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1

Efficient translation initiation dictates codon usage at gene start  

PubMed Central

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

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

2013-01-01

2

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

PubMed

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

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

2015-01-01

3

The rat ARF protein is translated from two closely spaced ATG start codons and can transcriptionally activate p53 in the absence of p53 protein stabilization.  

PubMed

We have analyzed the transcriptional start sites of the rat ARF gene and the amino acid sequence of the rat ARF tumor suppressor protein. The 5' end of the ratARF gene is similar to that of a number of cellular housekeeping genes in that it is CG-rich and does not contain an upstream TATA box motif to define a precise transcriptional start site. The transcription of the rat ARF gene is initiated at multiple start sites with one major start site accounting for 41% of transcription. The rat ARF protein contains two methionine ATG codons at its amino terminus separated by 10 amino acids. The translation of the major endogenous ARF protein species is initiated from the upstream methionine ATG codon. The upstream methionine ATG codon is predominantly used, despite the fact that it is both very close to the major transcriptional start site (6 bases downstream) and is in a less favorable nucleic acid sequence context than the downstream ATG, relative to the ideal sequence postulated for efficient initiation of translation. The downstream, inefficient rat ARF ATG is equivalent to the major mouse ARF ATG start codon. Both of these closely spaced ATGs can be utilized as a translational start codon to produce a nucleolar-localized ARF protein which can induce a p53-dependent inhibition of cell division and transcriptional activation of p53 in the absence of p53 stabilization. PMID:16760664

Hunt, Abigail E; Moule, Madeleine G; Fried, Mike

2006-06-01

4

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

PubMed Central

In eukaryotic cells initiation may occur from near-cognate codons that differ from AUG by a single nucleotide. The stringency of start codon selection impacts the efficiency of initiation at near-cognate codons and the efficiency of initiation at AUG codons in different contexts. We used a codon-optimized firefly luciferase reporter initiated with AUG or each of the nine near-cognate codons in preferred context to examine the stringency of start codon selection in the model filamentous fungus Neurospora crassa. In vivo results indicated that the hierarchy of initiation at start codons in N. crassa (AUG ? CUG > GUG > ACG > AUA ? UUG > AUU > AUC) is similar to that in human cells. Similar results were obtained by translating mRNAs in a homologous N. crassa in vitro translation system or in rabbit reticulocyte lysate. We next examined the efficiency of initiation at AUG, CUG, and UUG codons in different contexts in vitro. The preferred context was more important for efficient initiation from near-cognate codons than from AUG. These studies demonstrated that near-cognate codons are used for initiation in N. crassa. Such events could provide additional coding capacity or have regulatory functions. Analyses of the 5?-leader regions in the N. crassa transcriptome revealed examples of highly conserved near-cognate codons in preferred contexts that could extend the N termini of the predicted polypeptides. PMID:23396971

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

2013-01-01

5

Multiple start codons and phosphorylation result in discrete Rad52 protein species  

PubMed Central

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

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

2006-01-01

6

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

PubMed Central

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

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

2014-01-01

7

Secret Codon  

NSDL National Science Digital Library

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

Julie Yu

2008-01-01

8

A conformational change in the eukaryotic translation preinitiation complex and release of eIF1 signal recognition of the start codon.  

PubMed

During eukaryotic translation initiation, ribosomal 43S complexes scan mRNAs for the correct AUG codon at which to begin translation. Start codon recognition triggers GTP hydrolysis, committing the complex to engagement at that point on the mRNA. While fidelity at this step is essential, the nature of the codon recognition event and the mechanism by which it activates GTP hydrolysis are poorly understood. Here we report the changes that occur within the 43S.mRNA complex in response to AUG codon recognition. eIF1 and eIF1A are key players in assembly of 43S.mRNA complexes capable of locating initiation codons. We observed FRET between these two factors when bound to the 40S subunit. Using steady-state FRET, anisotropy, and kinetic analyses, we demonstrate that start codon recognition results in a conformational change and release of eIF1 from the ribosome. These rearrangements probably play a role in triggering GTP hydrolysis and committing the complex to downstream events. PMID:15664195

Maag, David; Fekete, Christie A; Gryczynski, Zygmunt; Lorsch, Jon R

2005-01-21

9

The C-Terminal Domain of Eukaryotic Initiation Factor 5 Promotes Start Codon Recognition by Its Dynamic Interplay with eIF1 and eIF2?  

E-print Network

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) ...

Luna, Rafael E.

10

Analysis of diversity and relationships among orchardgrass (Dactylis glomerata L.) accessions using start codon-targeted markers.  

PubMed

Orchardgrass, or cocksfoot, is an important perennial forage grass worldwide. The comprehensive understanding of orchardgrass accessions will benefit germplasm collection and breeding progress, and it will enhance efforts to improve forage yield and quality. Therefore, 24 novel, simple, polymorphic, and reliable start codon-targeted (SCoT) markers were used to analyze the diversity and genetic relationships among 95 orchardgrass accessions. In total, 273 polymorphic bands were detected with an average of 11.4 bands per primer. The average polymorphic rate for the species was 83.4%, suggesting a high discriminating ability of the SCoT technique for orchardgrass. The molecular variance analysis revealed that 69.13 and 30.87% of variation resided within and among groups, respectively, demonstrating that the orchardgrass germplasms had a higher level of genetic diversity within groups than among geographical regions and distributions. The distinct geographical divergence of orchardgrass was revealed between North America and Oceania. The unweighted pair-group method with arithmetic mean dendrogram revealed a separation of 7 main clusters between 95 accessions according to the geographical origin. Furthermore, each cluster was divided into subgroups mainly according to the origin of its state. The genetic divergence of orchardgrass might be influenced by the ecogeographical conditions, climatic types, breeding systems and gene flow with variations in cultures, bird migration, and breeder selection. These results could facilitate orchardgrass germplasm collection, management, and breeding worldwide. PMID:25036346

Jiang, L F; Qi, X; Zhang, X Q; Huang, L K; Ma, X; Xie, W G

2014-01-01

11

RNA Secondary Structure in the Coding Region of Dengue Virus Type 2 Directs Translation Start Codon Selection and Is Required for Viral Replication  

PubMed Central

Dengue virus is a positive-strand RNA virus and a member of the genus Flavivirus, which includes West Nile, yellow fever, and tick-borne encephalitis viruses. Flavivirus genomes are translated as a single polyprotein that is subsequently cleaved into 10 proteins, the first of which is the viral capsid (C) protein. Dengue virus type 2 (DENV2) and other mosquito-borne flaviviruses initiate translation of C from a start codon in a suboptimal context and have multiple in-frame AUGs downstream. Here, we show that an RNA hairpin structure in the capsid coding region (cHP) directs translation start site selection in human and mosquito cells. The ability of the cHP to direct initiation from the first start codon is proportional to its thermodynamic stability, is position dependent, and is sequence independent, consistent with a mechanism in which the scanning initiation complex stalls momentarily over the first AUG as it begins to unwind the cHP. The cHP of tick-borne flaviviruses is not maintained in a position to influence start codon selection, which suggests that this coding region cis element may serve another function in the flavivirus life cycle. Here, we demonstrate that the DENV2 cHP and both the first and second AUGs of C are necessary for efficient viral replication in human and mosquito cells. While numerous regulatory elements have been identified in the untranslated regions of RNA viral genomes, we show that the cHP is a coding-region RNA element that directs start codon selection and is required for viral replication. PMID:16474125

Clyde, Karen; Harris, Eva

2006-01-01

12

Translation of psbC mRNAs starts from the downstream GUG, not the upstream AUG, and requires the extended Shine-Dalgarno sequence in tobacco chloroplasts.  

PubMed

The plastid gene psbC encodes the CP43 subunit of PSII. Most psbC mRNAs of many organisms possess two possible initiation codons, AUG and GUG, and their coding regions are generally annotated from the upstream AUG. Using a chloroplast in vitro translation system, we show here that translation of the tobacco plastid psbC mRNA initiates from the GUG. This mRNA possesses a long Shine-Dalgarno (SD)-like sequence, GAGGAGGU, nine nucleotides upstream of the GUG. Point mutations in this sequence abolished translation, suggesting that a strong interaction between this extended SD-like sequence and the 3' end of 16S rRNA facilitates translation initiation from the GUG. PMID:17664183

Kuroda, Hiroshi; Suzuki, Haruka; Kusumegi, Takahiro; Hirose, Tetsuro; Yukawa, Yasushi; Sugiura, Masahiro

2007-09-01

13

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

PubMed

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. PMID:22941660

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

2012-11-01

14

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans  

E-print Network

Upstream ORFs (uORFs) are mRNA elements defined by a start codon in the 5? UTR that is out-of-frame with the main coding sequence. Although uORFs are present in approximately half of human and mouse transcripts, no study ...

Calvo, Sarah E.

15

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

E-print Network

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

Trumpower, Bernard L.

16

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

PubMed Central

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

2013-01-01

17

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

Microsoft Academic Search

BACKGROUND: Upstream open reading frames (uORFs) are elements found in the 5'-region of an mRNA transcript, capable of regulating protein production of the largest, or major ORF (mORF), and impacting organismal development and growth in fungi, plants, and animals. In Drosophila, approximately 40% of transcripts contain upstream start codons (uAUGs) but there is little evidence that these are translated and

Celine A Hayden; Giovanni Bosco

2008-01-01

18

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

Microsoft Academic Search

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

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

1989-01-01

19

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

SciTech Connect

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

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

2006-10-13

20

Transcription, Translation and Mutation Given this list of codons  

E-print Network

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

Prestwich, Ken

21

Properties of an Intergenic Terminator and Start Site Switch That Regulate IMD2 Transcription in Yeast  

Microsoft Academic Search

The IMD2 gene in Saccharomyces cerevisiae is regulated by intracellular guanine nucleotides. Regulation is exerted through the choice of alternative transcription start sites that results in synthesis of either an unstable short transcript terminating upstream of the start codon or a full-length productive IMD2 mRNA. Start site selection is dictated by the intracellular guanine nucleotide levels. Here we have mapped

M. Harley Jenks; Thomas W. O'Rourke; Daniel Reines

2008-01-01

22

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

PubMed

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

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

2015-01-01

23

Codon Distributions in DNA  

E-print Network

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

Som, A; Chakrabarti, J; Bandyopadhyay, D

2001-01-01

24

Codon distributions in DNA  

NASA Astrophysics Data System (ADS)

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

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

2001-05-01

25

Codon Evolution Mechanisms and Models  

E-print Network

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

Anisimova, Maria

26

Structure of the Saccharomyces cerevisiae HO gene and analysis of its upstream regulatory region.  

PubMed Central

The HO gene product of Saccharomyces cerevisiae is a site-specific endonuclease that initiates mating type interconversion. We have determined the nucleotide sequence of a 3,129-base-pair (bp) segment containing HO. The segment contains a single long open reading frame encoding a polypeptide of 586 amino acids, which has unusual (unbiased) codon usage and is preceded by 762 bp of upstream region. The predicted HO protein is basic (16% lysine and arginine) and is calculated to have a secondary structure that is 30% helical. The corresponding transcript is initiated approximately 50 nucleotides prior to the presumed initiation codon. Insertion of an Escherichia coli lacZ gene fragment into the putative HO coding segment inactivated HO and formed a hybrid HO-lacZ gene whose beta-galactosidase activity was regulated by the mating type locus in the same manner as HO (repressed by a 1-alpha 2). Upstream regions of 1,360 and 762 bp conferred strong repression; 436 bp led to partial constitutivity and 301 bp to full constitutivity. Thus, DNA sequences that confer repression of HO by a1-alpha 2 are at least 250 nucleotides upstream of the transcription start point and are within 436 nucleotides of the HO initiation codon. The progressive loss of repression suggests that both the -762 to -436 and the -436 to -301 intervals contain sites for regulation by a1-alpha 2. The HO gene contains two distinct regions that promote autonomous replication of plasmids in S. cerevisiae. These regions contain sequences that are homologous to the two conserved sequences that are associated with ARS activity. Images PMID:3025649

Russell, D W; Jensen, R; Zoller, M J; Burke, J; Errede, B; Smith, M; Herskowitz, I

1986-01-01

27

Primary acute lymphoblastic leukemia cells use a novel promoter and 5'noncoding exon for the human reduced folate carrier that encodes a modified carrier translated from an upstream translational start.  

PubMed

The human reduced folate carrier (hRFC) is reported to be regulated by up to seven alternatively spliced noncoding exons (A1, A2, A, B, C, D, and E). Noncoding exon and promoter usage was analyzed in RNAs from 27 childhood acute lymphoblastic leukemia (ALL) specimens by real-time PCR and/or 5' rapid amplification of cDNA ends (5' RACE) assay. By real-time PCR, total hRFC transcripts in ALL spanned a 289-fold range. Over 90% of hRFC transcripts were transcribed with A1, A2, and B 5' untranslated regions (UTRs). Analysis of 5' RACE clones showed that the A1 + A2 5'UTRs contained A1 sequence alone or a fusion of A1 and A2, implying the existence of a single, alternatively spliced 1021-bp A1/A2 noncoding region. High frequency sequence polymorphisms (AGG deletion, C/T transition) identified in the A1/A2 region by 5'RACE were confirmed in normal DNAs. By reporter assays in HepG2 hepatoma and Jurkat leukemia cells, A1/A2 promoter activity was localized to a 134-bp minimal region. Translation from an upstream AUG in the A1/A2 noncoding region in-frame with the normal translation start resulted in synthesis of a larger ( approximately 7 kDa) hRFC protein with transport properties altered from those for wild-type hRFC. Although there was no effect on transcript or protein stabilities, in vitro translation from A1/A2 transcripts was decreased compared with those with the B 5'UTR. Our results document the importance of the hRFC A1/A2 upstream region in childhood ALL and an intricate transcriptional and posttranscriptional regulation of hRFC-A1/A2 mRNAs. Furthermore, they suggest that use of the A1/A2 5'UTR may confer a transport phenotype distinct from the other 5'UTRs due to altered translation efficiency and transport properties. PMID:15297414

Flatley, Robin M; Payton, Scott G; Taub, Jeffrey W; Matherly, Larry H

2004-08-01

28

A Generalized Mechanistic Codon Model  

PubMed Central

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

Zaheri, Maryam; Dib, Linda; Salamin, Nicolas

2014-01-01

29

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

E-print Network

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

Magliery, Thomas J.

30

Codon Evolution Mechanisms and Models  

E-print Network

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

Anisimova, Maria

31

Efficient codon optimization with motif engineering  

E-print Network

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

Condon, Anne

32

Asociaciones Trasformacion de codons a aminoacidos  

E-print Network

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

Giménez, Domingo

33

What Drives Codon Choices in Human Genes?  

Microsoft Academic Search

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

Samuel Karlin; Jan Mrázek

1996-01-01

34

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

PubMed Central

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

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

1994-01-01

35

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

36

Rare codons regulate KRas oncogenesis  

PubMed Central

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

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

2013-01-01

37

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

PubMed Central

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

2010-01-01

38

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

E-print Network

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

Carbone, Alessandra

39

Point Counter Point UAR Codons for Glutamine  

E-print Network

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

Keeling, Patrick

40

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency  

E-print Network

Balanced Codon Usage Optimizes Eukaryotic Translational Efficiency Wenfeng Qian1 , Jian-Rong Yang1 in rapidly growing organisms. It is widely believed that synonymous codons are translated with unequal speeds and that translational efficiency is maximized by the exclusive use of rapidly translated codons. Here we estimate

Zhang, Jianzhi

41

Codon Usage Domains over Bacterial Chromosomes  

E-print Network

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

Kent, University of

42

Cloning and Characterization of Buffalo NANOG Gene: Alternative Transcription Start Sites, Splicing, and Polyadenylation in Embryonic Stem Cell-Like Cells  

PubMed Central

NANOG is a critical homeodomain transcription factor responsible for maintaining embryonic stem cell (ESC) self-renewal and pluripotency. In the present study, we isolated, sequenced, and characterized the NANOG gene in buffalo ESC-like cells. Here, we demonstrated that NANOG mRNA is expressed as multiple isoforms and uses four alternative transcriptional start sites (TSSs) and five different polyadenylation sites. The TSSs identified by 5?-RNA ligase-mediated rapid amplification of cDNA ends (RLM-5?-RACE) were positioned at 182, 95, 35, and 17 nucleotides upstream relative to the translation initiation codon. 3?-RACE experiment revealed the presence of tandem polyadenylation signals, which leads to the expression of at least five different 3?-untranslated regions (269, 314, 560, 566, and 829 nucleotides). Expression analysis showed that these alternatively polyadenylated transcripts expressed differentially. Sequence analysis showed that the open reading frame of buffalo NANOG codes for a 300-amino-acid-long protein. Further, results showed that alternative splicing leads to the expression of two types of transcript variants encoded by four and five exons. In silico analysis of cloned 5?-flanking region (3366 nucleotides upstream of translation start codon) identified several putative transcription factors binding sites in addition to a TATA box and CAAT box at ?30 and ?139?bp (upstream to the distal most TSS), respectively, in the buffalo NANOG promoter. PMID:22011250

Singh, Natwar; Sharma, Ruchi; George, Aman; Singla, Suresh K.; Palta, Prabhat; Manik, Radhaysham; Chauhan, Manmohan S.

2012-01-01

43

Upstream health law.  

PubMed

For the first time, entrepreneurs are aggressively developing new technologies and business models designed to improve individual and population health, not just to deliver specialized medical care. Consumers of these goods and services are not yet "patients"; they are simply people. As this sector of the health care industry expands, it is likely to require new forms of legal governance, which we term "upstream health law." PMID:25565619

Sage, William M; McIlhattan, Kelley

2014-12-01

44

Analysis of the 5'-upstream region of mouse P/Q-type Ca2+ channel alpha1A subunit gene for expression in pancreatic islet beta cells using transgenic mice and HIT-T15 cells.  

PubMed

The omega-agatoxin-IVA-sensitive P/Q-type Ca(2+) channel plays a role in insulin release from the pancreatic islets of beta cells. To dissect the molecular mechanisms underlying beta cell expression of the P/Q-type channel, we characterized the 5'-upstream region of the mouse alpha(1A) subunit gene using transgenic mice and HIT insulinoma cells. The E. coli lacZ reporter gene was expressed in pancreatic acini and islets in transgenic mice carrying the 6.3 kb or 3.0 kb of the 5'-upstream region, although those with 1.5 kb or 0. 5 kb of the 5'-upstream region failed to show reporter expression on histological examination. As the expression of alpha(1A)subunit gene could not be detected in acini using RT-PCR analysis, the reporter expression in acini might have been ectopic expression. When linked to the placental alkaline phosphatase reporter gene to examine promoter activity for beta cell expression, the 6.3 kb and 3.0 kb fragment of the 5'-upstream region, but not the smaller 1.5 kb fragment, were able to drive reporter gene expression in HIT cells. The sequence between 3.0 and 1.5 kb upstream of the start codon enhanced thymidine kinase promoter activity in HIT cells, but not in fibroblast NIH3T3 cells. These results suggested that the beta cell-specific elements of the alpha(1A) subunit gene are likely to be located in the distal upstream region (-3021 to-1563) of the 5'-upstream sequence and that the 6.3 kb fragment of the 5'-upstream region alone might be a lack of a negative cis-regulatory element(s) to suppress the alpha(1A) subunit gene expression in acini. PMID:10750023

Takahashi, E; Miyamoto, N; Nagasu, T

2000-04-01

45

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

SciTech Connect

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

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

1987-05-01

46

Biotechnology: Upstream Processing Associate  

NSDL National Science Digital Library

In this 2:31 video excerpted from Pathways to Technology, youâ??ll 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.

47

Reduced synonymous substitution rate at the start of enterobacterial genes.  

PubMed Central

Synonymous codon usage is less biased at the start of Escherichia coli genes than elsewhere. The rate of synonymous substitution between E.coli and Salmonella typhimurium is substantially reduced near the start of the gene, which suggests the presence of an additional selection pressure which competes with the selection for codons which are most rapidly translated. Possible competing sources of selection are the presence of secondary ribosome binding sites downstream from the start codon, the avoidance of mRNA secondary structure near the start of the gene and the use of sub-optimal codons to regulate gene expression. We provide evidence against the last of these possibilities. We also show that there is a decrease in the frequency of A, and an increase in the frequency of G along the E.coli genes at all three codon positions. We argue that these results are most consistent with selection to avoid mRNA secondary structure. PMID:8233796

Eyre-Walker, A; Bulmer, M

1993-01-01

48

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

PubMed Central

A human gene encoding an interferon-induced 15-kDa protein has been isolated from a genomic library. The gene appears to be single-copy and is composed of two exons, the first of which contains the ATG translation initiation codon. In vitro nuclear run-on assays showed that the transcription rate of the gene is stimulated after interferon treatment. To analyze transcriptional regulatory sequences, we constructed recombinant plasmids for use in transient transfection assays of HeLa cells. Constructs containing 115 nucleotides 5' to the transcription initiation site were found to be fully inducible by interferon. Assays of deletion mutants identified a critical element for interferon induction located between -115 and -96, just upstream of the "CCAAT box." Moreover, a DNA fragment including this region can confer interferon inducibility on a heterologous promoter (thymidine kinase) when cloned in either orientation upstream of the gene or downstream of the gene. These are properties characteristic of an enhancer element that is active only after treatment with interferon. This regulatory sequence may be shared by a group of interferon-induced genes, since a very similar sequence is present within the functional region near the RNA start site of another interferon-induced gene. Images PMID:3476954

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

1987-01-01

49

Site-specific codon bias in bacteria  

SciTech Connect

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

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

1996-03-01

50

Evolution of codon usage in bacteria.  

E-print Network

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

Henry, Ian

2007-01-01

51

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

E-print Network

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

Webb, Colleen

52

Studying Codon Usage: From sequence to function  

NASA Astrophysics Data System (ADS)

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

Hwa, Terry; Klumpp, Stefan; Dong, Jiajia

2007-03-01

53

Evolution of Codon Usage Bias in Drosophila  

Microsoft Academic Search

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

Jeffrey R. Powell; Etsuko N. Moriyama

1997-01-01

54

Di-codon Usage for Gene Classification  

NASA Astrophysics Data System (ADS)

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

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

55

Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae.  

PubMed

We have taken advantage of recently sequenced hemiascomycete fungal genomes to computationally identify additional genes potentially regulated by upstream open reading frames (uORFs). Our approach is based on the observation that the structure, including the uORFs, of the post-transcriptionally uORF regulated Saccharomyces cerevisiae genes GCN4 and CPA1 is conserved in related species. Thirty-eight candidate genes for which uORFs were found in multiple species were identified and tested. We determined by 5' RACE that 15 of these 38 genes are transcribed. Most of these 15 genes have only a single uORF in their 5' UTR, and the length of these uORFs range from 3 to 24 codons. We cloned seven full-length UTR sequences into a luciferase (LUC) reporter system. Luciferase activity and mRNA level were compared between the wild-type UTR construct and a construct where the uORF start codon was mutated. The translational efficiency index (TEI) of each construct was calculated to test the possible regulatory function on translational level. We hypothesize that uORFs in the UTR of RPC11, TPK1, FOL1, WSC3, and MKK1 may have translational regulatory roles while uORFs in the 5' UTR of ECM7 and IMD4 have little effect on translation under the conditions tested. PMID:16012843

Zhang, Zhihong; Dietrich, Fred S

2005-08-01

56

Universality and Shannon entropy of codon usage  

NASA Astrophysics Data System (ADS)

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

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

2003-12-01

57

Codon Constraints on Closed 2D Shapes  

E-print Network

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

Richards, Whitman

1984-05-01

58

Correlation matrix for quartet codon usage  

NASA Astrophysics Data System (ADS)

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

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

2005-06-01

59

Selection on Codon Bias Ruth Hershberg and Dmitri A. Petrov  

E-print Network

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

Petrov, Dmitri

60

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

E-print Network

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

Clark, Patricia L.

61

RESEARCH ARTICLE Open Access Context-dependent codon partition models  

E-print Network

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

Gent, Universiteit

62

Transfer RNA misidentification scrambles sense codon recoding.  

PubMed

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

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

2013-10-11

63

A Model of Codon Usage Bias  

NASA Astrophysics Data System (ADS)

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

Kloster, Morten; Tang, Chao

2007-03-01

64

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

E-print Network

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

Clore, G. Marius

65

Effect of Codon Message on Xylanase Thermal Activity*  

PubMed Central

Because the genetic codon is known for degeneracy, its effect on enzyme thermal property is seldom investigated. A dataset was constructed for GH10 xylanase coding sequences and optimal temperatures for activity (Topt). Codon contents and relative synonymous codon usages were calculated and respectively correlated with the enzyme Topt values, which were used to describe the xylanase thermophilic tendencies without dividing them into two thermophilic and mesophilic groups. After analyses of codon content and relative synonymous codon usages were checked by the Bonferroni correction, we found five codons, with three (AUA, AGA, and AGG) correlating positively and two (CGU and AGC) correlating negatively with the Topt value. The three positive codons are purine-rich codons, and the two negative codons have A-ends. The two negative codons are pyridine-rich codons, and one has a C-end. Comparable with the codon C- and A-ending features, C- and A-content within mRNA correlated negatively and positively with the Topt value, respectively. Thereby, codons have effects on enzyme thermal property. When the issue is analyzed at the residual level, the effect of codon message is lost. The codons relating to enzyme thermal property are selected by thermophilic force at nucleotide level. PMID:22707716

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

2012-01-01

66

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

NASA Astrophysics Data System (ADS)

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

Caniparoli, Luca; Marsili, Matteo; Vendruscolo, Michele

2013-04-01

67

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

PubMed Central

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

Xia, Xuhua

2015-01-01

68

REVISITING THE CODON ADAPTATION INDEX FROM A WHOLE-GENOME PERSPECTIVE  

E-print Network

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

Carbone, Alessandra

69

Universality and Shannon entropy of codon usage  

E-print Network

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

Frappat, L; Sciarrino, A; Sorba, Paul

2003-01-01

70

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

NASA Astrophysics Data System (ADS)

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

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

2000-03-01

71

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

PubMed Central

Background Upstream open reading frames (uORFs) are elements found in the 5'-region of an mRNA transcript, capable of regulating protein production of the largest, or major ORF (mORF), and impacting organismal development and growth in fungi, plants, and animals. In Drosophila, approximately 40% of transcripts contain upstream start codons (uAUGs) but there is little evidence that these are translated and affect their associated mORF. Results Analyzing 19,389 Drosophila melanogaster transcript annotations and 666,153 dipteran EST sequences we have identified 44 putative conserved peptide uORFs (CPuORFs) in Drosophila melanogaster that show evidence of negative selection, and therefore are likely to be translated. Transcripts with CPuORFs constitute approximately 0.3% of the total number of transcripts, a similar frequency to the Arabidopsis genome, and have a mean length of 70 amino acids, much larger than the mean length of plant CPuORFs (40 amino acids). There is a statistically significant clustering of CPuORFs at cytological band 57 (p = 10-5), a phenomenon that has never been described for uORFs. Based on GO term and Interpro domain analyses, genes in the uORF dataset show a higher frequency of ORFs implicated in mitochondrial import than the genome-wide frequency (p < 0.01) as well as methyltransferases (p < 0.02). Conclusion Based on these data, it is clear that Drosophila contain putative CPuORFs at frequencies similar to those found in plants. They are distinguished, however, by the type of mORF they tend to associate with, Drosophila CPuORFs preferentially occurring in transcripts encoding mitochondrial proteins and methyltransferases. This provides a basis for the study of CPuORFs and their putative regulatory role in mitochondrial function and disease. PMID:18237443

Hayden, Celine A; Bosco, Giovanni

2008-01-01

72

Sum rules of codon usage probabilities  

E-print Network

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

Frappat, L; Sorba, Paul

2003-01-01

73

Codon thermoelectric signature in molecular junctions  

NASA Astrophysics Data System (ADS)

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

Maciá, Enrique

2010-07-01

74

Sum rules for codon usage probabilities  

NASA Astrophysics Data System (ADS)

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

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

2003-05-01

75

Preferred and avoided codon pairs in three domains of life  

PubMed Central

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

Tats, Age; Tenson, Tanel; Remm, Maido

2008-01-01

76

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

77

RESEARCH Open Access Stop codons in bacteria are not selectively  

E-print Network

RESEARCH Open Access Stop codons in bacteria are not selectively equivalent Inna S Povolotskaya1 stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial

Paris-Sud XI, Université de

78

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

E-print Network

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

Plotkin, Joshua B.

79

An evolutionary perspective on synonymous codon usage in unicellular organisms  

Microsoft Academic Search

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

Paul M. Sharp; Wen-Hsiung Li

1986-01-01

80

Use and misuse of correspondence analysis in codon usage studies  

E-print Network

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

Thioulouse, Jean

81

Genome Landscapes and Bacteriophage Codon Usage Julius B. Lucks1  

E-print Network

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

Plotkin, Joshua B.

82

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

E-print Network

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

Guerra Hernández, Alejandro

83

All-codon scanning identifies p53 cancer rescue mutations  

E-print Network

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

Lathrop, Richard H.

84

Synonymous Codon Bias is Related to Selection for Translational Accuracy?  

E-print Network

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

Eyre-Walker, Adam

85

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

E-print Network

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

Cutler, Chris

86

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

E-print Network

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

Nielsen, Rasmus

87

Codon Preference Optimization Increases Heterologous PEDF Expression  

PubMed Central

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

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

2010-01-01

88

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

89

The effects of upstream DNA on open complex formation by Escherichia coli RNA polymerase  

PubMed Central

Binding of activators to upstream DNA sequences regulates transcription initiation by affecting the stability of the initial RNA polymerase (RNAP)–promoter complex and/or the rate of subsequent conformational changes required to form the open complex (RPO). Here we observe that the presence of nonspecific upstream DNA profoundly affects an early step in formation of the transcription bubble. Kinetic studies with the ?PR promoter and Escherichia coli RNAP reveal that the presence of DNA upstream of base pair -47 greatly increases the rate of forming RPO, without significantly affecting its rate of dissociation. We find that this increase is largely due to an acceleration of the rate-limiting step (isomerization) in RPO formation, a step that occurs after polymerase binds. Footprinting experiments reveal striking structural differences downstream of the transcription start site (+1) in the first kinetically significant intermediate when upstream DNA is present. On the template strand, the DNase I downstream boundary of this early intermediate is +20 when upstream DNA is present but is shortened by approximately two helical turns when upstream DNA beyond -47 is removed. KMnO4 footprinting reveals an identical initiation bubble (-11 to +2), but unusual reactivity of template strand upstream cytosines (-12, -14, and -15) on the truncated promoter. Based on this work, we propose that early wrapping interactions between upstream DNA and the polymerase exterior strongly affect the events that control entry and subsequent unwinding of the DNA start site in the jaws of polymerase. PMID:15626761

Davis, Caroline A.; Capp, Michael W.; Record, M. Thomas; Saecker, Ruth M.

2005-01-01

90

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

PubMed Central

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

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

2014-01-01

91

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

PubMed

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

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

2014-01-01

92

Genome-wide analysis of codon usage bias in Ebolavirus.  

PubMed

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

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

2015-01-22

93

Start Young!  

ERIC Educational Resources Information Center

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

Rubin, Penni

2002-01-01

94

Starting motor  

Microsoft Academic Search

This patent describes a starting motor having a housing, planetary reduction gears including an internal gear in the housing. The improvement consists of an elastic member having a first annular portion mounted in engagement with a fixed annular member of the housing and a plurality of protruding axially extending elastic portions providing a corrugated surface pressed into engagement with an

T. Tanaka; I Hamano

1989-01-01

95

Analysis of synonymous codon usage pattern in duck circovirus.  

PubMed

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

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

2015-02-25

96

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

PubMed Central

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

Moore, Gregory L.; Maranas, Costas D.

2002-01-01

97

Mega-scale Bioinformatics Investigation of Codon Bias in Vertebrates.  

E-print Network

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

Nabiyouni, Maryam

2011-01-01

98

Getting Started  

NSDL National Science Digital Library

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

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

2001-01-01

99

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

E-print Network

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

Graur, Dan

100

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

E-print Network

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

Moriyama, Etsuko

101

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

102

A whole-genome analysis of premature termination codons.  

PubMed

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

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

2011-11-01

103

Codon Capture and Ambiguous Intermediate Scenarios of Genetic Code Evolution  

E-print Network

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

Yamashita, Tatsuro

2011-01-01

104

Rare codons capacitate Kras-driven de novo tumorigenesis.  

PubMed

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

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

2014-12-01

105

Starting motor  

SciTech Connect

This patent describes a starting motor having a housing, planetary reduction gears including an internal gear in the housing. The improvement consists of an elastic member having a first annular portion mounted in engagement with a fixed annular member of the housing and a plurality of protruding axially extending elastic portions providing a corrugated surface pressed into engagement with an end portion of the internal gear, the elastic member being sandwiched between the internal gear and the housing member, the protruding axially extending elastic portions providing resilient means which flex and incline circumferentially under turning force from the internal gear and exert reactive thrust on the internal gear elastically so that the frictional force at the abutting surfaces of the protruding portions holds the internal gear in resilient engagement with the elastic member and the resilient means acts as a buffer to absorb rotary impact force developing in the planetary reduction gears.

Tanaka, T.; Hamano, I

1989-05-23

106

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...

107

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. PMID:22500751

Kaya, Tolga; Koser, Hur

2012-01-01

108

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

109

Transactivation of a DR1 PPRE by a human constitutive androstane receptor variant expressed from internal protein translation start sites  

Microsoft Academic Search

Downstream in-frame start codons produce amino- terminal-truncated human constitutive androstane receptor protein isoforms (NCARs). The NCARs are expressed in liver and in vitro cell systems following translation from in-frame methionine AUG start codons at positions 76, 80, 125, 128, 168 and 265 within the full-length CAR mRNA. The resulting CAR proteins lack the N-terminal DNA-binding domain (DBD) of the receptor,

Matthew A. Stoner; Scott S. Auerbach; Stephanie M. Zamule; Stephen C. Strom; Curtis J. Omiecinski

2007-01-01

110

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

PubMed

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

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

2012-01-01

111

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

112

Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast  

E-print Network

Recent analysis of genomic signatures in mammals, flies, and worms indicates that functional translational stop codon readthrough is considerably more abundant in metazoa than previously recognized, but this analysis ...

Jungreis, Irwin

113

Evidence of efficient stop codon readthrough in four mammalian genes  

E-print Network

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

Loughran, Gary

114

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

E-print Network

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

Erives, Albert J.

115

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

E-print Network

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

Gerstein, Mark

116

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

E-print Network

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

Carbone, Alessandra

117

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

E-print Network

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

Michel, Christian

118

All-codon scanning identifies p53 cancer rescue mutations  

PubMed Central

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

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

2010-01-01

119

The empirical codon mutation matrix as a communication channel  

PubMed Central

Background A number of evolutionary models have been widely used for sequence alignment, phylogenetic tree reconstruction, and database searches. These models focus on how sets of independent substitutions between amino acids or codons derive one protein sequence from its ancestral sequence during evolution. In this paper, we regard the Empirical Codon Mutation (ECM) Matrix as a communication channel and compute the corresponding channel capacity. Results The channel capacity of 4.1875 bit, which is needed to preserve the information determined by the amino acid distribution, is obtained with an exponential factor of 0.26 applied to the ECM matrix. Additionally, we have obtained the optimum capacity achieving codon distribution. Compared to the biological distribution, there is an obvious difference, however, the distribution among synonymous codons is preserved. More importantly, the results show that the biological codon distribution allows for a “transmission” at a rate very close to the capacity. Conclusion We computed an exponential factor for the ECM matrix that would still allow for preserving the genetic information given the redundancy that is present in the codon-to-amino acid mapping. This gives an insight how such a mutation matrix relates to the preservation of a species in an information-theoretic sense. PMID:24655606

2014-01-01

120

A model for codon position bias in RNA editing  

E-print Network

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

Liu, T; Liu, Tsunglin; Bundschuh, Ralf

2005-01-01

121

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

122

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

123

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

NASA Astrophysics Data System (ADS)

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

Lind, Christoffer; Sund, Johan; Åqvist, Johan

2013-12-01

124

Analysis of a shift in codon usage in Drosophila.  

PubMed

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

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

2003-01-01

125

Upstream urbanization exacerbates urban heat island effects  

NASA Astrophysics Data System (ADS)

Urban Heat Island (UHI) effects adversely impact weather, air quality, and climate. Previous studies have attributed UHI effects to localized, surface processes. Based on an observational and modeling study of an extreme UHI (heat wave) episode in the Baltimore metropolitan region, we find that upstream urbanization exacerbates UHI effects and that meteorological consequences of extra-urban development can cascade well downwind. Under southwesterly wind, Baltimore, MD, experienced higher peak surface temperatures and higher pollution concentrations than did the larger urban area of Washington, DC. Ultra-high resolution numerical simulations with National Land Cover Data (NLCD) of 2001 show a nonlocal, dynamical contribution to UHI effects; when the upstream urban area is replaced by natural vegetation (in the model) the UHI effects could be reduced by more than 25%. These findings suggest that judicious land-use and urban planning, especially in rapidly developing countries, could help alleviate UHI consequences including heat stress and smog.

Zhang, Da-Lin; Shou, Yi-Xuan; Dickerson, Russell R.

2009-12-01

126

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

PubMed Central

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

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

2004-01-01

127

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

PubMed Central

An AUG-initiated upstream open reading frame (uORF) encoding a potential polypeptide of 3 to 13 amino acids (aa) is found within the 5? untranslated region (UTR) of >75% of coronavirus genomes based on 38 reference strains. Potential CUG-initiated uORFs are also found in many strains. The AUG-initiated uORF is presumably translated following genomic 5?-end cap-dependent ribosomal scanning, but its function is unknown. Here, in a reverse-genetics study with mouse hepatitis coronavirus, the following were observed. (i) When the uORF AUG-initiating codon was replaced with a UAG stop codon along with a U112A mutation to maintain a uORF-harboring stem-loop 4 structure, an unimpaired virus with wild-type (WT) growth kinetics was recovered. However, reversion was found at all mutated sites within five virus passages. (ii) When the uORF was fused with genomic (main) ORF1 by converting three in-frame stop codons to nonstop codons, a uORF-ORF1 fusion protein was made, and virus replicated at WT levels. However, a frameshifting G insertion at virus passage 7 established a slightly 5?-extended original uORF. (iii) When uAUG-eliminating deletions of 20, 30, or 51 nucleotides (nt) were made within stem-loop 4, viable but debilitated virus was recovered. However, a C80U mutation in the first mutant and an A77G mutation in the second appeared by passage 10, which generated alternate uORFs that correlated with restored WT growth kinetics. In vitro, the uORF-disrupting nondeletion mutants showed enhanced translation of the downstream ORF1 compared with the WT. These results together suggest that the uORF represses ORF1 translation yet plays a beneficial but nonessential role in coronavirus replication in cell culture. PMID:24173235

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

2014-01-01

128

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

E-print Network

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

Namiko Mitarai; Kim Sneppen; Steen Pedersen

2008-09-25

129

Codon-based mutagenesis using dimer-phosphoramidites  

Microsoft Academic Search

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

Philippe Neuner; Riccardo Cortese; Paolo Monaci

1998-01-01

130

Symmetry and Codon Usage Correlations in the Genetic Code  

E-print Network

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

Frappat, L; Sorba, Paul

1998-01-01

131

Similarity analysis of DNA sequences based on codon usage  

NASA Astrophysics Data System (ADS)

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

Li, Chun; Yu, Xiaoqing; Helal, Nadia

2008-06-01

132

The Selection-Mutation-Drift Theory of Synonymous Codon Usage  

Microsoft Academic Search

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

Michael Bulmer

1991-01-01

133

The predicted truncation from a cancer-associated variant of the MSH2 initiation codon alters activity of the MSH2-MSH6 mismatch repair complex.  

PubMed

Lynch syndrome (LS) is caused by germline mutations in DNA mismatch repair (MMR) genes. MMR recognizes and repairs DNA mismatches and small insertion/deletion loops. Carriers of MMR gene variants have a high risk of developing colorectal, endometrial, ovarian, and other extracolonic carcinomas. We report on an ovarian cancer patient who carries a germline MSH2 c.1A>C variant which alters the translation initiation codon. Mutations affecting the MSH2 start codon have been described previously for LS-related malignancies. However, the patients often lack a clear family history indicative of LS and their tumors often fail to display microsatellite instability, a hallmark feature of LS. Therefore, the pathogenicity of start codon variants remains undefined. Loss of the MSH2 start codon has been predicted to result in a truncated protein translated from a downstream in-frame AUG that would lack the first 25 amino acids. We therefore purified recombinant MSH2(N?25)-MSH6 and MSH2(N?25)-MSH3 to examine their DNA lesion recognition and adenosine nucleotide processing functions in vitro. We found that the MSH2(N?25) mutant confers distinct biochemical defects on MSH2-MSH6, but does not have a significant effect on MSH2-MSH3. We confirmed that expression of the MSH2 c.1A>C cDNA results in the production of multiple protein products in human cells that may include the truncated and full-length forms of MSH2. An in vivo MMR assay revealed a slight reduction in MMR efficiency in these cells. These data suggest that mutation of the MSH2 initiation codon, while not a strong, high-risk disease allele, may have a moderate impact on disease phenotype. PMID:21837758

Cyr, Jennifer L; Brown, Graham D; Stroop, Jennifer; Heinen, Christopher D

2012-08-01

134

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

Microsoft Academic Search

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

James F Kane

1995-01-01

135

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.

136

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

Microsoft Academic Search

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

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

2008-01-01

137

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

E-print Network

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

Wu, Wei-Biao

138

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

E-print Network

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

Jayaram, Bhyravabotla

139

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

SciTech Connect

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

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

1995-12-01

140

Oligonucleotide Design and Codon Optimization for PCR-based Gene Synthesis  

E-print Network

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

Williams, Brian C.

141

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

E-print Network

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

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

2011-03-03

142

Tissue-specific codon usage and the expression of human genes  

E-print Network

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

Plotkin, Joshua B.

143

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria  

E-print Network

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

Forney, Larry J.

144

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

E-print Network

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

Fernandez, Thomas

145

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

E-print Network

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

146

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

E-print Network

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

Wong, Limsoon

147

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

E-print Network

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

Carbone, Alessandra

148

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

E-print Network

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

Forger, Frank Michael

149

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

E-print Network

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

Cai, Long

150

Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria  

E-print Network

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

Top, Eva

151

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

E-print Network

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

Clark, Patricia L.

152

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

E-print Network

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

Eyre-Walker, Adam

153

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

E-print Network

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

Herbeck, Joshua

154

LETTER TO THE EDITOR The effect of nonsense codons on splicing  

E-print Network

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

Tong, Liang

155

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

E-print Network

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

Eyre-Walker, Adam

156

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

E-print Network

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

Xia, Xuhua

157

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

E-print Network

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

Aldana, Maximino

158

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

E-print Network

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

Xia, Xuhua

159

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

E-print Network

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

Pilpel, Yitzhak

160

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

E-print Network

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

Eppstein, Margaret J.

161

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

E-print Network

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

Majewski, Jacek

162

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

E-print Network

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

Bundschuh, Ralf

163

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

E-print Network

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

Church, George M.

164

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

E-print Network

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

Magliery, Thomas J.

165

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

E-print Network

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

Herbeck, Joshua

166

Translation efficiency is determined by both codon bias and folding energy  

E-print Network

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

Ruppin, Eytan

167

ArticleFastTrack Good Codons, Bad Transcript: Large Reductions in  

E-print Network

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

168

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

E-print Network

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

Petrov, Dmitri

169

RESEARCH Open Access The role of codon selection in regulation of  

E-print Network

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

Pilpel, Yitzhak

170

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

E-print Network

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

Cutter, Asher D.

171

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

E-print Network

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

Herbeck, Joshua

172

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. PMID:18437580

2008-01-01

173

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

Microsoft Academic Search

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

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

2009-01-01

174

Virus-like particle formation and translational start site choice of the plant retrotransposon Tto1  

Microsoft Academic Search

Ty1\\/copia group retrotransposon Tto1 from tobacco was put under control of an inducible promoter for expression in Arabidopsis thaliana. The system was used to analyze intermediates of the transposition process. The Tto1 RNA 5? region has a complex structure and contains several AUG codons. We therefore sought to experimentally define the translation initiation site. Constructs starting at various positions within

Gudrun Böhmdorfer; Kerstin Luxa; Andrea Frosch; Andrea Tramontano; Srecko Jelenic; Martina Weber; Andreas Bachmair

2008-01-01

175

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

176

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...

177

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

PubMed Central

Background KRAS mutations in codons 12 and 13 are established predictive biomarkers for anti-EGFR therapy in colorectal cancer. Previous studies suggest that KRAS codon 61 and 146 mutations may also predict resistance to anti-EGFR therapy in colorectal cancer. However, clinicopathological, molecular, and prognostic features of colorectal carcinoma with KRAS codon 61 or 146 mutation remain unclear. Methods We utilized a molecular pathological epidemiology database of 1267 colon and rectal cancers in the Nurse’s Health Study and the Health Professionals Follow-up Study. We examined KRAS mutations in codons 12, 13, 61 and 146 (assessed by pyrosequencing), in relation to clinicopathological features, and tumor molecular markers, including BRAF and PIK3CA mutations, CpG island methylator phenotype (CIMP), LINE-1 methylation, and microsatellite instability (MSI). Survival analyses were performed in 1067 BRAF-wild-type cancers to avoid confounding by BRAF mutation. Cox proportional hazards models were used to compute mortality hazard ratio, adjusting for potential confounders, including disease stage, PIK3CA mutation, CIMP, LINE-1 hypomethylation, and MSI. Results KRAS codon 61 mutations were detected in 19 cases (1.5%), and codon 146 mutations in 40 cases (3.2%). Overall KRAS mutation prevalence in colorectal cancers was 40% (=505/1267). Of interest, compared to KRAS-wild-type, overall, KRAS-mutated cancers more frequently exhibited cecal location (24% vs. 12% in KRAS-wild-type; P?codon, though statistical power was limited for codon 61 mutants. Neither KRAS codon 61 nor codon 146 mutation was significantly associated with clinical outcome or prognosis in univariate or multivariate analysis [colorectal cancer-specific mortality hazard ratio (HR)?=?0.81, 95% confidence interval (CI)?=?0.29-2.26 for codon 61 mutation; colorectal cancer-specific mortality HR?=?0.86, 95% CI?=?0.42-1.78 for codon 146 mutation]. Conclusions Tumors with KRAS mutations in codons 61 and 146 account for an appreciable proportion (approximately 5%) of colorectal cancers, and their clinicopathological and molecular features appear generally similar to KRAS codon 12 or 13 mutated cancers. To further assess clinical utility of KRAS codon 61 and 146 testing, large-scale trials are warranted. PMID:24885062

2014-01-01

178

Selection of AUG initiation codons differs in plants and animals.  

PubMed Central

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

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

1987-01-01

179

Developmental Stage and Level of Codon Usage Bias in Drosophila  

PubMed Central

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

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

2008-01-01

180

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

E-print Network

A Study of the Purine/Pyrimidine Codon Occurrence with a Reduced Centered Variable With the three-letter alphabet {R,Y,N} (R = purine, Y = pyrimidine, N= R or Y), there are 26 codons (NNN being excluded): RNN, . ,NNY (six codons at two unspecified bases N), RRN,. ,NYY (12 codons at one unspecified

Michel, Christian

181

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

182

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

PubMed Central

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

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

2012-01-01

183

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

184

An upstream open reading frame within an IRES controls expression of a specific VEGF-A isoform  

PubMed Central

Vascular endothelial growth factor A (VEGF-A) is a potent secreted mitogen critical for physiological and pathological angiogenesis. Regulation of VEGF-A occurs at multiple levels, including transcription, mRNA stabilization, splicing, translation and differential cellular localization of various isoforms. Recent advances in our understanding of the posttranscriptional regulation of VEGF-A are comprised of the identification of stabilizing mRNA-binding proteins and the discovery of two internal ribosomal entry sites (IRES) as well as two alternative initiation codons in the 5?UTR of the VEGF-A mRNA. We have previously reported that VEGF-A translation initiation at both the AUG and CUG codons is dependent on the exon content of the coding region. In this report, we show that the expression of different VEGF-A isoforms is regulated by a small upstream open reading frame (uORF) located within an internal ribosome entry site, which is translated through a cap-independent mechanism. This uORF acts as a cis-regulatory element that regulates negatively the expression of the VEGF 121 isoform. Our data provide a framework for understanding how VEGF-A mRNAs are translated, and how the production of the VEGF 121 isoform is secured under non-hypoxic environmental conditions. PMID:18304943

Bastide, Amandine; Karaa, Zeineb; Bornes, Stéphanie; Hieblot, Corinne; Lacazette, Eric; Prats, Hervé

2008-01-01

185

Upstream/downstream: Issues in environmental ethics  

SciTech Connect

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

Scherer, D. (ed.)

1991-01-01

186

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

PubMed Central

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

Yadav, Manoj Kumar; Swati, D

2012-01-01

187

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

PubMed Central

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

Kloster, Morten; Tang, Chao

2008-01-01

188

Synonymous Codon Usage in TTSuV2: Analysis and Comparison with TTSuV1  

PubMed Central

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

Dai, Dingzhen

2013-01-01

189

Why Are Translationally SubOptimal Synonymous Codons Used in Escherichia coli ?  

Microsoft Academic Search

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

Nick G. C. Smith; Adam Eyre-Walker

2001-01-01

190

Codon usage correlations and crystal basis model of the genetic code  

NASA Astrophysics Data System (ADS)

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

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

2001-07-01

191

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

PubMed Central

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

Parisien, Marc; Yi, Chengqi; Pan, Tao

2012-01-01

192

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

Microsoft Academic Search

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

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

2004-01-01

193

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

PubMed Central

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

Morton, B R

2001-01-01

194

Calpain, an upstream regulator of thymocyte apoptosis.  

PubMed

Apoptosis is the common phenotype of programmed or physiologic cell death, the process used to remove excess or defunct cells during normal tissue maintenance. One of the most studied cell types with respect to apoptosis is the immature T cell from the thymus, which activates its death program in response to an enormous variety of agents. Previously, our group implicated the calcium-dependent cytosolic protease calpain as a participant in thymocyte apoptosis initiated by glucocorticoids or irradiation. We found that the calpain inhibitors N-acetyl-leu-leu-norleucinal (calpain inhibitor I) and carbenzoxy-val-phe-H (MDL 28,170) prevented dexamethasone-induced apoptosis of thymocytes; in this study, we show that two additional calpain active site inhibitors, L-3-carboxy-trans-2,3-epoxypropionyl-leu-amido-(4-guanidinio )butane ethyl ester (E64d) and carbenzoxy-leu-leu-tyr-CHN2 (ZLLY-CHN2), also prevent apoptosis in this model. Three compounds that inhibit lysosomal cysteine proteases, carbenzoxy-tyr-ala-CHN2 (ZYA-CHN2), ammonium chloride, and chloroquine, do not block apoptosis, indicating that the effect of the calpain inhibitors is not due to cross-inhibition of lysosomal proteases. In addition, I-benzyl-CH=C(SH)COOH (PD150606), a calpain inhibitor directed toward the calcium binding sites of calpain, also prevents apoptosis. Calpain is necessary for other models of programmed cell death that require new gene expression (induction models), those following treatment of thymocytes with the calcium ionophore A23187, ionomycin, or forskolin. However, two models of thymocyte apoptosis that do not require new gene expression (transduction models), those triggered by heat shock and by valinomycin, are calpain independent, as is calcium-triggered DNA fragmentation in isolated thymocyte nuclei. These experiments suggest an upstream regulatory role for calpain in a pathway to thymocyte apoptosis common to several inducers. PMID:9103432

Squier, M K; Cohen, J J

1997-04-15

195

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

PubMed Central

Background Porcine reproductive and respitatory syndrome virus (PRRSV) is a recently emerged pathogen and severely affects swine populations worldwide. The replication of PRRSV is tightly controlled by viral gene expression and the codon usage of translation initiation region within each gene could potentially regulate the translation rate. Therefore, a better understanding of the codon usage pattern of the initiation translation region would shed light on the regulation of PRRSV gene expression. Results In this study, the codon usage in the translation initiation region and in the whole coding sequence was compared in PRRSV ORF1a and ORFs2-7. To investigate the potential role of codon usage in affecting the translation initiation rate, we established a codon usage model for PRRSV translation initiation region. We observed that some non-preferential codons are preferentially used in the translation initiation region in particular ORFs. Although some positions vary with codons, they intend to use codons with negative CUB. Furthermore, our model of codon usage showed that the conserved pattern of CUB is not directly consensus with the conserved sequence, but shaped under the translation selection. Conclusions The non-variation pattern with negative CUB in the PRRSV translation initiation region scanned by ribosomes is considered the rate-limiting step in the translation process. PMID:22014033

2011-01-01

196

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

PubMed

Messenger RNA (mRNA) encodes a sequence of amino acids by using codons. For most amino acids, there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for changing the ribosome speed while keeping the amino acid sequence and hence the resulting protein. Recently, it has been noticed that the choice of the synonymous codon, via the resulting distribution of slow- and fast-translated codons, affects not only on the average speed of one ribosome translating the mRNA but also might have an effect on nearby ribosomes by affecting the appearance of 'traffic jams' where multiple ribosomes collide and form queues. To test this 'context effect' further, we here investigate the effect of the sequence of synonymous codons on the ribosome traffic by using a ribosome traffic model with codon-dependent rates, estimated from experiments. We compare the ribosome traffic on wild-type (WT) sequences and sequences where the synonymous codons were swapped randomly. By simulating translation of 87 genes, we demonstrate that the WT sequences, especially those with a high bias in codon usage, tend to have the ability to reduce ribosome collisions, hence optimizing the cellular investment in the translation apparatus. The magnitude of such reduction of the translation time might have a significant impact on the cellular growth rate and thereby have importance for the survival of the species. PMID:24104350

Mitarai, Namiko; Pedersen, Steen

2013-10-01

197

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

PubMed

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

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

2014-12-01

198

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

SciTech Connect

A number of point and insert mutations of the PrP gene (PRNP) have been linked to familial Creutzfeldt-Jakob disease (CJD) and Gerstmann-Straussler-Scheinker disease (GSS). Moreover, the methionine/valine homozygosity at the polymorphic codon 129 of PRNP may cause a predisposition to sporadic and iatrogenic CJD or may control the age at onset of familial cases carrying either the 144-bp insertion or codon 178, codon 198, and codon 210 pathogenic mutations in PRNP. In addition, the association of methionine or valine at codon 129 and the point mutation at codon 178 on the same allele seem to play an important role in determining either fatal familial insomnia or CJD. However, it is noteworthy that a relationship between codon 129 polymorphism and accelerated pathogenesis (early age at onset or shorter duration of the disease) has not been seen in familial CJD patients with codon 200 mutation or in GSS patients with codon 102 mutation, arguing that other, as yet unidentified, gene products or environmental factors, or both, may influence the clinical expression of these diseases. 17 refs.

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

1996-04-01

199

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

200

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

E-print Network

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

Namiko Mitarai; Steen Pedersen

2013-09-04

201

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

PubMed

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

Zeng, Kai; Charlesworth, Brian

2009-10-01

202

Catalytic Ignition and Upstream Reaction Propagation in a Platinum Tube  

NASA Technical Reports Server (NTRS)

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

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

2007-01-01

203

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

204

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

PubMed Central

Although the decoding rules have been largely elucidated, the physical-chemical reasons for the "correctness" of codon:anticodon duplexes have never been clear. In this work, on the basis of the available data, we propose that the correct codon:anticodon duplexes are those whose formation and interaction with the ribosomal decoding center are not accompanied by uncompensated losses of hydrogen and ionic bonds. Other factors such as proofreading, base-base stacking and aminoacyl-tRNA concentration contribute to the efficiency and accuracy of aminoacyl-tRNA selection, and certainly these factors are important; but we suggest that analyses of hydrogen and ionic bonding alone provides a robust first-order approximation of decoding accuracy. Thus our model can simplify predictions about decoding accuracy and error. The model can be refined with data, but is already powerful enough to explain all of the available data on decoding accuracy. Here we predict which duplexes should be considered correct, which duplexes are responsible for virtually all misreading, and we suggest an evolutionary scheme that gave rise to the mixed boxes of the genetic code. PMID:11453067

Lim, V I; Curran, J F

2001-01-01

205

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

206

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

207

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

E-print Network

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

Eyre-Walker, Adam

208

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

PubMed Central

Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C?T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C?T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages. PMID:24583580

Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

2014-01-01

209

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

Microsoft Academic Search

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

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

2008-01-01

210

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

Microsoft Academic Search

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

Hiroshi Akashi

1994-01-01

211

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

212

Downstream Secondary Structure Facilitates Recognition of Initiator Codons by Eukaryotic Ribosomes  

Microsoft Academic Search

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

Marilyn Kozak

1990-01-01

213

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

PubMed Central

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

Kumar, Chandra Shekhar; Kumar, Sachin

2014-01-01

214

Starting a Small Business  

NSDL National Science Digital Library

This is the first of several lessons on starting a small business. This class is intended for adults entrepreneurs who may be thinking of starting a business. This lesson gives economic information on small businesses. It also provides information to help the student determine whether they are ready to be a business owner and whether their particular business could succeed. QUESTION: If you were to start a small business or home occupation, what would it be? Create a document giving a brief description of a potential business idea. (You will not be required to share the information with class members.) LESSON: Please read the following articles. 1. Go to the ...

Duke, Sonya

2008-10-07

215

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias  

PubMed Central

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

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

2009-01-01

216

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

PubMed

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

Nissley, Daniel A; O'Brien, Edward P

2014-12-31

217

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

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

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

218

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

219

7. Keechelus Dam, showing upstream face and crest, with outlet ...  

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

7. Keechelus Dam, showing upstream face and crest, with outlet gate tower at left background. View to northeast. - Keechelus Dam, Yakima River, 10 miles northwest of Easton, Easton, Kittitas County, WA

220

26. UPSTREAM VIEW OF DISCHARGE END OF OUTLET STRUCTURE.... Volume ...  

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

26. UPSTREAM VIEW OF DISCHARGE END OF OUTLET STRUCTURE.... Volume XVI, No. 17, September 29, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

221

24. UPSTREAM VIEW OF A PORTION OF THE CLOSED CONDUIT ...  

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

24. UPSTREAM VIEW OF A PORTION OF THE CLOSED CONDUIT SECTION OF OUTLET WORKS.... Volume XVI, No. 15, August 16, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

222

7. VIEW WEST ALONG THE UPSTREAM SLOPE OF THE EMBANKMENT, ...  

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

7. VIEW WEST ALONG THE UPSTREAM SLOPE OF THE EMBANKMENT, SHOWING ROCK PAVING IN PROGRESS.... Volume XIX, No. 7, June 24, 1940. - Prado Dam, Embankment, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

223

22. UPSTREAM VIEW OF THE OUTLET CONTROL STRUCTURE AND THE ...  

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

22. UPSTREAM VIEW OF THE OUTLET CONTROL STRUCTURE AND THE PIER FOR THE SERVICE BRIDGE.... Volume XVIII, No. 12, January 29, 1940. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

224

16. VIEW EASTERLY ALONG THE UPSTREAM SIDE OF THE OGEE ...  

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

16. VIEW EASTERLY ALONG THE UPSTREAM SIDE OF THE OGEE SECTION OF THE SPILLWAY.... Volume XVIII, No. 13, January 29, 1940. - Prado Dam, Spillway, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

225

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

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

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

226

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

227

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

228

1. View from the northeast, looking upstream (southwest) toward bridge's ...  

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

1. View from the northeast, looking upstream (southwest) toward bridge's northeast elevation - Enloe Bridge No. 90021, Spanning Red River of North between Minnesota & North Dakota on County State Aid Highway 28, Wolverton, Wilkin County, MN

229

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

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

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

230

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

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

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

231

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

232

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

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

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

233

5. A VIEW LOOKING WEST, TOWARD THE UPSTREAM SIDE OF ...  

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

5. A VIEW LOOKING WEST, TOWARD THE UPSTREAM SIDE OF THE PIER, SHOWING THE DETERIORATED SHEARWATER EDGE, THE NORTHEAST ABUTMENT AND WING WALL. - Cement Plant Road Bridge, Spanning Leatherwood Creek on County Road 50 South, Bedford, Lawrence County, IN

234

3. AN IMAGE LOOKING SOUTH, TOWARD THE UPSTREAM SIDE OF ...  

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

3. AN IMAGE LOOKING SOUTH, TOWARD THE UPSTREAM SIDE OF THE CENTRAL PIER AND SHOWING THE SOUTHEAST ABUTMENT AND ERODED STARLING. - Cement Plant Road Bridge, Spanning Leatherwood Creek on County Road 50 South, Bedford, Lawrence County, IN

235

EVALUATING THE EFFECT OF UPSTREAM WATERSHED ACTIVITIES TO DOWNSTREAM STREAMFLOW  

EPA Science Inventory

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

236

1. Credit JTL General view looking upstream and towards New ...  

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

1. Credit JTL General view looking upstream and towards New Hampshire, unidentified 'crazy man' perched on top of arch. - Bellows Falls Arch Bridge, Spanning Connecticut River, North Walpole, Cheshire County, NH

237

DETAIL VIEW OF TOP OF DAM GATE STRUCTURE. UPSTREAM LOCK ...  

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

DETAIL VIEW OF TOP OF DAM GATE STRUCTURE. UPSTREAM LOCK GATE AT RIGHT REAR. LOOKING WEST. - Illinois Waterway, La Grange Lock and Dam, 3/4 mile south of Country 795N at Illinois River, Versailles, Brown County, IL

238

Typical Framing of Bridge Ends and New Walk on Upstream ...  

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

Typical Framing of Bridge Ends and New Walk on Upstream Side, Typical Sway Bracing Above Upper Stringers, Typical Sway Bracing Below Floor Beams - Covered Bridge, Spanning Connecticut River, Orford, Grafton County, NH

239

15. GUARD LOCKS VIEWED FROM THE NORTHWEST BANK: SHOWS UPSTREAM ...  

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

15. GUARD LOCKS VIEWED FROM THE NORTHWEST BANK: SHOWS UPSTREAM SIDE. GATEHOUSE ON THE LEFT, ISLAND IN THE CENTER, AND LOCK HOUSE ON THE RIGHT 1976 - Pawtucket Canal, Guard Locks, Lowell, Middlesex County, MA

240

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

241

Influence of a river valley constriction on upstream sedimentation  

E-print Network

INFLUENCE OF A RIVER VALLEY CONSTRICTION ON UPSTREAM SEDIMENTATION A Thesis by QUIN KINNEBREW Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirement for the degree of MASTER OF SCIENCE... December 1988 Major Subject: Geology INFLUENCE OF A RIVER VALLEY CONSTRICTION ON UPSTREAM SEDIMENTATION A Thesis by QUIN KINNEBREW Approved as to style and content by: (Chairman of Committee) Kenneth L. White (Member) Earl R. Hoskins (Member...

Kinnebrew, Quin

2012-06-07

242

Downstream price-cap regulation and upstream market power  

Microsoft Academic Search

Under “partial separation,” it is increasingly common for a utility’s upstream affiliate (e.g., an electric generation supplier)\\u000a to be unregulated while its downstream affiliate (e.g., the distribution company offering retail service) is subject to regulation.\\u000a When choosing the optimal form of downstream regulation, regulators may be confronted with the potential exercise of market\\u000a power by the upstream affiliate. This paper

James D. Reitzes

2008-01-01

243

Starting an Investment Club  

E-print Network

the treasurer and one other member are given these E-161 8-02 STARTING AN INVESTMENT CLUB Jason Johnson, Bill Thompson and Wade Polk* * Assistant Professor and Extension Economist?Management, Assistant Professor and Extension Economist, and Extension Program...

Johnson, Jason; Thompson, Bill; Polk, Wade

2002-08-12

244

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

PubMed Central

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

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

2014-01-01

245

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

E-print Network

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

Bedwell, David M.

246

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

E-print Network

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

Mukherjee, Amar

247

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

E-print Network

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

Petrov, Dmitri

248

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

E-print Network

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

Wagner, Andreas

249

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

E-print Network

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

Paris-Sud XI, Université de

250

Barriers impede upstream spawning migration of flathead chub  

USGS Publications Warehouse

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

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

2014-01-01

251

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

PubMed Central

Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life. Though the frequency of codon usage is not equal across species and within genome in the same species, the phenomenon is non random and is tissue-specific. Several factors such as GC content, nucleotide distribution, protein hydropathy, protein secondary structure, and translational selection are reported to contribute to codon usage preference. The synonymous codon usage patterns can be helpful in revealing the expression pattern of genes as well as the evolutionary relationship between the sequences. In this study, synonymous codon usage bias patterns were determined for the evolutionarily close proteins of albumin superfamily, namely, albumin, ?-fetoprotein, afamin, and vitamin D-binding protein. Our study demonstrated that the genes of the four albumin superfamily members have low GC content and high values of effective number of codons (ENC) suggesting high expressivity of these genes and less bias in codon usage preferences. This study also provided evidence that the albumin superfamily members are not subjected to mutational selection pressure. PMID:24707212

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

2014-01-01

252

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

PubMed

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

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

2003-10-23

253

High codon adaptation in citrus tristeza virus to its citrus host  

PubMed Central

Background Citrus tristeza virus (CTV), a member of the genus Closterovirus within the family Closteroviridae, is the causal agent of citrus tristeza disease. Previous studies revealed that the negative selection, RNA recombination and gene flow were the most important forces that drove CTV evolution. However, the CTV codon usage was not studied and thus its role in CTV evolution remains unknown. Results A detailed comparative analysis of CTV codon usage pattern was done in this study. Results of the study show that although in general CTV does not have a high degree of codon usage bias, the codon usage of CTV has a high level of resemblance to its host codon usage. In addition, our data indicate that the codon usage resemblance is only observed for the woody plant-infecting closteroviruses but not the closteroviruses infecting the herbaceous host plants, suggesting the existence of different virus-host interactions between the herbaceous plant-infecting and woody plant-infecting closteroviruses. Conclusion Based on the results, we suggest that in addition to RNA recombination, negative selection and gene flow, host plant codon usage selection can also affect CTV evolution. PMID:22698086

2012-01-01

254

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

PubMed

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

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

2008-12-01

255

Engine starting and stopping  

NASA Astrophysics Data System (ADS)

Different starter systems for jet engines are discussed: electric, cartridge, iso-propyl-nitrate, air, gas turbine, and hydraulic. The fuel system, ignition system, air flow control system, and actual starting mechanism of an air starter motor system are considered. The variation of engine parameters throughout a typical starting sequence are described, with reference to examples for an RB211-535 engine. Physical constraints on engine starting are considered: rotating stall, light up, the window between hang and stall, hang, compressor stall, and the effects of ambient conditions. The following are also discussed: contractual and airworthiness requirements; windmilling; inflight relighting; afterburning light up; combustion stability; and broken shafts. Graphics illustrating the above are presented.

Curnock, Barry

256

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

PubMed Central

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

Kober, Kord M.; Pogson, Grant H.

2013-01-01

257

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

PubMed Central

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

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

2014-01-01

258

Getting started information)  

E-print Network

Contents: Getting started (General information) 2 Customer Care 6 Health & Safety 7 Fire Safety as information that we are legally obliged to give (e.g. Health & Safety, fire evacuation procedures etc & twin). Lafrowda has 730 rooms in flats of up to 12 people. Each has a kitchen/diner/lounge area

Mumby, Peter J.

259

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

260

Starting Material Silicon substrate  

E-print Network

Starting Material Silicon substrate 150 mm, p-type, , 36-63 ohm-cm Attila Horvath 2005 #12;Pad Oxidation and Nitride Deposition Silicon substrate Pad oxide = 250A Silicon nitride = 2200A Attila Horvath 2005 #12;N-Well Photo and Nitride Etch Silicon substrate Pad oxide Silicon nitride Photo resist Attila

Healy, Kevin Edward

261

Home Start Evaluation Study.  

ERIC Educational Resources Information Center

Case studies of eight Home Start programs are given as the third section of an evaluation study. Communities involved are Binghamton, New York; Franklin, North Carolina; Cleveland, Ohio; Harrogate, Tennessee; Houston, Texas; Weslaco, Texas; Millville, Utah; Parkersburg, West Virginia. Although each study varies in format, each describes in detail…

High/Scope Educational Research Foundation, Ypsilanti, MI.

262

PAINTING CHECKLIST GETTING STARTED  

E-print Network

PAINTING CHECKLIST GETTING STARTED o Choose your colour scheme o Test colours using sample pots o Measure the area to be painted · Choose paint finish, matt, semi-gloss, gloss etc · Type of paint to use, water-based etc · State of repair of current surface · Painting over oil-based/gloss paint or wallpaper

Peters, Richard

263

StartMe  

NSDL National Science Digital Library

The StartMe application gives Internet users the opportunity to create their own personal browser startpage with their favorite bookmarks and RSS feeds. The drag and drop interface is user-friendly, particularly for computer neophytes. Visitors can also incorporate extensions for popular browsers or tweak the appearance of their startpage as they see fit. This version is compatible with all operating systems.

264

Home Start Evaluation Study.  

ERIC Educational Resources Information Center

Case studies of seven Home Start programs are given as the third section of an evaluation study. Communities involved are Huntsville, Alabama; Fairbanks, Alaska; Fort Defiance, Arizona; Dardanelle, Arkansas; Wichita, Kansas; Gloucester, Massachusetts; and Reno, Nevada. Although each study varies in format, each describes in detail the degree and…

High/Scope Educational Research Foundation, Ypsilanti, MI.

265

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...

266

Comparison of properties of upstream whistlers at different planets  

NASA Technical Reports Server (NTRS)

Whistler mode waves have been recorded in the upstream region of Mercury, Venus, Earth and Saturn. They are elliptically polarized and observed typically at frequencies between 0.1 to 4 Hz. These intrinsically right handed waves can be left-handed polarized in the spaceframe as a result of strong negative Doppler shift. The waves propagate at an angle between 10 and 60 deg to the background magnetic field, with (Delta B)/B rarely exceeding 0.1. Comprehensive studies of these waves at Earth and Venus indicate that upstream whistlers are generated at the shock rather than locally in the foreshock. In this paper, we compare properties of upstream whistlers at all these planets. We also discuss the utilization of selected properties of these waves to evaluate the effective Alfvenic Mach number and the shock thickness at Mercury where solar wind measurements are not available.

Orlowski, D. S.; Russell, C. T.

1995-01-01

267

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

268

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

PubMed

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

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

2014-01-01

269

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

PubMed Central

During normal translation, binding of a release factor to one of the three stop codons (UGA, UAA or UAG) results in termination of protein synthesis. However, modification of the initial uridine to a pseudouridine (?) allows efficient recognition and read-through of these stop codons by a transfer RNA (tRNA), although it requires formation of two normally forbidden purine-purine base pairs1. We have determined the crystal structure at 3.1 Å resolution of the 30S ribosomal subunit in complex with the anticodon stem loop of tRNASer bound to the ?AG stop codon in the A site. The ?A base pair at the first position is accompanied by the formation of purine-purine base pairs at the second and third positions of the codon, which display an unusual Watson-Crick/Hoogsteen geometry. The structure shows a previously unsuspected ability of the ribosomal decoding center to accommodate non-canonical base pairs. PMID:23812587

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

2013-01-01

270

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

Microsoft Academic Search

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

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

1979-01-01

271

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

E-print Network

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

Lin, Michael F. (Michael Fong-Jay)

2012-01-01

272

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

273

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

PubMed Central

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

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

2009-01-01

274

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

PubMed Central

Background Synonymous codon usage can affect many cellular processes, particularly those associated with translation such as polypeptide elongation and folding, mRNA degradation/stability, and splicing. Highly expressed genes are thought to experience stronger selection pressures on synonymous codons. This should result in codon usage bias even in species with relatively low effective population sizes, like mammals, where synonymous site selection is thought to be weak. Here we use phylogenetic codon-based likelihood models to explore patterns of codon usage bias in a dataset of 18 mammalian rhodopsin sequences, the protein mediating the first step in vision in the eye, and one of the most highly expressed genes in vertebrates. We use these patterns to infer selection pressures on key translational mechanisms including polypeptide elongation, protein folding, mRNA stability, and splicing. Results Overall, patterns of selection in mammalian rhodopsin appear to be correlated with post-transcriptional and translational processes. We found significant evidence for selection at synonymous sites using phylogenetic mutation-selection likelihood models, with C-ending codons found to have the highest relative fitness, and to be significantly more abundant at conserved sites. In general, these codons corresponded with the most abundant tRNAs in mammals. We found significant differences in codon usage bias between rhodopsin loops versus helices, though there was no significant difference in mean synonymous substitution rate between these motifs. We also found a significantly higher proportion of GC-ending codons at paired sites in rhodopsin mRNA secondary structure, and significantly lower synonymous mutation rates in putative exonic splicing enhancer (ESE) regions than in non-ESE regions. Conclusions By focusing on a single highly expressed gene we both distinguish synonymous codon selection from mutational effects and analytically explore underlying functional mechanisms. Our results suggest that codon bias in mammalian rhodopsin arises from selection to optimally balance high overall translational speed, accuracy, and proper protein folding, especially in structurally complicated regions. Selection at synonymous sites may also be contributing to mRNA stability and splicing efficiency at exonic-splicing-enhancer (ESE) regions. Our results highlight the importance of investigating highly expressed genes in a broader phylogenetic context in order to better understand the evolution of synonymous substitutions. PMID:24884412

2014-01-01

275

Getting Started with Android  

Microsoft Academic Search

\\u000a Android is hot, and many people are developing Android applications (apps for short). Perhaps you would also like to develop\\u000a apps, but are unsure about how to get started. Although you could study Google’s online Android Developer’s Guide (http:\\/\\/developer.android.com\\/guide\\/index.html) to acquire the needed knowledge, you might be overwhelmed by the vast amount\\u000a of information that this guide presents. In contrast,

Dave Smith; Jeff Friesen

276

How to use Big Data technologies to optimize operations in Upstream Petroleum Industry  

E-print Network

How to use Big Data technologies to optimize operations in Upstream Petroleum Industry Abdelkader generated by the Petroleum Industry and particularly its upstream segment? Upstream is no stranger to Big the desired outcomes? Keywords Big Data; Analytics; Upstream Petroleum Industry; Knowledge Management; KM

Paris-Sud XI, Université de

277

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

PubMed Central

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

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

2001-01-01

278

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

279

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

Microsoft Academic Search

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

Laurent Duret; Dominique Mouchiroud

1999-01-01

280

When to Start Antiretroviral Therapy  

MedlinePLUS

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

281

Transcriptional starts for cytadherence-related operons of Mycoplasma genitalium.  

PubMed

One mechanism of mycoplasma cytadherence possessed by several mycoplasmas, including Mycoplasma genitalium, necessitates coordination of multiple adhesins and adherence-associated proteins. The genes encoding these adherence-related proteins are located in three different regions of the M. genitalium genome and exhibit an operon-like organization with surrounding genes. To understand whether genes encoding adherence-related proteins in M. genitalium are regulated as operons, we performed transcriptional and reverse transcription-polymerase chain reaction (RT-PCR) analyses on the loci mg191 (encoding major cytadhesin P140 localized at the specialized tip organelle) and mg218 (encoding high molecular mass cytadherence-related protein MG218 required for tip-mediated adherence). Primer extension suggested that transcription of mg191 was under the control of two transcriptional starts, one immediately upstream of mg191 (Prm(MG191)) and the other upstream of mg190 (Prm(MG190)). In contrast, mg218 appeared to be transcribed by a single transcriptional start, located upstream of mg217. RT-PCR indicated that transcription was continuous from mg190 to mg192 and mg217 to mg219, suggesting that these loci constitute true operons. Additional data revealed heretofore undetected similarities between adherence-related operons of M. genitalium and Mycoplasma pneumoniae. PMID:14659545

Musatovova, Oxana; Dhandayuthapani, Subramanian; Baseman, Joel B

2003-12-01

282

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

E-print Network

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

Henkel, Werner

283

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

PubMed Central

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

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

2013-01-01

284

Upstream particle events close to the bow shock and 200 earth radii upstream - ISEE-1 and ISEE-3 observations  

NASA Technical Reports Server (NTRS)

Two energetic particle events (28 keV - 145 keV) upstream of the earth's bow shock have been investigated with two identical experiments of the Max-Planck-Institut/University of Maryland on ISEE-1 and ISEE-3. Close to the bow shock the particle distribution is more or less isotropic and indicates strong scattering of these particles in the upstream wave field. At ISEE-3 the particles move essentially scatter-free from the general bow shock direction. The temporal evolution of the particle bursts is discussed in terms of the interplanetary magnetic field topology and the scattering conditions.

Scholer, M.; Hovestadt, D.; Klecker, B.; Ipavich, F. M.; Gloeckler, G.

1980-01-01

285

Developmental approach to prevent adolescent suicides: research pathways to effective upstream preventive interventions.  

PubMed

The 2012 National Strategy for Suicide Prevention expands the current suicide prevention paradigm by including a strategic direction aimed at promoting healthy populations. Childhood and adolescence are key suicide prevention window periods, yet knowledge of suicide prevention pathways through universal interventions is limited (Aspirational Goal 11). Epidemiologic evidence suggests that prevention programs in normative social systems such as schools are needed for broad suicide prevention impact. Prevention trial results show that current universal prevention programs for children and young adolescents are effective in reducing adolescent emotional and behavioral problems that are risk factors for suicidal behavior, and in the case of the Good Behavior Game, suicide attempts. A developmentally sequenced upstream suicide prevention approach is proposed: (1) childhood programs to strengthen a broad set of self-regulation skills through family and school-based programs, followed by (2) adolescent programs that leverage social influences to prevent emerging risk behaviors such as substance abuse and strengthen relationships and skills. Key knowledge breakthroughs needed are evidence linking specific intervention strategies to reduced suicidal behaviors and mortality and their mechanisms of action. Short- and long-term objectives to achieve these breakthroughs include combining evidence from completed prevention trials, increasing motivators for prevention researchers to assess suicide-related outcome, and conducting new trials of upstream interventions in populations using efficient designs acceptable to communities. In conclusion, effective upstream prevention programs have been identified that modify risk and protective factors for adolescent suicide, and key knowledge breakthroughs can jump-start progress in realizing the suicide prevention potential of specific strategies. PMID:25145747

Wyman, Peter A

2014-09-01

286

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

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

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

287

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

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

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

288

BIOPROSPECTOR: DISCOVERING CONSERVED DNA MOTIFS IN UPSTREAM REGULATORY REGIONS  

E-print Network

610, Harvard University Cambridge MA 02138 (jliu@stat.stanford.edu) The development of genome these modifications greatly improve the performance of the program. Although testing and development are still step is to examine the upstream region of genes in the same expression pattern group and look

Liu, Xiaole Shirley

289

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

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

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

290

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

291

25. UPSTREAM VIEW OF LOWER END OF OUTLET STRUCTURE SHOWING ...  

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

25. UPSTREAM VIEW OF LOWER END OF OUTLET STRUCTURE SHOWING FORMS IN PLACE FOR GRAVITY WALL SECTIONS.... Volume XVI, No. 16, August 16, 1939. - Prado Dam, Outlet Works, Santa Ana River near junction of State Highways 71 & 91, Corona, Riverside County, CA

292

Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters  

E-print Network

Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters Alexander Bolshoy1 of the distribution of predicted intrinsic curvature along all available complete prokaryotic genomes, the genomes were divided into two groups. Curvature distribution in all prokaryotes of the first group indicated

Bolshoy, Alexander

293

Spill-Pattern Manipulation to Guide Migrant Salmon Upstream  

Microsoft Academic Search

Passage of upstream migrant sockeye salmon (Oncorhynchus nerka) and chinook salmon (O. tshawytscha) through the three pool-and-weir type fish ladders at Rock Island Dam on the Columbia River was controlled to a large extent by the proportion of the total flow discharged through the turbines and also by the location of the open spillway gates with respect to the ladders.

Bernie Leman; G. J. Paulik

1966-01-01

294

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

295

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

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

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

296

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

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

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

297

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

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

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

298

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

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

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

299

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

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

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

300

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

301

Upstream Drafting of a Flexible Body by its Downstream Neighbor  

Microsoft Academic Search

It is common knowledge that an upstream body influences its downstream neighbors in an open flow. This is often referred to as flow drafting or slipstreaming (either in the air or in water). In this talk, we present an experimental study on how the motion of a flapping flag is strongly affected by a downstream neighbor. In a flowing soap

Teis Schnipper; Jun Zhang

2010-01-01

302

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

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

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

303

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

304

ASSESSMENT OF THE IMPACT OF UPSTREAM LAND MANAGEMENT  

E-print Network

ASSESSMENT OF THE IMPACT OF UPSTREAM LAND MANAGEMENT MEASURES ON FLOOD FLOWS IN PICKERING model calibrated for two events in the Pickering Beck catchment, North Yorkshire, and a set reduction) is greater for the large event than the small event studied, which is an unusual but important

305

Human SNPs resulting in premature stop codons and protein truncation  

PubMed Central

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

2006-01-01

306

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

PubMed

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

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

2014-09-01

307

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

PubMed Central

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

Helftenbein, E

1985-01-01

308

StartUpNation  

NSDL National Science Digital Library

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

309

Minnesota: Early Head Start Initiatiive  

ERIC Educational Resources Information Center

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

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

2012-01-01

310

An upstream YY1 binding site on the HIV-1 LTR contributes to latent infection.  

PubMed

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. PMID:24116200

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

2013-01-01

311

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

PubMed

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. PMID:22243239

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

2011-12-01

312

Upstream Erosion and Sedimentation in small reservoirs in Burkina Faso  

NASA Astrophysics Data System (ADS)

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

de Boissezon, J.

2003-04-01

313

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

NASA Astrophysics Data System (ADS)

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

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

2014-01-01

314

Association analysis of polymorphisms in the upstream region of the human dopamine D4 receptor gene in schizophrenia.  

PubMed

Several studies have suggested that the transcriptional activity of the DRD4 gene may exert an important role in susceptibility to schizophrenia. To address this issue, we studied the association of schizophrenia and polymorphisms including -616C>G, -603T>del, -602G>del, 600G>C, -521C>T, -376C>T and a 120 bp tandem duplication polymorphism (120 bp repeat) in 1.2 kb upstream from the initiation codon in the promoter region of the DRD4 gene with 210 schizophrenic cases and 206 healthy controls. The results showed a significant excess of allele L of the 120 bp repeat in the schizophrenic patients compared to the controls (X(2)=8.585, df=1, P=0.003, OR=1.546, 95% CI=1.154-2.070). No significant difference was detected in the frequencies of genotype and allele of six other polymorphisms between the two groups. However, haplotypic distribution of 120 bp repeat, -616C>G, -602G>del, -521C>T and -376C>T was significantly different between case and control groups (P=0.005). This might cause the alteration of the transcriptional regulation of the DRD4 gene, as the consensus sequences of binding sites for several known transcription factors are involved in this region. PMID:14623368

Xing, Qing-he; Wu, Sheng-nan; Lin, Zhi-guang; Li, Hua-fang; Yang, Jian-dong; Feng, Guo-yin; Wang, Ming-tai; Yang, Wei-wei; He, Lin

2003-12-01

315

Start Smart: Steps to Starting a Business Workshop Registration The Start Smart workshop will cover  

E-print Network

and mail it with your check* or credit card information to: WSU Tri-Cities Business LINKS 2710 Crimson WayStart Smart: Steps to Starting a Business Workshop Registration The Start Smart workshop will cover: · How much money will you need to start and run the business until it is profitable? · What are your

Collins, Gary S.

316

Torque fluctuations caused by upstream mean flow and turbulence  

NASA Astrophysics Data System (ADS)

A series of studies are in progress investigating the effects of turbine-array-wake interactions for a range of atmospheric boundary layer states by means of the EnFlo meteorological wind tunnel. The small, three-blade model wind turbines drive 4-quadrant motor-generators. Only a single turbine in neutral flow is considered here. The motor-generator current can be measured with adequate sensitivity by means of a current sensor allowing the mean and fluctuating torque to be inferred. Spectra of torque fluctuations and streamwise velocity fluctuations ahead of the rotor, between 0.1 and 2 diameters, show that only the large-scale turbulent motions contribute significantly to the torque fluctuations. Time-lagged cross-correlation between upstream velocity and torque fluctuations are largest over the inner part of the blade. They also show the turbulence to be frozen in behaviour over the 2 diameters upstream of the turbine.

Farr, T. D.; Hancock, P. E.

2014-12-01

317

Electron-ion coupling upstream of relativistic collisionless shocks  

E-print Network

It is argued and demonstrated by particle-in-cell simulations that the synchrotron maser instability could develop at the front of a relativistic, magnetized shock. The instability generates strong low-frequency electromagnetic waves propagating both upstream and downstream of the shock. Upstream of the shock, these waves make electrons lag behind ions so that a longitudinal electric field arises and the electrons are accelerated up to the ion kinetic energy. Then thermalization at the shock front results in a plasma with equal temperatures of electrons and ions. Downstream of the shock, the amplitude of the maser-generated wave may exceed the strength of the shock-compressed background magnetic field. In this case the shock-accelerated particles radiate via nonlinear Compton scattering rather than via a synchrotron mechanism. The spectrum of the radiation differs, in the low-frequency band, from that of the synchrotron radiation, providing possible observational tests of the model.

Yuri Lyubarsky

2006-11-01

318

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

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

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

319

The effect of tRNA levels on decoding times of mRNA codons  

PubMed Central

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

Dana, Alexandra; Tuller, Tamir

2014-01-01

320

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

PubMed

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

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

2007-12-01

321

Interaction of upstream flow distortions with high Mach number cascades  

NASA Technical Reports Server (NTRS)

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

Englert, G. W.

1981-01-01

322

Positions of Trp codons in the leader peptide-coding region of the at operon influence anti-trap synthesis and trp operon expression in Bacillus licheniformis.  

PubMed

Tryptophan, phenylalanine, tyrosine, and several other metabolites are all synthesized from a common precursor, chorismic acid. Since tryptophan is a product of an energetically expensive biosynthetic pathway, bacteria have developed sensing mechanisms to downregulate synthesis of the enzymes of tryptophan formation when synthesis of the amino acid is not needed. In Bacillus subtilis and some other Gram-positive bacteria, trp operon expression is regulated by two proteins, TRAP (the tryptophan-activated RNA binding protein) and AT (the anti-TRAP protein). TRAP is activated by bound tryptophan, and AT synthesis is increased upon accumulation of uncharged tRNA(Trp). Tryptophan-activated TRAP binds to trp operon leader RNA, generating a terminator structure that promotes transcription termination. AT binds to tryptophan-activated TRAP, inhibiting its RNA binding ability. In B. subtilis, AT synthesis is upregulated both transcriptionally and translationally in response to the accumulation of uncharged tRNA(Trp). In this paper, we focus on explaining the differences in organization and regulatory functions of the at operon's leader peptide-coding region, rtpLP, of B. subtilis and Bacillus licheniformis. Our objective was to correlate the greater growth sensitivity of B. licheniformis to tryptophan starvation with the spacing of the three Trp codons in its at operon leader peptide-coding region. Our findings suggest that the Trp codon location in rtpLP of B. licheniformis is designed to allow a mild charged-tRNA(Trp) deficiency to expose the Shine-Dalgarno sequence and start codon for the AT protein, leading to increased AT synthesis. PMID:20061467

Levitin, Anastasia; Yanofsky, Charles

2010-03-01

323

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. PMID:19057713

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

324

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

PubMed

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

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

2014-08-10

325

Maryland Early Head Start Initiative  

ERIC Educational Resources Information Center

Since 2000, Maryland has provided state supplemental funds to Head Start and Early Head Start (EHS) programs to improve access. Local EHS programs may use funds, through child care partnerships, to extend the EHS day or year. Maryland's approach to building on EHS includes: (1) Increase the capacity of existing Head Start and EHS programs to…

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

2012-01-01

326

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

PubMed Central

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

Bohlke, Nina; Budisa, Nediljko

2014-01-01

327

How to use Big Data technologies to optimize operations in Upstream Petroleum Industry  

E-print Network

How to use Big Data technologies to optimize operations in Upstream Petroleum Industry Abdelkader for it to have value. But what about Big Data generated by the Petroleum Industry and particularly its upstream; Analytics; Upstream Petroleum Industry; Knowledge Management; KM; Business Intelligence; BI; Innovation

Boyer, Edmond

328

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

329

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

PubMed

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

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

2012-01-01

330

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

PubMed Central

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

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

2012-01-01

331

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

332

Upstream Drafting of a Flexible Body by its Downstream Neighbor  

NASA Astrophysics Data System (ADS)

It is common knowledge that an upstream body influences its downstream neighbors in an open flow. This is often referred to as flow drafting or slipstreaming (either in the air or in water). In this talk, we present an experimental study on how the motion of a flapping flag is strongly affected by a downstream neighbor. In a flowing soap film tunnel we introduce, in turn, passive as well as kinematically driven bodies in the wake of an otherwise freely flapping flag. We show how the flapping frequency and drag on the leading flag can be significantly manipulated by the downstream neighbor.

Schnipper, Teis; Zhang, Jun

2010-11-01

333

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

334

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

335

The Bastille Day Magnetic Clouds and Upstream Shocks: Near Earth Interplanetary Observations  

NASA Technical Reports Server (NTRS)

The energetic charged particle, interplanetary magnetic field, and plasma characteristics of the 'Bastille Day' shock and ejecta/magnetic cloud events at 1 AU occurring over the days 14-16 July 2000 are described. Profiles of MeV (WIND/LEMT) energetic ions help to organize the overall sequence of events from the solar source to 1 AU. Stressed are analyses of an outstanding magnetic cloud (MC2) starting late on 15 July and its upstream shock about 4 hours earlier in WIND magnetic field and plasma data. Also analyzed is a less certain, but likely, magnetic cloud (MC1) occurring early on 15 July; this was separated from MC2 by its upstream shock and many heliospheric current sheet (HCS) crossings. Other HCS crossings occurred throughout the 3-day period. Overall this dramatic series of interplanetary events caused a large multi-phase magnetic storm with min Dst lower than -300 nT. The very fast solar wind speed (greater than or equal to 1100 km/s) in and around the front of MC2 (for near average densities) was responsible for a very high solar wind ram pressure driving in the front of the magnetosphere to geocentric distances estimated to be as low as approx. 5 R(sub E), much lower than the geosynchronous orbit radius. This was consistent with magnetic field observations from two GOES satellites which indicated they were in the magnetosheath for extended times. A static force free field model is used to fit the two magnetic cloud profiles providing estimates of the clouds' physical and geometrical properties. MC2 was much larger than MCI, but their axes were nearly antiparallel, and their magnetic fields had the same left-handed helicity. MC2's axis and its upstream shock normal were very close to being perpendicular to each other, as might be expected if the cloud were driving the shock at the time of observation. The estimated axial magnetic flux carried by MC2 was 52 x 10(exp 20) Mx, which is about 5 times the typical magnetic flux estimated for other magnetic clouds in the WIND data over its first 4 years and is 17 times the flux of MC1. This large flux is due to both the strong axially-directed field of MC2 (46.8 nT on the axis) and the large radius (R(sub 0) = 0.189 AU) of the flux tube. MC2's average speed is consistent with the expected transit time from a halo-CME to which it is apparently related.

Lepping, R. P.; Berdichevsky, D. B.; Burlaga, L. F.; Lazarus, A. J.; Kasper, J.; Desch, M. D.; Wu, C.-C.; Reames, D. V.; Singer, H. J.; Singer, H. J.; Vondrak, Richard R. (Technical Monitor)

2001-01-01

336

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

337

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

Microsoft Academic Search

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

Iris Bahir; Menachem Fromer; Yosef Prat; Michal Linial

2009-01-01

338

CoDoNS: Replacing the DNS Hierarchy Venugopalan Ramasubramanian (Rama)  

E-print Network

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

Sirer, Emin Gun

339

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

Microsoft Academic Search

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

Mikita Suyama; David Torrents; Peer Bork

2006-01-01

340

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

E-print Network

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

Plotkin, Joshua B.

341

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

PubMed

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

Kessler, Michael D; Dean, Matthew D

2014-10-01

342

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

343

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

PubMed

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

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

2010-04-01

344

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

Microsoft Academic Search

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

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

1996-01-01

345

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

PubMed Central

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

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

2011-01-01

346

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

PubMed Central

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

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

2013-01-01

347

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

PubMed

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

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

2014-01-01

348

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

PubMed Central

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene. We outline a simple approach to assess the strength of RCB (RCBS) in genes as a guide to their likely expression levels and illustrate this with an analysis of Escherichia coli (E. coli) genome. Our efforts to quantitatively predict gene expression levels in E. coli met with a high level of success. Surprisingly, we observe a strong correlation between RCBS and protein length indicating natural selection in favour of the shorter genes to be expressed at higher level. The agreement of our result with high protein abundances, microarray data and radioactive data demonstrates that the genomic expression profile available in our method can be applied in a meaningful way to the study of cell physiology and also for more detailed studies of particular genes of interest. PMID:19131380

Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

2009-01-01

349

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

PubMed

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

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

2014-11-01

350

START Background Report START, September 2013 1 BACKGROUND REPORT  

E-print Network

-Shabaab, terrorism in Kenya, and extended attacks involving hostages in barricade situations. AL-SHABAAB Since: Global Terrorism Database #12;START Background Report © START, September 2013 2 Bombing/ Explosion 38/ Infrastructure Attack 2.37% Hijacking 0.36% Al-Shabaab Attack Types, 2007-2012 (n=548) Source: Global Terrorism

Hill, Wendell T.

351

A Start-up company to start your career  

E-print Network

-up company? · Tremendous job insecurity ­ Funding may disappear in an instant ­ Technology, or marketing, may · Technology push · Market pull · Direction and focus of company almost always changes · Must meet needsA Start-up company to start your career Professional Development Seminar March 6, 2013 #12;What

352

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

E-print Network

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

Nielsen, Rasmus

353

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

E-print Network

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

Paris-Sud XI, Université de

354

Maine: Early Head Start Initiatives  

ERIC Educational Resources Information Center

Maine has two initiatives that build on Early Head Start (EHS). The first initiative, Fund for a Healthy Maine, has since 2001 provided tobacco settlement money to existing Head Start and EHS programs to expand the number of children who receive full-day, full-year services. Local programs have the option of using these funds for EHS, depending on…

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

2012-01-01

355

Research Services START UP FUNDS  

E-print Network

/compliance/chreb/ Conjoint Faculties Research Ethics Board New website: www.ucalgary.ca/research/ethics/cfreb Animal Care-up spending (prior to any recruitment of research participants or the acquisition of animals) and timeResearch Services START UP FUNDS www.ucalgary.ca/research START UP FUNDS From time to time some

de Leon, Alex R.

356

Kansas: Early Head Start Initiative  

ERIC Educational Resources Information Center

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

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

2012-01-01

357

Nebraska: Early Head Start Initiative  

ERIC Educational Resources Information Center

Since 1999, Nebraska's Early Head Start Infant/Toddler Quality Initiative has supported Early Head Start (EHS) and community child care partnerships to improve the quality and professionalism of infant and toddler care. EHS programs apply to receive funding to establish partnerships with center-based or home-based child care.The initiative has…

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

2012-01-01

358

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

PubMed

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

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

2014-01-01

359

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

PubMed

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

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

2005-12-01

360

Hypersonic Flow Control Using Upstream Focused Energy Deposition  

NASA Technical Reports Server (NTRS)

A numerical study of centerline and off-centerline power deposition at a point upstream of a two-dimensional blunt body at Mach 6.5 at 30 km altitude are presented. The full Navier-Stokes equations are used. Wave drag, lift, and pitching moment are presented as a function of amount of power absorbed in the flow and absorption point location. It is shown that wave drag is considerably reduced. Modifications to the pressure distribution in the flow field due to the injected energy create lift and a pitching moment when the injection is off-centerline. This flow control concept may lead to effective ways to improve the performance and to stabilize and control hypersonic vehicles.

Riggins David W.; Nelson, H. F.

1999-01-01

361

Control of cavity flow by upstream mass injection  

NASA Astrophysics Data System (ADS)

The purpose of this investigation was to use mass-injection ahead of the cavity to control the shear flow across the cavity to reduce or eliminate cavity oscillations. A brief review and analysis of cavity flow, shear layer flow and mass-injection is presented. The results of an experimental study performed at a nominal Mach number of 1.8 are provided. Significant attenuation of cavity oscillations was observed experimentally with upstream mass-injection. The thickening of the cavity shear layer alters its stability characteristics such that its preferred vortex roll-up frequency falls outside of the natural frequencies of the cavity. As a result of the experimental investigation, it is concluded that mass-injection is effective in significantly reducing or eliminating cavity oscillations.

Vakili, Ahmad D.; Gauthier, Christian

1991-06-01

362

Upstream Swirl Effects on the Flow Inside a Labyrinth Seal  

NASA Technical Reports Server (NTRS)

The flow field inside a seven cavity tooth on rotor labyrinth seal was measured using a 3D laser Doppler anemometer system. The seal was operated at a Reynolds number of 24,000 and a Taylor number of 6,600 using water as the working fluid. Swirl vanes were placed upstream of the seal to produce positive, negative, and no preswirl. It was found that the axial and radial velocities were minimally effected. The tangential velocity, both in the clearance region and the seal cavities on the rotor, were greatly altered by the preswirl. By applying negative preswirl, the tangential velocity was suppressed, even in the seventh cavity. The turbulence levels decreased as the preswirl varied from negative to positive.

Morrison, Gerald L.; Johnson, Mark C.

1997-01-01

363

Numerical analysis of supersonic combustion ramjet with upstream fuel injection  

NASA Astrophysics Data System (ADS)

This paper describes possible fuel injection scheme for airbreathing engines that use hydrocarbon fuels. The basic idea is to inject fuel at the spike tip of the supersonic inlet to achieve mixing and combustion efficiency with a limited length combustion chamber. A numerical code, able to solve the full Navier-Stokes equations in turbulent and reacting flows, is employed to obtain numerical simulations of the thermo-fluidynamic fields at different scramjet flight conditions, at Mach numbers of M=6.5 and 8. The feasibility of the idea of the upstream injection is checked for a simple axisymmetric configuration and relatively small size. The results are discussed in connection with the potential benefits deriving from the use of new ultra high temperature ceramics (UHTC).

Savino, Raffaele; Pezzella, Giuseppe

2003-09-01

364

Radio Emission from Upstream of Earth's Bow Shock  

NASA Astrophysics Data System (ADS)

Bursty radio emissions are often generated upstream of Earth's bow shock as a result of the interaction of the supersonic and superalfvenic solar wind with Earth's magnetosphere. This radiation is therefore expected to be be very similar to type II solar radio bursts which are associated with travelling interplanetary shocks and coronal mass ejections. Here we demonstrate that a model which can successfully account for type II radio bursts can also explain many aspects of the terrestrial radio emissions. The model is analytic and quantitative; it combines reflection and acceleration of solar wind electrons at the bow shock stochastic growth theory predictions for the time-averaged production of Langmuir waves in the foreshock and nonlinear processes for the conversion of Langmuir energy into electromagnetic radiation at harmonics of the solar wind electron plasma frequency. The spatial distribution and flux levels of the radio emission predicted by this model are shown to agree remarkably well both qualitatively and quantitatively with spacecraft observations.

Kuncic, Zdenka; Cairns, Iver H.; Knock, Stuart; Robinson, Peter A.

365

Upstream and downstream processing of recombinant IgA.  

PubMed

Immunoglobulin A (IgA) is the most abundant antibody class in the human body and has a unique role in mediating immunity. The ever-increasing knowledge about the potential of IgAs has renewed interest in this antibody class for therapeutic use against a variety of infectious and malignant diseases, and as a preventive agent for mucosal pathogens. Despite the considerable therapeutic potential of IgA the exploration thereof has often been hampered due to difficulties in producing and purifying desired quantities. Large amounts of pure IgA will be required for in vivo studies. This work reviews current achievements and bottlenecks in upstream and downstream processing of recombinant IgA from a biotechnological point of view. We also highlight recent accomplishments with diverse expression systems and presents different affinity techniques for the capture of recombinant IgA to compare their purification potential. PMID:25257601

Reinhart, David; Kunert, Renate

2015-02-01

366

From Worker Health To Citizen Health: Moving Upstream  

PubMed Central

New rapid growth economies, urbanization, health systems crises and “big data” are causing fundamental changes in social structures and systems including health. These forces for change have significant consequences for occupational and environmental medicine and will challenge the specialty to think beyond workers and workplaces as the principal locus of innovation for health and performance. These trends are placing great emphasis on upstream strategies for addressing the complex systems dynamics of the social determinants of health. The need to engage systems in communities for healthier workforces is a shift in orientation from worker and workplace centric to citizen and community centric. This change for occupational and environmental medicine requires extending systems approaches in the workplace to communities which are systems of systems and which require different skills, data, tools and partnerships. PMID:24284749

Sepulveda, Martin-Jose

2014-01-01

367

Upstream Structures and Their Effects on the Magnetosphere  

NASA Technical Reports Server (NTRS)

Kinetic processes within the Earth's foreshock generate a profusion of plasma and magnetic field structures with sizes and durations ranging from the microscale (e.g. SLAMs, solitons, and density holes) to the mesoscale (e.g. foreshock cavities or boundaries, hot flow anomalies, and bubbles). Swept into the bow shock by the solar wind flow, the perturbations associated with these features batter the magnetosphere, driving a wide variety of magnetospheric effects, including large amplitude magnetopause motion, bursty reconnection and the generation of flux transfer events, enhanced pulsation activity within the magnetosphere, diffusion and energization of radiation belt particles, enhanced particle precipitation resulting in dayside aurora and riometer absorption, and the generation of field-aligned currents and magnetic impulse events in high-latitude ground magnetometers. This talk reviews the ever growing menagery of structures observed upstream from the bow shock, examines their possible interrelationships, and considers their magnetospheric consequences.

Sibeck, D. G.

2011-01-01

368

Ensemble streamflow prediction adjustment for upstream water use and regulation  

NASA Astrophysics Data System (ADS)

Hydrologic model forecasts are commonly biased in watersheds where water use and regulation activities cause flow alterations. Furthermore, direct accounting of such biases in forecast preparation is impractical as the information required is extensive and usually unavailable. This article introduces a new method to characterize the aggregate flow alteration biases and associated uncertainty in watersheds with important but largely undocumented water use and regulation activities. It also uses these assessments to adjust the ensemble streamflow predictions at downstream locations. The method includes procedures to (a) detect the presence of significant upstream regulation and water use influences; (b) correct the ensemble streamflow predictions and associated uncertainty for any biases in periods when such influences are detectable; and (c) assess the adjusted forecast reliability improvements. Applications in three watersheds of the American River in California demonstrate that the new method leads to significant forecast skill improvements and is also readily applicable to other regions.

Georgakakos, Aris P.; Yao, Huaming; Georgakakos, Konstantine P.

2014-11-01

369

Hitchhiking behaviour in the obligatory upstream migration of amphidromous snails  

PubMed Central

Migratory animals endure high stress during long-distance travel in order to benefit from spatio-temporally fluctuating resources, including food and shelter or from colonization of unoccupied habitats. Along with some fishes and shrimps, nerite snails in tropical to temperate freshwater systems are examples of amphidromous animals that migrate upstream for growth and reproduction after a marine larval phase. Here I report, to my knowledge, the first example of ‘hitchhiking’ behaviour in the obligatory migration of animals: the nerite snail Neritina asperulata appears to travel several kilometres as minute juveniles by firmly attaching to the shells of congeneric, subadult snails in streams of Melanesian Islands, presumably to increase the success rate of migration. PMID:19411267

Kano, Yasunori

2009-01-01

370

Assessing upstream fish passage connectivity with network analysis.  

PubMed

Hydrologic connectivity is critical to the structure, function, and dynamic process of river ecosystems. Dams, road crossings, and water diversions impact connectivity by altering flow regimes, behavioral cues, local geomorphology, and nutrient cycling. This longitudinal fragmentation of river ecosystems also increases genetic and reproductive isolation of aquatic biota such as migratory fishes. The cumulative effects on fish passage of many structures along a river are often substantial, even when individual barriers have negligible impact. Habitat connectivity can be improved through dam removal or other means of fish passage improvement (e.g., ladders, bypasses, culvert improvement). Environmental managers require techniques for comparing alternative fish passage restoration actions at alternative or multiple locations. Herein, we examined a graph-theoretic algorithm for assessing upstream habitat connectivity to investigate both basic and applied fish passage connectivity problems. First, we used hypothetical watershed configurations to assess general alterations to upstream fish passage connectivity with changes in watershed network topology (e.g., linear vs. highly dendritic) and the quantity, location, and passability of each barrier. Our hypothetical network modeling indicates that locations of dams with limited passage efficiency near the watershed outlet create a strong fragmentation signal but are not individually sufficient to disconnect the system. Furthermore, there exists a threshold in the number of dams beyond which connectivity declines precipitously, regardless of watershed topology and dam configuration. Watersheds with highly branched configurations are shown to be less susceptible to disconnection as measured by this metric. Second, we applied the model to prioritize barrier improvement in the mainstem of the Truckee River, Nevada, USA. The Truckee River application demonstrates the ability of the algorithm to address conditions common in fish passage projects including incomplete data, parameter uncertainty, and rapid application. This study demonstrates the utility of a graph-theoretic approach for assessing fish passage connectivity in dendritic river networks assuming full basin utilization for a given species, guild, or community of concern. PMID:24147411

McKay, S Kyle; Schramski, John R; Conyngham, Jock N; Fischenich, J Craig

2013-09-01

371

Explosion Clad for Upstream Oil and Gas Equipment  

NASA Astrophysics Data System (ADS)

Today's upstream oil and gas facilities frequently involve the combination of high pressures, high temperatures, and highly corrosive environments, requiring equipment that is thick wall, corrosion resistant, and cost effective. When significant concentrations of CO2 and/or H2S and/or chlorides are present, corrosion resistant alloys (CRA) can become the material of choice for separator equipment, piping, related components, and line pipe. They can provide reliable resistance to both corrosion and hydrogen embrittlement. For these applications, the more commonly used CRA's are 316L, 317L and duplex stainless steels, alloy 825 and alloy 625, dependent upon the application and the severity of the environment. Titanium is also an exceptional choice from the technical perspective, but is less commonly used except for heat exchangers. Explosion clad offers significant savings by providing a relatively thin corrosion resistant alloy on the surface metallurgically bonded to a thick, lower cost, steel substrate for the pressure containment. Developed and industrialized in the 1960's the explosion cladding technology can be used for cladding the more commonly used nickel based and stainless steel CRA's as well as titanium. It has many years of proven experience as a reliable and highly robust clad manufacturing process. The unique cold welding characteristics of explosion cladding reduce problems of alloy sensitization and dissimilar metal incompatibility. Explosion clad materials have been used extensively in both upstream and downstream oil, gas and petrochemical facilities for well over 40 years. The explosion clad equipment has demonstrated excellent resistance to corrosion, embrittlement and disbonding. Factors critical to insure reliable clad manufacture and equipment design and fabrication are addressed.

Banker, John G.; Massarello, Jack; Pauly, Stephane

2011-01-01

372

Correlation between upstream human activities and riverine antibiotic resistance genes.  

PubMed

Antimicrobial resistance remains a serious and growing human health challenge. The water environment may represent a key dissemination pathway of resistance elements to and from humans. However, quantitative relationships between landscape features and antibiotic resistance genes (ARGs) have not previously been identified. The objective of this study was to examine correlations between ARGs and putative upstream anthropogenic sources in the watershed. sul1 (sulfonamide) and tet(W) (tetracycline) were measured using quantitative polymerase chain reaction in bed and suspended sediment within the South Platte River Basin, which originates from a pristine region in the Rocky Mountains and runs through a gradient of human activities. A geospatial database was constructed to delineate surface water pathways from animal feeding operations, wastewater treatment plants, and fish hatchery and rearing units to river monitoring points. General linear regression models were compared. Riverine sul1 correlated with upstream capacities of animal feeding operations (R(2) = 0.35, p < 0.001) and wastewater treatment plants (R(2) = 0.34, p < 0.001). Weighting for the inverse distances from animal feeding operations along transport pathways strengthened the observed correlations (R(2) = 0.60-0.64, p < 0.001), suggesting the importance of these pathways in ARG dissemination. Correlations were upheld across the four sampling events during the year, and averaging sul1 measurements in bed and suspended sediments over all events yielded the strongest correlation (R(2) = 0.92, p < 0.001). Conversely, a significant relationship with landscape features was not evident for tet(W), which, in contrast to sul1, is broadly distributed in the pristine region and also relatively more prevalent in animal feeding operation lagoons. The findings highlight the need to focus attention on quantifying the contribution of water pathways to the antibiotic resistance disease burden in humans and offer insight into potential strategies to control the spread of ARGs. PMID:23035771

Pruden, Amy; Arabi, Mazdak; Storteboom, Heather N

2012-11-01

373

Ingestion into the upstream wheelspace of an axial turbine stage  

NASA Astrophysics Data System (ADS)

The upstream wheelspace of an axial air turbine stage complete with nozzle guide vanes (NGVs) and rotor blades (430 mm mean diameter) has been tested with the objective of examining the combined effect of NGVs and rotor blades on the level of mainstream ingestion for different seal flow rates. A simple axial clearance seal was used with the rotor spun up to 6650 rpm by drawing air through it from atmospheric pressure with a large centrifugal compressor. The effect of rotational speed was examined for several constant mainstream flow rates by controlling the rotor speed with an air brake. The circumferential variation in hub static pressure was measured at the trailing edge of the NGVs upstream of the seal gap and was found to affect ingestion significantly. The hub static pressure distribution on the rotor blade leading edges was rotor speed dependent and could not be measured in the experiments. The Denton three-dimensional CFD computer code was used to predict the smoothed time-dependent pressure field for the rotor together with the pressure distribution downstream of the NGVs. The level and distribution of mainstream ingestion, and thus, the seal effectiveness, was determined from nitrous oxide gas concentration measurements and related to static pressure measurements made throughout the wheelspace. With the axial clearance rim seal close to the rotor the presence of the blades had a complex effect. Rotor blades in connection with NGVs were found to reduce mainstream ingestion seal flow rates significantly, but a small level of ingestion existed even for very high levels of seal flow rate.

Green, T.; Turner, A. B.

1994-04-01

374

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

NASA Astrophysics Data System (ADS)

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

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

1985-06-01

375

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

376

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

E-print Network

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

F. M. Forger; R. S. Sachse

1998-08-04

377

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

NASA Astrophysics Data System (ADS)

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

Forger, Michael; Sachse, Sebastian

2000-08-01

378

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

PubMed

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

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

2012-01-01

379

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

PubMed Central

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

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

1985-01-01

380

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

Microsoft Academic Search

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

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

2001-01-01

381

Innovation and performance: The case of the upstream petroleum sector  

NASA Astrophysics Data System (ADS)

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 supply, Canada's oil sands development, and the potential that Canada may become an "energy superpower." The study examines the factors that drive companies involved in exploration, development, and production in the upstream petroleum sector to innovate and the impact of their innovation activities through major technologies on their performance. The thesis focuses on process innovation, which involves the adoption of new or significantly improved production processes, and is distinct from product innovation, which is based on the development and commercialization of a product with improved product characteristics to deliver new services to the consumer. The thesis provides a comprehensive review of the literature and develops an investigative model framework to examine the drivers of innovation and the impact of innovation on performance in the upstream petroleum sector. The research employs a survey questionnaire that was developed to obtain data and information, which was missing in the literature or not publicly available to test key relationships of innovation and performance indicators. In addition to the survey questionnaire, a number of knowledgeable experts in the industry were also interviewed. A total of 68 respondents completed the survey questionnaire, accounting for 40 percent of the firms in the industry. This percentage goes up to over 50 percent when account is taken of extremely small firms who could not fill out the survey. Further, the 68 respondents account for most of the industry revenues, production, and employment. The respondents include most of the key explorers, developers, and producers as well as the owners of the major projects and oil sands developments. Almost all firms in the industry with revenues above $1B with employees above 1000 responded to the survey. As well, many companies have joint project arrangements and farm-in agreements with other companies in the industry. Hence, this survey is considered highly representative of the industry. Industry associations were very helpful in providing advice, and in endorsing the circulation of the questionnaire. The results show that the sector relies more heavily on acquiring advanced machinery and equipment, processes and other external knowledge than on internal R&D. Advanced machinery and equipment includes embedded R&D. 3D and 4D seismic stand out as the most relied upon in exploration, horizontal wells in development activities, and field recovery in production. Increasing productive capacity, reducing costs and reducing environmental impact are the three main drivers of innovation. Collaboration is important to the sector and agreements with competitors and suppliers are ranked as most important. The main reason for collaboration is to gain access to external knowledge. Government tax incentives (e.g., the Scientific Research and Experimental Development) (SR&ED) tax credit and its fiscal framework are important in spurring R&D. Fiscal policies, on the other hand, are more important for acquiring advanced machinery and equipment, advanced processes, and other external knowledge. The study has several broad implications with respect to the application of technologies: (1) Without the adoption of major technologies, costs would have been substantially higher and productive capacity and productivity much lower. This study also contributes to the view that resources should not be treated as a fixed stock but as flow which can be improved. (2) The environment is an important driver of innovation, particularly environmental regulation. Providing the right mix of regulation and leaving firms to undertake innovation may result in fav

Persaud, A. C. Jai

382

Function of the upstream hypersensitive sites of the chicken beta-globin gene cluster in mice.  

PubMed Central

We have shown previously that the chicken beta A-globin gene, with its 3' enhancer, is expressed in a copy number-dependent manner in transgenic mice. The expression level was low but increased approximately 6-fold upon inclusion of 11 kb of upstream DNA containing four DNase I hypersensitive sites. To study the effect of the individual upstream hypersensitive sites on transgene expression, we produced lines of mice in which the individual upstream sites were linked to the beta A gene and enhancer. RNA levels were measured in blood from adult animals. With each of these four constructs, the level of transgene RNA per DNA copy varied over a > 20-fold range. These data suggest that addition of a hypersensitive site to the beta A-globin/enhancer region abrogates its position independent expression. The average beta A-globin expression per copy in the lines carrying an upstream site was comparable with that in lines without an upstream site. Thus, no single upstream hypersensitive site accounts for the higher level of beta A-globin expression seen in mice containing the complete upstream region. We had shown previously that control of the chicken beta-globin cluster is distributed between at least two regions, the beta A/epsilon enhancer and the upstream region. Our current results suggest that the control mediated by the upstream DNA is itself distributed and is not due to a single hypersensitive site. Images PMID:7784184

Reitman, M; Lee, E; Westphal, H

1995-01-01

383

Relation between mRNA expression and sequence information in Desulfovibrio vulgaris: Combinatorial contributions of upstream regulatory motifs and coding sequence features to variations in mRNA abundance  

SciTech Connect

ABSTRACT-The context-dependent expression of genes is the core for biological activities, and significant attention has been given to identification of various factors contributing to gene expression at genomic scale. However, so far this type of analysis has been focused whether on relation between mRNA expression and non-coding sequence features such as upstream regulatory motifs or on correlation between mRN abundance and non-random features in coding sequences (e.g. codon usage and amino acid usage). In this study multiple regression analyses of the mRNA abundance and all sequence information in Desulfovibrio vulgaris were performed, with the goal to investigate how much coding and non-coding sequence features contribute to the variations in mRNA expression, and in what manner they act together...

Wu, Gang; Nie, Lei; Zhang, Weiwen

2006-05-26

384

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

PubMed

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

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

1997-10-01

385

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

NASA Astrophysics Data System (ADS)

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

Sneppen, Kim; Semsey, Szabolcs

2014-12-01

386

Recognition of the amber UAG stop codon by release factor RF1  

SciTech Connect

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

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

2010-08-23

387

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

PubMed

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

Sneppen, Kim; Semsey, Szabolcs

2014-01-01

388

Environmental shaping of codon usage and functional adaptation across microbial communities  

PubMed Central

Microbial communities represent the largest portion of the Earth’s biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species’ boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a ‘functional metagenomics’ platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community. PMID:23921637

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

2013-01-01

389

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

PubMed Central

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

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

2014-01-01

390

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

PubMed Central

The APC gene was investigated in 31 unrelated polyposis coli families by SSCP analysis and the protein truncation test. Twenty-three germline mutations were identified which gave rise to a variety of different phenotypes. Some of these mutations have already been described; however we report six previously unpublished mutations. Typical disease symptoms were observed in families who harboured mutations between exon 4 (codon 169) and codon 1393 of exon 15. Mutations beyond codon 1403 were associated with more varied phenotype with respect to the development of extracolonic symptoms. In this report we provide support for the notion that there appears to be a correlation between the location of an APC mutation (beyond codon 1403) and extracolonic manifestations of familial adenomatous polyposis. Images PMID:8730280

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

1996-01-01

391

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

Microsoft Academic Search

The primary structure of human apolipoprotein (apo) B-48 has been deduced and shown by a combination of DNA excess hybridization, sequencing of tryptic peptides, cloned complementary DNAs, and intestinal messenger RNAs (mRNAs) to be the product of an intestinal mRNA with an in-frame UAA stop codon resulting from a C to U change in the codon CAA encoding Gln2153 in

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

1987-01-01

392

STARTing Again: What Happens After START I Expires?  

SciTech Connect

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

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

2007-08-01

393

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

E-print Network

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

Cutter, Asher D.

394

Rating Curve Estimation from Local Levels and Upstream Discharges  

NASA Astrophysics Data System (ADS)

Current technology allows for low cost and easy level measurements while the discharge measurements are still difficult and expensive. Thus, these are rarely performed and usually not in flood conditions because of lack of safety and difficulty in activating the measurement team in due time. As a consequence, long series of levels are frequently available without the corresponding discharge values. However, for the purpose of planning, management of water resources and real time flood forecasting, discharge is needed and it is therefore essential to convert local levels into discharge values by using the appropriate rating curve. Over this last decade, several methods have been proposed to relate local levels at a site of interest to data recorded at a river section located upstream where a rating curve is available. Some of these methods are based on a routing approach which uses the Muskingum model structure in different ways; others are based on the entropy concepts. Lately, fuzzy logic has been applied more and more frequently in the framework of hydraulic and hydrologic problems and this has prompted to the authors to use it for synthesising the rating curves. A comparison between all these strategies is performed, highlighting the difficulties and advantages of each of them, with reference to a long reach of the Po river in Italy, where several hydrometers and the relevant rating curves are available, thus allowing for both a parameterization and validation of the different strategies.

Franchini, M.; Mascellani, G.

2003-04-01

395

Long Conserved Fragments Upstream of Mammalian Polyadenylation Sites  

PubMed Central

Polyadenylation is a cotranscriptional nuclear RNA processing event involving endonucleolytic cleavage of the nascent, emerging pre-messenger RNA (pre-mRNA) from the RNA polymerase, immediately followed by the polymerization of adenine ribonucleotides, called the poly(A) tail, to the cleaved 3? end of the polyadenylation site (PAS). This apparently simple molecular processing step has been discovered to be connected to transcription and splicing therefore increasing its potential for regulation of gene expression. Here, through a bioinformatic analysis of cis-PAS–regulatory elements in mammals that includes taking advantage of multiple evolutionary time scales, we find unexpected selection pressure much further upstream, up to 200 nt, from the PAS than previously thought. Strikingly, close to 3,000 long (30–500 nt) noncoding conserved fragments (CFs) were discovered in the PAS flanking region of three remotely related mammalian species, human, mouse, and cow. When an even more remote transitional mammal, platypus, was included, still over a thousand CFs were found in the proximity of the PAS. Even though the biological function of these CFs remains unknown, their considerable sizes makes them unlikely to serve as protein recognition sites, which are typically ?15 nt. By harnessing genome wide DNaseI hypersensitivity data, we have discovered that the presence of CFs correlates with chromatin accessibility. Our study is important in highlighting novel experimental targets, which may provide new understanding about the regulatory aspects of polyadenylation. PMID:21705472

Gunderson, Samuel I.

2011-01-01

396

Rheotaxis facilitates upstream navigation of mammalian sperm cells  

E-print Network

A major puzzle in biology is how mammalian sperm determine and maintain the correct swimming direction during the various phases of the sexual reproduction process. Whilst chemotaxis is assumed to dominate in the immediate vicinity of the ovum, it is unclear which biochemical or physical cues guide spermatozoa on their long journey towards the egg cell. Currently debated mechanisms range from peristaltic pumping to temperature sensing (thermotaxis) and direct response to fluid flow variations (rheotaxis), but little is known quantitatively about their relative importance. Here, we report the first quantitative experimental study of mammalian sperm rheotaxis. Using microfluidic devices, we investigate systematically the swimming behavior of human and bull sperm over the whole range of physiologically relevant shear rates and viscosities. Our measurements show that the interplay of fluid shear, steric surface-interactions and chirality of the flagellar beat leads to a stable upstream spiraling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. To rationalise these findings, we identify a minimal mathematical model that is capable of describing quantitatively the experimental observations. The combined experimental and theoretical evidence supports the hypothesis that the shape and beat patterns of mammalian sperm cells have evolved to optimally exploit rheotaxis for long-distance navigation.

Vasily Kantsler; Jörn Dunkel; Martyn Blayney; Raymond E. Goldstein

2014-05-26

397

Resistance to MEK Inhibitors: Should We Co-Target Upstream?  

NSDL National Science Digital Library

Aberrant activation of the ERK pathway is common in human tumors. This pathway consists of a three-tiered kinase module [comprising the kinases RAF, mitogen-activated protein kinase (MAPK) kinase (MEK), and extracellular signal–regulated kinase (ERK)] that functions as a negative feedback amplifier to confer robustness and stabilization of pathway output. Because this pathway is frequently dysregulated in human cancers, intense efforts are under way to develop selective inhibitors of the ERK pathway as anticancer drugs. Although promising results have been reported in early trials for inhibitors of RAF or MEK, resistance invariably occurs. Amplification of the upstream oncogenic driver of ERK signaling has been identified as a mechanism for MEK inhibitor resistance in cells with mutant BRAF or KRAS. Increased abundance of the oncogenic driver (either KRAS or BRAF in the appropriate cellular context) in response to prolonged drug treatment results in increased flux through the ERK pathway and restoration of ERK activity above the threshold required for cell growth. For patients with BRAF mutant tumors, the results suggest that the addition of a RAF inhibitor to a MEK inhibitor may delay or overcome drug resistance. The data thus provide a mechanistic basis for ongoing trials testing concurrent treatment with RAF and MEK inhibitors.

Poulikos I. Poulikakos (Memorial Sloan-Kettering Cancer Center;Program in Molecular Pharmacology and Chemistry REV); David B. Solit (Memorial Sloan-Kettering Cancer Center;Human Oncology and Pathogenesis Program REV)

2011-03-29

398

Upstream entrainment in numerical simulations of spatially evolving round jets  

NASA Astrophysics Data System (ADS)

Direct numerical simulation is used to study the effect of entrainment near the inflow nozzle on spatially evolving round jets. Inflow entrainment is obtained by providing a buffer region upstream of the inflow nozzle. Simulations are performed at Reynolds numbers of 300 (laminar) and 2400 (turbulent), respectively. Simulations without the inflow buffer are contrasted to those with the buffer region. The potential core is seen to close earlier in the presence of inflow entrainment. As a result, near-field turbulent intensities and pressure fluctuations on the jet centerline are noticeably affected. It is suggested that inflow entrainment results in an effective co-flow, whose effect on the volumetric flow rate near the inflow nozzle is appreciable for both laminar and turbulent jets. When plotted in similarity variables, the far-field solutions with and without inflow entrainment agree well with each other, and experiment. The results suggest the importance of allowing for inflow entrainment in simulations of turbulent jets, particularly for studies where near-field behavior is important.

Babu, Pradeep C.; Mahesh, Krishnan

2004-10-01

399

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

PubMed Central

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

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

2014-01-01

400

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

PubMed Central

The origin and early evolution of sex chromosomes are currently poorly understood. The Neurospora tetrasperma mating-type (mat) chromosomes have recently emerged as a model system for the study of early sex chromosome evolution, since they contain a young (<6 million years ago [Mya]), large (>6.6-Mb) region of suppressed recombination. Here we examined preferred-codon usage in 290 genes (121,831 codon positions) in order to test for early signs of genomic degeneration in N. tetrasperma mat chromosomes. We report several key findings about codon usage in the region of recombination suppression, including the following: (i) this region has been subjected to marked and largely independent degeneration among gene alleles; (ii) the level of degeneration is magnified over longer periods of recombination suppression; and (iii) both mat a and mat A chromosomes have been subjected to deterioration. The frequency of shifts from preferred codons to nonpreferred codons is greater for shorter genes than for longer genes, suggesting that short genes play an especially significant role in early sex chromosome evolution. Furthermore, we show that these degenerative changes in codon usage are best explained by altered selection efficiency in the recombinationally suppressed region. These findings demonstrate that the fungus N. tetrasperma provides an effective system for the study of degenerative genomic changes in young regions of recombination suppression in sex-regulating chromosomes. PMID:21335530

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

2011-01-01

401

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

PubMed

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

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

2014-01-01

402

Direct Correlations of Large-Amplitude Waves with Suprathermal Protons in the Upstream Solar Wind  

Microsoft Academic Search

SUMMARY We present here the results of direct correlations of magnetometer, plasma wave detector, plasma probe, and Lepedea proton data taken simultaneously by experiments aboard Ogo 5 during a large upstream wave event, on March 10, 1968. Direct correlation of Lepedea fluxes with magnetometer fluctuations shows that the large upstream wave amplitudes occur when enhanced fluxes of protons with Ep

F. L. Scarf; R. W. Fredricks; L. A. Frank; C. T. Russell; P. J. Coleman; M. Neugebauer

1970-01-01

403

The Caenorhabditis elegans Werner Syndrome Protein Functions Upstream of ATR and ATM in Response to DNA  

E-print Network

The Caenorhabditis elegans Werner Syndrome Protein Functions Upstream of ATR and ATM in Response syndrome protein, a RecQ helicase, mutations of which are associated with premature aging and increased-S (2010) The Caenorhabditis elegans Werner Syndrome Protein Functions Upstream of ATR and ATM in Response

Gartner, Anton

404

Methods of upstream power backoff on very high speed digital subscriber lines  

Microsoft Academic Search

This article describes the near-far problem in the upstream direction of VDSL, which results when the lengths of VDSL loops in a binder vary significantly. Methods of upstream power backoff to mitigate the near-far problem are then described. Simulation results are presented, and the performances of the methods are discussed

Krista S. Jacobsen; Texas Instruments

2001-01-01

405

The bow shocks and upstream waves of Venus and Mars D.A. Brain *  

E-print Network

at the two planets (and at other solar system bodies) suggest that similar processes are at work at both processes occurring at the shock. A variety of waves have been observed upstream from many solar system compared to each other in terms of their solar wind interaction. Upstream from each planet the most distant

California at Berkeley, University of

406

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

NASA Technical Reports Server (NTRS)

Observations with the Los Alamos Scientific Laboratory/Max-Planck-Institut crossed-fan solar wind ion experiment on ISEE I 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 by 7-10 km/s as it enters the wave region. At times, average speed changes as large as 25-40 km/s are observed. Superposed upon these changes in average flow speed are large amplitude (+ or - 15) fluctuations in flow speed associated with the waves themselves. The observations suggest that the solar wind deceleration is the result of momentum transfer from reflected bow shock ions to the wind via the long-period waves as the reflected ion beams go unstable. The broad angular distributions of the diffuse ions thus appear to be produced as a consequence of the disruption of reflected ion beams.

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

1980-01-01

407

An upstream promoter element of the Acanthamoeba castellanii TBP gene binds a DNA sequence specific transcription activating protein, TPBF.  

PubMed Central

We have characterized a positive-acting element in the upstream portion of the Acanthamoeba TBP gene promoter. The 27 bp element (TPE), located within the promoter between -97 and -70, stimulates transcription in an orientation independent fashion and tolerates modest changes in its distance from the TATA box. The TPE does not, however, function synergistically nor when positioned 3000 bp 5' or 260 base pairs 3' of the transcription start site. The TPE binds a DNA sequence-dependent factor, TPBF, which we have partly purified. TPBF was characterized using in vitro transcription, DNase I footprinting, methylation interference and electrophoretic mobility shift assays. TPBF does not have a counterpart in HeLa cells, but nonetheless strongly stimulates transcription of the Acanthamoeba TBP gene in mammalian extracts. Our results also suggest that there are additional positively and negatively acting elements within the TBP gene promoter, for which a model is presented. Images PMID:8414988

Liu, F; Bateman, E

1993-01-01

408

"Upstream Thinking": the catchment management approach of a water provider  

NASA Astrophysics Data System (ADS)

Human activities have large impacts on water quality and provision. Water companies throughout the UK are faced with the consequences of poor land management and need to find appropriate solutions to decreasing water quality. This is particularly true in the South West of England, where 93% of the drinking water is sourced from rivers and reservoirs: large areas of drained peatlands (i.e. Exmoor and Dartmoor National Parks) are responsible for a significant input of dissolved organic carbon (DOC) discolouring the water, whilst poorly managed farming activities can lead to diffuse pollution. Alongside the direct environmental implications, poor water quality is partly increasing water treatment costs and will drive significant future investment in additional water treatment, with further repercussions on customers. This highlights the need for water companies throughout the UK, and further afield, to be more involved in catchment management. "Upstream Thinking" is South West Water's (SWW) approach to catchment management, where working with stakeholders to improve water quality upstream aims to avoid increasingly costly solutions downstream. This approach has led the company to invest in two major areas of work: (1) The Farmland programme where problematic farm management practices and potential solutions are identified, typically 40% of the required investment is then offered in exchange for a legal undertaking to maintain the new farm assets in good condition for 25 years; (2) The Mires programme which involves heavy investment in peatland restoration through the blocking of open ditches in order to improve water storage and quality in the long term. From these two projects, it has been clear that stakeholder involvement of groups such as local farmers, the Westcountry Rivers Trust, the Exmoor National Park Authority, the Environment Agency, Natural England and the Exmoor Society is essential, first because it draws in catchment improvement expertise which is not directly held within the company, and second because it shows how local communities and groups are considered and valued by the company. Monitoring changes and providing a solid scientific base is also undertaken to prove the concept and justify any investment. The work carried out so far has highlighted that SWW's collaborative approach to catchment management is changing the relationship between private water suppliers in the UK and stakeholders or groups having an impact on water quality. This results in a progressive move from a situation where the polluter has to pay, to rewarding providers of clean water instead. The value of ecosystem payments of this kind is being discussed with the appropriate authorities (i.e. Natural England, and the Department for Environment, Food and Rural Affairs) so that it can form part of ensuring sustainable water supplies in future, with all the environmental and ecological benefits of clear raw waters in rivers, lakes and streams.

Grand-Clement, E.; Ross, M.; Smith, D.; Anderson, K.; Luscombe, D.; Le Feuvre, N.; Brazier, R. E.

2012-04-01

409

Expressions of heparanase and upstream stimulatory factor in hepatocellular carcinoma  

PubMed Central

Background The expression of heparanase (HPSE) was associated with postoperative metastatic recurrence in patients with hepatocellular carcinoma (HCC). The six E-box binding sites in the core promoter of the HPSE gene suggested that transcription factors of E-box such as upstream stimulatory factor (USF) might regulate the transcription of the HPSE gene. The aim of our study is to measure the levels of HPSE and USF expression and investigate the relationship between USF expression and clinicopathological parameters in patients with HCC. Methods HPSE, USF1 and USF2 expressions in human HCC cell lines (BEL-7402, HepG2 and HCCLM3) and 15 fresh human HCC tissue samples were measured by real-time reverse transcriptase-PCR and Western blot analysis. The normal liver cell line QSG7701 or fresh normal liver tissue samples obtained from 15 additional surgical patients with hepatic rupture was used as a control. The protein expressions were determined by immunohistochemistry in paraffin-embedded human HCC tissues and corresponding non-neoplastic tumor surrounding tissues (NTST) of 57 patients. Results HPSE, USF1 and USF2 mRNA expressions were increased in HCC cell lines and HCC tissues compared with normal liver cell line and normal liver tissue. The protein expressions of HPSE, USF1 and USF2 in HCC cell lines and HCC tissues were also increased. Both USF1 and USF2 expressions were positively correlated with HPSE. USF1 and USF2 expressions were increased in patients with liver cirrhosis, worse tissue differentiation, advanced HCC stages and metastatic recurrence. Conclusions Increased USF in HCC is associated with HPSE expression. USF might be an important factor in regulating HPSE expression and act as a novel marker of metastatic recurrence of HCC patients. PMID:25149140

2014-01-01

410

START-UP ACCIDENT ANALYSIS  

Microsoft Academic Search

S>Analog computer studies are made of two main areas of interest during ; a start-up accident; the ability of drivedown circuitry to shut down the reactor ; before reaching the power range, and the self shut-down characteristics of the ; reactor if the accident progresses into the power range. The results indicate ; that period drivedown circuitry would have to

MacNaughton

1958-01-01

411

Math Club Starting in Kindergarten  

ERIC Educational Resources Information Center

Starting a math club as early as kindergarten and having a range of grade levels in attendance can be successful. With the help of the older students, the varied age groups are entertained and excited about attending math club. The purpose of the club is to enrich the classroom mathematics curriculum with hands-on activities and to have members…

Perry, Ann M.

2011-01-01

412

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.

413

Start Where Your Students Are  

ERIC Educational Resources Information Center

Starting where your students are means understanding how currencies are negotiated and traded in the classroom. Any behavior that students use to acquire the knowledge and skills needed in the classroom functions as currency. Teachers communicate the kinds of currencies they accept in their classrooms, such as getting good grades; students do…

Jackson, Robyn R.

2010-01-01

414

Entrepreneur Training Program. Getting Started.  

ERIC Educational Resources Information Center

This student workbook on starting a small business is part of the entrepreneur training program at Ocean County (New Jersey) Vocational-Technical Schools. The workbook consists of 16 units containing goals and objectives, study questions, exercises, sample materials, and information sheets. Unit topics are as follows: being a small business owner;…

De Maria, Richard

415

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.

416

Ethical Imperative For Head Start  

ERIC Educational Resources Information Center

A Head Start Program should foster an ethically valid situation. Such a situation would encourage the physical, mental, social, emotional and ethical growth and development of the four-year-old with due concern for his needs, interests and special potentialities. (Author)

Pratt, Grace K.

1972-01-01

417

MAKING WAVES, DENVER HEAD START.  

ERIC Educational Resources Information Center

THIS DOCUMENT PROVIDES A DESCRIPTIVE SURVEY OF PROJECT HEAD START ACTIVITIES IN DENVER, COLORADO. THE PRIMARY EDUCATIONAL OBJECTIVES OF THE PROGRAM ARE CITED AS (1) CONCEPT DEVELOPMENT THROUGH EXPERIENCES IN AN ENLARGED ENVIRONMENT, (2) SELF-CONCEPT DEVELOPMENT THROUGH SUCCESSFUL INTERACTION WITH TEACHERS AND WITH PEERS, AND (3) THE DEVELOPMENT OF…

Denver Opportunity, CO.

418

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner.  

PubMed

Upstream open reading frames (uORFs) are often found in the 5'-leader regions of eukaryotic mRNAs and can negatively modulate the translational efficiency of the downstream main ORF. Although the effects of most uORFs are thought to be independent of their encoded peptide sequences, certain uORFs control translation of the main ORF in a peptide sequence-dependent manner. For genome-wide identification of such peptide sequence-dependent regulatory uORFs, exhaustive searches for uORFs with conserved amino acid sequences have been conducted using bioinformatic analyses. However, whether the conserved uORFs identified by these bioinformatic approaches encode regulatory peptides has not been experimentally determined. Here we analyzed 16 recently identified Arabidopsis thaliana conserved uORFs for the effects of their amino acid sequences on the expression of the main ORF using a transient expression assay. We identified five novel uORFs that repress main ORF expression in a peptide sequence-dependent manner. Mutational analysis revealed that, in four of them, the C-terminal region of the uORF-encoded peptide is critical for the repression of main ORF expression. Intriguingly, we also identified one exceptional sequence-dependent regulatory uORF, in which the stop codon position is not conserved and the C-terminal region is not important for the repression of main ORF expression. PMID:25618853

Ebina, Isao; Takemoto-Tsutsumi, Mariko; Watanabe, Shun; Koyama, Hiroaki; Endo, Yayoi; Kimata, Kaori; Igarashi, Takuya; Murakami, Karin; Kudo, Rin; Ohsumi, Arisa; Noh, Abdul Latif; Takahashi, Hiro; Naito, Satoshi; Onouchi, Hitoshi

2015-02-18

419

Fundamental role of start/stop regulators in whole DNA and new trinucleotide classification.  

PubMed

The origin and logic of genetic code are two of greatest mysteries of life sciences. Analyzing DNA sequences we showed that the start/stop trinucleotides have broader importance than just marking start and stop of exons in coding DNA. On this basis, here we introduced new classification of trinucleotides and showed that all A+T rich trinucleotides consisting of three different nucleotides arise from start-ATG, stop-TGA and stop-TAG using their complement, reverse complement and reverse transformations. Due to the same transformations during generations of crossing-over they can switch from one form to the other. By direct process the start-ATG and stop-TAG can irreversibly transform into stop-TAA. By transformation into A+T rich trinucleotides and 16/32 C+G rich they can lose the start/stop function and take the role of a sense codon in reversible way. The remaining 16 C+G trinucleotides cannot directly transform into start/stop trinucleotides and thus remain a firm skeleton for structuring the C+G rich DNA. We showed that start/stops strongly enrich the A+T rich noncoding DNA through frequently extended forms. From the evolutionary viewpoint the start/stops are chief creators of prevailing A+T rich noncoding DNA, and of more stable coding DNA. We propose that start/stops have basic role as "seeds" in trinucleotide evolution of noncoding and coding sequences and lead to asymmetry between A+T and C+G rich DNA. By dynamical transformations during evolution they enabled pronounced phylogenetic broadness, keeping the regulator function. PMID:24042127

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

2013-12-01

420

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

PubMed Central

Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. Here, we present the first integrated stoichiometric multiscale model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655, which describes the sequence-specific synthesis and function of almost 2000 gene products at molecular detail. We added linear constraints, which couple enzyme synthesis and catalysis reactions. Comparison with experimental data showed improvement of growth phenotype prediction with the multiscale model over E. coli’s metabolic model alone. Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. We addressed the question of whether the bias in synonymous codon usage could affect the growth phenotype and environmental niches that an organism can occupy. We created two classes of in silico strains, one with more biased codon usage and one with more equilibrated codon usage than the wildtype. The reduced growth phenotype in biased strains was caused by tRNA supply shortage, indicating that expansion of tRNA gene content or tRNA codon recognition allow E. coli to respond to changes in codon usage bias. Our analysis suggests that in order to maximize growth and to adapt to new environmental niches, codon usage and tRNA content must co-evolve. These results provide further evidence for the mutation-selection-drift balance theory of codon usage bias. This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors. PMID:23029152

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

2012-01-01

421

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

PubMed

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

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

2014-10-12

422

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

423

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

PubMed Central

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

424

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

PubMed Central

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

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

2009-01-01

425

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

PubMed Central

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

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

2014-01-01

426

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

PubMed Central

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

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

1989-01-01

427

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

NASA Astrophysics Data System (ADS)

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

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

428

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

PubMed Central

Receptor activator of nuclear factor (NF)-?B ligand (RANKL), a master cytokine that drives osteoclast differentiation, activation and survival, exists in both transmembrane and extracellular forms. To date, studies on physiological role of RANKL have been mainly carried out with extracellular RANKL probably due to difficulties in achieving high level expression of functional transmembrane RANKL (mRANKL). In the present study, we took advantage of codon optimization and response surface methodology to optimize the soluble expression of mRANKL in E. coli. We optimized the codon usage of mRANKL sequence to a preferred set of codons for E. coli changing its codon adaptation index from 0.64 to 0.76, tending to increase its expression level in E. coli. Further, we utilized central composite design to predict the optimum combination of variables (cell density before induction, lactose concentration, post-induction temperature and post-induction time) for the expression of mRANKL. Finally, we investigated the effects of various experimental parameters using response surface methodology. The best combination of response variables was 0.6 OD600, 7.5 mM lactose, 26°C post-induction temperature and 5 h post-induction time that produced 52.4 mg/L of fusion mRANKL. Prior to functional analysis of the protein, we purified mRANKL to homogeneity and confirmed the existence of trimeric form of mRANKL by native gel electrophoresis and gel filtration chromatography. Further, the biological activity of mRANKL to induce osteoclast formation on RAW264.7 cells was confirmed by tartrate resistant acid phosphatase assay and quantitative real-time polymerase chain reaction assays. Importantly, a new finding from this study was that the biological activity of mRANKL is higher than its extracellular counterpart. To the best of our knowledge, this is the first time to report heterologous expression of mRANKL in soluble form and to perform a comparative study of functional properties of both forms of RANKL. PMID:24809485

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

2014-01-01

429

PILOT TESTING OF MERCURY OXIDATION CATALYSTS FOR UPSTREAM OF WET FGD SYSTEMS  

SciTech Connect

This document summarizes progress on Cooperative Agreement DE-FC26-01NT41185, Pilot Testing of Mercury Oxidation Catalysts for Upstream of Wet FGD Systems, during the time period October 1, 2002 through December 31, 2002. The objective of this project is to demonstrate at pilot scale the use of solid honeycomb catalysts to promote the oxidation of elemental mercury in the flue gas from coal combustion. The project is being funded by the U.S. DOE National Energy Technology Laboratory under Cooperative Agreement DE-FC26-01NT41185. EPRI, Great River Energy (GRE), and City Public Service (CPS) of San Antonio are project co-funders. URS Group is the prime contractor. The mercury catalytic oxidation process under development uses catalyst materials applied to honeycomb substrates to promote the oxidation of elemental mercury in the flue gas from coal-fired power plants that have wet lime or limestone flue gas desulfurization (FGD) systems. Oxidized mercury is removed in the wet FGD absorbers and co-precipitates with the byproducts from the FGD system. The co-precipitated mercury does not appear to adversely affect the disposal or reuse properties of the FGD byproduct. The current project testing previously identified, effective catalyst materials at a larger, pilot scale and in a commercial form, to provide engineering data for future fullscale designs. The pilot-scale tests will continue for up to 14 months at each of two sites to provide longer-term catalyst life data. This is the fifth full reporting period for the subject Cooperative Agreement. During this period, project efforts included starting up the pilot unit with three catalysts at the first site, conducting catalyst activity measurements, completing comprehensive flue gas sampling and analyses, and procuring additional catalysts for the pilot unit. This technical progress report provides an update on these efforts.

Gary M. Blythe

2003-01-21

430

Heliospheric Termination Shock Motion Due to Fluctuations in the Solar Wind Upstream Conditions: Spherically Symmetric Model  

NASA Technical Reports Server (NTRS)

Large-scale fluctuations in the solar wind plasma upstream of the heliospheric termination shock (TS) will cause inward and outward motions of the shock. Using numerical techniques, we extend an earlier strictly one-dimensional (planar) analytic gas dynamic model to spherical symmetry to investigate the features of global behavior of shock motion. Our starting point is to establish a steady numerical solution of the gasdynamic equations describing the interaction between the solar wind and the interstellar medium. We then introduce disturbances of the solar wind dynamic pressure at an inner boundary, and follow the subsequent evolution of the system, especially the motion of the termination shock. Our model solves spherically symmetric gasdynamic equations as an initial-boundary value problem. The equations in conservative form are solved using a fully implicit Total Variation Diminishing (TVD) upwind scheme with Roe-type Riemann solver. Boundary conditions are given by the solar wind parameters on an inner spherical boundary, where they are allowed to vary with time for unsteady calculations, and by a constant pressure (roughly simulating the effect of the local interstellar medium) on an outer boundary. We find that immediately after the interaction, the shock moves with speeds given by the earlier analogous analytic models. However, as the termination shock propagates it begins to slow down, seeking a new equilibrium position. In addition, the disturbance transmitted through the TS, either a shock or rarefaction wave, will encounter the heliopause boundary and be reflected back. The reflected signal will encounter the TS, causing it to oscillate. The phenomenon may be repeated for a number of reflections, resulting in a "ringing" of the outer heliosphere.

Ratkiewicz, R.; Barnes, A.; Molvik, G. A.; Spreiter, J. R.; Stahara, S. S.; Cuzzi, Jeffery N. (Technical Monitor)

1995-01-01

431

30 CFR 75.1913 - Starting aids.  

...2014-07-01 2014-07-01 false Starting aids. 75.1913 Section 75.1913 Mineral Resources...Diesel-Powered Equipment § 75.1913 Starting aids. (a) Volatile fuel starting aids shall be used in accordance with...

2014-07-01

432

30 CFR 75.1913 - Starting aids.  

Code of Federal Regulations, 2012 CFR

...2012-07-01 2012-07-01 false Starting aids. 75.1913 Section 75.1913 Mineral Resources...Diesel-Powered Equipment § 75.1913 Starting aids. (a) Volatile fuel starting aids shall be used in accordance with...

2012-07-01

433

30 CFR 75.1913 - Starting aids.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false Starting aids. 75.1913 Section 75.1913 Mineral Resources...Diesel-Powered Equipment § 75.1913 Starting aids. (a) Volatile fuel starting aids shall be used in accordance with...

2013-07-01

434

30 CFR 75.1913 - Starting aids.  

Code of Federal Regulations, 2011 CFR

...2011-07-01 2011-07-01 false Starting aids. 75.1913 Section 75.1913 Mineral Resources...Diesel-Powered Equipment § 75.1913 Starting aids. (a) Volatile fuel starting aids shall be used in accordance with...

2011-07-01

435

30 CFR 75.1913 - Starting aids.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false Starting aids. 75.1913 Section 75.1913 Mineral Resources...Diesel-Powered Equipment § 75.1913 Starting aids. (a) Volatile fuel starting aids shall be used in accordance with...

2010-07-01

436

Drug Abuse Prevention Starts with Parents  

MedlinePLUS

... Abuse Prevention Starts with Parents Ages & Stages Listen Drug Abuse Prevention Starts with Parents Article Body Drugs, including ... for a time when drugs may be offered. Drug abuse prevention starts with parents learning how to talk ...

437

Aquareovirus effects syncytiogenesis by using a novel member of the FAST protein family translated from a noncanonical translation start site.  

PubMed

As nonenveloped viruses, the aquareoviruses and orthoreoviruses are unusual in their ability to induce cell-cell fusion and syncytium formation. While an extraordinary family of fusion-associated small transmembrane (FAST) proteins is responsible for orthoreovirus syncytiogenesis, the basis for aquareovirus-induced syncytiogenesis is unknown. We now report that the S7 genome segment of an Atlantic salmon reovirus is polycistronic and uses a noncanonical CUG translation start codon to produce a 22-kDa integral membrane protein responsible for syncytiogenesis. The aquareovirus p22 protein represents a fourth distinct member of the FAST family with a unique repertoire and arrangement of structural motifs. PMID:19297495

Racine, Trina; Hurst, Tara; Barry, Chris; Shou, Jingyun; Kibenge, Frederick; Duncan, Roy

2009-06-01

438

Aquareovirus Effects Syncytiogenesis by Using a Novel Member of the FAST Protein Family Translated from a Noncanonical Translation Start Site?  

PubMed Central

As nonenveloped viruses, the aquareoviruses and orthoreoviruses are unusual in their ability to induce cell-cell fusion and syncytium formation. While an extraordinary family of fusion-associated small transmembrane (FAST) proteins is responsible for orthoreovirus syncytiogenesis, the basis for aquareovirus-induced syncytiogenesis is unknown. We now report that the S7 genome segment of an Atlantic salmon reovirus is polycistronic and uses a noncanonical CUG translation start codon to produce a 22-kDa integral membrane protein responsible for syncytiogenesis. The aquareovirus p22 protein represents a fourth distinct member of the FAST family with a unique repertoire and arrangement of structural motifs. PMID:19297495

Racine, Trina; Hurst, Tara; Barry, Chris; Shou, Jingyun; Kibenge, Frederick; Duncan, Roy

2009-01-01

439

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

PubMed Central

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

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

2013-01-01

440

Apolipoprotein B-48 is the product of a messenger RNA with an organ-specific in-frame stop codon  

SciTech Connect

The primary structure of human apolipoprotein (apo) B-48 has been deduced and shown by a combination of DNA excess hybridization, sequencing of tryptic peptides, cloned complementary DNAs, and intestinal messenger RNAs (mRNAs) to be the product of an intestinal mRNA with an in-frame UAA stop codon resulting from a C to U change in the codon CAA encoding Gln/sup 2153/ in apoB-100 mRNA. The carboxyl-terminal Ile/sup 2152/ of apoB-48 purified from chylous ascites fluid has apparently been cleaved from the initial translation product, leaving Met/sup 2151/ as the new carboxyl-terminus. These data indicate that approx.85% of the intestinal mRNAs terminate within approx. 0.1 to 1.0 kilobase downstream from the stop codon. The other approx. 15% have lengths similar to hepatic apoB-100 mRNA even though they have the same in-frame stop codon. The organ-specific introduction of a stop codon to a mRNA appears unprecedented and might have implications for cryptic polyadenylation signal recognition and RNA processing.

Chen, S.H.; Habib, G.; Yang, C.Y.; Gu, Z.W.; Lee, B.R.; Weng, S.A.; Silberman, S.R.; Cai, S.J.; Deslypere, J.P.; Rosseneu, M.; Gotton, A.M. Jr.

1987-10-16

441

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

PubMed

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

Das, Gunajyoti; Lyngdoh, R H Duncan

2012-08-01

442

Experience with the use of the Codonics Safe Label System(™) to improve labelling compliance of anaesthesia drugs.  

PubMed

The Codonics Safe Labeling System(™) (http://www.codonics.com/Products/SLS/flash/) is a piece of equipment that is able to barcode scan medications, read aloud the medication and the concentration and print a label of the appropriate concentration in the appropriate colour code. We decided to test this system in our facility to identify risks, benefits and usability. Our project comprised a baseline survey (25 anaesthesia cases during which 212 syringes were prepared from 223 drugs), an observational study (47 cases with 330 syringes prepared) and a user acceptability survey. The baseline compliance with all labelling requirements was 58%. In the observational study the compliance using the Codonics system was 98.6% versus 63.8% with conventional labelling. In the user acceptability survey the majority agreed the Codonics machine was easy to use, more legible and adhered with better security than the conventional preprinted label. However, most were neutral when asked about the likelihood of flexibility and customisation and were dissatisfied with the increased workload. Our findings suggest that the Codonics labelling machine is user-friendly and it improved syringe labelling compliance in our study. However, staff need to be willing to follow proper labelling workflow rather than batch label during preparation. Future syringe labelling equipment developers need to concentrate on user interface issues to reduce human factor and workflow problems. Support logistics are also an important consideration prior to implementation of any new labelling system. PMID:24967766

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

2014-07-01

443

Start codon FokI and intron 8 BsmI variants in the vitamin D receptor gene and susceptibility to colorectal cancer  

Microsoft Academic Search

Epidemiological evidence suggests the protective effect of vitamin D against colorectal cancer (CRC) and the polymorphisms\\u000a in vitamin D receptor (VDR) gene may influence the development of CRC. In this study the possible association of VDR FokI\\u000a and BsmI gene polymorphisms with CRC risk was examined. A total of 904 subjects, including 452 cases with CRC and 452 controls\\u000a were

Touraj Mahmoudi; Khatoon Karimi; Seyed Reza Mohebbi; Seyed Reza Fatemi; Mohammad Reza Zali

444

Shock Excursion Due to Fluctuations in the Solar Wind Upstream Conditions  

NASA Technical Reports Server (NTRS)

Large-scale fluctuations in the solar wind upstream of the termination shock will cause inward and outward motions of the shock. In earlier work, Barnes analyzed such motion by calculating of the response of a planar gasdynamic shock to upstream disturbances. We now generalize this analysis to the case of a spherically symmetric shock. Our procedure is first to solve numerically the set of gasdynamic equations describing the interaction between the solar wind and the interstellar medium to establish a dynamic equilibrium. The next step is to impose upstream fluctuations of the solar wind dynamical pressure on this equilibrium state at an inner boundary, and then to follow the subsequent shock motion.

Ratkiewicz, Romana E.; Barnes, A.; Molvik, G. A.; Spreiter, J. R.; Stahara, S. S.; Cuzzi, Jeffrey N. (Technical Monitor)

1994-01-01

445

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

PubMed

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

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

2004-08-01

446

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

PubMed Central

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

Allnér, Olof; Nilsson, Lennart

2011-01-01

447

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

NASA Astrophysics Data System (ADS)

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

Gorban, Alexander; Popova, Tatyana; Zinovyev, Andrey

2005-08-01

448

Structural insights into eRF3 and stop codon recognition by eRF1  

PubMed Central

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

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

2009-01-01

449

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

PubMed

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

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

2012-02-01

450

Codon optimisation improves the expression of Trichoderma viride sp. endochitinase in Pichia pastoris.  

PubMed

The mature cDNA of endochitinase from Trichoderma viride sp. was optimised based on the codon bias of Pichia pastoris GS115 and synthesised by successive PCR; the sequence was then transformed into P. pastoris GS115 via electroporation. The transformant with the fastest growth rate on YPD plates containing 4?mg/mL G418 was screened and identified. This transformant produced 23.09?U/mL of the recombinant endochitinase, a 35% increase compared to the original strain bearing the wild-type endochitinase cDNA. The recombinant endochitinase was sequentially purified by ammonia sulphate precipitation, DE-52 anion-exchange chromatography and Sephadex G-100 size-exclusion chromatography. Thin-layer chromatography indicated that the purified endochitinase could hydrolyse chito-oligomers or colloidal chitin to generate diacetyl-chitobiose (GlcNAc)? as the main product. This study demonstrates (1) a means for high expression of Trichoderma viride sp. endochitinase in P. pastoris using codon optimisation and (2) the preparation of chito-oligomers using endochitinase. PMID:24154717

Yu, Ping; Yan, Yuan; Gu, Qing; Wang, Xiangyang

2013-01-01

451

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

452

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

PubMed Central

Reliable inference of ancestral sequences can be critical to identifying both patterns and causes of molecular evolution. Robustness of ancestral inference is often assumed among closely related species, but tests of this assumption have been limited. Here, we examine the performance of inference methods for data simulated under scenarios of codon bias evolution within the Drosophila melanogaster subgroup. Genome sequence data for multiple, closely related species within this subgroup make it an important system for studying molecular evolutionary genetics. The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. Maximum parsimony inference, which has been widely employed in analyses of Drosophila codon bias evolution, was compared to an approach that attempts to account for uncertainty in ancestral inference by weighting ancestral reconstructions by their posterior probabilities. The latter approach employs maximum likelihood estimation of rate and base composition parameters. For equilibrium and most non-equilibrium scenarios that were investigated, the probabilistic method appears to generate reliable ancestral codon bias inferences for molecular evolutionary studies within the D. melanogaster subgroup. These reconstructions are more reliable than parsimony inference, especially when codon usage is strongly skewed. However, inference biases are considerable for both methods under particular departures from stationarity (i.e., when adaptive evolution is prevalent). Reliability of inference can be sensitive to branch lengths, asymmetry in substitution rates, and the locations and nature of lineage-specific processes within a gene tree. Inference reliability, even among closely related species, can be strongly affected by (potentially unknown) patterns of molecular evolution in lineages ancestral to those of interest. PMID:17957249

Akashi, Hiroshi; Goel, Piyush; John, Anoop

2007-01-01

453

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

SciTech Connect

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

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

1998-07-01

454

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

PubMed Central

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

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

2011-01-01

455

Evidence for specularly reflected ions upstream from the quasi-parallel bow shock  

NASA Technical Reports Server (NTRS)

Ion velocity distributions in the form of bunches of gyrating particles traveling along helical paths have been observed moving sunward immediately upstream from quasi-parallel parts of the earth's bow shock using Los Alamos/Garching instruments on ISEE-1 and -2. These distributions have characteristics which indicate that they are produced by the nearly specular reflection at the shock of a portion of the incident solar wind ions. In particular, the guiding center motion and the gyrospeeds of the gyrating ions are quantitatively consistent with simple geometrical considerations for specular reflection. These considerations reveal that specularly reflected ions can escape upstream when the angle between the upstream magnetic field and the local shock normal is less than 45 deg but not when the angle is greater than 45 deg. These upstream gyrating ions are an important signature of one of the processes by which solar wind streaming energy is dissipated into other forms of energy at the shock.

Gosling, J. T.; Thomsen, M. F.; Bame, S. J.; Feldman, W. C.; Paschmann, G.; Sckopke, N.

1982-01-01

456

Regulation of the human. beta. -actin promoter by upstream and intron domains  

SciTech Connect

The authors have identified three regulatory domains of the complex human {beta}-actin gene promoter. They span a region of about 3,000 bases, from not more than {minus}2,011 bases upstream of the mRNA cap site to within the 5{prime} intron (832 bases long). A distal upstream domain contains at least one enhancer-like element. A proximal upstream domain, with a CArG (for CC(A+T rich){sub 6}GG) motif found in all known mammalian actin genes, seems to confer serum, but not growth factor, inducibility. The third domain is within the evolutionarily conserved 3{prime} region of the first intron and contains a 13 base-pair sequence, identical to the upstream sequence with the CArG motif. This domain also contains sequences that are both serum and fibroblast growth inducible.

Ng, Sunyu (Linus Pauling Institute of Science and Medicine, Palo Alto, CA (USA))(Institute of Molecular Biology, Nankang (China)); Gunning, P.; Kedes, L. (Stanford Univ. School of Medicine, Palo Alto, CA (USA)); Liu, Shuhui (Institute of Molecular Biology, Taipei (China) National Tsing Hua Univ., Hsinchu (China)); Leavitt, J. (Linus Pauling Institute of Science and Medicine, Palo Alto, CA (USA))

1989-01-25

457

Upstream Financial Review of the Global Oil and Natural Gas Industry 2013  

EIA Publications

This analysis focuses on financial and operating trends of the oil and natural gas production business segment, often referred to as upstream operations, of 42 global oil and natural gas producing companies

2014-01-01

458

Measurement of Emissions from Produced Water Ponds: Upstream Oil and Gas Study #1; Final Report  

EPA Science Inventory

Significant uncertainty exists regarding air pollutant emissions from upstream oil and gas production operations. Oil and gas operations present unique and challenging emission testing issues due to the large variety and quantity of potential emissions sources. This report summ...

459

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

460

Effects of upstream surface heat fluxes on the evolution of the South China Sea summer monsoon  

Microsoft Academic Search

Summary  This study uses a regional climate model to investigate the effects of upstream surface heat fluxes on the evolution of the\\u000a East Asian summer monsoon, especially the South China Sea (SCS) summer monsoon onset and its subsequent evolution. Upstream\\u000a refers to the regions west of the SCS: Bay of Bengal (BOB), Indochina Peninsula (ICP) and the Indian subcontinent (IND). Five

X. Shi; J. C. L. Chan; K. C. Chow; Y. Ding

2008-01-01

461

Association of low-frequency waves with suprathermal ions in the upstream solar wind  

Microsoft Academic Search

Observations obtained upstream of the earth's bowshock with the LASL\\/MPI plasma instruments and the UCLA magnetometers on ISEE-1 and 2 have revealed a striking relationship between the presence of low-frequency fluctuations in solar wind density and field strength and the different types of distribution functions of upstream ions. Waves are absent when the ions have the beamlike distribution of the

G. Paschmann; N. Sckopke; S. J. Bame; J. R. Asbridge; J. T. Gosling; C.T. Russell; E. W. Greenstadt

1979-01-01

462

30- to 100keV Protons Upstream From the Earth’s Bow Shock  

Microsoft Academic Search

Protons of 30 to 100 keV are found upstream from the bow shock whenever interplanetary magnetic fields connect the spacecraft and bow shock. Their energy spectrum is closely power law, d J\\/dE o: E- with v usually close to 3. The spectrum is sharply cut off above 100 keV. The protons do not appear upstream of a boundary determined by

R. P. Lin; C.-I. Meng; K. A. Anderson

1974-01-01

463

6. Oblique view of upstream side of Bridge Number 310.58, ...  

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

6. Oblique view of upstream side of Bridge Number 310.58, 135mm lens. Note ashlar stone masonry abutment built in 1886, Tunnel 15 at left. Heavy vegetation cover, steep banks, and lack of streamside footing precluded full elevation views of the upstream and downstream sides of this bridge. - Southern Pacific Railroad Shasta Route, Bridge No. 310.58, Milepost 310.58, Sims, Shasta County, CA

464

Upstream migration of adult chum and pink salmon in the Shibetsu River  

Microsoft Academic Search

The migratory behavior and swimming patterns of anadromous upstream migratory fish have been poorly described in the Shibetsu\\u000a River in eastern Hokkaido, Japan. In this 2004 study, we used electromyogram (EMG) transmitters and depth\\/ temperature (DT)\\u000a loggers to compare the upstream migratory behavior of adult male chum salmon (Oncorhynchus keta) and pink salmon (O. gorbuscha) in the canalized and reconstructed

Y. Makiguchi; H. Nii; K. Nakao; H. Ueda

2007-01-01

465

Upstream migration of adult chum and pink salmon in the Shibetsu River  

Microsoft Academic Search

The migratory behavior and swimming patterns of anadromous upstream migratory fish have been poorly described in the Shibetsu\\u000a River in eastern Hokkaido, Japan. In this 2004 study, we used electromyogram (EMG) transmitters and depth\\/ temperature (DT)\\u000a loggers to compare the upstream migratory behavior of adult male chum salmon (Oncorhynchus keta) and pink salmon (O. gorbuscha) in the canalized and reconstructed

Y. Makiguchi; H. Nii; K. Nakao; H. Ueda

466

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

Microsoft Academic Search

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

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

2000-01-01

467

Start: Statler Hotel (star) Finish: Upson Hall  

E-print Network

Start: Statler Hotel (star) Finish: Upson Hall Duration: 1.30h Main route: Red arrows that start from Statler Hotel and end at Upson Hall 2nd route: Orange dashed line that starts from Statler Hotel and meets read line at McGraw Tower #12;3rd route: Red arrow backwards, starting from Statler Hotel 4th

Keinan, Alon

468

The Home Start Demonstration Program: An Overview.  

ERIC Educational Resources Information Center

Following a discussion of the Home Start program and its evaluation plan, the 16 Office of Child Development-funded Home Start projects in the United States are described. Home start is a 3-year Head Start demonstration program, aimed at the 3-5 years of age range, which focuses on enhancing the quality of children's lives by building upon…

Office of Child Development (DHEW), Washington, DC.

469

Russian joint ventures, upstream deals hit fast clip  

SciTech Connect

This paper reports that Russia is stepping up the pace of joint ventures and imports of petroleum technology and hardware. Among the latest action: Polar Lights, a 50-50 venture of Conoco Timan-Pechora Ltd. and Arkhangelskgeologia (AAG), started drilling in the first new-field oil-development project in Russia to include a US partner; The governments of Oman and the Kazakhstan republic signed an agreement covering oil and gas exploration, field development, and production in Kazakhstan; Phibro Energy Inc., Greenwich, Conn., last week reported the sale and delivery of the first full cargo of Russian crude oil produced and exported by a Russian-American joint venture; Era Aviation Inc., Anchorage, Alas., is sending two helicopters with crewmen to Russia to help assess the feasibility of oil and gas development off Sakhalin Island; In deals involving Canadian companies, SNC-Lavalin Inc., Montreal, received a contract for initial work on a $350 million (US) modernization of the Volvograd refinery in southern Russia.

Not Available

1992-06-29

470

Defragged Binary I Ching Genetic Code Chromosomes Compared to Nirenberg’s and Transformed into Rotating 2D Circles and Squares and into a 3D 100% Symmetrical Tetrahedron Coupled to a Functional One to Discern Start From Non-Start Methionines through a Stella Octangula  

PubMed Central

Background Three binary representations of the genetic code according to the ancient I Ching of Fu-Xi will be presented, depending on their defragging capabilities by pairing based on three biochemical properties of the nucleic acids: H-bonds, Purine/Pyrimidine rings, and the Keto-enol/Amino-imino tautomerism, yielding the last pair a 32/32 single-strand self-annealed genetic code and I Ching tables. Methods Our working tool is the ancient binary I Ching's resulting genetic code chromosomes defragged by vertical and by horizontal pairing, reverse engineered into non-binaries of 2D rotating 4×4×4 circles and 8×8 squares and into one 3D 100% symmetrical 16×4 tetrahedron coupled to a functional tetrahedron with apical signaling and central hydrophobicity (codon formula: 4[1(1)+1(3)+1(4)+4(2)]; 5:5, 6:6 in man) forming a stella octangula, and compared to Nirenberg's 16×4 codon table (1965) pairing the first two nucleotides of the 64 codons in axis y. Results One horizontal and one vertical defragging had the start Met at the center. Two, both horizontal and vertical pairings produced two pairs of 2×8×4 genetic code chromosomes naturally arranged (M and I), rearranged by semi-introversion of central purines or pyrimidines (M' and I') and by clustering hydrophobic amino acids; their quasi-identity was disrupted by amino acids with odd codons (Met and Tyr pairing to Ile and TGA Stop); in all instances, the 64-grid 90° rotational ability was restored. Conclusions We defragged three I Ching representations of the genetic code while emphasizing Nirenberg's historical finding. The synthetic genetic code chromosomes obtained reflect the protective strategy of enzymes with a similar function, having both humans and mammals a biased G-C dominance of three H-bonds in the third nucleotide of their most used codons per amino acid, as seen in one chromosome of the i, M and M' genetic codes, while a two H-bond A-T dominance was found in their complementary chromosome, as seen in invertebrates and plants. The reverse engineering of chromosome I' into 2D rotating circles and squares was undertaken, yielding a 100% symmetrical 3D geometry which was coupled to a previously obtained genetic code tetrahedron in order to differentiate the start methionine from the methionine that is acting as a codifying non-start codon. PMID:23431415

Castro-Chavez, Fernando

2012-01-01

471

A search for upstream pressure pulses associated with flux transfer events: An AMPTE/ISEE case study  

NASA Technical Reports Server (NTRS)

On September 19, 1984, the Active Magnetospheric Particle Tracers Explorers (AMPTE) United Kingdom Satellite (UKS) and Ion Release Module (IRM) and International Sun Earth Explorers (ISEE) 1 and 2 spacecraft passed outbound through the dayside magnetopause at about the same time. The AMPTE spacecraft pair crossed first and were in the near-subsolar magnetosheath for more than an hour. Meanwhile the ISEE pair, about 5 R(sub E) to the south, observed flux transfer event (FTE) signatures. We use the AMPTE UKS and IRM plasma and field observations of magnetosheath conditions directly upstream of the subsolar magnetopause to check whether pressure pulses are responsible for the FTE signatures seen at ISEE. Pulses in both the ion thermal pressure and the dynamic pressure are observed in the magnetosheath early on when IRM and UKS are close to the magnetopause, but not later. These large pulses appear to be related to reconnection going on at the magnetopause nearby. AMPTE magnetosheath data far from the magnetopause do not show a pressure pulse correlation with FTEs at ISEE. Moreover, the magnetic pressure and tension effects seen in the ISEE FTEs are much larger than any pressure effects seen in the magnetosheath. A superposed epoch analysis based on small-amplitude peaks in the AMPTE magnetosheath total static pressure (nkT + B(exp 2)/2 mu(sub 0)) hint at some boundary effects, less than 5 nT peak-to-peak variations in the ISEE 1 and 2 B(sub N) signature starting about 1 min after the pressure peak epoch. However, these variations are much smaller than the standard deviations of the B(sub N) field component. Thus the evidence from this case study suggests that upstream magnetosheath pressure pulses do not give rise to FTEs, but may produce very small amplitude signatures in the magnetic field at the magnetopause.

Elphic, R. C.; Baumjohann, W.; Cattell, C. A.; Luehr, H.; Smith, M. F.

1994-01-01

472

Role of p53 Codon 72 Arginine Allele in Cell Survival in vitro and in the Clinical Outcome of Patients with Advanced Breast Cancer  

Microsoft Academic Search

Background: The p53 codon 72 polymorphism, which results in either an arginine or proline residue, plays a different role in vitro and in vivo in cell survival and drug resistance. We verified, in vitro, the impact of the arginine allele on cell survival under normoxia and hypoxia, and investigated in vivo the role of p53 codon 72 arginine homozygosity in

I. Vannini; W. Zoli; A. Tesei; M. Rosetti; P. Sansone; G. Storci; A. Passardi; I. Massa; M. Ricci; D. Gusolfino; F. Fabbri; P. Ulivi; G. Brigliadori; D. Amadori; M. Bonafe

2008-01-01

473

First step toward a virus-derived vector for gene cloning and expression in spiroplasmas, organisms which read UGA as a tryptophan codon: synthesis of chloramphenicol acetyltransferase in Spiroplasma citri.  

PubMed Central

Spiroplasmas are wall-less procaryotes in which the UGA codon serves not as a stop signal but as a code for the amino acid tryptophan. Spiroplasma genes that contain UGA codons thus cannot be studied in the usual Escherichia coli cloning and expression systems. Although this problem can be circumvented by using UGA-suppressor strains of E. coli, spiroplasmas themselves would provide a more efficient cloning and expression host. We have now successfully employed the replicative form (RF) of a filamentous spiroplasma virus (SpV1) to clone and express the E. coli-derived chloramphenicol acetyltransferase (CAT) gene in Spiroplasma citri. The CAT gene was inserted in one of the four intergenic regions of the SpV1 RF and introduced into cells by electroporation. Both the RF and the virion DNA produced by the transfected cells contained the CAT gene sequences. Northern blot analysis, primer extension, and S1 mapping showed that transcription of the CAT gene started from a promoter located on the SpV1 RF and was terminated downstream of the CAT gene, still within the viral RF. Expression of the CAT gene was demonstrated by acetylation of chloramphenicol by cell-free extracts from the transfected spiroplasmas. Images PMID:1706702

Stamburski, C; Renaudin, J; Bove, J M

1991-01-01

474

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

PubMed

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

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

2014-05-01

475

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

PubMed

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

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

1996-11-01

476

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

NASA Astrophysics Data System (ADS)

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

Mantzaris, Alexander V.; Husmeier, Dirk

477

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

PubMed Central

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

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

2012-01-01

478

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

PubMed

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

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

2012-11-15

479

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

SciTech Connect

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

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

1993-09-01

480

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

PubMed

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

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

2011-01-01