legislature to expand educational choices for high school students. In 1991-1992, there were less than 1,000 students participating; in 1998-1999 there were…

Meld, Andrea

363

Near Field of Starting Plumes  

Microsoft Academic Search

Although steady jets and plumes have been studied extensively in the past, there is relatively little known about the initial stages of starting buoyant jets. The present investigation examined buoyancy-driven flows resulting from cylindrical containers w ith length to diameter ratios (L\\/D) between 2 and 13. Density ratios up to ten percent were utilized. A technique was developed to release

H. Johari; M. Gharib; D. Dabiri

1997-01-01

364

Maintenance Posture for Quick Start.  

National Technical Information Service (NTIS)

Quick Start is an aircraft modification which installed cartridge starters on all engines of the B-52G/H and non-fan KC-135 aircraft. Routine peacetime use of the modification was suspended due to an excessive amount of smoke and toxic gases created by th...

J. M. Connolly

1981-01-01

365

Self start flyback power supply  

SciTech Connect

A switching regulator power supply operates at a variable high frequency with low power dissipation and a minimum of complexity. The transformer primary windings are included as part of a self starting circuit which starts a pulse generator having a fixed pulse width and variable frequency. During a first cycle of operation, the self starting circuit in response to the input rectified AC power after a predetermined period of time applies sufficient voltage which enables the pulse generator to begin generating a first output pulse of fixed pulse width. This causes the primary windings to store energy and feedback energy to the self starting circuit which increases the voltage applied to the generator causing it to begin normal operation at maximum frequency. An error circuit coupled to the secondary winding compares the output DC supply voltage to a reference voltage and generates an error signal which is applied through a DC coupling circuit for adjusting the frequency of the pulse generator to existing line and load conditions.

Fenter, W.S.

1983-08-23

366

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

Microsoft Academic Search

Human prion protein gene (PRNP) is considered an important gene in determining the incidence of human transmissible spongiform encephalopathies or prion\\u000a diseases. Polymorphisms of PRNP at codon 129 in Europeans and codon 219 in Japanese may play an important role in the susceptibility to sporadic Creutzfeldt–Jakob\\u000a disease (CJD); data regarding codon 129 in the Japanese population have led to divergent

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

2005-01-01

367

Decoding the Decoding Region: Analysis of Eukaryotic Release Factor (eRF1) Stop Codon-Binding Residues  

Microsoft Academic Search

Peptide synthesis in eukaryotes terminates when eukaryotic release factor 1 (eRF1) binds to an mRNA stop codon and occupies the ribosomal A site. Domain 1 of the eRF1 protein has been implicated in stop codon recognition in a number of experimental studies. In order to further pinpoint the residues of this protein involved in stop codon recognition, we sequenced and

Han Liang; Jonathan Y. Wong; Qing Bao; Andre R. O. Cavalcanti; Laura F. Landweber

2005-01-01

368

Comparative study on factors influencing the codon and amino acid usage in Lactobacillus sakei 23K and 13 other lactobacilli  

Microsoft Academic Search

In this study, major factors shaping codon and amino acid usage variation Lactobacillus sakei 23K were investigated. It included 13 other Lactobacillus species for a comparative analysis. The correspondence analysis (COA) showed that in 13 species the major trend of synonymous\\u000a codon usage was highly correlated with gene expression level as assessed by the “Codon Adaptation Index” (CAI) values. In

Kinshuk Chandra Nayak

369

Codon usage bias from tRNA's point of view: Redundancy, specialization, and efficient decoding for translation optimization  

Microsoft Academic Search

The selection-mutation-drift theory of codon usage plays a major role in the theory of molecular evolution by explaining the co-evolution of codon usage bias and tRNA content in the framework of translation optimization. Because most studies have focused only on codon usage, we analyzed the tRNA gene pool of 102 bacterial species. We show that as minimal generation times get

Eduardo P. C. Rocha

2004-01-01

370

Synonymous Codon Choices in the Extremely GC-Poor Genome of Plasmodium falciparum: Compositional Constraints and Translational Selection  

Microsoft Academic Search

.   We have analyzed the patterns of synonymous codon preferences of the nuclear genes of Plasmodium falciparum, a unicellular parasite characterized by an extremely GC-poor genome. When all genes are considered, codon usage is strongly\\u000a biased toward A and T in third codon positions, as expected, but multivariate statistical analysis detects a major trend among\\u000a genes. At one end genes

Héctor Musto; Héctor Romero; Alejandro Zavala; Kamel Jabbari; Giorgio Bernardi

1999-01-01

371

An Upstream YY1 Binding Site on the HIV-1 LTR Contributes to Latent Infection  

PubMed Central

During HIV-1 infection a population of latently infected cells is established. This population is the major obstacle preventing total eradication of the virus from AIDS patients. HIV-1 latency is thought to arise by various mechanisms including repressive chromatin modifications. Transcription factors such as YY1 have been shown to facilitate repressive chromatin modifications by the recruitment of histone deacetylases. In this study, we identified a novel binding site for YY1 on the HIV-1 LTR, 120 nucleotides upstream of the transcription start site. We show that YY1 can bind to this site in vitro and in vivo and that binding to the LTR is dissociated upon T cell activation. Overexpression of YY1 causes an increase in the proportion of cells that produce latent infections. These observations, in combination with previous results, demonstrate that YY1 plays a prominent role in controlling the establishment and maintenance of latent HIV-1 provirus in unstimulated cells.

Bernhard, Wendy; Barreto, Kris; Raithatha, Sheetal; Sadowski, Ivan

2013-01-01

372

Experimental Measurements of Starting Loads and Model Behaviors in the Indraft Supersonic Wind Tunnel  

NASA Astrophysics Data System (ADS)

Measurements of starting load in the indraft supersonic wind tunnel of Muroran Institute of Technology were conducted for Mach 2, 3 and 4 conditions with AGARD-B model. The high speed photographs were taken for the behaviors of the wind tunnel model. Those photographs make clear that the oscillations of the model coincide with the measured starting load oscillation and starting loads were caused by two shock waves. The first shock wave is the reflection shock, which is generated at the nozzle throat by expansion wave reflection. The second one is asymmetric oblique shock waves (AOS) coming from the upstream. AOS can generate the asymmetric conical shock (ACS) around the nose cone of the model, which would have directly caused the starting loads on the wind tunnel model. Based on those observations, the authors presented the conical shock theory, which is the alternative starting load prediction theory to the normal shock theory.

Minato, Ryojiro; Mizobata, Kazuhide; Kuwata, Komei

373

Influence of Codon Bias on Heterologous Production of Human Papillomavirus Type 16 Major Structural Protein L1 in Yeast  

PubMed Central

Heterologous gene expression is dependent on multistep processes involving regulation at the level of transcription, mRNA turnover, protein translation, and posttranslational modifications. Codon bias has a significant influence on protein yields. However, sometimes it is not clear which parameter causes observed differences in heterologous gene expression as codon adaptation typically optimizes many sequence properties at once. In the current study, we evaluated the influence of codon bias on heterologous production of human papillomavirus type 16 (HPV-16) major structural protein L1 in yeast by expressing five variants of codon-modified open reading frames (OFRs) encoding HPV-16 L1 protein. Our results showed that despite the high toleration of various codons used throughout the length of the sequence of heterologously expressed genes in transformed yeast, there was a significant positive correlation between the gene's expression level and the degree of its codon bias towards the favorable codon usage. The HPV-16 L1 protein expression in yeast can be optimized by adjusting codon composition towards the most preferred codon adaptation, and this effect most probably is dependent on the improved translational elongation.

Norkiene, Milda; Gedvilaite, Alma

2012-01-01

374

Tentoxin sensitivity of chloroplasts determined by codon 83 of beta subunit of proton-ATPase.  

PubMed

Tentoxin is a naturally occurring phytotoxic peptide that causes seedling chlorosis and arrests growth in sensitive plants and algae. In vitro, it inhibits activity of the beta subunit of the plastid proton-adenosine triphosphatase (ATPase) from sensitive species. Plastid atpB genes from six closely related, tentoxin-sensitive or -resistant Nicotiana species differ at codon 83, according to their response to the toxin: glutamate correlated with resistance and aspartate correlated with sensitivity. The genetic relevance of this site was confirmed in Chlamydomonas reinhardtii by chloroplast transformation. The alga, normally tentoxin-resistant, was rendered tentoxin-sensitive by mutagenesis of its plastid atpB gene at codon 83. Codon 83 may represent a critical site on the beta subunit that does not compete with nucleotide binding or other catalytic activities. PMID:1387730

Avni, A; Anderson, J D; Holland, N; Rochaix, J D; Gromet-Elhanan, Z; Edelman, M

1992-08-28

375

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

PubMed

Synonymous codon usage patterns are shaped by a balance between mutation, drift, and natural selection. To date, detection of translational selection in vertebrates has proven to be a challenging task, obscured by small long-term effective population sizes in larger animals and the existence of isochores in some species. The consensus is that, in such species, natural selection is either completely ineffective at overcoming mutational pressures and genetic drift or perhaps is effective but so weak that it is not detectable. The aim of this research is to understand the interplay between mutation, selection, and genetic drift in vertebrates. We observe that although variation in mutational bias is undoubtedly the dominant force influencing codon usage, translational selection acts as a weak additional factor influencing synonymous codon usage. These observations indicate that translational selection is a widespread phenomenon in vertebrates and is not limited to a few species. PMID:23883522

Doherty, Aoife; McInerney, James O

2013-07-24

376

The effect of altered codon usage on luciferase activity in tobacco, maize and wheat  

Microsoft Academic Search

A comparison of the wild-type firefly luciferase reporter gene to a codon-modified gene, available from Promega, demonstrates\\u000a that in tobacco cell cultures, an increase in G+C content of 1.8%, as a consequence of 36 A\\/T?G\\/C synonymous codon alterations\\u000a and removal of the lysosomal targeting sequence, has no significant effect on expression. In maize Black Mexican Sweet cells\\u000a and wheat scutellum,

D. M. Lonsdale; L. J. Moisan; A. J. Harvey

1998-01-01

377

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

378

Effect of sequence context at stop codons on efficiency of reinitiation in GCN4 translational control.  

PubMed Central

Translational control of the GCN4 gene involves two short open reading frames in the mRNA leader (uORF1 and uORF4) that differ greatly in the ability to allow reinitiation at GCN4 following their own translation. The low efficiency of reinitiation characteristic of uORF4 can be reconstituted in a hybrid element in which the last codon of uORF1 and 10 nucleotides 3' to its stop codon (the termination region) are substituted with the corresponding nucleotides from uORF4. To define the features of these 13 nucleotides that determine their effects on reinitiation, we separately randomized the sequence of the third codon and termination region of the uORF1-uORF4 hybrid and selected mutant alleles with the high-level reinitiation that is characteristic of uORF1. The results indicate that many different A+U-rich triplets present at the third codon of uORF1 can overcome the inhibitory effect of the termination region derived from uORF4 on the efficiency of reinitiation at GCN4. Efficient reinitiation is not associated with codons specifying a particular amino acid or isoacceptor tRNA. Similarly, we found that a diverse collection of A+U-rich sequences present in the termination region of uORF1 could restore efficient reinitiation at GCN4 in the presence of the third codon derived from uORF4. To explain these results, we propose that reinitiation can be impaired by stable base pairing between nucleotides flanking the uORF1 stop codon and either the tRNA which pairs with the third codon, the rRNA, or sequences located elsewhere in GCN4 mRNA. We suggest that these interactions delay the resumption of scanning following peptide chain termination at the uORF and thereby lead to ribosome dissociation from the mRNA. Images

Grant, C M; Hinnebusch, A G

1994-01-01

379

p53 codon 72 polymorphism in patients with gastric and colorectal cancer in a Korean population  

Microsoft Academic Search

Background  The common p53 codon 72 polymorphism has been investigated as a risk factor for cancer in different populations; however,\\u000a the results have been inconsistent. This study investigated the risk of developing gastric or colorectal cancer associated\\u000a with the p53 codon 72 polymorphism in a Korean population.\\u000a \\u000a \\u000a \\u000a \\u000a Methods  We conducted a large-scale case–control study that included 2,213 gastric cancer patients; 1,829 colorectal

Hye-Rim Song; Sun-Seog Kweon; Hee Nam Kim; Jin-Mei Piao; Woo-Jun Yun; Jin-Su Choi; Jun-Eul Hwang; Ju-Young Yoon; Hyeong-Rok Kim; Young-Kyu Park; Soo-Hyun Kim; Yoo-Duk Choi; Min-Ho Shin

380

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

381

Resolution of translation start site for the human Kell glycoprotein.  

PubMed

BACKGROUND: The human Kell blood group system currently contains 35 antigens determined by allelic polymorphisms in the Kell glycoprotein, a single-pass Type II transmembrane protein. The Kell glycoprotein was initially cloned through screening of a cDNA library; however, direct amino acid sequencing of most of the Kell glycoprotein has not been reported. The N-terminus of the Kell glycoprotein contains two potential translational start sites, which result in differences in the cytoplasmic tail. STUDY DESIGN AND METHODS: Protein extracts were isolated from human red blood cell membranes and were digested with trypsin. The resulting peptides were subjected to liquid chromatography-tandem mass spectrometry, allowing resolution of peptides from the N-terminus of the Kell glycoprotein. RESULTS: Peptides were isolated and sequenced that correspond to the upstream methionine start site predicted by the full cDNA sequence. No evidence of internal translation initiation at Methionine 20 was detected. CONCLUSIONS: These findings identify the translational start site and define the full cytoplasmic tail of the human Kell glycoprotein. PMID:23721226

Blacken, Grady R; Zimring, James C; Fu, Xiaoyun

2013-05-30

382

Hospital health promotion: swimming or sinking in an upstream business?  

PubMed

Healthy People 2000 (HP 2000) calls on hospitals to offer health promotion programs addressing priority health needs of the community. Historically, this upstream initiative has not been present in health care. With the increasing provision of these programs, this case study examined their content to further understand potential public health impact. The health promotion programs offered to the community--both the general public and corporate employees--by an urban Midwest hospital were assessed over 1 year. This article presents a content analysis of 216 programs that was conducted by measuring seven variables: target group, presentation format, fee, health focus, program providers, contact frequency, and activity. Based on this single case study, hospitals appear to be addressing objectives set forth by HP 2000 for community hospitals. Although moving upstream with health promotion, an analysis of program content suggests modifications may be necessary in order to serve as effective interventions for health priorities. PMID:14610973

Hilgerson, Lori L; Prohaska, Thomas R

2003-01-01

383

Addressing poor nutrition to promote heart health: Moving upstream  

PubMed Central

Current dietary recommendations for cardiovascular disease prevention suggest dietary patterns that promote achieving healthy weight, emphasize vegetables, legumes, fruit, whole grains, fish and nuts, substituting mono-unsaturated fats for saturated fats and restricting dietary sodium to less than 2300 mg/day. However, trends in nutrient intake and food consumption patterns suggest that the need for improvement in the dietary patterns of Canadians is clear. Influencing eating behaviour requires more than addressing nutrition knowledge and perceptions of healthy eating – it requires tackling the context within which individuals make choices. A comprehensive approach to improving nutrition includes traditional downstream strategies such as counselling to improve knowledge and skills; midstream strategies such as using the media to change social norms; and upstream strategies such as creating supportive environments through public policy including regulatory measures. While the evidence base for more upstream strategies continues to grow, key examples of comprehensive approaches to population change provide a call to action.

Raine, Kim D

2010-01-01

384

Diffuse minor ions upstream of simulated quasi-parallel shocks  

Microsoft Academic Search

We have performed a number of one-dimensional hybrid (particle ions, massless fluid electrons) simulations of quasi-parallel collisionless shocks in order to elucidate the origin of diffuse upstream minor ions. Minor ions are treated self-consistently by the hybrid code; however, a number of runs have also been performed wherein the minor ions are treated as test particles. We have investigated the

K. J. Trattner; M. Scholer

1994-01-01

385

Upstream gyrating ion events: Cluster observations and simulations  

Microsoft Academic Search

Localized events of low-frequency quasi-monochromatic waves in the 30s range observed by Cluster in the upstream region of Earth are analyzed. They are associated with a gyro-motion of the two ion populations consisting of the incoming solar wind protons and the back-streaming ions from the shock. A coordinate system is chosen in which one axis is parallel to the ambient

K. Sauer; M. Fraenz; E. Dubinin; C. Mazelle; A. Korth; H. Rème; I. Dandouras; K.-H. Glassmeier

2005-01-01

386

VIEW SOUTH SOUTHWEST LOOKING UPSTREAM FROM ENTRANCE TO LOCKS 35 ...  

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

VIEW SOUTH SOUTHWEST LOOKING UPSTREAM FROM ENTRANCE TO LOCKS 35 AND 71. THE BRIDGE IN THE VIEW IS NOTED FOR ITS EXTRAORDINARY WIDTH (475 FT.) RELATIVE TO ITS MODEST SPAN (116 FT. 10 IN.). WHEN CONSTRUCTED IN 1914 IT WAS CLAIMED TO BE THE WIDEST BRIDGE IN THE WORLD. MAIN STREET CROSSES IT DIAGONALLY, ALONG WITH TWO CROSS STREETS. - New York State Barge Canal, Lockport Locks, Richmond Avenue, Lockport, Niagara County, NY

387

8. SEDIMENTATION CHAMBER, VIEW UPSTREAM (PLANK COVER REMOVED FOR CLARITY). ...  

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

8. SEDIMENTATION CHAMBER, VIEW UPSTREAM (PLANK COVER REMOVED FOR CLARITY). BOX FLUME DROPS SLIGHTLY INTO CHAMBER ON LEFT SIDE. CHAMBER IS A SERIES OF BAFFLES DESIGNED TO SLOW THE FLOW OF WATER. FLOW IS REDUCED TO ALLOW PARTICULATES TO SETTLE TO THE BOTTOM. TWO SCREENS (NOT SHOWN) FILTER LARGER DEBRIS. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI

388

Steepened channels upstream of knickpoints: Controls on relict landscape response  

NASA Astrophysics Data System (ADS)

The morphology of a relict landscape provides important insight into erosion rates and processes prior to base level fall. Fluvial knickpoints are commonly thought to form a leak-proof moving boundary between a rejuvenated landscape below and a relict landscape above. We argue that fluvial rejuvenation may leak farther upstream, depending on the rate and style of knickpoint migration. The outer margin of a relict landscape should therefore be used with caution in tectonic geomorphology studies, as channel steepening upstream of knickpoints could reduce the relict area. We explore the response of the Roan Plateau to knickpoint retreat triggered by late Cenozoic upper Colorado River incision. Multiple knickpoints (100-m waterfalls) separate a low-relief, upper landscape from incised canyons below. Two digital elevation model data sets (10-m U.S. Geological Survey and 1-m Airborne Laser Swath Mapping) indicate steeper channels above waterfalls relative to concave channels farther upstream. The steepened reaches are several kilometers long, correspond to doubling of slope, and exhibit channel narrowing and an increase in hillslope angle. We compare two mechanisms for generating steepened reaches. The first uses a recent model for erosion amplification due to flow acceleration at the waterfall lip. The second acknowledges that waterfall lips may be limited to the outcrop of a resistant formation. Subtle structural warping of the stratigraphy can lead to lowering of the waterfall lip as it retreats, thus lowering base level for upstream channels. Results of numerical modeling experiments suggest the latter mechanism is more consistent with our observations of long, mildly steepened reaches.

Berlin, Maureen M.; Anderson, Robert S.

2009-09-01

389

Retail Zone Pricing and Simulated Price Effects of Upstream Mergers  

Microsoft Academic Search

Despite the oft?recognized reality of zone pricing by food retailers, this form of price discrimination has received very little attention within the context of upstream merger analysis. Promoting this issue to ‘center stage’, we relax the conventional merger simulation assumption of uniform pass?through by retailers. Relaxing this assumption allows us to explore the potential impacts of zone pricing on post?merger

Geoffrey M. Pofahl; ORAL CAPPS JR.; H. Alan Love

2006-01-01

390

Upstream particles observed in the earth's foreshock region  

Microsoft Academic Search

On the basis of primarily an extensive study of fully three-dimensional plasma data, we describe the interrelationships of the upstream particles and plasma waves observed in the earth's foreshock region. The University of Iowa LEPEDEAs detect ions and electrons from 1 eV to 45 keV over all except approx.2% of the unit sphere. Comparisons are made with high time resolution

T. E. Eastman; R. R. Anderson; L. A. Frank; G. K. Parks

1981-01-01

391

Conserved upstream open reading frames in higher plants  

Microsoft Academic Search

BACKGROUND: Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are

Michael K Tran; Carolyn J Schultz; Ute Baumann

2008-01-01

392

Methods of testing HEPA filters with short upstream approaches  

SciTech Connect

The design of an air cleaning system to be used in a high gamma radiation field presented unique problems for in-place Dioctyl phthalate (DOP) leak testing. The design required remotely changeable HEPA (High Efficiency Particulates Air) filters in a throw-away, stainless steel housing, located underground in a stainless steel-lined concrete pit. The conventional approach of providing ten duct diameters of upstream mixing for the dispersion of testing the second filter stage in the system. To establish aerosol (DOP) injection ports that could provide mixing in accordance with ANSI N510-80, a full-scale housing was built. The housing and components were built of plexiglas to view the DOP streams. A series of tests were designed in which the following factors were varied: (1) aerosol distributors, (2) aerosol distributor locations, (3) baffle design, and (4) baffle location. DOP concentration measurements were taken immediately upstream of the filters. The uniformity score, as determined by ANSI N510-80, was defined as the larger of maximum minus average divided by average, or average minus minimum divided by the average values of DOP concentration. Three tests met the uniformity score requirement of 0.20, but all three had ten duct diameters of upstream mixing. The type of aerosol distributor, duct length, and flow rate were found to most affect the uniformity score. 5 figs.

Kirk, G.Q.; Childress, C.E.; Schmoyer, D.D.

1988-01-01

393

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

394

Determination of the Relative Importance of Gene Function or Taxonomic Grouping to Codon Usage Bias Using Cluster Analysis and SVMs  

Microsoft Academic Search

The codon usage patterns of 2,552 major histocompatibility complex (MHC) sequences from 33 primate species, and the consequent subsets of sequences obtained by removing species with most abundant sequences was observed. The correlation between function and species with regards to MHC codon usage patterns was analyzed using cluster analysis and support vector machines (SVMs). The results show that gene function

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

2006-01-01

395

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

ERIC Educational Resources Information Center

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

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

2009-01-01

396

Mutation pressure shapes codon usage in the GC-Rich genome of foot-and-mouth disease virus.  

PubMed

Foot-and-mouth disease (FMD) is economically the most important viral-induced livestock disease worldwide. In this study, we report the results of a survey of codon usage bias of FMD virus (FMDV) representing all seven serotypes (A, O, C, Asia 1, SAT 1, SAT 2, and SAT 3). Correspondence analysis, a commonly used multivariate statistical approach, was carried out to analyze synonymous codon usage bias. The analysis showed that the overall extent of codon usage bias in FMDV is low. Furthermore, the good correlation between the frequency of G + C at the synonymous third position of sense codons (GC3S) content at silent sites of each sequence and codon usage bias suggested that mutation pressure rather than natural (translational) selection is the most important determinant of the codon bias observed. In addition, other factors, such as the lengths of open reading frame (ORF) and the hydrophobicity of genes also influence the codon usage variation among the genomes of FMDV in a minor way. The result of phylogenetic analyses based on the relative synonymous codon usage (RSCU) values indicated a few obvious phylogenetic incongruities, which suggest that more FMDV genome diversity may exist in nature than is currently indicated. Our work might give some clues to the features of FMDV genome and some evolutionary information of this virus. PMID:17768673

Zhong, Jincheng; Li, Yanmin; Zhao, Sheng; Liu, Shenggang; Zhang, Zhidong

2007-09-01

397

Enhanced expression in tobacco of the gene encoding green fluorescent protein by modification of its codon usage  

Microsoft Academic Search

The gene encoding green fluorescent protein (GFP) from Aequorea victoria was resynthesized to adapt its codon usage for expression in plants by increasing the frequency of codons with a C or a G in the third position from 32 to 60%. The strategy for constructing the synthetic gfp gene was based on the overlap extension PCR method using 12 long

Odette Mendes; Emil J. H. Wolbert; A. Douwe de Boer

1997-01-01

398

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

Microsoft Academic Search

DNA vaccination elicits humoral and cellular immune responses and has been shown to confer protection against several viral, bacterial, and parasitic pathogens. Here we report that optimized codon usage of an injected DNA sequence considerably increases both humoral and cellular immune responses. We recently generated a synthetic human immunodeficiency virus type 1 gp120 sequence in which most wild-type codons were

STEFANIE ANDRE; BRIAN SEED; JOSEF EBERLE; WINFRIED SCHRAUT; ANDREAS BULTMANN; JURGEN HAAS

1998-01-01

399

Does the prion protein gene 129 codon polymorphism influence sleep? Evidence from a fatal familial insomnia kindred  

Microsoft Academic Search

Objective: Experimental and clinical evidence in prion diseases suggests that the prion protein gene (PRNP) plays a role in regulating sleep.Methods: Seventeen healthy individuals belonging to a single fatal familial insomnia pedigree, 8 carriers and 9 non-carriers of the PRNP codon 178 mutation, underwent polysomnography and spectral electroencephalographic (EEG) analysis. All were also characterized with regard to the codon 129

Giuseppe Plazzi; Pasquale Montagna; Manolo Beelke; Lino Nobili; Fabrizio De Carli; Pietro Cortelli; Stefano Vandi; Patrizia Avoni; Paolo Tinuper; Pierluigi Gambetti; Elio Lugaresi; Franco Ferrillo

2002-01-01

400

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

Microsoft Academic Search

Wigglesworthia glossinidia brevipalpis, the obligate bacterial endosymbiont of the tsetse fly Glossinabrevipalpis,ischaracterizedbyextremegenomereductionandATnucleotidecomposition bias. Here, multivariate statistical analyses are used to test the hypothesis that mutational bias and genetic drift shape synonymous codon usage and amino acid usage of Wigglesworthia. The results show that synonymous codon usage patterns vary little across the genome and do not distinguish genes of putative high

J. T. Herbeck

2003-01-01

401

Codon Optimization of Gene Fragments Encoding Plasmodium falciparum Merzoite Proteins Enhances DNA Vaccine Protein Expression and Immunogenicity in Mice  

Microsoft Academic Search

In contrast to conventional vaccines, DNA and other subunit vaccines exclusively utilize host cell molecules for transcription and translation of proteins. The adenine plus thymine content of Plasmodium falciparum gene sequences (80%) is much greater than that of Homo sapiens (59%); consequently, codon usage is markedly different. We hypothesized that modifying codon usage of P. falciparum genes encoded by DNA

DAVID L. NARUM; SANJAI KUMAR; WILLIAM O. ROGERS; STEVEN R. FUHRMANN; HONG LIANG; MIRANDA OAKLEY; ALEM TAYE; B. KIM LEE SIM; STEPHEN L. HOFFMAN

2001-01-01

402

Identification and Repair of Positive Binding Antibodies Containing Randomly Generated Amber Codons from Synthetic Phage Display Libraries  

Microsoft Academic Search

Phage display technology allows for the rapid isolation and characterization of monoclonal antibodies that have vast potential for therapeutic and diagnostic applications. However, the panning process, which utilizes a host strain that suppresses termination by the amber codon, has an inherent bias toward clones containing randomly generated amber stop codons, complicating identification of positive binding antibodies when the antibody genes

Warren D. Marcus; Stuart M. Lindsay; Michael R. Sierks

2006-01-01

403

Codon-optimized fluorescent proteins designed for expression in low-GC gram-positive bacteria.  

PubMed

Fluorescent proteins have wide applications in biology. However, not all of these proteins are properly expressed in bacteria, especially if the codon usage and genomic GC content of the host organism are not ideal for high expression. In this study, we analyzed the DNA sequences of multiple fluorescent protein genes with respect to codons and GC content and compared them to a low-GC gram-positive bacterium, Bacillus anthracis. We found high discrepancies for cyan fluorescent protein (CFP), yellow fluorescent protein (YFP), and the photoactivatable green fluorescent protein (PAGFP), but not GFP, with regard to GC content and codon usage. Concomitantly, when the proteins were expressed in B. anthracis, CFP- and YFP-derived fluorescence was undetectable microscopically, a phenomenon caused not by lack of gene transcription or degradation of the proteins but by lack of protein expression. To improve expression in bacteria with low genomic GC contents, we synthesized a codon-optimized gfp and constructed optimized photoactivatable pagfp, cfp, and yfp, which were in contrast to nonoptimized genes highly expressed in B. anthracis and in another low-GC gram-positive bacterium, Staphylococcus aureus. Using optimized GFP as a reporter, we were able to monitor the activity of the protective antigen promoter of B. anthracis and confirm its dependence on bicarbonate and regulators present on virulence plasmid pXO1. PMID:19181829

Sastalla, Inka; Chim, Kannie; Cheung, Gordon Y C; Pomerantsev, Andrei P; Leppla, Stephen H

2009-01-30

404

The significance of p53 codon 72 polymorphism for the development of cervical adenocarcinomas  

PubMed Central

Infection with the human papillomavirus is an important co-factor in the development of cervical carcinomas. Accordingly, HPV DNA is recognised in most of these tumours. Polymorphism of the p53 gene, codon 72, is also considered a risk factor in the development of cervical carcinoma. However, this finding is contradicted by several observers. In the present investigation, 111 cases of adenocarcinoma of the cervix collected through the Swedish Cancer Registry and 188 controls (females with normal cytology at organised gynaecological screening) were analysed with regard to p53, codon 72, polymorphism using a PCR- and SSCP-based technique. In the controls, 9% showed pro/pro, 44% pro/arg and 47% arg/arg, whereas in the invasive adenocarcinomas, the corresponding figures were 0%, 29% and 71%, respectively. The difference was statistically significant (P = 0.001). HPV DNA was identified in 86 tumours (HPV 18 in 48, HPV 16 in 31 and HPV of unknown type in 7 cases) and 25 tumours were HPV negative. The p53, codon 72, genotypes observed in HPV-positive and HPV-negative cervical adenocarcinomas were not statistically different (P = 0.690). The results indicate that women homozygotic for arg/arg in codon 72 of the p53 gene are at an increased risk for the development of cervical adenocarcinomas. However, this genetic disposition seems to be unrelated to the HPV infection. © 2001 Cancer Research Campaign??http://www.bjcancer.com

Andersson, S; Rylander, E; Strand, A; Sallstrom, J; Wilander, E

2001-01-01

405

The KIT Exon 11 Stop Codon Mutation in Gastrointestinal Stromal Tumors: What Is the Clinical Meaning?  

PubMed Central

Background/Aims Gastrointestinal stromal tumors (GISTs) strongly express a receptor tyrosine kinase (RTK, c-KIT-CD117) harboring a KIT mutation that causes constitutive receptor activation leading to the development and growth of tumors; 35% of GISTs without KIT mutations have platelet-derived growth factor receptor alpha (PDGFRA) mutations, and the type of mutation plays an important role in the response to treatment. This study aimed to establish the frequency of stop codon mutations in the RTKs, KIT, and PDGFRA, in GISTs and correlate this molecular alteration with protein expression and treatment responsiveness. Methods Seventy-nine GISTs were analyzed for both KIT and PDGFRA mutations. Immunohistochemical expression was studied in tissue microarray blocks. Results We found three rare KIT mutations in exon 11 that induced a stop codon, two at position 563 and one at position 589, which have never been described before. All three tumors were CD117-, DOG1-, and CD34-positive. Two patients with a KIT stop codon mutation did not respond to imatinib therapy and died shortly after treatment. Conclusions The association between stop codon mutations in KIT and patient survival, if confirmed in a larger population, may be useful in choosing effective therapies.

Michelucci, Angela; Chiappetta, Caterina; Cacciotti, Jessica; Veccia, Norman; Astri, Elisa; Leopizzi, Martina; Prosperi Porta, Romana; Petrozza, Vincenzo; Della Rocca, Carlo; Bevilacqua, Generoso; Cavazzana, Andrea

2013-01-01

406

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

2013-06-30

407

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

PubMed

Codon use among the three domains of life is not confined to the universal genetic code. With only 22 tRNA genes in mammalian mitochondria, exceptions from the universal code are necessary for proper translation. A particularly interesting deviation is the decoding of the isoleucine AUA codon as methionine by the one mitochondrial-encoded tRNA(Met). This tRNA decodes AUA and AUG in both the A- and P-sites of the metazoan mitochondrial ribosome. Enrichment of posttranscriptional modifications is a commonly appropriated mechanism for modulating decoding rules, enabling some tRNA functions while restraining others. In this case, a modification of cytidine, 5-formylcytidine (f(5)C), at the wobble position-34 of human mitochondrial tRNA(f5CAU)(Met) (hmtRNA(f5CAU)(Met)) enables expanded decoding of AUA, resulting in a deviation in the genetic code. Visualization of the codon•anticodon interaction by X-ray crystallography revealed that recognition of both A and G at the third position of the codon occurs in the canonical Watson-Crick geometry. A modification-dependent shift in the tautomeric equilibrium toward the rare imino-oxo tautomer of cytidine stabilizes the f(5)C34•A base pair geometry with two hydrogen bonds. PMID:23781103

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

2013-06-18

408

Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas  

Microsoft Academic Search

DNA sequence polymorphism and codon usage bias were investigated in a set of 41 nuclear loci in the Pacific oyster Crassostrea gigas. Our results revealed a very high level of DNA polymorphism in oysters, in the order of magnitude of the highest levels reported in animals to date. A total of 290 single nucleotide polymorphisms (SNPs) were detected, 76 of

C. Sauvage; N. Bierne; S. Lapègue; P. Boudry

2007-01-01

409

Codon conservation in the influenza A virus genome defines RNA packaging signals  

Microsoft Academic Search

Genome segmentation facilitates reassortment and rapid evolution of influenza A virus. However, segmentation complicates particle assembly as virions must contain all eight vRNA species to be infectious. Specific packaging signals exist that extend into the coding regions of most if not all segments, but these RNA motifs are poorly defined. We measured codon variability in a large dataset of sequences

Julia R. Gog; Emmanuel Dos Santos Afonso; Rosa M. Dalton; India Leclercq; Laurence Tiley; Debra Elton; Johann C. von Kirchbach; Nadia Naffakh; Nicolas Escriou; Paul Digard

2007-01-01

410

Codon optimization of bacterial luciferase ( lux ) for expression in mammalian cells  

Microsoft Academic Search

Expression of the bacterial luciferase (lux) system in mammalian cells would culminate in a new generation of bioreporters for in vivo monitoring and diagnostics technology. Past efforts to express bacterial luciferase in mammalian cells have resulted in only modest gains due in part to low overall expression of the bacterial genes. To optimize expression, we have designed and synthesized codon-optimized

Stacey S. Patterson; Hebe. M. Dionisi; Rakesh K. Gupta; Gary S. Sayler

2005-01-01

411

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

412

Incorporating PCA and fuzzy-ART techniques into achieve organism classification based on codon usage consideration  

Microsoft Academic Search

To recognize the DNA sequence and mine the hidden information to achieve the classification of organisms are viewed as a difficult work to biologists. As we know, the amino acids are the basic elements to construct DNA. Hence, if the codon usage of amino acids can be analyzed well, the useful information about classification of organisms may be obtained. However,

Kun-Lin Hsieh; I-Ching Yang

2008-01-01

413

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

Microsoft Academic Search

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

Mariusz Zoltowski; Nicolaus Copernicus

2007-01-01

414

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

415

p53 Codon 72 Arg Homozygotes Are Associated with an Increased Risk of Cutaneous Melanoma  

Microsoft Academic Search

The p53 gene plays an important role in cell cycle control, facilitating DNA repair activities in response to DNA damage. Aberrant cell cycle control impairs DNA repair and increases the probability of mutations that can lead to carcinogenesis. The p53 gene is polymorphic at codon 72 (Arg\\/Pro) of its protein, which is functionally distinct, leading to inquiry into its role

Hongbing Shen; Zhensheng Liu; Sara S. Strom; Margaret R. Spitz; Jeffrey E. Lee; Jeffrey E. Gershenwald; Merrick I. Ross; Paul F. Mansfield; Madeleine Duvic; Honnavara N. Ananthaswamy; Qingyi Wei

2003-01-01

416

Differential Trends in the Codon Usage Patterns in HIV-1 Genes  

PubMed Central

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

Pandit, Aridaman; Sinha, Somdatta

2011-01-01

417

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

418

Cooperation between upstream and downstream elements of the adenovirus major late promoter for maximal late phase-specific transcription.  

PubMed Central

Transcription from the adenovirus major late promoter (MLP) is greatly stimulated during lytic infection, after replication of the viral DNA has started. This replication-dependent activation has previously been shown to be mediated by a positive regulatory cellular protein(s). Binding of this factor(s) to sequence elements (DE1 and DE2), located between positions +76 and +124, with respect to the MLP transcriptional startsite, is detected only after the onset of DNA replication. Using a cell-free transcription system which mimics the late phase induction of the MLP and DNA binding assays, we now present evidence showing that maximal stimulation also depends on the MLP upstream element (UE), without involving increased DNA binding activity of the corresponding factor (UEF) during the lytic cycle. Our results indicate that the upstream and downstream elements act cooperatively on transcription efficiency, although no direct interactions between the cognate factors could be demonstrated. These observations strongly suggest that the elevated rate of transcription originating at the MLP startsite, late in infection, results from the simultaneous action of factors bound at the upstream and downstream elements onto a common target within the basal transcription machinery. Images

Mondesert, G; Kedinger, C

1991-01-01

419

Upstream mononucleotide A-repeats play a cis-regulatory role in mammals through the DICER1 and Ago proteins.  

PubMed

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. PMID:23935075

Aporntewan, Chatchawit; Pin-On, Piyapat; Chaiyaratana, Nachol; Pongpanich, Monnat; Boonyaratanakornkit, Viroj; Mutirangura, Apiwat

2013-08-08

420

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

421

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

422

Deceleration of the solar wind upstream from the earth's bow shock and the origin of diffuse upstream ions  

Microsoft Academic Search

Observations with the Los Alamos Scientific Laboratory\\/Max-Planck-Institut crossed-fan solar wind ion experiment on ISEE 1 reveal that the solar wind is decelerated and deflected away from the direction of the earth's bow shock as it enters that portion of the upstream region populated by 'diffuse' bow shock ions and long-period (10--60 s) waves. Typically, the average directed velocity vector changes

S. J. Bame; J. R. Asbridge; W. C. Feldman; J. T. Gosling; G. Paschmann; N. Sckopke

1980-01-01

423

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

424

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

PubMed Central

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

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

2013-01-01

425

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

PubMed Central

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

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

2009-01-01

426

Two-codon T-box riboswitch binding two tRNAs.  

PubMed

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 tRNA(Asn) and tRNA(Glu). 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. PMID:23858450

Saad, Nizar Y; Stamatopoulou, Vassiliki; Brayé, Mélanie; Drainas, Denis; Stathopoulos, Constantinos; Becker, Hubert Dominique

2013-07-15

427

XRCC1 codon 399 and ERCC2 codon 751 polymorphism, smoking, and drinking and risk of esophageal squamous cell carcinoma in a North Indian population.  

PubMed

XRCC1 (X-ray cross-complementing group 1) codon 399 and ERCC2 (excision repair cross-complementing group 2) codon 751 polymorphisms were studied in esophageal squamous cell carcinoma (ESQCC) in a North Indian population. Peripheral blood samples of 120 cases and 160 age-and-gender matching controls were collected from North India and the two polymorphisms were studied by means of polymerase chain reaction-restriction fragment length polymorphism techniques. The data were analyzed with a logistic regression model. The XRCC1 codon 399 Gln/Gln genotype was significantly associated with reduced risk of ESQCC (OR = 0.31, 95% CI = 0.12-0.78, P = 0.01). In smokers, the XRCC1 Arg/Gln genotype was marginally and statistically nonsignificantly (OR = 1.5) associated with increased risk of this cancer. In drinkers, the XRCC1 Gln/Gln genotype was significantly protective (OR = 0.06, 95% CI = 0.007-0.605, P = 0.03), whereas ERCC2 (Lys/Gln-Gln/Gln) was marginally associated with increased risk (OR = 2.1, 95% CI = 0.46-9.44). Upon analysis of gene-gene interaction, a relationship was observed, although statistically nonsignificant, between combined genotypes of XRCC1 (Arg/Gln-Gln/Gln)-ERCC2 Gln/Gln (OR = 0.33, 95% CI = 0.09-1.16) and XRCC1 (Gln/Gln)-ERCC2 (Lys/Gln) (OR = 0.36, 95% CI = 0.11-1.17) and reduced risk of ESQCC in the North Indian population. These observations suggest that the Gln/Gln genotype of XRCC1 might play an important role in DNA repair in ESQCC. PMID:17556064

Sobti, Ranbir Chander; Singh, Jagmohan; Kaur, Pushpinder; Pachouri, Suparna S; Siddiqui, Ehtesham A; Bindra, Harnish Singh

2007-06-01

428

77 FR 3838 - Notice of Availability of Proposed New Starts/Small Starts Policy Guidance  

Federal Register 2010, 2011, 2012, 2013

...FTA-2010-0009] Notice of Availability of Proposed New Starts/Small Starts Policy Guidance AGENCY: Federal Transit Administration...Administration's (FTA) Proposed Policy Guidance on New Starts/Small Starts and requests your comments on it....

2012-01-25

429

Ingredients: where pet food starts.  

PubMed

Every clinician is asked "What should I feed my pet?" Understanding the ingredients in pet food is an important part of making the best recommendation. Pet food can be as simple as one ingredient or as complicated as containing more than 60 ingredients. Pet food and its ingredients are regulated by the Food and Drug Administration and state feed officials. Part of that regulation is the review and definition of ingredients. Existing ingredients change and new ingredients become available so the need for ingredient definitions grows. Ingredients for product formulations are chosen based on their nutrient content, digestibility, palatability, functionality, availability, and cost. As an example, a typical, nutritionally complete dry dog food with 42 ingredients is examined and the ingredients are discussed here. Safe, healthy pet food starts with safe ingredients sourced from well-monitored suppliers. The ultimate goal of both veterinarians and pet food manufacturers is the same--long healthy lives for dogs and cats. PMID:18656839

Thompson, Angele

2008-08-01

430

When to start antiretroviral therapy.  

PubMed

Antiretrovirals perform superbly in combating HIV infection. But when to initiate therapy in asymptomatic, nonpregnant, hepatitis-free, HIV-infected persons is not securely established. Of two completed randomized trials using modern therapy, a Haitian trial demonstrated a benefit to initiating therapy between 200 and 350 CD4 cells/mm(3) as compared with less than 200 CD4 cells/mm(3) and an international trial demonstrated a benefit to starting at greater than 350 CD4 cells/mm(3) as compared with less than 250 CD4 cells/mm(3). Many observational cohorts support initiating treatment at less than 350 CD4 cells/mm(3). Of these, three large studies supported initiation at less than 350 cells/mm(3), less than 450 CD4 cells/mm(3), and less than 500 CD4 cells/mm(3), respectively, but only the last supported starting at higher counts. Such studies are not probative, given the problem of confounding. No conventional antiretroviral regimen is free of long-term adverse effects, especially over decades of use. All are expensive and require expensive monitoring. When resources are restricted, initiation of antiretrovirals for persons with high CD4 count diverts treatment from more needy persons. Pathophysiological considerations favor universal treatment because antiretrovirals mitigate systemic inflammation, which aggravates atherosclerosis. There are suggestions that HIV hastens the natural decline of cognitive, renal, and pulmonary function as well as bone mineral loss; the mechanism(s) are uncertain, as is the ability of antiretrovirals to counteract the probable acceleration. The four major guideline panels, although all have issued updates in the past year, are not consistent in recommendations for treatment of HIV-infected persons with counts greater than 350 CD4 cells/mm(3). PMID:21308456

Rhame, Frank S

2011-02-01

431

Starting a TALEN Core Facility  

PubMed Central

Targeted gene modifications have been advanced by the use of engineered nucleases that make a double strand break (DSB) in genomic DNA. When the cell responds to the DSB by either the imperfect repair process of non-homologous end joining (NHEJ) or by homologous recombination (HR) from a donor template, a targeted modification can result. Since the first engineered nucleases were made in 1996 by fusing a zinc finger DNA binding domain to a FokI cleavage domain, Zinc Finger Nucleases (ZFNs) have progressed considerably to the point of clinical trials for HIV. More recently in 2009, a DNA binding motif called Transcription Activator Like Effector (TALE) was discovered to have a simple code for sequence recognition. Using the same concept as in ZFNs, TALEs were fused to a FokI cleavage domain to engineer Transcription Activator Like Effector Nucleases (TALENs). Although ZFNs are several years ahead of TALENs on research and optimization, TALENs are quickly proving to be capable of similar performance but with a much simpler design. There are commercial vendors as well as core facilities producing ZFNs and TALENs and multiple TALEN assembly kits that have been made publicly available. These TALEN assembly kits can be used to construct a custom nuclease for virtually any genome region of interest. With the idea of starting a TALEN core facility service for a private institution, a comparison of the assembly methods was made to determine which method was best suited. This presentation will introduce the TALEN structure, compare assembly methods from a core facility perspective and highlight the first experiences of starting a TALEN core facility.

Delventhal, Kym

2013-01-01

432

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

433

Study on a noise reduction system of CATV network upstream for data communication  

Microsoft Academic Search

All cable modems used in the CATV network use the same upstream and downstream frequencies to establish bidirectional communication with their central system. The upstream frequency band usually suffers from ingress impulse noises that cause severe interference to upstream communication. We have developed a method to detect, at the central system, the places where these noises get into the coaxial

M. Nakamura; Y. Yang; K. Wasaki; Y. Shidama

2003-01-01

434

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

2013-09-13

435

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

436

Identification of a novel first exon in the human dystrophin gene and of a new promoter located more than 500 kb upstream of the nearest known promoter  

SciTech Connect

The dystrophin gene, which is muted in patients with Duchenne and Becker muscular dystrophies, is the largest known human gene. Five alternative promoters have been characterized until now. Here we show that a novel dystrophin isoform with a different first exon can be produced through transcription initiation at a previously-unidentified alternative promoter. The case study presented is that of patient with Duchenne muscular dystrophy who had a deletion extending from 5{prime} end of the dystrophin gene to exon 2, including all promoters previously mapped in the 5{prime} part of the gene. Transcripts from lymphoblastoid cells were found to contain sequences corresponding to exon 3, indicating the presence of new promoter upstream of this exon. The nucleotide sequence of amplified cDNA corresponding to the 5{prime} end of the new transcript indicated that the 5{prime} end of exon 3 was extended by 9 codons, only the last (most 3{prime}) of which codes for methionine. The genomic nucleotide sequence upstream from the new exon, as determined using inverse polymerase chain reaction, revealed the presence of sequences similar to a TATA box, an octamer motif and an MEF-2 element. The identified promoter/exon did not map to intron 2, as might have been expected, but to a position more than 500 kb upstream of the most 5{prime} of the previously-identified promoters, thereby adding 500 kb to the dystrophin gene. The sequence of part of the new promoter region is very similar to that of certain medium reiteration frequency repetitive sequences. These findings may help us understand the molecular evolution of the dystrophin gene.

Yanagawa, H.; Nishio, H.; Takeshima, Y. [Kobe Univ. School of Medicine (Japan)] [and others

1994-09-01

437

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

438

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

439

POSTRANSLATIONAL MODIFICATIONS OF P53: UPSTREAM SIGNALING PATHWAYS.  

SciTech Connect

The p53 tumor suppressor is a tetrameric transcription factor that is posttranslational modified at >20 different sites by phosphorylation, acetylation, or sumoylation in response to various cellular stress conditions. Specific posttranslational modifications, or groups of modifications, that result from the activation of different stress-induced signaling pathways are thought to modulate p53 activity to regulate cell fate by inducing cell cycle arrest, apoptosis, or cellular senescence. Here we review recent progress in characterizing the upstream signaling pathways whose activation in response to various genotoxic and non-genotoxic stresses result in p53 posttranslational modifications.

ANDERSON,C.W.APPELLA,E.

2003-10-23

440

2. View of Potomac River at Great Falls looking upstream ...  

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

2. View of Potomac River at Great Falls looking upstream from Observation Tower. The majestic character of this wild and untrammeled spot is vividly shown. Scanty flow is evidenced by light colored normal water line markings on rock formation. Washington Agueduct Dam is shown in upper portion. Maryland on right and Virginia on left. Natives quoted as saying the water was as low or lower than during the drought conditions of 1930. Mr. Horyduzak, Photographer, 1943. - Potowmack Company: Great Falls Canal & Locks, Great Falls, Fairfax County, VA

441

Swimming upstream: the strengths of women who survive homelessness.  

PubMed

A study of the strengths and personal resources of women who had overcome homelessness revealed that the experience of homelessness for these women was a temporary state of disruption resulting from an effort to free themselves from conditions associated with despair, such as abuse or addictions, and to search for a better life. Personal, interpersonal, and transpersonal categories of strengths were identified that enabled these women to move in a positive direction toward health and self-actualization. The synthesizing metaphor "swimming upstream" describes the stoic determination required to go against the overwhelming negative forces of their environment. PMID:7515608

Montgomery, C

1994-03-01

442

Codon pairs of the HIV-1 vif gene correlate with CD4+ T cell count  

PubMed Central

Background The human APOBEC3G (A3G) protein activity is associated with innate immunity against HIV-1 by inducing high rates of guanosines to adenosines (G-to-A) mutations (viz., hypermutation) in the viral DNA. If hypermutation is not enough to disrupt the reading frames of viral genes, it may likely increase the HIV-1 diversity. To counteract host innate immunity HIV-1 encodes the Vif protein that binds A3G protein and form complexes to be degraded by cellular proteolysis. Methods Here we studied the pattern of substitutions in the vif gene and its association with clinical status of HIV-1 infected individuals. To perform the study, unique vif gene sequences were generated from 400 antiretroviral-naïve individuals. Results The codon pairs: 78–154, 85–154, 101–157, 105–157, and 105–176 of vif gene were associated with CD4+ T cell count lower than 500 cells per mm3. Some of these codons were located in the 81LGQGVSIEW89 region and within the BC-Box. We also identified codons under positive selection clustered in the N-terminal region of Vif protein, between 21WKSLVK26 and 40YRHHY44 regions (i.e., 31, 33, 37, 39), within the BC-Box (i.e., 155, 159) and the Cullin5-Box (i.e., 168) of vif gene. All these regions are involved in the Vif-induced degradation of A3G/F complexes and the N-terminal of Vif protein binds to viral and cellular RNA. Conclusions Adaptive evolution of vif gene was mostly to optimize viral RNA binding and A3G/F recognition. Additionally, since there is not a fully resolved structure of the Vif protein, codon pairs associated with CD4+ T cell count may elucidate key regions that interact with host cell factors. Here we identified and discriminated codons under positive selection and codons under functional constraint in the vif gene of HIV-1.

2013-01-01

443

Rapid communication Overcoming codon bias: A method for high-level overexpression of Plasmodium and other AT-rich parasite genes in Escherichia coli  

Microsoft Academic Search

Parasite genes often use codons which are rarely used in the highly expressed genes of Escherichia coli, possibly resulting in translational stalling and lower yields of recombinant protein. We have constructed the ''RIG'' plasmid to overcome the potential codon-bias problem seen in Plasmodium genes. RIG contains the genes that encode three tRNAs (Arg, Ile, Gly), which recognise rare codons found

Arthur M. Baca; Wim G. J. Hol

444

Quantitative codon optimisation of DNA libraries encoding sub-random peptides: design and characterisation of a novel library encoding transmembrane domain peptides  

Microsoft Academic Search

Codons for amino acids sharing similar chemical properties seem to cluster on the genetic codon table. Such a geographical distribution of the codons was exploited to create chemically synthe- sised DNA that encodes peptide libraries containing only a subset of the 20 natural amino acids. The frequency of each amino acid in the subset was further optimised by quantitatively manipulating

Ola Larsson; Dorit Thormeyer; Arian Asinger; Bjorn Wihlen; Claes Wahlestedt; Zicai Liang

2002-01-01

445

Cold start fuel enrichment circuit  

SciTech Connect

A cold start and knock prevention circuit is described having an output node providing a fuel enrichment signal for an internal combustion engine, comprising in combination: transducer means sensing audio signals indicative of engine combustion and occurring within a combustion chamber of the engine and converting the audio signals into an electrical output voltage including a portion representing background noise and a portion representing detonation; means for adjust the amplitude of the transducer output voltage; means sampling the portion of the transducer output voltage representing background noise and controlling the adjusting means to decrease the amplitude of the transducer output voltage for increased sensed background noise and to increase the amplitude of the transducer output voltage for decreased sensed background noise; detonation threshold means responsive to a predetermined increase in the amplitude of the portion of the transducer output voltage representing detonation above the amplitude of the portion of the transducer output voltage representing background noise, and outputting a fuel enrichment signal to the output node; a thermistor connected to the output node and sensing engine temperature; a voltage source biasing the thermistor such that the voltage across the thermistor varies with engine temperature and provides an output fuel enrichment signal at the output node.

Staerzi, R.E.; Radtke, N.H.; Hummel, L.S.

1988-08-16

446

Specific Mutations in KRAS Codons 12 and 13, and Patient Prognosis in 1075 BRAF-wild-type Colorectal Cancers  

PubMed Central

Purpose To assess prognostic roles of various KRAS oncogene mutations in colorectal cancer, BRAF mutation status must be controlled for because BRAF mutation is associated with poor prognosis, and almost all BRAF mutants are present among KRAS-wild-type tumors. Taking into account experimental data supporting a greater oncogenic effect of codon 12 mutations compared to codon 13 mutations, we hypothesized that KRAS codon 12 mutated colorectal cancers might behave more aggressively than KRAS-wild-type tumors and codon 13 mutants. Experimental design Utilizing molecular pathological epidemiology database of 1261 rectal and colon cancers, we examined clinical outcome and tumor biomarkers of KRAS codon 12 and 13 mutations in 1075 BRAF-wild-type cancers (i.e., controlling for BRAF status). Cox proportional hazards model was used to compute mortality hazard ratio (HR), adjusting for potential confounders, including stage, PIK3CA mutations, microsatellite instability, CpG island methylator phenotype, and LINE-1 methylation. Results Compared to patients with KRAS-wild-type/BRAF-wild-type cancers (N=635), those with KRAS codon 12 mutations (N=332) experienced significantly higher colorectal cancer-specific mortality [log-rank P=0.0001; multivariate HR=1.30; 95% confidence interval (CI), 1.02–1.67; P=0.037], whereas KRAS codon 13 mutated cases (N=108) were not significantly associated with prognosis. Among the seven most common KRAS mutations, c.35G>T (p.G12V; N=93) was associated with significantly higher colorectal cancer-specific mortality (log-rank P=0.0007; multivariate HR=2.00, 95% CI, 1.38–2.90, P=0.0003) compared to KRAS-wild-type/BRAF-wild-type cases. Conclusions KRAS codon 12 mutations (in particular, c.35G>T), but not codon 13 mutations, are associated with inferior survival in BRAF-wild-type colorectal cancer. Our data highlight the importance of accurate molecular characterization in colorectal cancer.

Imamura, Yu; Morikawa, Teppei; Liao, Xiaoyun; Lochhead, Paul; Kuchiba, Aya; Yamauchi, Mai; Qian, Zhi Rong; Nishihara, Reiko; Meyerhardt, Jeffrey A.; Haigis, Kevin M.; Fuchs, Charles S.; Ogino, Shuji

2013-01-01

447

The human mitochondrial tRNAMet: Structure/function relationship of a unique modification in the decoding of unconventional codons  

PubMed Central

Human mitochondrial mRNAs utilize the universal AUG and the unconventional isoleucine AUA codons for methionine. In contrast to translation in the cytoplasm, human mitochondria use one tRNA, hmtRNAMetCAU, to read AUG and AUA codons at both the peptidyl- (P-), and aminoacyl-(A-) sites of the ribosome. The hmtRNAMetCAU has a unique post-transcriptional modification, 5-formylcytidine, at the wobble position 34 (f5C34), and a cytidine substituting for the invariant uridine at position 33 of the canonical “U-turn” in tRNAs. The structure of the tRNA's anticodon stem and loop domain (hmtASLMetCAU), determined by NMR restrained molecular modeling, revealed how the f5C34 modification facilitates the decoding of AUA at the P- and A-sites. The f5C34 defined a reduced conformational space for the nucleoside, in what appears to have restricted the conformational dynamics of the anticodon bases of the modified hmtASLMetCAU. The hmtASLMetCAU exhibited a “C-turn” conformation that has some characteristics of the U-turn motif. Codon binding studies with both E. coli and bovine mitochondrial ribosomes revealed that the f5C34 facilitates AUA binding in the A-site and suggested that the modification favorably alters the ASL's binding kinetics. Mitochondrial translation by many organisms including humans sometimes initiates with the universal isoleucine codons AUU and AUC. The f5C34 enabled P-site codon binding to these normally isoleucine codons. Thus, the physicochemical properties of this one modification, f5C34, expand codon recognition from the traditional AUG to the non-traditional, synonymous codons AUU and AUC as well as AUA, in the reassignment of universal codons in the mitochondria.

Bilbille, Yann; Gustilo, Estella M.; Harris, Kimberly A.; Jones, Christie N.; Lusic, Hrvoje; Kaiser, Robert J.; Delaney, Michael O.; Spremulli, Linda L.; Deiters, Alexander; Agris, Paul F.

2011-01-01

448

On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli  

PubMed Central

A recent investigation concluded that codon bias did not affect expression of green fluorescent protein (GFP) variants in Escherichia coli, while stability of an mRNA secondary structure near the 5? end played a dominant role. We demonstrate that combining the two variables using regression trees or support vector regression yields a biologically plausible model with better support in the GFP data set and in other experimental data: codon usage is relevant for protein levels if the 5? mRNA structures are not strong. Natural E. coli genes had weaker 5? mRNA structures than the examined set of GFP variants and did not exhibit a correlation between the folding free energy of 5? mRNA structures and protein expression.

Supek, Fran; Smuc, Tomislav

2010-01-01

449

Degradation of mRNAs that lack a stop codon: A decade of nonstop progress  

PubMed Central

Nonstop decay is the mechanism of identifying and disposing aberrant transcripts that lack in-frame stop codons. It is hypothesized that these transcripts are identified during translation when the ribosome arrives at the 3? end of the mRNA and stalls. Presumably the ribosome stalling recruits additional cofactors, Ski7 and the exosome complex. The exosome degrades the transcript using either one of is ribonucleolytic activities and the ribosome and the peptide are both released. Additional precautionary measures by the nonstop decay pathway may include translational repression of the nonstop transcript after translation, and proteolysis of the released peptide by the proteasome. This surveillance mechanism protects the cells from potentially harmful truncated proteins, but it may also be involved in mediating critical cellular functions of transcripts that are prone to stop codon read-through. Important advances have been made in the past decade as we learn that nonstop decay may have implications in human disease.

Klauer, A. Alejandra; van Hoof, Ambro

2013-01-01

450

A POPULATION-SPECIFIC HTR2B STOP CODON PREDISPOSES TO SEVERE IMPULSIVITY  

PubMed Central

SUMMARY Impulsivity, describing action without foresight, is an important feature of several psychiatric diseases, suicidality and violent behavior. The complex origins of impulsivity hinder identification of the genes influencing both it and diseases with which it is associated. We performed exon-centric sequencing of impulsive individuals in a founder population, targeting fourteen genes belonging to the serotonin and dopamine domain. A stop codon in HTR2B that is common (MAF >1%) but exclusive to Finns was identified. Expression of the gene in the human brain was assessed, as well as the molecular functionality of the stop codon that was associated with psychiatric diseases marked by impulsivity in both population and family-based analyses. Knockout of Htr2b increased impulsive behaviors in mice, indicative of predictive validity. Our study shows the potential for identifying and tracing effects of rare alleles in complex behavioral phenotypes using founder populations, and suggests a role for HTR2B in impulsivity.

Bevilacqua, Laura; Doly, Stephane; Kaprio, Jaakko; Yuan, Qiaoping; Tikkanen, Roope; Paunio, Tiina; Zhou, Zhifeng; Wedenoja, Juho; Maroteaux, Luc; Diaz, Silvina; Belmer, Arnaud; Hodgkinson, Colin A.; Dell'Osso, Liliana; Suvisaari, Jaana; Coccaro, Emil; Rose, Richard J; Peltonen, Leena; Virkkunen, Matti; Goldman, David

2011-01-01

451

Lack of IRS-1 codon 513 and 972 polymorphism in Pima Indians  

SciTech Connect

Insulin receptor substrate-1 (IRS-1), a 1242 amino acid protein, an endogenous substrate for the insulin receptor tyrosine kinase, mediates many or all of the metabolic actions of insulin. Recently, polymorphism at codons 513 and 972 of the IRS-1 gene resulting in 2 amino acid substitutions that were associated with type II diabetes were found in a Caucasian population. Using allele specific oligonucleotide (ASO) hybridization, we screened 242 diabetic and 190 nondiabetic Pima Indians, a population with a very high prevalence of type II diabetes. Neither of the two mutations was present in either diabetic or nondiabetic subjects. We conclude that polymorphism at codons 513 and 972 of the IRS-1 gene observed in certain Caucasian populations is very rare or absent in Pima Indians. 20 refs., 2 figs., 1 tab.

Celi, F.S.; Silver, K.; Walston, J. [and others

1995-09-01

452

Evolutionary Basis of Codon Usage and Nucleotide Composition Bias in Vertebrate DNA Viruses  

Microsoft Academic Search

Understanding the extent and causes of biases in codon usage and nucleotide composition is essential to the study of viral\\u000a evolution, particularly the interplay between viruses and host cells or immune responses. To understand the common features\\u000a and differences among viruses we analyzed the genomic characteristics of a representative collection of all sequenced vertebrate-infecting\\u000a DNA viruses. This revealed that patterns

Laura A. Shackelton; Colin R. Parrish; Edward C. Holmes

2006-01-01

453

Translation efficiency is determined by both codon bias and folding energy.  

PubMed

Synonymous mutations do not alter the protein produced yet can have a significant effect on protein levels. The mechanisms by which this effect is achieved are controversial; although some previous studies have suggested that codon bias is the most important determinant of translation efficiency, a recent study suggested that mRNA folding at the beginning of genes is the dominant factor via its effect on translation initiation. Using the Escherichia coli and Saccharomyces cerevisiae transcriptomes, we conducted a genome-scale study aiming at dissecting the determinants of translation efficiency. There is a significant association between codon bias and translation efficiency across all endogenous genes in E. coli and S. cerevisiae but no association between folding energy and translation efficiency, demonstrating the role of codon bias as an important determinant of translation efficiency. However, folding energy does modulate the strength of association between codon bias and translation efficiency, which is maximized at very weak mRNA folding (i.e., high folding energy) levels. We find a strong correlation between the genomic profiles of ribosomal density and genomic profiles of folding energy across mRNA, suggesting that lower folding energies slow down the ribosomes and decrease translation efficiency. Accordingly, we find that selection forces act near uniformly to decrease the folding energy at the beginning of genes. In summary, these findings testify that in endogenous genes, folding energy affects translation efficiency in a global manner that is not related to the expression levels of individual genes, and thus cannot be detected by correlation with their expression levels. PMID:20133581

Tuller, Tamir; Waldman, Yedael Y; Kupiec, Martin; Ruppin, Eytan

2010-02-02

454

Translation efficiency is determined by both codon bias and folding energy  

PubMed Central

Synonymous mutations do not alter the protein produced yet can have a significant effect on protein levels. The mechanisms by which this effect is achieved are controversial; although some previous studies have suggested that codon bias is the most important determinant of translation efficiency, a recent study suggested that mRNA folding at the beginning of genes is the dominant factor via its effect on translation initiation. Using the Escherichia coli and Saccharomyces cerevisiae transcriptomes, we conducted a genome-scale study aiming at dissecting the determinants of translation efficiency. There is a significant association between codon bias and translation efficiency across all endogenous genes in E. coli and S. cerevisiae but no association between folding energy and translation efficiency, demonstrating the role of codon bias as an important determinant of translation efficiency. However, folding energy does modulate the strength of association between codon bias and translation efficiency, which is maximized at very weak mRNA folding (i.e., high folding energy) levels. We find a strong correlation between the genomic profiles of ribosomal density and genomic profiles of folding energy across mRNA, suggesting that lower folding energies slow down the ribosomes and decrease translation efficiency. Accordingly, we find that selection forces act near uniformly to decrease the folding energy at the beginning of genes. In summary, these findings testify that in endogenous genes, folding energy affects translation efficiency in a global manner that is not related to the expression levels of individual genes, and thus cannot be detected by correlation with their expression levels.

Tuller, Tamir; Waldman, Yedael Y.; Kupiec, Martin; Ruppin, Eytan

2010-01-01

455

Codon optimization of the calf prochymosin gene and its expression in Kluyveromyces lactis  

Microsoft Academic Search

Chymosin as an important industrial enzyme widely used in cheese manufacture. The yeast Kluyveromyces lactis is a promising host strain for expression of the chymosin gene. However, low yields (80 U\\/ml in shake flask cultures) were\\u000a obtained when the K. lactis strain GG799 was used to express chymosin. We hypothesized that the codon-usage bias of the host may have resulted in

Zhen FengLanwei; Lanwei Zhang; Xue Han; Yanhe Zhang

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