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1

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

SciTech Connect

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

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

1991-04-01

2

Why has nature invented three stop codons of DNA and only one start codon?  

PubMed

We examine the standard genetic code with three stop codons. Assuming that the synchronization period of length 3 in DNA or RNA is violated during the transcription or translation processes, the probability of reading a frameshifted stop codon is higher than if the code would have only one stop codon. Consequently, the synthesis of RNA or proteins will soon terminate. In this way, cells do not produce undesirable proteins and essentially save energy. This hypothesis is tested on the AT-rich Drosophila genome, where the detection of frameshifted stop codons is even higher than the theoretical value. Using the binomial theorem, we establish the probability of reading a frameshifted stop codon within n steps. Since the genetic code is largely redundant, there is still space for some hidden secondary functions of this code. In particular, because stop codons do not contain cytosine, random C ? U and C ? T mutations in the third position of codons increase the number of hidden frameshifted stops and simultaneously the same amino acids are coded. This evolutionary advantage is demonstrated on the genomes of several simple species, e.g. Escherichia coli. PMID:22483666

K?ížek, Michal; K?ížek, Pavel

2012-07-01

3

High-level tetracycline resistance mediated by efflux pumps Tet(A) and Tet(A)-1 with two start codons.  

PubMed

Efflux is the most common mechanism of tetracycline resistance. Class A tetracycline efflux pumps, which often have high prevalence in Enterobacteriaceae, are encoded by tet(A) and tet(A)-1 genes. These genes have two potential start codons, GTG and ATG, located upstream of the genes. The purpose of this study was to determine the start codon(s) of the class A tetracycline resistance (tet) determinants tet(A) and tet(A)-1, and the tetracycline resistance level they mediated. Conjugation, transformation and cloning experiments were performed and the genetic environment of tet(A)-1 was analysed. The start codons in class A tet determinants were investigated by site-directed mutagenesis of ATG and GTG, the putative translation initiation codons. High-level tetracycline resistance was transferred from the clinical strain of Klebsiella pneumoniae 10-148 containing tet(A)-1 plasmid pHS27 to Escherichia coli J53 by conjugation. The transformants harbouring recombinant plasmids that carried tet(A) or tet(A)-1 exhibited tetracycline MICs of 256-512 µg ml(-1), with or without tetR(A). Once the ATG was mutated to a non-start codon, the tetracycline MICs were not changed, while the tetracycline MICs decreased from 512 to 64 µg ml(-1) following GTG mutation, and to ?4 µg ml(-1) following mutation of both GTG and ATG. It was presumed that class A tet determinants had two start codons, which are the primary start codon GTG and secondary start codon ATG. Accordingly, two putative promoters were predicted. In conclusion, class A tet determinants can confer high-level tetracycline resistance and have two start codons. PMID:25102906

Wang, Weixia; Guo, Qinglan; Xu, Xiaogang; Sheng, Zi-Ke; Ye, Xinyu; Wang, Minggui

2014-11-01

4

Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes  

PubMed Central

Summary: The correct translation of mRNA depends critically on the ability to initiate at the right AUG codon. For most mRNAs in eukaryotic cells, this is accomplished by the scanning mechanism, wherein the small (40S) ribosomal subunit attaches to the 5? end of the mRNA and then inspects the leader base by base for an AUG in a suitable context, using complementarity with the anticodon of methionyl initiator tRNA (Met-tRNAiMet) as the key means of identifying AUG. Over the past decade, a combination of yeast genetics, biochemical analysis in reconstituted systems, and structural biology has enabled great progress in deciphering the mechanism of ribosomal scanning. A robust molecular model now exists, describing the roles of initiation factors, notably eukaryotic initiation factor 1 (eIF1) and eIF1A, in stabilizing an “open” conformation of the 40S subunit with Met-tRNAiMet bound in a low-affinity state conducive to scanning and in triggering rearrangement into a “closed” conformation incompatible with scanning, which features Met-tRNAiMet more tightly bound to the “P” site and base paired with AUG. It has also emerged that multiple DEAD-box RNA helicases participate in producing a single-stranded “landing pad” for the 40S subunit and in removing the secondary structure to enable the mRNA to traverse the 40S mRNA-binding channel in the single-stranded form for base-by-base inspection in the P site. PMID:21885680

Hinnebusch, Alan G.

2011-01-01

5

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

PubMed Central

Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous disorder associated with bone fragility and susceptibility to fractures after minimal trauma. OI type V has an autosomal-dominant pattern of inheritance and is not caused by mutations in the type I collagen genes COL1A1 and COL1A2. The most remarkable and pathognomonic feature, observed in ?65% of affected individuals, is a predisposition to develop hyperplastic callus after fractures or surgical interventions. To identify the molecular cause of OI type V, we performed whole-exome sequencing in a female with OI type V and her unaffected parents and searched for de novo mutations. We found a heterozygous de novo mutation in the 5?-untranslated region of IFITM5 (the gene encoding Interferon induced transmembrane protein 5), 14 bp upstream of the annotated translation initiation codon (c.?14C>T). Subsequently, we identified an identical heterozygous de novo mutation in a second individual with OI type V by Sanger sequencing, thereby confirming that this is the causal mutation for the phenotype. IFITM5 is a protein that is highly enriched in osteoblasts and has a putative function in bone formation and osteoblast maturation. The mutation c.?14C>T introduces an upstream start codon that is in frame with the reference open-reading frame of IFITM5 and is embedded into a stronger Kozak consensus sequence for translation initiation than the annotated start codon. In vitro, eukaryotic cells were able to recognize this start codon, and they used it instead of the reference translation initiation signal. This suggests that five amino acids (Met-Ala-Leu-Glu-Pro) are added to the N terminus and alter IFITM5 function in individuals with the mutation. PMID:22863195

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

2012-01-01

6

Structural Changes Enable Start Codon Recognition by the Eukaryotic Translation Initiation Complex  

PubMed Central

Summary During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit. Here, we present a cryoEM reconstruction of a yeast preinitiation complex at 4.0 Å resolution with initiator tRNA in the PIN state, prior to eIF1 release. The structure reveals stabilization of the codon-anticodon duplex by the N-terminal tail of eIF1A, changes in the structure of eIF1 likely instrumental in its subsequent release, and changes in the conformation of eIF2. The mRNA traverses the entire mRNA cleft and makes connections to the regulatory domain of eIF2?, eIF1A, and ribosomal elements that allow recognition of context nucleotides surrounding the AUG codon.

Hussain, Tanweer; Llácer, Jose L.; Fernández, Israel S.; Munoz, Antonio; Martin-Marcos, Pilar; Savva, Christos G.; Lorsch, Jon R.; Hinnebusch, Alan G.; Ramakrishnan, V.

2014-01-01

7

Mutations in Caenorhabditis elegans eIF2? Permit Translation Initiation From Non-AUG Start Codons  

PubMed Central

Recognition of the AUG start codon on mRNAs during translation initiation in eukaryotes occurs in a preinitiation complex that includes small ribosomal subunits and multiple translation initiation factors. The complexity of this process and the lack of appropriate tools have prevented its genetic study in multicellular organisms. Here we describe a genetic system in the nematode Caenorhabditis elegans to study how the AUG start codon is selected. We have generated a sensitive reporter assay that allows for the isolation of mutants with reduced fidelity to recognize the AUG start codon. Two mutants were identified to have dominant missense mutations in iftb-1, which encodes the ?-subunit of eIF2 (eIF2?). Both mutations occur in a conserved region located outside of the C2–C2 zinc finger domain where yeast SUI3 mutations are localized in Saccharomyces cerevisiae eIF2?. C. elegans iftb-1, as well as mutant eIF2?s carrying the equivalent SUI3 mutations, are able to initiate translation at non-AUG codons that retain two potential base-pairing interactions with the anticodon of the initiator methionyl tRNA. These analyses further support the critical role of eIF2? in start codon selection, and two functional domains within eIF2? are likely involved, one defined by our C. elegans mutants and the other by the yeast SUI3 mutants. PMID:20215469

Zhang , Yinhua; Maduzia , Lisa L.

2010-01-01

8

Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning  

PubMed Central

SUMMARY Translation of Hepatitis C viral proteins requires an internal ribosome entry site (IRES) located in the 5? untranslated region of the viral mRNA. The core domain of the Hepatitis C virus (HCV) IRES contains a four-way helical junction that is integrated within a predicted pseudoknot. This domain is required for positioning the mRNA start codon correctly on the 40S ribosomal subunit during translation initiation. Here we present the crystal structure of this RNA, revealing a complex double-pseudoknot fold that establishes the alignment of two helical elements on either side of the four-helix junction. The conformation of this core domain constrains the open reading frame’s orientation for positioning on the 40S ribosomal subunit. This structure, representing the last major domain of HCV-like IRESs to be determined at near-atomic resolution, provides the basis for a comprehensive cryo-electron microscopy-guided model of the intact HCV IRES and its interaction with 40S ribosomal subunits. PMID:22000514

Berry, Katherine E.; Waghray, Shruti; Mortimer, Stefanie A.; Bai, Yun; Doudna, Jennifer A.

2011-01-01

9

Association of vitamin D receptor gene start codon (Fok1) polymorphism with high myopia  

PubMed Central

Background: High myopia caused primarily due to abnormal emmetropization and excessive axial ocular elongation is associated with sight-threatening ocular pathology. Muscular dysfunction of ocular ciliary muscles due to altered intracellular calcium levels can result in defective mechanotransduction of the eye and retinal defocus. The vitamin D3 receptor (VDR; a intracellular hormone receptor) is known to mediate calcium homeostasis, influencing the development of myopia. Materials and Methods: In the present study, a total of 206 high myopia, 98 low myopia and 250 control samples were analyzed for VDR gene Fok1 (exon 2 start codon) polymorphism using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Results: High myopia patients revealed decrease in the frequency of ff homozygotes (8.3%) as compared to control group (14.0%), with a corresponding increase in frequency of FF homozygotes (68.9% in high myopia vs. 62.8% in controls). The frequency of f allele carriers (Ff and ff) was increased in females of high myopia (35.6%) and low myopia cases (45.4%). Elevated frequency of f allele was found only in early age at onset cases of high myopia (0.227) and later age at onset (10–20 years) cases of low myopia (0.273) as well as in low myopia cases with parental consanguinity (0.458) (P 0.035; ?2 = 6.692*). Conclusion: The results suggest that VDR gene might not be playing a direct role in the development of myopia, but might contribute indirectly to the risk conferred by mechanical stress factors or growth/development related factors through its role in calcium homeostasis and regulation of ciliary muscle function. PMID:21897619

Annamaneni, Sandhya; Bindu, Chintala Hema; Reddy, Kasu Prasad; Vishnupriya, Satti

2011-01-01

10

A Conformational Change in the Eukaryotic Translation Preinitiation Complex and Release of eIF1 Signal Recognition of the Start Codon  

Microsoft Academic Search

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

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

2005-01-01

11

Secret Codon  

NSDL National Science Digital Library

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

Yu, Julie

2008-01-01

12

Dissociation of eIF1 from the 40S ribosomal subunit is a key step in start codon selection in vivo  

Microsoft Academic Search

Selection of the AUG start codon is a key step in translation initiation requiring hydrolysis of GTP in the eIF2•GTPMet-tRNAi Met ternary complex (TC) and subsequent Pi release from eIF2•GDPPi. It is thought that eIF1 prevents recognition of non-AUGs by promoting scanning and blocking Pi release at non-AUG codons. We show that Suimutations in Saccharomyces cerevisiae eIF1, which increase initiation

Yuen-Nei Cheung; David Maag; Sarah F. Mitchell; Christie A. Fekete; Mikkel A. Algire; Julie E. Takacs; Nikolay Shirokikh; Tatyana Pestova; Jon R. Lorsch; Alan G. Hinnebusch

2007-01-01

13

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

14

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

PubMed

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

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

2014-08-01

15

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

PubMed

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

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

2013-10-15

16

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

PubMed Central

Furvina®, also denominated G1 (MW 297), is a synthetic nitrovinylfuran [2-bromo-5-(2-bromo-2-nitrovinyl)-furan] antibiotic with a broad antimicrobial spectrum. An ointment (Dermofural®) containing G1 as the only active principle is currently marketed in Cuba and successfully used to treat dermatological infections. Here we describe the molecular target and mechanism of action of G1 in bacteria and demonstrate that in vivo G1 preferentially inhibits protein synthesis over RNA, DNA and cell wall synthesis. Furthermore, we demonstrate that G1 targets the small ribosomal subunit, binds at or near the P-decoding site and inhibits its function interfering with the ribosomal binding of fMet-tRNA during 30S initiation complex (IC) formation ultimately inhibiting translation. Notably, this G1 inhibition displays a bias for the nature (purine vs. pyrimidine) of the 3?-base of the codon, occurring efficiently only when the mRNA directing 30S IC formation and translation contains the canonical AUG initiation triplet or the rarely found AUA triplet, but hardly occurs when the mRNA start codon is either one of the non-canonical triplets AUU or AUC. This codon discrimination by G1 is reminiscent, though of opposite type of that displayed by IF3 in its fidelity function, and remarkably does not occur in the absence of this factor. PMID:22941660

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

2012-01-01

17

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.

18

A mutation in the start codon of ?-crystallin D leads to nuclear cataracts in the Dahl SS/Jr-Ctr strain.  

PubMed

Cataracts are a major cause of blindness. The most common forms of cataracts are age- and UV-related and develop mostly in the elderly, while congenital cataracts appear at birth or in early childhood. The Dahl salt-sensitive (SS/Jr) rat is an extensively used model of salt-sensitive hypertension that exhibits concomitant renal disease. In the mid-1980s, cataracts appeared in a few animals in the Dahl S colony, presumably the result of a spontaneous mutation. The mutation was fixed and bred to establish the SS/Jr-Ctr substrain. The SS/Jr-Ctr substrain has been used exclusively by a single investigator to study the role of steroids and hypertension. Using a classical positional cloning approach, we localized the cataract gene with high resolution to a less than 1-Mbp region on chromosome 9 using an F1(SS/Jr-Ctr × SHR) × SHR backcross population. The 1-Mbp region contained only 13 genes, including 4 genes from the ?-crystallins (Cryg) gene family, which are known to play a role in cataract formation. All of the ?-crystallins were sequenced and a novel point mutation in the start codon (ATG ? GTG) of the Crygd gene was identified. This led to the complete absence of the CRYGD protein in the eyes of the SS/Jr-Ctr strain. In summary, the identification of the genetic cause in this novel cataract model may provide an opportunity to better understand the development of cataracts, particularly in the context of hypertension. PMID:23404175

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

2013-04-01

19

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

PubMed

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

Mulpuri, Sujatha; Muddanuru, Tarakeswari; Francis, George

2013-06-01

20

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

PubMed Central

Cataracts are a major cause of blindness. The most common forms of cataracts are age and UV related and develops mostly in the elderly, while congenital cataracts appear at birth or in early childhood. The Dahl salt-sensitive (SS/Jr) rat is an extensively used model of salt-sensitive hypertension that exhibits concomitant renal disease. In the mid 1980’s, cataracts appeared in a few animals in the Dahl S colony, presumably the result of a spontaneous mutation. The mutation was fixed and bred to establish the SS/Jr-Ctr substrain. The SS/Jr-Ctr substrain has been exclusively used by a single investigator to study the role of steroids and hypertension. Using a classical positional cloning approach, we localized the cataract gene with high-resolution to a less than 1 Mbp region on chromosome 9 using an F1 (SS/Jr-Ctr X SHR) X SHR backcross population. The 1 Mbp region contained only 13 genes, including 4 genes from the ?-crystallins (Cryg) gene family which are known to play a role in cataract formation. All of the ?-crystallins were sequenced and a novel point mutation in the start codon (ATG ? GTG) of the Crygd gene was identified which led to the complete absence of CRYGD protein in the eyes of the SS/Jr-Ctr strain. In summary, the identification of the genetic cause in this novel cataract model may provide an opportunity to better understand the development of cataracts, particularly in the context of hypertension. PMID:23404175

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

2013-01-01

21

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

22

Quantifying Position-Dependent Codon Usage Bias  

PubMed Central

Although the mapping of codon to amino acid is conserved across nearly all species, the frequency at which synonymous codons are used varies both between organisms and between genes from the same organism. This variation affects diverse cellular processes including protein expression, regulation, and folding. Here, we mathematically model an additional layer of complexity and show that individual codon usage biases follow a position-dependent exponential decay model with unique parameter fits for each codon. We use this methodology to perform an in-depth analysis on codon usage bias in the model organism Escherichia coli. Our methodology shows that lowly and highly expressed genes are more similar in their codon usage patterns in the 5?-gene regions, but that these preferences diverge at distal sites resulting in greater positional dependency (pD, which we mathematically define later) for highly expressed genes. We show that position-dependent codon usage bias is partially explained by the structural requirements of mRNAs that results in increased usage of A/T rich codons shortly after the gene start. However, we also show that the pD of 4- and 6-fold degenerate codons is partially related to the gene copy number of cognate-tRNAs supporting existing hypotheses that posit benefits to a region of slow translation in the beginning of coding sequences. Lastly, we demonstrate that viewing codon usage bias through a position-dependent framework has practical utility by improving accuracy of gene expression prediction when incorporating positional dependencies into the Codon Adaptation Index model. PMID:24710515

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

2014-01-01

23

Upstream Processing  

NSDL National Science Digital Library

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

2009-09-24

24

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

ERIC Educational Resources Information Center

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

Szeberenyi, Jozsef

2009-01-01

25

Conserved upstream open reading frames in higher plants  

PubMed Central

Background Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants. Results We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs. Conclusion This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important. PMID:18667093

Tran, Michael K; Schultz, Carolyn J; Baumann, Ute

2008-01-01

26

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

27

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

PubMed Central

Background Codon usage analysis has been a classical topic for decades and has significances for studies of evolution, mRNA translation, and new gene discovery, etc. While the codon usage varies among different members of the plant kingdom, indicating the necessity for species-specific study, this work has mostly been limited to model organisms. Recently, the development of deep sequencing, especial RNA-Seq, has made it possible to carry out studies in non-model species. Result RNA-Seq data of Chinese bayberry was analyzed to investigate the bias of codon usage and codon pairs. High frequency codons (AGG, GCU, AAG and GAU), as well as low frequency ones (NCG and NUA codons) were identified, and 397 high frequency codon pairs were observed. Meanwhile, 26 preferred and 141 avoided neighboring codon pairs were also identified, which showed more significant bias than the same pairs with one or more intervening codons. Codon patterns were also analyzed at the plant kingdom, organism and gene levels. Changes during plant evolution were evident using RSCU (relative synonymous codon usage), which was even more significant than GC3s (GC content of 3rd synonymous codons). Nine GO categories were differentially and independently influenced by CAI (codon adaptation index) or GC3s, especially in 'Molecular function’ category. Within a gene, the average CAI increased from 0.720 to 0.785 in the first 50 codons, and then more slowly thereafter. Furthermore, the preferred as well as avoided codons at the position just following the start codon AUG were identified and discussed in relation to the key positions in Kozak sequences. Conclusion A comprehensive codon usage Table and number of high-frequency codon pairs were established. Bias in codon usage as well as in neighboring codon pairs was observed, and the significance of this in avoiding DNA mutation, increasing protein production and regulating protein synthesis rate was proposed. Codon usage patterns at three levels were revealed and the significance in plant evolution analysis, gene function classification, and protein translation start site predication were discussed. This work promotes the study of codon biology, and provides some reference for analysis and comprehensive application of RNA-Seq data from other non-model species. PMID:24160180

2013-01-01

28

Codon Usage Domains over Bacterial  

Microsoft Academic Search

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

Antoine Danchin; Mudassar Iqbal; Matteo Marsili; Massimo Vergassola

29

TTG serves as an initiation codon for the ribosomal protein MvaS7 from the archaeon Methanococcus vannielii.  

PubMed

The ribosomal protein MvaS7 from the methanogenic archaeon Methanococcus vannielii is a protein of 188 amino acids, i.e., it is 42 amino acids longer than previously suggested. The triplet TTG serves as a start codon. The methanogenic translation initiation region that includes the rare TTG start codon is recognized in Escherichia coli. PMID:7592355

Golderer, G; Dlaska, M; Gröbner, P; Piendl, W

1995-10-01

30

Divergence in codon usage of Lactobacillus species.  

PubMed Central

We have analyzed codon usage patterns of 70 sequenced genes from different Lactobacillus species. Codon usage in lactobacilli is highly biased. Both inter-species and intra-species heterogeneity of codon usage bias was observed. Codon usage in L. acidophilus is similar to that in L. helveticus, but dissimilar to that in L. bulgaricus, L. casei, L. pentosus and L. plantarum. Codon usage in the latter three organisms is not significantly different, but is different from that in L. bulgaricus. Inter-species differences in codon usage can, at least in part, be explained by differences in mutational drift. L. bulgaricus shows GC drift, whereas all other species show AT drift. L. acidophilus and L. helveticus rarely use NNG in family-box (a set of synonymous) codons, in contrast to all other species. This result may be explained by assuming that L. acidophilus and L. helveticus, but not other species examined, use a single tRNA species for translation of family-box codons. Differences in expression level of genes are positively correlated with codon usage bias. Highly expressed genes show highly biased codon usage, whereas weakly expressed genes show much less biased codon usage. Codon usage patterns at the 5'-end of Lactobacillus genes is not significantly different from that of entire genes. The GC content of codons 2-6 is significantly reduced compared with that of the remainder of the gene. The possible implications of a reduced GC content for the control of translation efficiency are discussed. PMID:8152923

Pouwels, P H; Leunissen, J A

1994-01-01

31

The three dominant female-sterile mutations of the Drosophila ovo gene are point mutations that create new translation-initiator AUG codons.  

PubMed

The Drosophila ovo gene, which encodes a putative transcription factor (Ovo) with TFIIIA-like zinc fingers, is required for female germline survival and proper oogenesis. Three dominant female-sterile ovoD mutations cause ovarian abnormalities that define an allelic series, with ovoD1 displaying the stronger phenotype and ovoD3 the weaker. We report here that all three ovoD mutations are point mutations that create new in-frame methionine codons in the 5' part of ovo. There are two types of overlapping ovo transcription units, ovo alpha and ovo beta. By using various ovo-lacZ reporter genes, we determined that the long Ovo isoforms starting at methionine M1, present in transcripts ovo alpha, are expressed at low levels only in mature oocytes. Short Ovo isoforms are translated from methionine M373, the first in-frame start codon present in transcript ovo beta, and correspond to the activity defined by recessive loss of function ovo mutations. The new AUGs created in ovoD mutations all are located upstream of the M373 initiation site. Our results support the hypothesis that they can substitute for M373 as translation starts and initiate the synthesis of Ovo proteins that have extra amino acids at their N termini. We propose that premature expression of long Ovo protein isoforms occurs in ovoD mutants and interferes with wild-type Ovo function in controlling female germline differentiation. PMID:9012532

Mével-Ninio, M; Fouilloux, E; Guénal, I; Vincent, A

1996-12-01

32

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

33

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

PubMed Central

To understand the diversity of transcripts in yeast (Saccharomyces cerevisiae) we analyzed the transcriptional landscapes for cells grown under 18 different environmental conditions. Each sample was analyzed using RNA-sequencing, and a total of 670,446,084 uniquely mapped reads and 377,263 poly-adenylated end tags were produced. Consistent with previous studies, we find that the majority of yeast genes are expressed under one or more different conditions. By directly comparing the 5? and 3? ends of the transcribed regions, we find extensive differences in transcript ends across many conditions, especially those of stationary phase, growth in grape juice, and salt stimulation, suggesting differential choice of transcription start and stop sites is pervasive in yeast. Relative to the exponential growth condition (i.e., YPAD), transcripts differing at the 5? ends and 3? ends are predicted to differ in their annotated start codon in 21 genes and their annotated stop codon in 63 genes. Many (431) upstream open reading frames (uORFs) are found in alternate 5? ends and are significantly enriched in transcripts produced during the salt response. Mutational analysis of five genes with uORFs revealed that two sets of uORFs increase the expression of a reporter construct, indicating a role in activation which had not been reported previously, whereas two other uORFs decreased expression. In addition, RNA binding protein motifs are statistically enriched for alternate ends under many conditions. Overall, these results demonstrate enormous diversity of transcript ends, and that this heterogeneity is regulated under different environmental conditions. Moreover, transcript end diversity has important biological implications for the regulation of gene expression. In addition, our data also serve as a valuable resource for the scientific community. PMID:23390610

Waern, Karl; Snyder, Michael

2013-01-01

34

Upstream waves at Mars  

NASA Technical Reports Server (NTRS)

Weak, about 0.15 nT, narrow band emissions at the proton gyro frequency are observed by the Phobos magnetometer MAGMA, upstream from the bow shock of Mars. These waves are left-hand elliptically polarized. They may be associated with the pick up of protons from the Martian hydrogen exosphere. Strong turbulence, similar to that observed at the terrestrial bow shock, is found on occasion in the upstream region when the IMF connects to the bow shock. On two occasions this turbulence occurred when the spacecraft crossed the orbit of Phobos. This coincidence raises the possibility that material in the orbits of Phobos interacts with the solar wind in such a way to either affect the direction of the IMF or to cause instabilities in the solar wind plasma. However, since on a third occasion these waves did not occur, these waves may be shock associated rather than Phobos associated.

Russell, C. T.; Luhmann, J. G.; Schwingenschuh, K.; Riedler, W.; Eroshenko, E.

1992-01-01

35

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

PubMed Central

In eukaryotes, the polypeptide release factor 1 (eRF1) is involved in translation termination at all three stop codons. However, the mechanism for decoding stop codons remains unknown. A direct interaction of eRF1 with the stop codons has been postulated. Recent studies focus on eRF1 from ciliates in which some stop codons are reassigned to sense codons. Using an in vitro assay based on mammalian ribosomes, we show that eRF1 from the ciliate Euplotes aediculatus responds to UAA and UAG as stop codons and lacks the capacity to decipher the UGA codon, which encodes cysteine in this organism. This result strongly suggests that in ciliates with variant genetic codes eRF1 does not recognize the reassigned codons. Recent hypotheses describing stop codon discrimination by eRF1 are not fully consistent with the set of eRF1 sequences available so far and require direct experimental testing. PMID:11463747

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

2001-01-01

36

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

37

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

PubMed Central

The analysis of DNA composition and codon usage reveals many factors that influence the evolution of genes and genomes. In this chapter, we show how to use CodonExplorer, a web tool and interactive database that contains millions of genes, to better understand the principles governing evolution at the single gene and whole-genome level. We present principles and practical procedures for using analyses of GC content and codon usage frequency to identify highly expressed or horizontally transferred genes and to study the relative contribution of different types of mutation to gene and genome composition. CodonExplorer’s combination of a user-friendly web interface and a comprehensive genomic database makes these diverse analyses fast and straightforward to perform. CodonExplorer is thus a powerful tool that facilitates and automates a wide range of compositional analyses. PMID:19378146

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

2010-01-01

38

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

PubMed Central

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

Kliman, Richard M.

2014-01-01

39

The Effects of Codon Context on In Vivo Translation Speed  

PubMed Central

We developed a bacterial genetic system based on translation of the his operon leader peptide gene to determine the relative speed at which the ribosome reads single or multiple codons in vivo. Low frequency effects of so-called “silent” codon changes and codon neighbor (context) effects could be measured using this assay. An advantage of this system is that translation speed is unaffected by the primary sequence of the His leader peptide. We show that the apparent speed at which ribosomes translate synonymous codons can vary substantially even for synonymous codons read by the same tRNA species. Assaying translation through codon pairs for the 5?- and 3?- side positioning of the 64 codons relative to a specific codon revealed that the codon-pair orientation significantly affected in vivo translation speed. Codon pairs with rare arginine codons and successive proline codons were among the slowest codon pairs translated in vivo. This system allowed us to determine the effects of different factors on in vivo translation speed including Shine-Dalgarno sequence, rate of dipeptide bond formation, codon context, and charged tRNA levels. PMID:24901308

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

2014-01-01

40

Codon Usage Domains over Bacterial Chromosomes  

E-print Network

to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One between bias and tRNA abundance was early remarked both in Escherichia coli and Saccharomyces cerevisiae in ribosomal proteins and some additional genes, highly expressed under exponential growth conditions [5

Kent, University of

41

Downstream Labeling and Upstream Competition  

Microsoft Academic Search

Abstract This paper,analyses the impact,of labeling in a context where,the products,come from a supply chain. We consider a case where there is an information,problem,about product quality in the downstream part of the chain, but not in the upstream part. We show that the implementation,of a label to solve this information,problem,affects competition in the upstream part of the chain. In particular,

Olivier BONROY; Stéphane LEMARIÉ; INRA SFER CIRAD

42

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

43

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

44

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

45

Selection on codon bias in yeast: a transcriptional hypothesis  

PubMed Central

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

Trotta, Edoardo

2013-01-01

46

Causes and Implications of Codon Usage Bias in RNA Viruses  

PubMed Central

Choice of synonymous codons depends on nucleotide/dinucleotide composition of the genome (termed mutational pressure) and relative abundance of tRNAs in a cell (translational pressure). Mutational pressure is commonly simplified to genomic GC content; however mononucleotide and dinucleotide frequencies in different genomes or mRNAs may vary significantly, especially in RNA viruses. A series of in silico shuffling algorithms were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses. Total GC content was a poor descriptor of viral genome composition and causes of codon usage bias. Genomic nucleotide content was the single most important factor of synonymous codon usage. Moreover, the choice between compatible amino acids (e.g., leucine and isoleucine) was strongly affected by genomic nucleotide composition. Dinucleotide composition at codon positions 2-3 had additional effect on codon usage. Together with mononucleotide composition bias, it could explain almost the entire codon usage bias in RNA viruses. On the other hand, strong dinucleotide content bias at codon position 3-1 found in some viruses had very little effect on codon usage. A hypothetical innate immunity sensor for CpG in RNA could partially explain the codon usage bias, but due to dependence of virus translation upon biased host translation machinery, experimental studies are required to further explore the source of dinucleotide bias in RNA viruses. PMID:23451064

Belalov, Ilya S.; Lukashev, Alexander N.

2013-01-01

47

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

48

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

49

Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance  

PubMed Central

Background Genetic mutation, selective pressure for translational efficiency and accuracy, level of gene expression, and protein function through natural selection are all believed to lead to codon usage bias (CUB). Therefore, informative measurement of CUB is of fundamental importance to making inferences regarding gene function and genome evolution. However, extant measures of CUB have not fully accounted for the quantitative effect of background nucleotide composition and have not statistically evaluated the significance of CUB in sequence analysis. Results Here we propose a novel measure--Codon Deviation Coefficient (CDC)--that provides an informative measurement of CUB and its statistical significance without requiring any prior knowledge. Unlike previous measures, CDC estimates CUB by accounting for background nucleotide compositions tailored to codon positions and adopts the bootstrapping to assess the statistical significance of CUB for any given sequence. We evaluate CDC by examining its effectiveness on simulated sequences and empirical data and show that CDC outperforms extant measures by achieving a more informative estimation of CUB and its statistical significance. Conclusions As validated by both simulated and empirical data, CDC provides a highly informative quantification of CUB and its statistical significance, useful for determining comparative magnitudes and patterns of biased codon usage for genes or genomes with diverse sequence compositions. PMID:22435713

2012-01-01

50

Complex Codon Usage Pattern and Compositional Features of Retroviruses  

PubMed Central

Retroviruses infect a wide range of organisms including humans. Among them, HIV-1, which causes AIDS, has now become a major threat for world health. Some of these viruses are also potential gene transfer vectors. In this study, the patterns of synonymous codon usage in retroviruses have been studied through multivariate statistical methods on ORFs sequences from the available 56 retroviruses. The principal determinant for evolution of the codon usage pattern in retroviruses seemed to be the compositional constraints, while selection for translation of the viral genes plays a secondary role. This was further supported by multivariate analysis on relative synonymous codon usage. Thus, it seems that mutational bias might have dominated role over translational selection in shaping the codon usage of retroviruses. Codon adaptation index was used to identify translationally optimal codons among genes from retroviruses. The comparative analysis of the preferred and optimal codons among different retroviral groups revealed that four codons GAA, AAA, AGA, and GGA were significantly more frequent in most of the retroviral genes inspite of some differences. Cluster analysis also revealed that phylogenetically related groups of retroviruses have probably evolved their codon usage in a concerted manner under the influence of their nucleotide composition. PMID:24288576

RoyChoudhury, Sourav; Mukherjee, Debaprasad

2013-01-01

51

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.  

PubMed Central

A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression. PMID:3547335

Sharp, P M; Li, W H

1987-01-01

52

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

PubMed Central

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

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

2009-01-01

53

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

54

Rapid divergence of codon usage patterns within the rice genome  

PubMed Central

Background Synonymous codon usage varies widely between genomes, and also between genes within genomes. Although there is now a large body of data on variations in codon usage, it is still not clear if the observed patterns reflect the effects of positive Darwinian selection acting at the level of translational efficiency or whether these patterns are due simply to the effects of mutational bias. In this study, we have included both intra-genomic and inter-genomic comparisons of codon usage. This allows us to distinguish more efficiently between the effects of nucleotide bias and translational selection. Results We show that there is an extreme degree of heterogeneity in codon usage patterns within the rice genome, and that this heterogeneity is highly correlated with differences in nucleotide content (particularly GC content) between the genes. In contrast to the situation observed within the rice genome, Arabidopsis genes show relatively little variation in both codon usage and nucleotide content. By exploiting a combination of intra-genomic and inter-genomic comparisons, we provide evidence that the differences in codon usage among the rice genes reflect a relatively rapid evolutionary increase in the GC content of some rice genes. We also noted that the degree of codon bias was negatively correlated with gene length. Conclusion Our results show that mutational bias can cause a dramatic evolutionary divergence in codon usage patterns within a period of approximately two hundred million years. The heterogeneity of codon usage patterns within the rice genome can be explained by a balance between genome-wide mutational biases and negative selection against these biased mutations. The strength of the negative selection is proportional to the length of the coding sequences. Our results indicate that the large variations in synonymous codon usage are not related to selection acting on the translational efficiency of synonymous codons. PMID:17288579

Wang, Huai-Chun; Hickey, Donal A

2007-01-01

55

Upstream open reading frames regulate the expression of the nuclear Wnt13 isoforms  

PubMed Central

Wnt proteins control cell survival and cell fate during development. Although Wnt expression is tightly regulated in a spatio-temporal manner, the mechanisms involved both at the transcriptional and translational levels are poorly defined. We have identified a downstream translation initiation codon, AUG(+74), in Wnt13B and Wnt13C mRNAs responsible for the expression of Wnt13 nuclear forms. In this report, we demonstrate that the expression of the nuclear Wnt13C form is translationaly regulated in response to stress and apoptosis. Though the 5’-leaders of both Wnt13C and Wnt13B mRNAs have an inhibitory effect on translation, they did not display an internal ribosome entry site activity as demonstrated by dicistronic reporter assays. However, mutations or deletions of the upstream AUG(?99) and AUG(+1) initiation codons abrogate these translation inhibitory effects, demonstrating that Wnt13C expression is controlled by upstream open reading frames. Since long 5’-untranslated region with short upstream open reading frames characterize other Wnt transcipts, our present data on the translational control of Wnt13 expression open the way to further studies on the translation control of Wnt expression as a modulator of their subcellular localization and activity. PMID:18155664

Tang, Tao; Rector, Kyle; Barnett, Corey D.; Mao, Catherine D.

2008-01-01

56

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

Microsoft Academic Search

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

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

1988-01-01

57

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

PubMed

RNA polymerase, purified from Methanococcus vannielii, was shown by exonuclease III footprinting to bind to a 49-base-pair (bp) region of DNA in the intergenic region upstream of mcrB. S1 nuclease protection experiments demonstrated that transcription initiation in vivo occurs within this region at 32 or 33 bp 5' to the ATG translation initiation codon of mcrB and 19 or 20 bp 3' to a TATA box. PMID:2832392

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

1988-04-01

58

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

SciTech Connect

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

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

1988-04-01

59

Readthrough strategies for stop codons in Duchenne muscular dystrophy  

Microsoft Academic Search

Duchenne muscular dystrophy is due to mutations of the dystrophin gene. These are large deletions or duplications in 80% of cases, while premature stop codons (nonsense point mutations) account for 7% of cases. This subgroup of patients may take advantage of the properties of the antibi- otic gentamicin to suppress stop codons (readthrough). The efficiency of the readthrough varies inversely

S. AURINO; V. N IGRO

60

Press Start  

NASA Astrophysics Data System (ADS)

This level sets the stage for the design philosophy called “Triadic Game Design” (TGD). This design philosophy can be summarized with the following sentence: it takes two to tango, but it takes three to design a meaningful game or a game with a purpose. Before the philosophy is further explained, this level will first delve into what is meant by a meaningful game or a game with a purpose. Many terms and definitions have seen the light and in this book I will specifically orient at digital games that aim to have an effect beyond the context of the game itself. Subsequently, a historical overview is given of the usage of games with a serious purpose which starts from the moment we human beings started to walk on our feet till our contemporary society. It turns out that we have been using games for all kinds of non-entertainment purposes for already quite a long time. With this introductory material in the back of our minds, I will explain the concept of TGD by means of a puzzle. After that, the protagonist of this book, the game Levee Patroller, is introduced. Based on the development of this game, the idea of TGD, which stresses to balance three different worlds, the worlds of Reality, Meaning, and Play, came into being. Interested? Then I suggest to quickly “press start!”

Harteveld, Casper

61

Ecological Adaptation in Bacteria: Speciation Driven by Codon Selection  

PubMed Central

In bacteria, physiological change may be effected by a single gene acquisition, producing ecological differentiation without genetic isolation. Natural selection acting on such differences can reduce the frequency of genotypes that arise from recombination at these loci. However, gene acquisition can only account for recombination interference in the fraction of the genome that is tightly linked to the integration site. To identify additional loci that contribute to adaptive differences, we examined orthologous genes in species of Enterobacteriaceae to identify significant differences in the degree of codon selection. Significance was assessed using the Adaptive Codon Enrichment metric, which accounts for the variation in codon usage bias that is expected to arise from mutation and drift; large differences in codon usage bias were identified in more genes than would be expected to arise from stochastic processes alone. Genes in the same operon showed parallel differences in codon usage bias, suggesting that changes in the overall levels of gene expression led to changes in the degree of adaptive codon usage. Most significant differences between orthologous operons were found among those involved with specific environmental adaptations, whereas "housekeeping" genes rarely showed significant changes. When considered together, the loci experiencing significant changes in codon selection outnumber potentially adaptive gene acquisition events. The identity of genes under strong codon selection seems to be influenced by the habitat from which the bacteria were isolated. We propose a two-stage model for how adaptation to different selective regimes can drive bacterial speciation. Initially, gene acquisitions catalyze rapid ecological differentiation, which modifies the utilization of genes, thereby changing the strength of codon selection on them. Alleles develop fitness variation by substitution, producing recombination interference at these loci in addition to those flanking acquired genes, allowing sequences to diverge across the entire genome and establishing genetic isolation (i.e., protection from frequent homologous recombination). PMID:22740635

Retchless, Adam C.; Lawrence, Jeffrey G.

2012-01-01

62

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

63

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

64

Properties and determinants of codon decoding time distributions  

PubMed Central

Background Codon decoding time is a fundamental property of mRNA translation believed to affect the abundance, function, and properties of proteins. Recently, a novel experimental technology--ribosome profiling--was developed to measure the density, and thus the speed, of ribosomes at codon resolution. Specifically, this method is based on next-generation sequencing, which theoretically can provide footprint counts that correspond to the probability of observing a ribosome in this position for each nucleotide in each transcript. Results In this study, we report for the first time various novel properties of the distribution of codon footprint counts in five organisms, based on large-scale analysis of ribosomal profiling data. We show that codons have distinctive footprint count distributions. These tend to be preserved along the inner part of the ORF, but differ at the 5' and 3' ends of the ORF, suggesting that the translation-elongation stage actually includes three biophysical sub-steps. In addition, we study various basic properties of the codon footprint count distributions and show that some of them correlate with the abundance of the tRNA molecule types recognizing them. Conclusions Our approach emphasizes the advantages of analyzing ribosome profiling and similar types of data via a comparative genomic codon-distribution-centric view. Thus, our methods can be used in future studies related to translation and even transcription elongation.

2014-01-01

65

Measure of synonymous codon usage diversity among genes in bacteria  

PubMed Central

Background In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synonymous codon usage among all genes within a genome. Results The application of Dmean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for Helicobacter pylori, but based on Dmean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity. Conclusion We recommend that Dmean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature. PMID:19480720

Suzuki, Haruo; Saito, Rintaro; Tomita, Masaru

2009-01-01

66

Mutations that convert the four leucine codons of the Salmonella typhimurium leu leader to four threonine codons.  

PubMed Central

In Salmonella typhimurium, expression of the leucine operon is regulated by a transcription attenuation mechanism. According to a current model of attenuation, elevated expression of this operon requires that a ribosome stall at one of four adjacent codons for leucine on a leader RNA. We used oligonucleotide-directed mutagenesis to convert the four leucine codons of the S. typhimurium leu leader to four threonine codons. Analysis of the resulting mutant operon showed that almost all regulation by leucine had been abolished. The mutant operon was, instead, partially derepressed by a limitation for charged threonine tRNA. These results provide direct evidence for the function for the four leucine codons postulated by the attenuator model. An unexpected observation made during these studies was that the wild-type leu operon was partially derepressed by starvation for threonine. PMID:3922957

Carter, P W; Weiss, D L; Weith, H L; Calvo, J M

1985-01-01

67

Regulation of ribonucleotide reductase M2 expression by the upstream AUGs  

PubMed Central

Ribonucleotide reductase catalyzes a rate-limiting reaction in DNA synthesis by converting ribonucleotides to deoxyribonucleotides. It consists of two subunits and the small one, M2 (or R2), plays an essential role in regulating the enzyme activity and its expression is finely controlled. Changes in the M2 level influence the dNTP pool and, thus, DNA synthesis and cell proliferation. M2 gene has two promoters which produce two major mRNAs with 5?-untranslated regions (5?-UTRs) of different lengths. In this study, we found that the M2 mRNAs with the short (63 nt) 5?-UTR can be translated with high efficiency whereas the mRNAs with the long (222 nt) one cannot. Examination of the long 5?-UTR revealed four upstream AUGs, which are in the same reading frame as the unique physiological translation initiation codon. Further analysis demonstrated that these upstream AUGs act as negative cis elements for initiation at the downstream translation initiation codon and their inhibitory effect on M2 translation is eIF4G dependent. Based on the findings of this study, we conclude that the expression of M2 is likely regulated by fine tuning the translation from the mRNA with a long 5?-UTR during viral infection and during the DNA replication phase of cell proliferation. PMID:15888728

Dong, Zizheng; Liu, Yang; Zhang, Jian-Ting

2005-01-01

68

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

Microsoft Academic Search

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

Fran Supek; Kristian Vlahovicek

2004-01-01

69

Codon usage bias, tRNA modifications and translational selection in bacteria  

Microsoft Academic Search

In this thesis, codon usage bias is studied in a large number of bacterial genomes. The codon frequency of each codon is measured as a fraction of the total number of codons for each amino acid, which can be used to calculate the potential selection strength in a genome according to the population genetics theory of selection, mutation and drift.

Wenqi Ran

2010-01-01

70

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

Microsoft Academic Search

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

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

2005-01-01

71

Codon Preference Optimization Increases Prokaryotic Cystatin C Expression  

PubMed Central

Gene expression is closely related to optimal vector-host system pairing in many prokaryotes. Redesign of the human cystatin C (cysC) gene using the preferred codons of the prokaryotic system may significantly increase cysC expression in Escherichia coli (E. coli). Specifically, cysC expression may be increased by removing unstable sequences and optimizing GC content. According to E. coli expression system codon preferences, the gene sequence was optimized while the amino acid sequence was maintained. The codon-optimized cysC (co-cysC) and wild-type cysC (wt-cysC) were expressed by cloning the genes into a pET-30a plasmid, thus transforming the recombinant plasmid into E. coli BL21. Before and after the optimization process, the prokaryotic expression vector and host bacteria were examined for protein expression and biological activation of CysC. The recombinant proteins in the lysate of the transformed bacteria were purified using Ni2+-NTA resin. Recombinant protein expression increased from 10% to 46% based on total protein expression after codon optimization. Recombinant CysC purity was above 95%. The significant increase in cysC expression in E. coli expression produced by codon optimization techniques may be applicable to commercial production systems. PMID:23093857

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

2012-01-01

72

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

73

Swimming Upstream: How to Reduce Homelessness in  

E-print Network

Swimming Upstream: How to Reduce Homelessness in Tempe's Emerging Urban Setting David V. Summers of the Tempe First United Methodist Church, provides vital support services to homeless and working poor people

Zhang, Junshan

74

Characteristics of synonymous codon usage bias in the beginning region of West Nile virus.  

PubMed

Adaptation in the overall codon usage pattern of West Nile virus (WNV) to that of two hosts was estimated based on the synonymous codon usage value (RSCU). Synonymous codon usage biases for the beginning coding sequence of this virus were also analyzed by calculating the usage fluctuation for each synonymous codon along the target region (the first 270 codon sites of the whole coding sequence of WNV). Adaptation of WNV to Anopheles gambiae regarding the overall codon usage revealed a mixture of synonymous codon usage patterns between this virus and its vector. Regarding the adaptation of WNV to its dead-end host and codon usage, although a mixture of overall codon usage patterns exists, the number of codons with reversed tendency codon usage is lower than that between the virus and its vector. In addition, some codons with low RSCU values for this virus are highly selected in the beginning translation region of WNV, while codons with low RSCU values in this region tend to pair with tRNAs present in low abundance in the host, suggesting that highly selected codons in a specific region in the beginning region of WNV are, to some degree, influenced by the corresponding low tRNA abundance of hosts to regulate the translation speed of the WNV polyprotein. PMID:25222233

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

2014-01-01

75

Insights & Perspectives Quadruplet codons: One small step for a  

E-print Network

for proteins An expanded genetic code could address fundamental questions about algorithmic information quadruplet codons, paving the way for studies on fundamental ques- tions about the origin of the genetic code to an infinitesimal fraction of the total volume, a full quadruplet genetic code would essentially double the infor

Chen, Irene

76

All-codon scanning identifies p53 cancer rescue mutations  

E-print Network

,2 , Linda V. Hall1 , Kirsty Salmon1 , G. Wesley Hatfield1,3,4 , Richard H. Lathrop1,2,5, * and Peter Kaiser6 of Microbiology and Molecular Genetics, 4 Department of Chemical Engineering and Materials Science, 5 Department with modified properties. We describe the fast and simple All- Codon Scanning (ACS) strategy that creates

Lathrop, Richard H.

77

The Starting Early Starting Smart Story.  

ERIC Educational Resources Information Center

Starting Early Starting Smart (SESS) is an early childhood public/private initiative designed to identify new, empirical knowledge about the effectiveness of integrating substance abuse prevention, addictions treatment, and mental health services with primary health care and childcare service settings (e.g., Head Start, day care, preschool) to…

Casey Family Programs, Seattle, WA.

78

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

Microsoft Academic Search

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

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

1985-01-01

79

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

Microsoft Academic Search

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

Xuhua Xia

80

Do universal codon-usage patterns minimize the effects of mutation and translation error?  

Microsoft Academic Search

BACKGROUND: Do species use codons that reduce the impact of errors in translation or replication? The genetic code is arranged in a way that minimizes errors, defined as the sum of the differences in amino-acid properties caused by single-base changes from each codon to each other codon. However, the extent to which organisms optimize the genetic messages written in this

Roberto Marquez; Sandra Smit; Rob Knight

2005-01-01

81

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 selection favors certain synony- mous codons which aid translation in Escherichia coli, yet codons not favored by translational selection persist. We use the frequency distributions of synonymous poly

Eyre-Walker, Adam

82

Genome-Wide Analysis of Codon Usage and Influencing Factors in Chikungunya Viruses  

PubMed Central

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

Tong, Yigang

2014-01-01

83

Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes  

Microsoft Academic Search

BACKGROUND: Codon usage bias has been widely reported to correlate with GC composition. However, the quantitative relationship between codon usage bias and GC composition across species has not been reported. RESULTS: Based on an informatics method (SCUO) we developed previously using Shannon informational theory and maximum entropy theory, we investigated the quantitative relationship between codon usage bias and GC composition.

Xiu-Feng Wan; Dong Xu; Andris Kleinhofs; Jizhong Zhou

2004-01-01

84

Downstream labeling and upstream price competition  

Microsoft Academic Search

This paper analyses the economic consequences of labeling in a setting with two vertically related markets. Labeling on the downstream market affects upstream price competition through two effects: a differentiation effect and a ranking effect. The magnitude of these two effects determines who in the supply chain will receive the benefits and who will bear the burden of labeling. For

Olivier Bonroy; Stéphane Lemarié

2012-01-01

85

Upstream urbanization exacerbates urban heat island effects  

Microsoft Academic Search

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.

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

2009-01-01

86

A TALE OF FOUR UPSTREAM TAILINGS DAMS  

Microsoft Academic Search

The evaluation and performance of four upstream-constructed tailings dams in South America are presented. All four dams were constructed beginning in the 1990's. The juxtaposition of the same design to four sites, each with unique site and operating conditions, led not surprisingly to four different outcomes. These outcomes ranged from outright failure, to construction of a toe buttress, slope flattening,

T. E. Martin; E. C. McRoberts; M. P. Davies

87

Housing Starts: May 1984.  

National Technical Information Service (NTIS)

This report presents statistics on new housing units started from 1964 to 1984. Statistics cover new privately owned housing units started in permit - issuing places, units authorized but not started in permit - issuing places, and manufacturers's shipmen...

1984-01-01

88

Starting Time Ending Time Starting Time  

E-print Network

Starting Time Ending Time Starting Time Name Of The Department/Unit Organizing The Event N How Would You Like Parking Arrangements Handled? Attendant Time (3 hour minimun): ) r e b m u N t n u-business hours. We may not be able to provide parking, depending on time of day and location. Consider public

Sjölander, Kimmen

89

Starting Time Ending Time Starting Time  

E-print Network

Starting Time Ending Time Starting Time Name Of The Department/Unit Organizing The Event N How Would You Like Parking Arrangements Handled? Attendant Time (3 hour minimun): Campus Department to schedule your event during non-business hours. We may not be able to provide parking, depending on time

Sjölander, Kimmen

90

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

91

Evolution of Advection Upstream Splitting Method Schemes  

NASA Technical Reports Server (NTRS)

This paper focuses on the evolution of advection upstream splitting method(AUSM) schemes. The main ingredients that have led to the development of modern computational fluid dynamics (CFD) methods have been reviewed, thus the ideas behind AUSM. First and foremost is the concept of upwinding. Second, the use of Riemann problem in constructing the numerical flux in the finite-volume setting. Third, the necessity of including all physical processes, as characterised by the linear (convection) and nonlinear (acoustic) fields. Fourth, the realisation of separating the flux into convection and pressure fluxes. The rest of this review briefly outlines the technical evolution of AUSM and more details can be found in the cited references. Keywords: Computational fluid dynamics methods, hyperbolic systems, advection upstream splitting method, conservation laws, upwinding, CFD

Liou, Meng-Sing

2010-01-01

92

Admissible upstream conditions for slender compressible vortices  

NASA Technical Reports Server (NTRS)

The influence of the compressibility on the flow in slender vortices is being studied. The dependence of the breakdown of the slender-vortex approximation on the upstream conditions is demonstrated for various Reynolds numbers and Mach numbers. Compatibility conditions, which have to be satisfied if the vortex is to remain slender, are discussed in detail. The general discussions are supplemented by several sample calculations.

Liu, C. H.; Krause, E.; Menne, S.

1986-01-01

93

Upstream reciprocity and the evolution of gratitude.  

PubMed

If someone is nice to you, you feel good and may be inclined to be nice to somebody else. This every day experience is borne out by experimental games: the recipients of an act of kindness are more likely to help in turn, even if the person who benefits from their generosity is somebody else. This behaviour, which has been called 'upstream reciprocity', appears to be a misdirected act of gratitude: you help somebody because somebody else has helped you. Does this make any sense from an evolutionary or a game theoretic perspective? In this paper, we show that upstream reciprocity alone does not lead to the evolution of cooperation, but it can evolve and increase the level of cooperation if it is linked to either direct or spatial reciprocity. We calculate the random walks of altruistic acts that are induced by upstream reciprocity. Our analysis shows that gratitude and other positive emotions, which increase the willingness to help others, can evolve in the competitive world of natural selection. PMID:17254983

Nowak, Martin A; Roch, Sébastien

2007-03-01

94

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

95

A Shift in the Third-Codon-Position Nucleotide Frequency in Alcohol Dehydrogenase Genes in the Genus Drosophila  

Microsoft Academic Search

Examination of the relative frequency of occurrence of alternative synonymous codons for any one amino acid (codon usage) for proteins within and among species suggests that codon usage pattern is a significant component of both genomic expression and expression of individual genes. This generalization implies a functional role of codon usage and that synonymous substitution rates may differ between lineages

William T. Starmer; David T. Sullivan

96

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

Microsoft Academic Search

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

Brian R. Morton

1993-01-01

97

Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance.  

PubMed

We present a comprehensive analysis of stop codon usage in bacteria by analyzing over eight million coding sequences of 4684 bacterial sequences. Using a newly developed program called "stop codon counter," the frequencies of the three classical stop codons TAA, TAG, and TGA were analyzed, and a publicly available stop codon database was built. Our analysis shows that with increasing genomic GC content the frequency of the TAA codon decreases and that of the TGA codon increases in a reciprocal manner. Interestingly, the release factor 1-specific codon TAG maintains a more or less uniform frequency (?20%) irrespective of the GC content. The low abundance of TAG is also valid with respect to expression level of the genes ending with different stop codons. In contrast, the highly expressed genes predominantly end with TAA, ensuring termination with either of the two release factors. Using three model bacteria with different stop codon usage (Escherichia coli, Mycobacterium smegmatis, and Bacillus subtilis), we show that the frequency of TAG and TGA codons correlates well with the relative steady state amount of mRNA and protein for release factors RF1 and RF2 during exponential growth. Furthermore, using available microarray data for gene expression, we show that in both fast growing and contrasting biofilm formation conditions, the relative level of RF1 is nicely correlated with the expression level of the genes ending with TAG. PMID:25217634

Korkmaz, Gürkan; Holm, Mikael; Wiens, Tobias; Sanyal, Suparna

2014-10-31

98

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

99

Genome-wide selection on codon usage at the population level in the fungal model organism Neurospora crassa.  

PubMed

Many organisms exhibit biased codon usage in their genome, including the fungal model organism Neurospora crassa. The preferential use of subset of synonymous codons (optimal codons) at the macroevolutionary level is believed to result from a history of selection to promote translational efficiency. At present, few data are available about selection on optimal codons at the microevolutionary scale, that is, at the population level. Herein, we conducted a large-scale assessment of codon mutations at biallelic sites, spanning more than 5,100 genes, in 2 distinct populations of N. crassa: the Caribbean and Louisiana populations. Based on analysis of the frequency spectra of synonymous codon mutations at biallelic sites, we found that derived (nonancestral) optimal codon mutations segregate at a higher frequency than derived nonoptimal codon mutations in each population; this is consistent with natural selection favoring optimal codons. We also report that optimal codon variants were less frequent in longer genes and that the fixation of optimal codons was reduced in rapidly evolving long genes/proteins, trends suggestive of genetic hitchhiking (Hill-Robertson) altering codon usage variation. Notably, nonsynonymous codon mutations segregated at a lower frequency than synonymous nonoptimal codon mutations (which impair translational efficiency) in each N. crassa population, suggesting that changes in protein composition are more detrimental to fitness than mutations altering translation. Overall, the present data demonstrate that selection, and partly genetic interference, shapes codon variation across the genome in N. crassa populations. PMID:22334579

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

2012-08-01

100

Translational effects of differential codon usage among intragenic domains of new genes in Drosophila.  

PubMed

Evolved codon usages often pose a technical challenge over the expressing of eukaryotic genes in microbial systems because of changed translational machinery. In the present study, we investigated the translational effects of intragenic differential codon usage on the expression of the new Drosophila gene, jingwei (jgw), a chimera derived from two unrelated parental genes: Ymp and Adh. We found that jgw possesses a strong intragenic differential usage of synonymous codons, i.e. the Adh-derived C-domain has a significantly higher codon bias than that of the Ymp-derived N-domain (P=0.0023 by t-test). Additional evolutionary analysis revealed the heterogeneous distribution of rare codons, implicating its role in gene regulation and protein translation. The in vitro expression of jgw further demonstrated that the heterogeneous distribution of rare codons has played a role in regulating gene expression, particularly, affecting the quality of protein translation. PMID:15833448

Zhang, Jianming; Long, Manyuan; Li, Liming

2005-05-01

101

Upstream waves at Mars: Phobos observations  

SciTech Connect

The region upstream from the Mars subsolar bow shock is surveyed for the presence of MHD wave phenomena using the high temporal resolution data from the MAGMA magnetometer. Strong turbulence is observed when the magnetic field is connected to the Mars bow shock in such a way as to allow diffuse ions to reach the spacecraft. On 2 occasions this turbulence occurred upon crossing the Phobos orbit. Also weak, {minus}0.15 nT, waves are observed at the proton gyro frequency. These waves are left-hand elliptically polarized and may be associated with the pick-up of protons from the Mars hydrogen exosphere.

Russell, C.T.; Luhmann, J.G. (Univ. of California, Los Angeles (USA)); Schwingenschuh, K.; Riedler, W. (Space Research Institute, Graz (Austria)); Yeroshenko, Ye. (IZMIRAN, Moscow (USSR))

1990-05-01

102

Manufacturing Technician-Upstream: John Condosta  

NSDL National Science Digital Library

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

2009-09-24

103

Upstream basin circulation of rotating, hydraulically controlled flows  

E-print Network

Upstream basin circulation of rotating, hydraulically controlled flows Adele Morrison Australian in the overturning motivates an improved understanding of the overflows and the associated upstream basin circulation-critical transitions [4]. A feature of hydraulically controlled flows is that the stratification in the basin upstream

Lebovitz, Norman

104

Lung cancer risk in relation to TP53 codon 47 and codon 72 polymorphism in Bangladeshi population.  

PubMed

The objective of this study was to determine whether p53 codon 47 and codon 72 polymorphisms are associated with increased risk of lung cancer in Bangladeshi population. We carried out a case-control study and examined the genotype distribution Pro47Ser and Arg72Pro single-nucleotide polymorphisms along with tobacco smoking in the predisposition of lung cancer by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) approach. The study included 106 lung cancer patients and 116 control subjects from Bangladesh. Lung cancer risk was estimated as odds ratio (OR) and 95 % confidence interval (CI) using conditional logistic regression models adjusting for age, sex, and smoking. No significant association was found between Pro47Ser SNP and lung cancer. The frequencies of p53 codon 72 polymorphisms (Arg/Arg, Arg/Pro, and Pro/Pro) in lung cancer were 25.5, 37.7, and 36.8 %, respectively; frequencies in the controls were 53.4, 30.2, and 16.4 %, respectively (p?codon 72 genotype distributions. When classified by smoking status, the effects of Arg72Pro polymorphism on lung cancer risk was only found to be significant (? (2) ?=?33.94, p?=?0.00000004) in case of heavy smokers (40 packs per year or more). We conclude that not Pro47Ser SNP but Arg72Pro SNP is involved in susceptibility to developing lung cancer, at least in Bangladeshi population. PMID:25034526

Mostaid, Md Shaki; Ahmed, Maizbha Uddin; Islam, Mohammad Safiqul; Bin Sayeed, Muhammad Shahdaat; Hasnat, Abul

2014-10-01

105

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

PubMed Central

Isoacceptors of Ala-, Arg-, Glu-, Gln-, Ile-, Leu-, Lys-, Ser-, Thr- and Val-tRNAs from wheat germ have been resolved by reverse phast chromatography. Codon recognition properties have been determined on isolated fractions of each of these aa-tRNAs and codon assignments have been made to a number of isoacceptors. Evolutionary changes which have occurred in patterns of codon recognition by isoacceptor aa-tRNAs in wheat germ and other organisms are discussed. PMID:251931

Hatfield, D; Rice, M

1978-01-01

106

Premature Stop Codon in MMP20 Causing Amelogenesis Imperfecta  

PubMed Central

Proteolytic enzymes are necessary for the hardening of dental enamel during development, and mutations in the kallikrein 4 (KLK4) and enamelysin (MMP20) genes cause autosomal recessive amelogenesis imperfecta (ARAI). So far, only one KLK4 and two MMP20 mutations have been reported. We have identified an ARAI-causing point mutation (c.l02G>A, g.l02G>A, and p.W34X) in exon 1 of MMP20 in a proband with autosomal recessive hypoplastic-hypomaturation amelogenesis imperfecta. The G to A transition changes the tryptophan (W) codon (TGG) at amino acid position 34 into a translation termination (X) codon (TGA). No disease-causing sequence variations were detected in KLK4. The affected enamel is thin, with mild spacing in the anterior dentition. The enamel layer is hypomineralized, does not contrast with dentin on radiographs, and tends to chip away from the underlying dentin. An intrinsic yellowish pigmentation is evident even during eruption. The phenotype supports current ideas concerning the function of enamelysin. PMID:18096894

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

2009-01-01

107

Nevada Head Start, 2002.  

ERIC Educational Resources Information Center

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

Biagi, Kathy

108

The Head Start Debates  

ERIC Educational Resources Information Center

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

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

2004-01-01

109

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

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

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

110

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

111

Ambushing the ambush hypothesis: predicting and evaluating off-frame codon frequencies in Prokaryotic Genomes  

PubMed Central

Background In this paper, we address the evidence for the Ambush Hypothesis. Proposed by Seligmann and Pollock, this hypothesis posits that there exists a selection for off-frame stop codons (OSCs) to counteract the possible deleterious effects of translational frameshifts, including the waste of resources and potential cytotoxicity. Two main types of study have been used to support the hypothesis. Some studies analyzed codon usage and showed that codons with more potential to create OSCs seem to be favored over codons with lower potential; they used this finding to support the Ambush Hypothesis. Another study used 342 bacterial genomes to evaluate the hypothesis directly, finding significant excesses of OSCs in these genomes. Results We repeated both analyses with newer datasets and searched for other factors that could explain the observed trends. In the first case, the relative frequency of codons with the potential to create OSCs is directly correlated with the GC content of organisms, as stop codons are GC-poor. When evaluating the frequency of OSCs directly in 1,976 bacterial genomes we also detected a significant excess. However, when comparing the excess of OSCs with similarly obtained results for the frequency of out-of-frame sense codons, some sense codons have a more significant excess than stop codons. Conclusions Two avenues of study have been used to support the Ambush Hypothesis. Using the same methods as these previous studies, we demonstrate that the evidence in support of the Ambush Hypothesis does not hold up against more rigorous testing. PMID:23799949

2013-01-01

112

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

113

Corporation-induced diseases, upstream epidemiologic surveillance, and urban health.  

PubMed

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

Jahiel, René I

2008-07-01

114

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

115

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

116

A micronucleus-specific sequence exists in the 5'-upstream region of calmodulin gene in Tetrahymena thermophila.  

PubMed Central

Tetrahymena thermophila possesses a transcriptionally inactive micronucleus and an active macronucleus. Both nuclei are developed from micronucleus-derived germ nuclei during conjugation. Extensive DNA rearrangement and transcriptional activation are known to be involved in macronuclear development, but little has been known about these processes in a particular functional gene. Therefore the micro- and macronuclear genomic DNAs for calmodulin gene were analyzed. A 1,384 bp micronucleus-specific sequence located about 3.5 kb upstream of calmodulin gene has been found, suggesting DNA rearrangement during macronuclear development. The micronucleus-specific sequence had 85% A + T, no extensive ORF, ATTAs at both ends, and two palindromic structures just outside of both ends. Interestingly, the micronucleus-specific sequence included a T-rich tract, T16CT5, in the middle, and a nearly complementary A-rich tract, A5TA10GA5, existed 7 bp upstream from the initiation codon. In addition, there was a 20 bp repetitive sequence TAAT(TAAC)4 about 100 bp upstream of the micronucleus-specific sequence and also in the promoter region of calmodulin gene. Although the functional significance of the micronucleus-specific sequence remains unclear, T16CT5 and TAAT(TAAC)4 elements might exert an influence on transcription of the calmodulin gene. Stringent Southern hybridization revealed that this micronucleus-specific sequence or very similar sequence(s) were abundant in the Tetrahymena micronuclear genome. Images PMID:8506136

Katoh, M; Hirono, M; Takemasa, T; Kimura, M; Watanabe, Y

1993-01-01

117

Sequences Required for Paramutation of the Maize B Gene Map to a Region Containing the Promoter and Upstream Sequences  

PubMed Central

The b gene encodes a transcriptional regulator of the maize anthocyanin biosynthetic pathway. Certain b alleles participate in paramutation, an allele-specific interaction that heritably alters transcription. The moderately transcribed B' allele heritably reduces the transcription of the highly transcribed B-I allele in a B'/B-I heterozygote, such that the B-I allele becomes B'. To identify the cis-acting sequences required for paramutation, we used B' or B-I alleles to isolate intragenic recombinants with B-Peru, an allele that is insensitive to paramutation and has distinct tissue-specific regulation. Physical mapping of the recombinant alleles showed that most of the crossovers were in a small region near the 5' end of the b-transcribed region. Analysis of the recombinant alleles revealed that the ability to cause and respond to paramutation and the control of tissue-specific expression both localize to the 5' region of the gene. The 3' boundary of these functions lies just upstream of the translation initiation codon. The 5' boundary has been estimated to be no more than 0.1 cM further upstream (1-150 kb). Thus, sequences critical for paramutation lie upstream of the b coding sequences and may include transcriptional regulatory sequences. PMID:7498778

Patterson, G. I.; Kubo, K. M.; Shroyer, T.; Chandler, V. L.

1995-01-01

118

The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr.  

PubMed

To gain insights into the relationship between codon bias, mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in degree of codon bias and level of gene expression. Individual structural elements (helices) were inferred using the comparative method. For each gene, four types of randomization simulations were performed to maintain/remove codon bias and/or to maintain or alter third-codon position nucleotide composition (N3). In the weakly expressed, weakly biased gene Adhr, the potential for secondary structure formation was found to be much stronger than in the highly expressed, highly biased gene Adh. This is consistent with the observation of approximately equal G and C percentages in Adhr ( approximately 31% across species), whereas in Adh the N3 distribution is shifted toward C (42% across species). Perturbing the N3 distribution to approximately equal amounts of A, G, C, and T increases the potential for secondary structure formation in Adh, but decreases it in Adhr. On the other hand, simulations that reduce codon bias without changing N3 content indicate that codon bias per se has only a weak effect on the formation of secondary structures. These results suggest that, for these two drosophilid genes, secondary structure is a relatively independent, negative regulator of gene expression. Whereas the degree of codon bias is positively correlated with level of gene expression, strong individual secondary structural elements may be selected for to retard mRNA translation and to decrease gene expression. PMID:11606539

Carlini, D B; Chen, Y; Stephan, W

2001-10-01

119

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

Microsoft Academic Search

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

CHRISTIAN J. MICHEL

1989-01-01

120

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

121

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, 2003) Although the surface proteins of human influenza A virus evolve rapidly and continually produce the sequence evolution of three influenza A genes over the past two decades. We study codon usage

Plotkin, Joshua B.

122

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

123

Vertebrate codon bias indicates a highly GC-rich ancestral genome.  

PubMed

Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences. PMID:23376453

Nabiyouni, Maryam; Prakash, Ashwin; Fedorov, Alexei

2013-04-25

124

Comprehensive analysis of the overall codon usage patterns in equine infectious anemia virus  

PubMed Central

Background Equine infectious anemia virus (EIAV) is an important animal model for understanding the relationship between viral persistence and the host immune response during lentiviral infections. Comparison and analysis of the codon usage model between EIAV and its hosts is important for the comprehension of viral evolution. In our study, the codon usage pattern of EIAV was analyzed from the available 29 full-length EIAV genomes through multivariate statistical methods. Finding Effective number of codons (ENC) suggests that the codon usage among EIAV strains is slightly biased. The ENC-plot analysis demonstrates that mutation pressure plays a substantial role in the codon usage pattern of EIAV, whereas other factors such as geographic distribution and host translation selection also take part in the process of EIAV evolution. Comparative analysis of codon adaptation index (CAI) values among EIAV and its hosts suggests that EIAV utilize the translational resources of horse more efficiently than that of donkey. Conclusion The codon usage bias in EIAV is slight and mutation pressure is the main factor that affects codon usage variation in EIAV. These results suggest that EIAV genomic biases are the result of the co-evolution of genome composition and the ability to evade the host’s immune response. PMID:24359511

2013-01-01

125

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

E-print Network

codon-usage trends defined by base compositional properties of individual nematode genomes. Introduction,orskewedlevelsofpolymor- phism at synonymous sites (Bennetzen and Hall 1982; Sharp and Li 1987; Akashi 1995; Duret and Mouchiroud, genomes exhibiting the strongest biases in codon usage cor- respond to species of bacteria and yeast

Cutter, Asher D.

126

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 Carbone Received: 27 July 2007 / Accepted: 7 December 2007 Ã? Springer Science+Business Media, LLC 2008 spectrum of related phage species. Based on a large-scale codon bias analysis of 116 DNA phages hosted

Carbone, Alessandra

127

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

PubMed Central

Background Translational power is the cellular rate of protein synthesis normalized to the biomass invested in translational machinery. Published data suggest a previously unrecognized pattern: translational power is higher among rapidly growing microbes, and lower among slowly growing microbes. One factor known to affect translational power is biased use of synonymous codons. The correlation within an organism between expression level and degree of codon bias among genes of Escherichia coli and other bacteria capable of rapid growth is commonly attributed to selection for high translational power. Conversely, the absence of such a correlation in some slowly growing microbes has been interpreted as the absence of selection for translational power. Because codon bias caused by translational selection varies between rapidly growing and slowly growing microbes, we investigated whether observed differences in translational power among microbes could be explained entirely by differences in the degree of codon bias. Although the data are not available to estimate the effect of codon bias in other species, we developed an empirically-based mathematical model to compare the translation rate of E. coli to the translation rate of a hypothetical strain which differs from E. coli only by lacking codon bias. Results Our reanalysis of data from the scientific literature suggests that translational power can differ by a factor of 5 or more between E. coli and slowly growing microbial species. Using empirical codon-specific in vivo translation rates for 29 codons, and several scenarios for extrapolating from these data to estimates over all codons, we find that codon bias cannot account for more than a doubling of the translation rate in E. coli, even with unrealistic simplifying assumptions that exaggerate the effect of codon bias. With more realistic assumptions, our best estimate is that codon bias accelerates translation in E. coli by no more than 60% in comparison to microbes with very little codon bias. Conclusions While codon bias confers a substantial benefit of faster translation and hence greater translational power, the magnitude of this effect is insufficient to explain observed differences in translational power among bacterial and archaeal species, particularly the differences between slowly growing and rapidly growing species. Hence, large differences in translational power suggest that the translational apparatus itself differs among microbes in ways that influence translational performance. PMID:15636642

Dethlefsen, Les; Schmidt, Thomas M

2005-01-01

128

The distribution function of diffuse ions and the magnetic field power spectrum upstream of Earth's bow shock  

Microsoft Academic Search

During two diffuse energetic ion events upstream of the Earth's bow shock with radial interplanetary magnetic field conditions comprehensive energy spectra of the protons and power spectra of the magnetic field fluctuations were obtained with the instrumentation on AMPTE\\/IRM. For diffuse ions a continuous distribution from ? 5 keV (starting above the solar wind energy) to the instrumental limit (230

E. Möbius; M. Scholer; N. Sckopke; H. Lühr; G. Paschmann; D. Hovestadt

1987-01-01

129

A Gibbs sampling method to detect over-represented motifs in the upstream regions of co-expressed genes  

Microsoft Academic Search

Microarray experiments can reveal useful information on the transcriptional regulation. We try to find regulatory elements in the region upstream of translation start of coexpressed genes. Here we present a modification to the original Gibbs Sampling algorithm [12]. We introduce a probability distribution to estimate the number of copies of the motif in a sequence. The second modification is the

Gert Thijs; Kathleen Marchal; Magali Lescot; Stephane Rombauts; Bart De Moor; Pierre Rouzé; Yves Moreau

2001-01-01

130

Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis  

PubMed Central

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 sites in those three distantly related multicellular eukaryotes. Surprisingly, there is a strong negative correlation between codon usage and protein length. This effect is not due to a smaller size of highly expressed proteins. Thus, for a same-expression pattern, the selective pressure on codon usage appears to be lower in genes encoding long rather than short proteins. This puzzling observation is not predicted by any of the current models of selection on codon usage and thus raises the question of how translation efficiency affects fitness in multicellular organisms. PMID:10200288

Duret, Laurent; Mouchiroud, Dominique

1999-01-01

131

Start with Science  

ERIC Educational Resources Information Center

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

Erickson, Susan

2012-01-01

132

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

133

World trends: Improving fortunes restore upstream health  

SciTech Connect

After a decade of recovery from the oil price collapse of 1986, the global upstream industry appears headed for a period of renewed strength and growth. Underpinning the prosperity is steady unrelenting growth in crude demand. Stronger global crude demand and heavy natural gas usage in the US are driving higher prices. Operators are reacting to better prices with larger drilling programs. Also boosting drilling levels are crude production expansion projects that many countries have underway in response to perceived future demand. Not surprisingly, World Oil`s outlook calls for global drilling to rise 4.5% to 60,273 wells, a second straight annual increase. Better US activity is helping, but so are stronger-than-expected numbers in Canada. Meanwhile, World Oil`s 51st annual survey of governments and operators indicates that global oil production rose 1.4% last year, to 62,774 million bpd. That was not enough, however, to keep up with demand. The paper discusses financial performance, business practices, other factors, and operating outlook. A table lists the 1996 forecasts, estimated wells drilled in 1995, and total wells and footage drilled in 1994 by country. A second table lists global crude and condensate production and wells actually producing in 1995 versus 1994.

NONE

1996-08-01

134

Why Kids Start  

MedlinePLUS

... to portray smokers as cool, sexy, independent, fun, attractive, and living on the edge – images that are ... 2009, contains several provisions aimed at preventing young people from starting to smoke. >> Learn More A A ...

135

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... 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

136

Polymorphism distribution of prion protein codon 117, 129 and 171 in Taiwan.  

PubMed

Prion diseases compass transmissible spongiform neurodegenerative diseases from various causes, including the genetic and infectious ones. We investigated the prevalence of codon 117, 129 and 171 polymorphism in prion protein (PrP) in Taiwanese, mainly for the sake of the informative absence of this genetic distribution. Our subjects were 419 aged ones of Han ethic origin. We evaluated the PrP gene (PRNP) polymorphism by restriction fragment length polymorphism, after amplification of their genomic DNAs by polymerase chain reactions with specific primers, digested by restriction enzyme PvuII (for codon 117), NspI (for codon 129), and BbvI (for codon 171), respectively, and confirmed by nucleotide sequencing. All of the subjects were homozygotes at codon 117 (Ala/Ala, gca/gca) and 171 (Asn/Asn, aac/aac). There were no valine homozygotes (Val/Val) in our 419 subjects, and nine subjects (2.1%) showed methionine-valine heterozygosity (Mal/Val, atg/gtg). The methionine homozygotes (Met/Met) comprised the major population (97.9%), and the prevalence of distribution is different to that seen in Caucasians. The almost 100% conservation of the domain from codon 117 to 171 implies the warranty of PrP in cellular functions. The high prevalence of Met/Met alleles in Taiwan did not imply an increased risk of CJD, and the genetic susceptibility of CJD by codon 129 of PrP may be still elusive for the infectivity. PMID:17410475

Wang, Kaw-Chen; Wang, Vinchi; Sun, Ming-Chieh; Chiueh, Ti-I; Soong, Bing-Wen; Shan, Din-E

2007-01-01

137

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

PubMed Central

Background Different proteins are required in widely different quantities to build a living cell. In most organisms, transcription control makes a major contribution to differential expression. This is not the case in trypanosomatids where most genes are transcribed at an equivalent rate within large polycistronic clusters. Thus, trypanosomatids must use post-transcriptional control mechanisms to balance gene expression requirements. Results Here, the evidence for translational selection, the enrichment of 'favoured' codons in more highly expressed genes, is explored. A set of highly expressed, tandem-repeated genes display codon bias in Trypanosoma cruzi, Trypanosoma brucei and Leishmania major. The tRNA complement reveals forty-five of the sixty-one possible anticodons indicating widespread use of 'wobble' tRNAs. Consistent with translational selection, cognate tRNA genes for favoured codons are over-represented. Importantly, codon usage (Codon Adaptation Index) correlates with predicted and observed expression level. In addition, relative codon bias is broadly conserved among syntenic genes from different trypanosomatids. Conclusion Synonymous codon bias is correlated with tRNA gene copy number and with protein expression level in trypanosomatids. Taken together, the results suggest that translational selection is the dominant mechanism underlying the control of differential protein expression in these organisms. The findings reveal how trypanosomatids may compensate for a paucity of canonical Pol II promoters and subsequent widespread constitutive RNA polymerase II transcription. PMID:18173843

Horn, David

2008-01-01

138

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

PubMed Central

Background Activating point mutations of GNAS at codon 201 have been detected in approximately two thirds of intraductal papillary mucinous neoplasms (IPMNs) of the pancreas. Intraductal papillary neoplasms of the bile ducts (IPNBs) morphologically resemble pancreatic IPMNs. This study sought to assess the mutational status of GNAS at codon 201 in IPNBs. Methods Thirty-four patients were included. DNA from microdissected IPNBs was subjected to a polymerase chain reaction and ligation method for the detection of GNAS mutations at codon 201 and of KRAS mutations at codon 12. Mutational status was compared with clinical and pathologic data. Results The IPNBs had a median diameter of 3.5 cm and were located intrahepatically (n= 6), extrahepatically (n= 13), both intra- and extrahepatically (n= 4) or in the gallbladder (intracystic papillary neoplasms, n= 11). Most exhibited pancreatobiliary differentiation (n= 20), high-grade dysplasia (n= 26) and an associated adenocarcinoma (n= 20). Analysis of GNAS codon 201 identified only one mutant sample in a multifocal intestinal subtype intrahepatic IPNB with high-grade dysplasia. Six lesions harboured a KRAS codon 12 mutation. Conclusions GNAS codon 201 mutations are uncommon in IPNBs, by contrast with pancreatic IPMNs. More comprehensive molecular profiling is needed to uncover the pathways involved in IPNB development. PMID:22954004

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

2012-01-01

139

Allosteric mechanism for codon-dependent tRNA selection on ribosomes.  

PubMed Central

We suggest that the interaction between a codon and its cognate tRNA induces conformational changes in the tRNA. We further suggest that sites on the ribosome preferentially bind tRNA in those conformations which require proper matching of codon and anticodon. According to this model, the codon functions as an allosteric effector which influences the conformation at various sites in the tRNA. This is made possible by the ribosome, which we suggest traps tRNA molecules in those conformation states that maximize the energy difference between cognate and noncognate codon-anticodon interactions. Studies of the interactions between tRNA molecules and their cognate codons in the absence of the ribosome have suggested that triplet-triplet interaction between codon and anticodon is far too weak to account for the specificity of the tRNA selection mechanism during protein synthesis. In contrast, we suggest that such affinity measurements do not adequately describe the interaction between a codon and its cognate tRNA. Thus, such experiments can not detect conformational changes in the tRNA, and, in particular, those stabilized by the ribosome. PMID:1060103

Kurland, C G; Rigler, R; Ehrenberg, M; Blomberg, C

1975-01-01

140

Transcription attenuation in Salmonella typhimurium: the significance of rare leucine codons in the leu leader.  

PubMed Central

The leucine operon of Salmonella typhimurium is controlled by a transcription attenuation mechanism. Four adjacent leucine codons within a 160-nucleotide leu leader RNA are thought to play a central role in this mechanism. Three of the four codons are CUA, a rarely used leucine codon within enteric bacteria. To determine whether the nature of the leucine codon affects the regulation of the leucine operon, we used oligonucleotide-directed mutagenesis to first convert one CUA of the leader to CUG and then convert all three CUA codons to CUG. CUG is the most frequently used leucine codon in enteric bacteria. A mutant having (CUA)2CUGCUC in place of (CUA)3CUC has an altered response to leucine limitation, requiring a slightly higher degree of limitation to effect derepression. Changing (CUA)3CUC to (CUG)3CUC has more dramatic effects upon operon expression. First, the basal level of expression is lowered to the point that the mutant grows more slowly than the parent in a minimal medium lacking leucine. Second, the response of the mutant to a leucine limitation is dramatically altered such that even a strong limitation elicits only a modest degree of derepression. If the mutant is grown under conditions of leucyl-tRNA limitation rather than leucine limitation, complete derepression can be achieved, but only at a much higher degree of limitation than for the wild-type operon. These results provide a clear-cut example of codon usage having a dramatic effect upon gene expression. PMID:3534884

Carter, P W; Bartkus, J M; Calvo, J M

1986-01-01

141

Start School Later  

NSDL National Science Digital Library

Last month, Pediatrics, the official journal of the American Academy of Pediatrics (AAP), issued a formal policy statement concerning School Start Times for Adolescents (http://pediatrics.aappublications.org/content/early/2014/08/19/peds.2014-1697.abstract?sid=3f739b0e-a552-4a4a-bd0a-907809e20255). In essence, the AAP called for schools to start later, citing sleep deprivation among teenagers as âÂÂan important public health issue.â This site from Start School Later, a group advocating for âÂÂhealth, safety and equity in education,â provides good, if somewhat one-sided, information on the topic. If youâÂÂre unfamiliar, start with Research & Info, which provides links to a number of informative sites about adolescent sleep needs and the impact of early school start times. Success Stories takes readers to schools around the country that have experimented with, and benefited from, later start times. If you're inspired, you can also Get Involved. Whatever your position on the issue, this is an informative and interesting site.

142

Psychiatric Advance Directives: Getting Started  

MedlinePLUS

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

143

Suppression of Premature Termination Codons as a Therapeutic Approach  

PubMed Central

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

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

2012-01-01

144

NECTAR: a database of codon-centric missense variant annotations  

PubMed Central

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

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

2014-01-01

145

Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type.  

PubMed Central

The poor printing of our previous Figure 2 (1) is corrected. Codon usage in mRNA sequences just published is also given. A new correspondence analysis is done, based on simultaneous comparison in all mRNA of use of the 61 codons. This analysis reinforces our claim that most genes in a genome, or genome type, have the same coding strategy; that is, they show similar choices among synonymous codons, or among degenerate bases (2). Like analysis on frequency variation in the amino acids coded reveals an entirely different pattern. PMID:6159596

Grantham, R; Gautier, C; Gouy, M

1980-01-01

146

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease  

PubMed Central

Upstream open reading frames (uORFs) are major gene expression regulatory elements. In many eukaryotic mRNAs, one or more uORFs precede the initiation codon of the main coding region. Indeed, several studies have revealed that almost half of human transcripts present uORFs. Very interesting examples have shown that these uORFs can impact gene expression of the downstream main ORF by triggering mRNA decay or by regulating translation. Also, evidence from recent genetic and bioinformatic studies implicates disturbed uORF-mediated translational control in the etiology of many human diseases, including malignancies, metabolic or neurologic disorders, and inherited syndromes. In this review, we will briefly present the mechanisms through which uORFs regulate gene expression and how they can impact on the organism's response to different cell stress conditions. Then, we will emphasize the importance of these structures by illustrating, with specific examples, how disturbed uORF-mediated translational control can be involved in the etiology of human diseases, giving special importance to genotype-phenotype correlations. Identifying and studying more cases of uORF-altering mutations will help us to understand and establish genotype-phenotype associations, leading to advancements in diagnosis, prognosis, and treatment of many human disorders. PMID:23950723

Barbosa, Cristina; Peixeiro, Isabel; Romao, Luisa

2013-01-01

147

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

148

Monochromatic precursor starts  

NASA Astrophysics Data System (ADS)

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

Rietveld, M. T.

1980-05-01

149

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

150

Genetic association between p53 codon 72 polymorphism and risk of cutaneous squamous cell carcinoma.  

PubMed

This study was designed to obtain a conclusive result about the relevance of p53 codon 72 polymorphism to the risk of cutaneous squamous cell carcinoma (SCC). We performed an updated meta-analysis of 3,792 subjects (1,349 cancer cases and 2,443 controls) to summarize the data available for p53 codon 72 polymorphism and SCC risk. The association was estimated by odds ratios (ORs) with 95% confidence intervals (CIs). The meta-analysis showed no statistical significance for SCC risk associated with any of the genetic models of p53 codon 72 polymorphism. The analyses by ethnic subgroup also failed to produce significant associations. This study suggests that p53 codon 72 polymorphism does not appear to represent a significant susceptibility factor for SCC in Caucasians. PMID:24353089

Liu, Ting; Lei, Zeyuan; Pan, ZhengYing; Chen, Yu; Li, Xiang; Mao, TongChun; He, Qian; Fan, Dongli

2014-04-01

151

Evidence of abundant stop codon readthrough in Drosophila and other Metazoa  

E-print Network

While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions ...

Jungreis, Irwin

152

Exonic transcription factor binding directs codon choice and affects protein evolution.  

PubMed

Genomes contain both a genetic code specifying amino acids and a regulatory code specifying transcription factor (TF) recognition sequences. We used genomic deoxyribonuclease I footprinting to map nucleotide resolution TF occupancy across the human exome in 81 diverse cell types. We found that ~15% of human codons are dual-use codons ("duons") that simultaneously specify both amino acids and TF recognition sites. Duons are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons. More than 17% of single-nucleotide variants within duons directly alter TF binding. Pervasive dual encoding of amino acid and regulatory information appears to be a fundamental feature of genome evolution. PMID:24337295

Stergachis, Andrew B; Haugen, Eric; Shafer, Anthony; Fu, Wenqing; Vernot, Benjamin; Reynolds, Alex; Raubitschek, Anthony; Ziegler, Steven; LeProust, Emily M; Akey, Joshua M; Stamatoyannopoulos, John A

2013-12-13

153

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

PubMed Central

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

2014-01-01

154

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

Microsoft Academic Search

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

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

2002-01-01

155

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

Microsoft Academic Search

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

Brigitte Weiss-Brummer; Alexander Hiittenhofer; Fritz Kaudewitz

1984-01-01

156

Mammalian Mutation Pressure, Synonymous Codon Choice, and mRNA Degradation  

Microsoft Academic Search

The usage of synonymous codons (SCs) in mammalian genes is highly correlated with local base composition and is therefore thought to be determined by mutation pressure. The usage is nonetheless structured. For instance, mammals share with Saccharomyces and Drosophila most preferences for the C-ending over the G-ending codon (or vice versa) within each fourfold-degenerate SC family and the fact that

Jubao Duan; Marcos A. Antezana

2003-01-01

157

Analysis of PRNP Gene Codon 129 Polymorphism in the Greek Population  

Microsoft Academic Search

Creutzfeldt–Jakob disease (CJD) is a fatal transmissible neurodegenerative prion disease with a rapid progression comprising\\u000a familial, sporadic, iatrogenic and variant forms. A polymorphism at codon 129 of PRNP gene has been implicated in the development\\u000a of variant CJD. We examined Met\\/Val allele frequencies and the genotype distribution, with respect to the polymorphic codon\\u000a 129 of PRNP gene in 348 healthy

Angelica A. Saetta; Nikolaos V. Michalopoulos; George Malamis; Polyanthi I. Papanastasiou; Niki Mazmanian; Maria Karlou; Anastasios Kouzoupis; Penelope Korkolopoulou; Efstratios Patsouris

2006-01-01

158

Starting up the upstarts.  

PubMed

Venture capitalists pour $1 billion a year into health care--and that investment may be the most overlooked indicator of new business opportunities. Signs show that companies focused on consolidation and cost-cutting are off the A list for risk capital. Instead, venture capitalists are targeting start-ups that save money on the front lines by truly managing care. PMID:9435477

Greene, J

1997-12-20

159

Blogs: Getting Started  

ERIC Educational Resources Information Center

Blogs are communication tools, they serve as vehicles to transmit messages. Before deciding to blog, one needs to devise a strategy on how this medium will fit in with his or her communication needs. This will also help later in deciding which features one will need to include in his or her blog. This article discusses ways on how to start and…

Dyrud, Marilyn A.; Worley, Rebecca B.; Schultz, Benjamin

2005-01-01

160

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.

161

PHP: Getting Started Introduction  

E-print Network

PHP: Getting Started Introduction This document describes the basic syntax for PHP code, how to execute PHP scripts, methods for sending output to the browser, how to comment your code, and the handling of whitespace. Basic PHP syntax PHP code typically resides in a plaintext file with a .php extension. The code

Vander Zanden, Brad

162

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

163

RCDI/eRCDI: a web-server to estimate codon usage deoptimization  

PubMed Central

Background The Relative Codon Deoptimization Index (RCDI) was developed by Mueller et al. (2006) as measure of codon deoptimization by comparing how similar is the codon usage of a gene and the codon usage of a reference genome. Findings RCDI/eRCDI is a web application server that calculates the Relative Codon Deoptimization Index and a new expected value for the RCDI (eRCDI). The RCDI is used to estimate the similarity of the codon frequencies of a specific gene in comparison to a given reference genome. The eRCDI is determined by generating random sequences with similar G+C and amino acid composition to the input sequences and may be used as an indicator of the significance of the RCDI values. RCDI/eRCDI is freely available at http://genomes.urv.cat/CAIcal/RCDI. Conclusions This web server will be a useful tool for genome analysis, to understand host-virus phylogenetic relationships or to infer the potential host range of a virus and its replication strategy, as well as in experimental virology to ease the step of gene design for heterologous protein expression. PMID:20356391

2010-01-01

164

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

PubMed

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

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

2014-02-01

165

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

166

Waltz Quick Start  

E-print Network

ion. For a more detailed explanation of the facilities and functions of the Waltz visualization system refer to the Waltz User Manual [Rob96]. ffl The Generalization Process splits the data into spatially connected groups. ffl A specialization is formed from a subset (selection) of these groups. ffl The results are displayed in multiple abstract views of the same data. These abstractions are formed by losing or augmenting the data to facilitate in the understanding of the data. Waltz implicitly connects the abstractions together as Linkages. By default most of the Linkages between the different abstractions are switched on; they are turned off by using the Linkages Form. 1.1 Starting a Waltz Session A Waltz session is started by typing the command: % waltz 1.2 Finishing a Waltz Session The session is ended by selecting the Quit option from the File menu at the top of the Waltz canvas; or by typing Alt q (the hot key configuration of the menu command). Waltz Quick Start Version...

unknown authors

1996-01-01

167

New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae  

PubMed Central

Stop codon readthrough may be promoted by the nucleotide environment or drugs. In such cases, ribosomes incorporate a natural suppressor tRNA at the stop codon, leading to the continuation of translation in the same reading frame until the next stop codon and resulting in the expression of a protein with a new potential function. However, the identity of the natural suppressor tRNAs involved in stop codon readthrough remains unclear, precluding identification of the amino acids incorporated at the stop position. We established an in vivo reporter system for identifying the amino acids incorporated at the stop codon, by mass spectrometry in the yeast Saccharomyces cerevisiae. We found that glutamine, tyrosine and lysine were inserted at UAA and UAG codons, whereas tryptophan, cysteine and arginine were inserted at UGA codon. The 5? nucleotide context of the stop codon had no impact on the identity or proportion of amino acids incorporated by readthrough. We also found that two different glutamine tRNAGln were used to insert glutamine at UAA and UAG codons. This work constitutes the first systematic analysis of the amino acids incorporated at stop codons, providing important new insights into the decoding rules used by the ribosome to read the genetic code. PMID:25056309

Blanchet, Sandra; Cornu, David; Argentini, Manuela; Namy, Olivier

2014-01-01

168

New insights into the incorporation of natural suppressor tRNAs at stop codons in Saccharomyces cerevisiae.  

PubMed

Stop codon readthrough may be promoted by the nucleotide environment or drugs. In such cases, ribosomes incorporate a natural suppressor tRNA at the stop codon, leading to the continuation of translation in the same reading frame until the next stop codon and resulting in the expression of a protein with a new potential function. However, the identity of the natural suppressor tRNAs involved in stop codon readthrough remains unclear, precluding identification of the amino acids incorporated at the stop position. We established an in vivo reporter system for identifying the amino acids incorporated at the stop codon, by mass spectrometry in the yeast Saccharomyces cerevisiae. We found that glutamine, tyrosine and lysine were inserted at UAA and UAG codons, whereas tryptophan, cysteine and arginine were inserted at UGA codon. The 5' nucleotide context of the stop codon had no impact on the identity or proportion of amino acids incorporated by readthrough. We also found that two different glutamine tRNA(Gln) were used to insert glutamine at UAA and UAG codons. This work constitutes the first systematic analysis of the amino acids incorporated at stop codons, providing important new insights into the decoding rules used by the ribosome to read the genetic code. PMID:25056309

Blanchet, Sandra; Cornu, David; Argentini, Manuela; Namy, Olivier

2014-11-01

169

The Characteristics of Rare Codon Clusters in the Genome and Proteins of Hepatitis C Virus; a Bioinformatics Look  

PubMed Central

BACKGROUND Recent studies suggest that rare codon clusters are functionally important for protein activity. METHODS Here, for the first time we analyzed and reported rare codon clusters in Hepatitis C Virus (HCV) genome and then identified the location of these rare codon clusters in the structure of HCV protein. This analysis was performed using the Sherlocc program that detects statistically relevant conserved rare codon clusters. RESULTS By this program, we identified the rare codon cluster in three regions of HCV genome; NS2, NS3, and NS5A coding sequence of HCV genome. For further understanding of the role of these rare codon clusters, we studied the location of these rare codon clusters and critical residues in the structure of NS2, NS3 and NS5A proteins. We identified some critical residues near or within rare codon clusters. It should be mentioned that characteristics of these critical residues such as location and situation of side chains are important in assurance of the HCV life cycle. CONCLUSION The characteristics of these residues and their relative status showed that these rare codon clusters play an important role in proper folding of these proteins. Thus, it is likely that these rare codon clusters may have an important role in the function of HCV proteins. This information is helpful in development of new avenues for vaccine and treatment protocols. PMID:25349685

Fattahi, Mohammadreza; Malekpour, Abdorrasoul; Mortazavi, Mojtaba; Safarpour, Alireza; Naseri, Nasrin

2014-01-01

170

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

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

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

171

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

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

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

172

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

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

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

173

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

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

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

174

Some considerations in the stability analysis of upstream tailings dams  

Microsoft Academic Search

Upstream constructed tailings dams represent a significant challenge to the geotechnical engineer in terms of analysis of their stability, in large part because the shear strength of the loose sands and fine grained or \\

T. E. Martin; E. C. McRoberts

175

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

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

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

176

STEEL ERECTION. View of upstream side of bridge, looking north ...  

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

STEEL ERECTION. View of upstream side of bridge, looking north from the old suspension bridge at unjoined cantilever arms - South Fork Trinity River Bridge, State Highway 299 spanning South Fork Trinity River, Salyer, Trinity County, CA

177

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

178

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

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

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

179

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...

180

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

181

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

182

2. STONE ARCH BRIDGE. TIMBERS ON THE UPSTREAM FACE OF ...  

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

2. STONE ARCH BRIDGE. TIMBERS ON THE UPSTREAM FACE OF THE PIER PROTECTED THE STONEWORK FROM DAMAGE FROM ICE FLOWS, BARGES, ETC. - Lockport Historic District, Stone Arch Bridge, Spanning Des Plaines River at Ninth Street, Lockport, Will County, IL

183

35. VIEW OF UPSTREAM SIDE OF SPILLWAY. RESERVOIR, PARAPET AND ...  

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

35. VIEW OF UPSTREAM SIDE OF SPILLWAY. RESERVOIR, PARAPET AND FLASHBOARDS ARE AT LOWER LEFT; GATE OPERATING ROOM WINDOWS ARE AT CENTER TO UPPER RIGHT - Bartlett Dam, Verde River, Phoenix, Maricopa County, AZ

184

3. Upstream face of Rock Creek Diversion Dam, closeup of ...  

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

3. Upstream face of Rock Creek Diversion Dam, close-up of gates, looking southeast - Bitter Root Irrigation Project, Rock Creek Diversion Dam, One mile east of Como Dam, west of U.S. Highway 93, Darby, Ravalli County, MT

185

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

186

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

187

Unit 6, upstream from Hickory Street Bridge Johnstown Local ...  

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

Unit 6, upstream from Hickory Street Bridge - Johnstown Local Flood Protection Project, Beginning on Conemaugh River approx 3.8 miles downstream from confluence of Little Conemaugh & Stony Creek Rivers at Johnstown, Johnstown, Cambria County, PA

188

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

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

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

189

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

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

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

190

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

PubMed Central

Background Heterologous gene expression is an important tool for synthetic biology that enables metabolic engineering and the production of non-natural biologics in a variety of host organisms. The translational efficiency of heterologous genes can often be improved by optimizing synonymous codon usage to better match the host organism. However, traditional approaches for optimization neglect to take into account many factors known to influence synonymous codon distributions. Results Here we define an alternative approach for codon optimization that utilizes systems level information and codon context for the condition under which heterologous genes are being expressed. Furthermore, we utilize a probabilistic algorithm to generate multiple variants of a given gene. We demonstrate improved translational efficiency using this condition-specific codon optimization approach with two heterologous genes, the fluorescent protein-encoding eGFP and the catechol 1,2-dioxygenase gene CatA, expressed in S. cerevisiae. For the latter case, optimization for stationary phase production resulted in nearly 2.9-fold improvements over commercial gene optimization algorithms. Conclusions Codon optimization is now often a standard tool for protein expression, and while a variety of tools and approaches have been developed, they do not guarantee improved performance for all hosts of applications. Here, we suggest an alternative method for condition-specific codon optimization and demonstrate its utility in Saccharomyces cerevisiae as a proof of concept. However, this technique should be applicable to any organism for which gene expression data can be generated and is thus of potential interest for a variety of applications in metabolic and cellular engineering. PMID:24636000

2014-01-01

191

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

Microsoft Academic Search

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

Jean-Claude Perez

2010-01-01

192

StartUpNation  

NSDL National Science Digital Library

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

193

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

PubMed

The evolution of codon bias, the unequal usage of synonymous codons, is thought to be due to natural selection for the use of preferred codons that match the most abundant species of isoaccepting tRNA, resulting in increased translational efficiency and accuracy. We examined this hypothesis by introducing 1, 6, and 10 unpreferred codons into the Drosophila alcohol dehydrogenase gene (Adh). We observed a significant decrease in ADH protein production with number of unpreferred codons, confirming the importance of natural selection as a mechanism leading to codon bias. We then used this empirical relationship to estimate the selection coefficient (s) against unpreferred synonymous mutations and found the value (s >or= 10(-5)) to be approximately one order of magnitude greater than previous estimates from population genetics theory. The observed differences in protein production appear to be too large to be consistent with current estimates of the strength of selection on synonymous sites in D. melanogaster. PMID:12586711

Carlini, David B; Stephan, Wolfgang

2003-01-01

194

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

195

Clinical Implications of Mutations at Reverse Transcriptase Codon 135 on Response to NNRTI-Based Therapy  

PubMed Central

To evaluate the impact of mutations at reverse transcriptase codon 135 on treatment outcomes in patients receiving NNRTI-based antiretroviral therapy, a total of 68 patients (30 with and 38 without baseline mutations at codon 135) were evaluated. Median increases in CD4 counts were 135 and 90 cells/mm3 (p=0.32), virologic suppression (HIV RNA < 400 copies/mL) was achieved in 16 (53%) and 16 (42%) patients (p=0.50), while NNRTI resistance was detected in 10/14 (71%) and 16/22 (73%) in patients with and without mutations at codon 135, respectively. Patients who experienced a virologic breakthrough and had a baseline mutation at codon 135 were more likely to evolve a single NNRTI resistance mutation (8/14 vs 4/22, p=0.029) but less likely to evolve multiple NNRTI resistance mutations (2/14 vs 12/22, p = 0.033). Mutations at codon 135 do not affect response rates, but affect the pattern of development of NNRTI resistance mutations. This has important implications for the subsequent use of newer NNRTIs such as etravirine in salvage therapy. PMID:19440454

Tossonian, Harout K; Raffa, Jesse D; Grebely, Jason; Viljoen, Mark; Mead, Annabel; Khara, Milan; McLean, Mark; Krishnamurthy, Ashok; DeVlaming, Stanley; Conway, Brian

2007-01-01

196

Two-codon T-box riboswitch binding two tRNAs  

PubMed Central

T-box riboswitches control transcription of downstream genes through the tRNA-binding formation of terminator or antiterminator structures. Previously reported T-boxes were described as single-specificity riboswitches that can bind specific tRNA anticodons through codon–anticodon interactions with the nucleotide triplet of their specifier loop (SL). However, the possibility that T-boxes might exhibit specificity beyond a single tRNA had been overlooked. In Clostridium acetobutylicum, the T-box that regulates the operon for the essential tRNA-dependent transamidation pathway harbors a SL with two potential overlapping codon positions for tRNAAsn and tRNAGlu. To test its specificity, we performed extensive mutagenic, biochemical, and chemical probing analyses. Surprisingly, both tRNAs can efficiently bind the SL in vitro and in vivo. The dual specificity of the T-box is allowed by a single base shift on the SL from one overlapping codon to the next. This feature allows the riboswitch to sense two tRNAs and balance the biosynthesis of two amino acids. Detailed genomic comparisons support our observations and suggest that “flexible” T-box riboswitches are widespread among bacteria, and, moreover, their specificity is dictated by the metabolic interconnection of the pathways under control. Taken together, our results support the notion of a genome-dependent codon ambiguity of the SLs. Furthermore, the existence of two overlapping codons imposes a unique example of tRNA-dependent regulation at the transcriptional level. PMID:23858450

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

2013-01-01

197

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

198

Two-step model of stop codon recognition by eukaryotic release factor eRF1  

PubMed Central

Release factor eRF1 plays a key role in the termination of protein synthesis in eukaryotes. The eRF1 consists of three domains (N, M and C) that perform unique roles in termination. Previous studies of eRF1 point mutants and standard/variant code eRF1 chimeras unequivocally demonstrated a direct involvement of the highly conserved N-domain motifs (NIKS, YxCxxxF and GTx) in stop codon recognition. In the current study, we extend this work by investigating the role of the 41 invariant and conserved N-domain residues in stop codon decoding by human eRF1. Using a combination of the conservative and non-conservative amino acid substitutions, we measured the functional activity of >80 mutant eRF1s in an in vitro reconstituted eukaryotic translation system and selected 15 amino acid residues essential for recognition of different stop codon nucleotides. Furthermore, toe-print analyses provide evidence of a conformational rearrangement of ribosomal complexes that occurs during binding of eRF1 to messenger RNA and reflects stop codon decoding activity of eRF1. Based on our experimental data and molecular modelling of the N-domain at the ribosomal A site, we propose a two-step model of stop codon decoding in the eukaryotic ribosome. PMID:23435318

Kryuchkova, Polina; Grishin, Alexander; Eliseev, Boris; Karyagina, Anna; Frolova, Ludmila; Alkalaeva, Elena

2013-01-01

199

Evidence of abundant stop codon readthrough in Drosophila and other metazoa.  

PubMed

While translational stop codon readthrough is often used by viral genomes, it has been observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions in 12 species of Drosophila and showed that for 149 genes, the open reading frame following the stop codon has a protein-coding conservation signature, hinting that stop codon readthrough might be common in Drosophila. We return to this observation armed with deep RNA sequence data from the modENCODE project, an improved higher-resolution comparative genomics metric for detecting protein-coding regions, comparative sequence information from additional species, and directed experimental evidence. We report an expanded set of 283 readthrough candidates, including 16 double-readthrough candidates; these were manually curated to rule out alternatives such as A-to-I editing, alternative splicing, dicistronic translation, and selenocysteine incorporation. We report experimental evidence of translation using GFP tagging and mass spectrometry for several readthrough regions. We find that the set of readthrough candidates differs from other genes in length, composition, conservation, stop codon context, and in some cases, conserved stem-loops, providing clues about readthrough regulation and potential mechanisms. Lastly, we expand our studies beyond Drosophila and find evidence of abundant readthrough in several other insect species and one crustacean, and several readthrough candidates in nematode and human, suggesting that functionally important translational stop codon readthrough is significantly more prevalent in Metazoa than previously recognized. PMID:21994247

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

2011-12-01

200

Enhanced Production of Recombinant Mycobacterium tuberculosis Antigens in Escherichia coli by Replacement of Low-Usage Codons  

Microsoft Academic Search

A major obstacle to development of subunit vaccines and diagnostic reagents for tuberculosis is the inability to produce large quantities of these proteins. To test the hypothesis that poor expression of some mycobacterial genes in Escherichia coli is due, in part, to the presence of low-usage E. coli codons, we used site-directed mutagenesis to convert low-usage codons to high-usage codons

DAVID L. LAKEY; RAMA K. R. VOLADRI; KATHRYN M. EDWARDS; CYNTHIA HAGER; BUKA SAMTEN; ROBERT S. WALLIS; PETER F. BARNES; DOUGLAS S. KERNODLE

2000-01-01

201

Hemoglobin E and codon 17 nonsense: Two ?-globin gene mutations common in Southeast Asia detected by the use of ARMS  

Microsoft Academic Search

Summary Hemoglobin E (codon 26 GAG?AAG) and codon 17 nonsense (AAG?TAG), two clinically important mutations of the ß-globin gene, are common in Southeast Asia. The detection of these mutations using allele-specific PCR is described. Together with the previously reported method for the detection of the common Southeast asian codon 41–42 frameshift mutation (del CTTT), it is possible to identify the

H. Steger; A. Eigel; G. Flatz; J. Horst

1993-01-01

202

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

203

Codon-optimized antibiotic resistance gene improves efficiency of transient transformation in Frankia.  

PubMed

Frankia is a unique actinobacterium having abilities to fix atmospheric dinitrogen and to establish endosymbiosis with trees, but molecular bases underlying these interesting characteristics are poorly understood because of a lack of stable transformation system. Extremely high GC content of Frankia genome (more than 70 percent) can be a hindrance to successful transformation. We generated a synthetic gentamicin resistance gene whose codon usage is optimized to Frankia (fgmR) and evaluated its usefulness as a selection marker using a transient transformation system. Success rate of transient transformation and cell growth in selective culture were significantly increased by use of fgmR instead of a native gentamicin resistance gene, suggesting that codon optimization improved translation efficiency of the marker gene and increased antibiotic resistance. Our result shows that similarity in codon usage pattern is an important factor to be taken into account when exogenous transgenes are expressed in Frankia cells. PMID:24287650

Kucho, Ken-Ichi; Kakoi, Kentaro; Yamaura, Masatoshi; Iwashita, Mari; Abe, Mikiko; Uchiumi, Toshiki

2013-11-01

204

Clustering in Large Networks Does Not Promote Upstream Reciprocity  

PubMed Central

Upstream reciprocity (also called generalized reciprocity) is a putative mechanism for cooperation in social dilemma situations with which players help others when they are helped by somebody else. It is a type of indirect reciprocity. Although upstream reciprocity is often observed in experiments, most theories suggest that it is operative only when players form short cycles such as triangles, implying a small population size, or when it is combined with other mechanisms that promote cooperation on their own. An expectation is that real social networks, which are known to be full of triangles and other short cycles, may accommodate upstream reciprocity. In this study, I extend the upstream reciprocity game proposed for a directed cycle by Boyd and Richerson to the case of general networks. The model is not evolutionary and concerns the conditions under which the unanimity of cooperative players is a Nash equilibrium. I show that an abundance of triangles or other short cycles in a network does little to promote upstream reciprocity. Cooperation is less likely for a larger population size even if triangles are abundant in the network. In addition, in contrast to the results for evolutionary social dilemma games on networks, scale-free networks lead to less cooperation than networks with a homogeneous degree distribution. PMID:21998641

Masuda, Naoki

2011-01-01

205

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

206

UGA suppression by normal tRNA Trp in Escherichia coli: codon context effects.  

PubMed Central

The nucleotide sequences at the 3' side of in-phase UGA termination codons in mRNAs of various prokaryotic genes were re-examined. An adenine (A) residue is found to be adjacent to the 3' side of UGA in mRNAs which code for readthrough proteins by the suppression of UGA by normal Escherichia coli tRNA Trp. It is suggested that the nature of the nucleotide following a UGA codon determines whether the UGA signals inefficiently or efficiently the termination of polypeptide chain synthesis: an A residue at this position permits the UGA readthrough process. PMID:7015288

Engelberg-Kulka, H

1981-01-01

207

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

PubMed Central

Translational control of the GCN4 gene involves two short open reading frames in the mRNA leader (uORF1 and uORF4) that differ greatly in the ability to allow reinitiation at GCN4 following their own translation. The low efficiency of reinitiation characteristic of uORF4 can be reconstituted in a hybrid element in which the last codon of uORF1 and 10 nucleotides 3' to its stop codon (the termination region) are substituted with the corresponding nucleotides from uORF4. To define the features of these 13 nucleotides that determine their effects on reinitiation, we separately randomized the sequence of the third codon and termination region of the uORF1-uORF4 hybrid and selected mutant alleles with the high-level reinitiation that is characteristic of uORF1. The results indicate that many different A+U-rich triplets present at the third codon of uORF1 can overcome the inhibitory effect of the termination region derived from uORF4 on the efficiency of reinitiation at GCN4. Efficient reinitiation is not associated with codons specifying a particular amino acid or isoacceptor tRNA. Similarly, we found that a diverse collection of A+U-rich sequences present in the termination region of uORF1 could restore efficient reinitiation at GCN4 in the presence of the third codon derived from uORF4. To explain these results, we propose that reinitiation can be impaired by stable base pairing between nucleotides flanking the uORF1 stop codon and either the tRNA which pairs with the third codon, the rRNA, or sequences located elsewhere in GCN4 mRNA. We suggest that these interactions delay the resumption of scanning following peptide chain termination at the uORF and thereby lead to ribosome dissociation from the mRNA. Images PMID:8264629

Grant, C M; Hinnebusch, A G

1994-01-01

208

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...

209

Development of GPON upstream physical-media-dependent prototypes  

Microsoft Academic Search

This paper presents three new gigabit-capable passive optical network (GPON) physical-media-dependent (PMD) prototypes: a burst-mode optical transmitter, an avalanche photodiode\\/transimpedance amplifier (APD-TIA), and a burst-mode optical receiver. With these, point-to-multipoint (P2MP) upstream transmission can be realized in a high-performance GPON at 1.25 Gb\\/s. Performance measurements on the new burst-mode upstream PMD modules comply with GPON uplink simulations. The laser transmitter

Xing-Zhi Qiu; Peter Ossieur; Johan Bauwelinck; Yanchun Yi; Dieter Verhulst; Jan Vandewege; Benoit De Vos; Paolo Solina

2004-01-01

210

From Head Start to Sure Start: Reflections on Policy Transfer  

ERIC Educational Resources Information Center

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

Welshman, John

2010-01-01

211

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

212

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

Microsoft Academic Search

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

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

2001-01-01

213

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

ERIC Educational Resources Information Center

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

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

2009-01-01

214

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

E-print Network

and confirm that nonsense errors can play an important role in shaping codon usage bias. r 2005 Elsevier Ltd bias, nonsense errors, and ribosome recycling Michael A. Gilchrista,�, Andreas Wagnerb a Department errors and codon usage bias can have a large effect on the probability that a ribosome will completely

Wagner, Andreas

215

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

Microsoft Academic Search

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

J. T. Herbeck

2003-01-01

216

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

PubMed Central

Background: Endometriosis is a female health disorder that occurs when cells from the lining of the uterus grow in other areas of the body. The cause of endometriosis is unknown. Objective: The purpose of this study was to investigate TP53 gene codon 72 polymorphism in women with endometriosis and compared it with healthy samples in Isfahan. Materials and Methods: We undertook a case-control study to examine the possible association of the TP53 gene codon 72 polymorphism with the risk of endometriosis in Isfahan. Ninety whole blood specimens from normal people as controls and ninety endometriosis specimens were analyzed. p53 codon 72 genotypes were identified using allele-specific polymerase chain reaction. Results: Frequency of genotype Arg/Arg (Arginine/Arginine) in the samples of endometriosis was 28.9% and in healthy samples 42.2%. Frequency of genotype Pro/Pro (Proline/Proline) in the samples of endometriosis was 15.6% and in healthy ones. Frequency of heterozygote's Arg/Pro was 55.6% in endometriosis samples and 54.45% in healthy ones 3.3%. By comparing statistical genotype Pro/Pro with two other genotypes in both groups there was a statistical meaningful difference between control group and endometriosis group. [p=0.009, CI=95%, OR=5.34 (1047-19.29)]. Conclusion: Recent research shows that genotype Pro/Pro codon72 exon4 TP53 gene may be one predisposing genetic factor for endometriosis in Isfahan. PMID:24639781

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

2013-01-01

217

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

Microsoft Academic Search

BACKGROUND: To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein

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

2009-01-01

218

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

E-print Network

Asked Questions'' category: The extraction and assembly of exons from large DNA sequence databasesAn Example in Kleisli: Codon Usage Extraction Made Easy Jiren Wang and Limsoon Wong Bio in this paper. First, we wanted to build a system that could extract coding sequences of a specified organism

Wong, Limsoon

219

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

Microsoft Academic Search

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

Les Dethlefsen; Thomas M. Schmidt

2005-01-01

220

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

Microsoft Academic Search

We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of Buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in Escherichia coli, a close free-living relative. We sought to discriminate genes of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the

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

2003-01-01

221

Strong short-range correlations and dichotomic codon classes in coding DNA sequences  

NASA Astrophysics Data System (ADS)

The study of correlation structures in DNA sequences is of great interest because it allows us to obtain structural and functional information about underlying genetic mechanisms. In this paper we present a study of the correlation structure of protein coding sequences of DNA based on a recently developed mathematical representation of the genetic code. A fundamental consequence of such representation is that codons can be assigned a parity class (odd-even). Such parity can be obtained by means of a nonlinear algorithm acting on the chemical character of the codon bases. In the same setting the Rumer’s class can be naturally described and a new dichotomic class, the hidden class, can be defined. Moreover, we show that the set of DNA’s base transformations associated to the three dichotomic classes can be put in a compact group-theoretic framework. We use the dichotomic classes as a coding scheme for DNA sequences and study the mutual dependence between such classes. The same analysis is carried out also on the chemical dichotomies of DNA bases. In both cases, the statistical analysis is performed by using an entropy-based dependence metric possessing many desirable properties. We obtain meaningful tests for mutual dependence by using suitable resampling techniques. We find strong short-range correlations between certain combinations of dichotomic codon classes. These results support our previous hypothesis that codon classes might play an active role in the organization of genetic information.

Gonzalez, Diego Luis; Giannerini, Simone; Rosa, Rodolfo

2008-11-01

222

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

223

Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids  

Microsoft Academic Search

We have explored compositional variation at synonymous (codon usage) and nonsynonymous (amino acid usage) positions in three complete genomes of Buchnera, endosymbiotic bacteria of aphids, and also in their orthologs in Escherichia coli, a close free-living relative. We sought to discriminate genes of variable expression levels in order to weigh the relative contributions of mutational bias and selection in the

C. Rispe; F. Delmotte; Ham van R. C. H. J; A. Moya

2004-01-01

224

DNA Mismatch Repair and Synonymous Codon Evolution in Mammals Adam Eyre-Walker  

E-print Network

DNA Mismatch Repair and Synonymous Codon Evolution in Mammals Adam Eyre-Walker Institute of Cell to predict the expected relationship between the rate of substitution and G+C content at silent sites. It was found that the silent-substitution rate should decline with increasing G+C content over most of the G

Eyre-Walker, Adam

225

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

Microsoft Academic Search

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

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

2007-01-01

226

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

227

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

228

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

229

RESEARCH ARTICLE Evaluating the effects of upstream lakes and wetlands  

E-print Network

, USA K. S. Cheruvelil Department of Fisheries and Wildlife, Lyman Briggs College, Michigan State and Wildlife, James Madison College, Michigan State University, 370 North Case Hall, East Lansing, MI 48824RESEARCH ARTICLE Evaluating the effects of upstream lakes and wetlands on lake phosphorus

230

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

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

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

231

7. GENERAL VIEW LOOKING NORTH, SHOWING UPSTREAM SIDE OF POWERHOUSE ...  

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

7. GENERAL VIEW LOOKING NORTH, SHOWING UPSTREAM SIDE OF POWERHOUSE #1; ADMINISTRATIVE OFFICES ARE VISIBLE AT CENTER/LEFT WITH ELEVATOR TOWER IN LEFT BACKGROUND; GANTRY CRANE IS VISIBLE IN FAR RIGHT BACKGROUND. - Bonneville Project, Powerhouse No.1, Spanning Bradford Slough, from Bradford Island, Bonneville, Multnomah County, OR

232

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

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

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

233

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

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

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

234

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

235

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

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

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

236

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

237

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

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

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

238

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

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

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

239

11. VIEW OF UPSTREAM ELEVATION OF BIG DALTON DAM SHOWING ...  

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

11. VIEW OF UPSTREAM ELEVATION OF BIG DALTON DAM SHOWING CONSTRUCTION OF THE ARCH WALLS, TAKEN ON SEPTEMBER 11, 1928 (PHOTOGRAPHER UNKNOWN). PICTURE WAS DEVELOPED FROM COPY NEGATIVES WHICH WERE TAKEN ON 6/5/1973 BY PHOTOGRAPHER GATSON OF L.A. COUNTY PUBLIC WORKS. - Big Dalton Dam, 2600 Big Dalton Canyon Road, Glendora, Los Angeles County, CA

240

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

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

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

241

6. AERATOR VIEWED UPSTREAM. DETAIL OF FLUSH VALVE AND VIEW ...  

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

6. AERATOR VIEWED UPSTREAM. DETAIL OF FLUSH VALVE AND VIEW INTO BOX FLUME. NOTE WRENCH TO OPEN VALVE AND REMAINS OF OLD SHOVEL USED FOR MAINTENANCE. TRASH SCREEN MESH IS SEEN AT BOTTOM LEFT. - Kalaupapa Water Supply System, Waikolu Valley to Kalaupapa Settlement, Island of Molokai, Kalaupapa, Kalawao County, HI

242

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

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

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

243

2. Upstream face of Rock Creek Diversion Dam, looking east ...  

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

2. Upstream face of Rock Creek Diversion Dam, looking east (Canal slide gates to left, Rock Creek diversion gate to right in raised position) - Bitter Root Irrigation Project, Rock Creek Diversion Dam, One mile east of Como Dam, west of U.S. Highway 93, Darby, Ravalli County, MT

244

1. Upstream face of Rock Creek Diversion Dam, looking east ...  

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

1. Upstream face of Rock Creek Diversion Dam, looking east (Overflow weir right, diversion section into Irrigation District Canal to left) - Bitter Root Irrigation Project, Rock Creek Diversion Dam, One mile east of Como Dam, west of U.S. Highway 93, Darby, Ravalli County, MT

245

Characterization of pore pressure conditions in upstream tailings dams  

Microsoft Academic Search

Conventional upstream tailings dams are unique structures in that their shear strength and pore pressure conditions are often difficult to characterize, particularly during the design stage. Selection of shear strength models based on understanding contractant versus dilatant, and drained versus undrained, behaviour in shear was the subject of a companion paper. This paper addresses the complexity of proper characterization of

T. E. Martin

246

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

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

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

247

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

248

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

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

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

249

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

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

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

250

45. View of upstream face of fish screens at Dingle ...  

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

45. View of upstream face of fish screens at Dingle Basin, looking northwest from south side of basin. Photo by Brian C. Morris, Puget Power, 1989. - Puget Sound Power & Light Company, White River Hydroelectric Project, 600 North River Avenue, Dieringer, Pierce County, WA

251

43. View of log boom (upstream) protecting fish screens at ...  

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

43. View of log boom (upstream) protecting fish screens at Dingle Basin, looking southwest from north side of basin. Photo by Brian C. Morris, PUget Power, 1989. - Puget Sound Power & Light Company, White River Hydroelectric Project, 600 North River Avenue, Dieringer, Pierce County, WA

252

Funding Category START-Programme  

E-print Network

Funding Category START-Programme Programme aims The fundamental aim of the START-Programme of awards between subject areas. The START Programme is one of the most generously supported research programmes in Austria. As such, it attracts considerable media attention and thus contributes significantly

Fuchs, Clemens

253

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

254

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

255

p53 codon 72 polymorphism and human papillomavirus associated skin cancer  

PubMed Central

Background/Aims—Non-melanoma skin cancers frequently harbour multiple human papillomavirus (HPV) types. A recent report suggests that a polymorphism of the p53 tumour suppressor gene that results in the substitution of a proline residue with an arginine residue at position 72 of the p53 protein might act as a risk factor in HPV associated malignancies. This study aimed to determine the following: (1) the relation between HPV infection and the development of cutaneous squamous cell carcinoma (SCC), and (2) whether there is a correlation between p53 codon 72 polymorphism and the development of SCC. Methods—Blood samples were taken from 55 patients with skin cancer (both renal transplant recipients and immunocompetent patients with skin cancer) and 115 ethnically matched volunteers. A polymerase chain reaction based assay was used to determine p53 codon 72 genotypes. In addition, 49 benign and malignant lesions from 34 of the patients with skin cancer and 20 normal human skin samples from 20 of the control volunteers were examined for HPV. Results—The proportions of p53 codon 72 genotypes found were 78% arginine homozygous, 2% proline homozygous, and 20% heterozygous among patients with skin cancer and 79% arginine homozygous, 3.5% proline homozygous, and 17.5% heterozygous among the control population. Statistical analysis showed no significant differences in the distribution of the two p53 isoforms between the patients with skin cancer and the control population. The predominant viral types detected in both the patients and the control group were EV associated HPVs, although the incidence was lower in normal skin samples than in malignant lesions or viral warts. Conclusions—These results suggest that in a Celtic population there is no correlation between the presence of HPV, the p53 codon 72 arginine polymorphism, and the development of skin cancer. Key Words: p53 codon 72 polymorphism • human papillomavirus • skin cancer PMID:11429426

O'Connor, D; Kay, E; Leader, M; Atkins, G; Murphy, G; Mabruk, M

2001-01-01

256

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

PubMed Central

A partial nucleotide sequence that included 1,693 base pairs of the M12 (emm12) gene of group A streptococci (strain CS24) and adjacent upstream DNA was determined. Type 12 M protein-specific mRNA of strain CS24 is transcribed from two promoters (P1 and P3) separated by 30 bases. The transcription start sites of the emm12 gene were located more than 400 bases downstream of a deletion that causes decreased M-protein gene transcription in strain CS64. Deletion analysis of M protein-expressing plasmids indicated that an upstream region greater than 1 kilobase is required for M-protein gene expression. The M-protein gene transcriptional unit appears to be monocistronic. Analysis of the emm12 DNA sequence revealed three major repeat regions. Two copies of each repeat, A and B, existed within the variable 5' end of the gene; repeat C demarcated the 5' end of the constant region shared by emm12 and emm6. Images PMID:2445730

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

1987-01-01

257

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

258

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

PubMed Central

During HIV-1 infection a population of latently infected cells is established. This population is the major obstacle preventing total eradication of the virus from AIDS patients. HIV-1 latency is thought to arise by various mechanisms including repressive chromatin modifications. Transcription factors such as YY1 have been shown to facilitate repressive chromatin modifications by the recruitment of histone deacetylases. In this study, we identified a novel binding site for YY1 on the HIV-1 LTR, 120 nucleotides upstream of the transcription start site. We show that YY1 can bind to this site in vitro and in vivo and that binding to the LTR is dissociated upon T cell activation. Overexpression of YY1 causes an increase in the proportion of cells that produce latent infections. These observations, in combination with previous results, demonstrate that YY1 plays a prominent role in controlling the establishment and maintenance of latent HIV-1 provirus in unstimulated cells. PMID:24116200

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

2013-01-01

259

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

NASA Astrophysics Data System (ADS)

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

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

1989-02-01

260

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

Microsoft Academic Search

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

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

2007-01-01

261

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

262

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

PubMed Central

Genome biology of mosquitoes holds potential in developing knowledge-based control strategies against vectorborne diseases such as malaria, dengue, West Nile, and others. Although the genomes of three major vector mosquitoes have been sequenced, attempts to elucidate the relationship between intron and codon usage bias across species in phylogenetic contexts are limited. In this study, we investigated the relationship between intron content and codon bias of orthologous genes among three vector mosquito species. We found an antagonistic relationship between codon usage bias and the intron number of genes in each mosquito species. The pattern is further evident among the intronless and the intron-containing orthologous genes associated with either low or high codon bias among the three species. Furthermore, the covariance between codon bias and intron number has a directional component associated with the species phylogeny when compared with other nonmosquito insects. By applying a maximum likelihood–based continuous regression method, we show that codon bias and intron content of genes vary among the insects in a phylogeny-dependent manner, but with no evidence of adaptive radiation or species-specific adaptation. We discuss the functional and evolutionary significance of antagonistic relationships between intron content and codon bias. PMID:24187589

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

2013-01-01

263

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

PubMed

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

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

2014-02-15

264

Papillomavirus Capsid Protein Expression Level Depends on the Match between Codon Usage and tRNA Availability  

PubMed Central

Translation of mRNA encoding the L1 and L2 capsid proteins of papillomavirus (PV) is restricted in vivo to differentiated epithelial cells, although transcription of the L1 and L2 late genes occurs more widely. The codon composition of PV late genes is quite different from that of most mammalian genes. To test the possibility that PV late gene codon composition determines the efficiency of PV late gene expression in some cell types, synthetic bovine papillomavirus type 1 (BPV1) late genes were constructed with codon composition modified to resemble the typical mammalian gene. Expression of these genes from a strong promoter in Cos-1 cells was compared with expression of wild-type BPV1 late genes from the same promoter. Both unmodified and modified PV late genes were transcribed in Cos-1 cells, but only the codon-modified genes were translated. In vitro translation of wild-type but not synthetic BPV1 L1 mRNA was markedly enhanced by addition of aminoacyl-tRNAs. Codon composition thus limits BPV1 late gene translation in Cos-1 cells, and this limitation can be overcome by modification of the codon composition of the genes or by provision of excess tRNA. Replacement of codons in the green fluorescent protein (gfp) gene with those frequently used in PV late genes did not alter gfp transcription in Cos-1 cells but almost abolished translation, supporting the hypothesis that the observed differences in efficiency of translation of modified and unmodified PV capsid genes were related to codon usage rather than mRNA structure. As tRNA populations vary within and between tissues in the same eukaryotic organism, we speculate that matching of tRNA availability to codon usage may be one determinant of the restriction of expression of PV late genes to differentiated epithelium. PMID:10233959

Zhou, Jian; Liu, Wen Jun; Peng, Shi Wen; Sun, Xiao Yi; Frazer, Ian

1999-01-01

265

Explosion Clad for Upstream Oil and Gas Equipment  

Microsoft Academic Search

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.

John G. Banker; Jack Massarello; Stephane Pauly

2011-01-01

266

Hot, diamagnetic cavities upstream from the earth's bow shock  

Microsoft Academic Search

An unusual type of plasma structure was observed by ISEE-1 and -2 upstream from the earth's bow shock on eight occasions during the first 2 years of the mission. These events typically last approx.1-2 minutes and have very striking magnetic field and plasma signatures. The magnitude of the field is strongly reduced within the events, with the low-field region (the

M. F. Thomsen; J. T. Gosling; S. A. Fuselier; S. J. Bame; C.T. Russell

1986-01-01

267

Microgravity induced selective lesions in immunosignaling: Upstream targets in lymphocytes  

NASA Astrophysics Data System (ADS)

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

Sundaresan, A.; Pellis, N.

268

Catalytic Ignition and Upstream Reaction Propagation in Monolith Reactors  

NASA Technical Reports Server (NTRS)

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

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

2007-01-01

269

Short wavelength ion waves upstream of the earth's bow shock  

NASA Technical Reports Server (NTRS)

The identification and explanation of short wavelength antenna interference effects observed in spacecraft plasma wave data have provided an important new method of determining limits on the wavelength, direction of propagation, and Doppler shift of short wavelength electrostatic waves. Using the ISEE-1 wideband electric field data, antenna interference effects have been identified in the ion waves upstream of the earth's bow shock. This identification implies that wavelengths of the upstream ion waves are shorter than the antenna length. The interference effects also provide new measurements of the direction of propagation of the ion waves. The new measurements show that the wave vectors of the ion waves are not parallel to the interplanetary magnetic field (IMF) as previously reported. The direction of propagation does not appear to be controlled by the IMF. In addition, analysis of the Doppler shift of the short wavelength ion waves has provided a measurement of the dispersion relation. The upper limit of the rest frame frequency was found to be on the order of the ion plasma frequency. At this frequency, the wavelength is on the order of a few times the Debye length. The results of this study now provide strong evidence that the ion waves in the upstream region are Doppler-shifted ion acoustic waves. Previously announced in STAR as N83-36328

Fuselier, S. A.; Gurnett, D. A.

1984-01-01

270

An upstream open reading frame represses expression of Lc, a member of the R/B family of maize transcriptional activators  

SciTech Connect

The R/B genes of maize encode a family of basic helix-loop-helix proteins that determine where and when the anthocyanin-pigment pathway will be expressed in the plant. Previous studies showed that allelic diversity among family members reflects differences in gene expression, specifically in transcription initiation. The authors present evidence that the R gene Lc is under translational control. They demonstrate that the 235-nt transcript leader of Lc represses expression 25- to 30-fold in an in vivo assay. Repression is mediated by the presence in cis of a 38-codon upstream open reading frame. Furthermore, the coding capacity of the upstream open reading frame influences the magnitude of repression. It is proposed that translational control does not contribute to tissue specificity but prevents overexpression of the Lc protein. The diversity of promoter and 5' untranslated leader sequences among the R/B genes provides an opportunity to study the coevolution of transcriptional and translational mechanisms of gene regulation. 36 refs., 5 figs.

Damiani, R.D. Jr.; Wessler, S.R. (Univ. of Georgia, Athens, GA (United States))

1993-09-01

271

Enhanced bacterial expression of several mammalian cytochrome P450s by codon optimization and chaperone coexpression  

PubMed Central

To elucidate the effect of codon optimization and chaperone coexpression on the heterologous expression of mammalian cytochrome P450s in Escherichia coli, the expression of P450s 2B1, 2S1, 2U1, 2W1, and 27C1 were investigated. With codon optimization for N-terminus or the entire gene, the expression levels of P450 27C1, 2U1 and 2W1 increased 22-fold, 3.6-fold and 2.1-fold respectively, while those for P450s 2B1 and 2S1 remained unchanged. With coexpression of E. coli molecular chaperones GroEL/ES, the expression level increased up to 14-fold for P450 27C1, and 3- to 5-fold for P450s 2B1, 2S1, and 2W1. Simultaneous application of these two techniques resulted in synergetic effects. PMID:19557307

Qiao, Jing; Zhang, Zhi-Gang; Guengerich, F. Peter; Liu, Yan; Pei, Xiao-Qiong

2014-01-01

272

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

SciTech Connect

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

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

1995-09-01

273

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

PubMed Central

Nonstop decay is the mechanism of identifying and disposing aberrant transcripts that lack in-frame stop codons. It is hypothesized that these transcripts are identified during translation when the ribosome arrives at the 3? end of the mRNA and stalls. Presumably the ribosome stalling recruits additional cofactors, Ski7 and the exosome complex. The exosome degrades the transcript using either one of is ribonucleolytic activities and the ribosome and the peptide are both released. Additional precautionary measures by the nonstop decay pathway may include translational repression of the nonstop transcript after translation, and proteolysis of the released peptide by the proteasome. This surveillance mechanism protects the cells from potentially harmful truncated proteins, but it may also be involved in mediating critical cellular functions of transcripts that are prone to stop codon read-through. Important advances have been made in the past decade as we learn that nonstop decay may have implications in human disease. PMID:22740367

Klauer, A. Alejandra; van Hoof, Ambro

2013-01-01

274

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

275

Research Services START UP FUNDS  

E-print Network

Research Services START UP FUNDS www.ucalgary.ca/research START UP FUNDS From time to time some of their research program. The nature of the grants can vary. For example, some grants are discretionary allowing the researcher to use the funds for a wide variety of activities such as travel, office furniture, students

de Leon, Alex R.

276

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

277

The roles of individual eukaryotic translation initiation factors in ribosomal scanning and initiation codon selection  

PubMed Central

To elucidate an outline of the mechanism of eukaryotic translation initiation, 48S complex formation was analyzed on defined mRNAs in reactions reconstituted in vitro from fully purified translation components. We found that a ribosomal 40S subunit, eukaryotic initiation factor (eIF) 3, and the eIF2 ternary complex form a 43S complex that can bind to the 5?-end of an unstructured 5?-untranslated region (5?-UTR) and in the presence of eIF1 scan along it and locate the initiation codon without a requirement for adenosine triphosphate (ATP) or factors (eIF4A, eIF4B, eIF4F) associated with ATP hydrolysis. Scanning on unstructured 5?-UTRs was enhanced by ATP, eIFs 4A and 4B, and the central domain of the eIF4G subunit of eIF4F. Their omission increased the dependence of scanning on eIFs 1 and 1A. Ribosomal movement on 5?-UTRs containing even weak secondary structures required ATP and RNA helicases. eIF4F was essential for scanning, and eIFs 4A and 4B were insufficient to promote this process in the absence of eIF4F. We report that in addition to its function in scanning, eIF1 also plays a principal role in initiation codon selection. In the absence of eIF1, 43S complexes could no longer discriminate between cognate and noncognate initiation codons or sense the nucleotide context of initiation codons and were able to assemble 48S complexes on 5?-proximal AUG triplets located only 1, 2, and 4 nt from the 5?-end of mRNA. PMID:12435632

Pestova, Tatyana V.; Kolupaeva, Victoria G.

2002-01-01

278

Aminoglycoside suppression at UAG, UAA and UGA codons in Escherichia coli and human tissue culture cells  

Microsoft Academic Search

Summary  We have compared the suppression of nonsense mutations by aminoglycoside antibiotics inEscherichia coli and in human 293 cells. Six nonsense alleles of the chloramphenicol acetyl transferase (cat) gene, in the vector pRSVcat, were suppressed by growth in G418 and paromomycin. Readthrough at UAG, UAA and UGA codons was monitored with enzyme assays\\u000a for chloramphenicol acetyl transferase (CAT), in stably transformed

Robin Martin; Anne E. Mogg; Louise A. Heywood; Lars Nitschke; Julian F. Burke

1989-01-01

279

Recurrent mutations at codon 625 of the splicing factor SF3B1 in uveal melanoma.  

PubMed

Uveal melanoma is the most common primary cancer of the eye and often results in fatal metastasis. Here, we describe mutations occurring exclusively at codon 625 of the SF3B1 gene, encoding splicing factor 3B subunit 1, in low-grade uveal melanomas with good prognosis. Thus, uveal melanoma is among a small group of cancers associated with SF3B1 mutations, and these mutations denote a distinct molecular subset of uveal melanomas. PMID:23313955

Harbour, J William; Roberson, Elisha D O; Anbunathan, Hima; Onken, Michael D; Worley, Lori A; Bowcock, Anne M

2013-02-01

280

Glutathione Peroxidase Codon 198 Polymorphism Variant Increases Lung Cancer Risk1  

Microsoft Academic Search

Human cellular glutathione peroxidase 1 (hGPX1) is a selenium-depen- dent enzyme that participates in the detoxification of hydrogen peroxide and a wide range of organic peroxides. We conducted a case-control study nested within the a-Tocopherol, b-Carotene Cancer Prevention Study cohort to evaluate the association between the proline to leucine polymor- phism at codon 198 of hGPX1 and lung cancer risk.

Duminda Ratnasinghe; Joseph A. Tangrea; Mark R. Andersen; Michael J. Barrett; Jarmo Virtamo; Philip R. Taylor; Demetrius Albanes

281

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

PubMed

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

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

2013-09-01

282

Relationship between codon biased genes, microarray expression values and physiological characteristics of Streptococcus pneumoniae  

Microsoft Academic Search

A codon-profile strategy was used to predict gene expression levels in Streptococcus pneumoniae. Predicted highly expressed (PHE) genes included those encoding glycolytic and fermentative enzymes, sugar-conversion systems and carbohydrate-transporters. Additionally, some genes required for infection that are involved in oxidative metabolism and hydrogen peroxide production were PHE. Low expression values were predicted for genes encoding specific regulatory proteins like two-component

Antonio J. Martin-Galiano; Jerry M. Wells; Adela G. de la Campa

2004-01-01

283

Effect of codon optimisation on the production of recombinant fish growth hormone in Pichia pastoris.  

PubMed

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; Huy, Teh Ser; Mohamed, Zulqarnain

2014-01-01

284

Codon insertion and deletion functions as a somatic diversification mechanism in human antibody repertoires  

PubMed Central

It has been suggested that codon insertion and/or deletion may represent a mechanism that, along with hypermutation, contributes to the affinity maturation of antibodies. We used repertoire cloning to examine human antibodies directed against 3 carbohydrate antigens and 1 protein antigen for the presence of such modifications. We find that both the insertion and deletion of codons occur frequently in antigen-specific responses following vaccination. Codon insertions and deletions were observed most often in the complementarity determining regions, and less frequently in the framework regions, of VH, V?, and V? gene segments, and involved motifs known to be preferred targets of somatic hypermutation. Clonal lineage analysis shows that these events occur through out the course of the somatic maturation of individual antibody clones. We also determined that these alterations of paratope structure have varying effects on the relative affinity of the binding site for its cognate antigen. Reviewers This article was reviewed by Mark Shlomchik, Deborah Dunn-Walters (nominated by Dr. Andrew Macpherson), and Rachel M. Gerstein. Open peer review Reviewed by Mark Shlomchik, Deborah Dunn-Walters (nominated by Dr. Andrew Macpherson), and Rachel M. Gerstein. For the full reviews, please go to the Reviewers' comments section. PMID:16942619

Reason, Donald C; Zhou, Jianhui

2006-01-01

285

General trends in selectively driven codon usage biases in the domain archaea.  

PubMed

Since the advent of rapid techniques for sequencing DNA in the mid 70's, it became clear that all codons coding for the same amino acid are not used according to neutral expectations. In the last 30 years, several theories were proposed for explaining this fact. However, the most important concepts were the result of analyses carried out in Bacteria, and unicellular and multicellular eukaryotes like mammals (in other words, in two of the three Domains of life). In this communication, we study the main forces that shape codon usage in Archaeae under an evolutionary perspective. This is important because, as known, the orthologous genes related with the informational system in this Domain (replication, transcription and translation) are more similar to eukaryotes than to Bacteria. Our results show that the effect of selection acting at the level of translation is present in the Domain but mainly restricted to only a phylum (Euryarchaeota) and therefore is not as extended as in Bacteria. Besides, we describe the phylogenetic distribution of translational optimal codons and estimate the effect of selection acting at the level of accuracy. Finally, we discuss these results under some peculiarities that characterize this Domain. PMID:25239794

Iriarte, Andrés; Jara, Eugenio; Leytón, Lucía; Diana, Leticia; Musto, Héctor

2014-10-01

286

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

2013-01-01

287

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

PubMed

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

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

2013-01-01

288

Codon Optimization Significantly Improves the Expression Level of a Keratinase Gene in Pichia pastoris  

PubMed Central

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

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

2013-01-01

289

Analysis of PRNP gene codon 129 polymorphism in the Greek population.  

PubMed

Creutzfeldt-Jakob disease (CJD) is a fatal transmissible neurodegenerative prion disease with a rapid progression comprising familial, sporadic, iatrogenic and variant forms. A polymorphism at codon 129 of PRNP gene has been implicated in the development of variant CJD. We examined Met/Val allele frequencies and the genotype distribution, with respect to the polymorphic codon 129 of PRNP gene in 348 healthy individuals from the region of Athens, Greece. The following genotype frequencies were observed in the Greek population: Met/Met 50%, Met/Val 39% and Val/Val 11%. The presence of the Methionine allele frequencies in various European populations, according to the published data, increases gradually from northwestern to southeastern countries, implying the presence of a cline. The distribution of genotypes of Met homozygotes displays random declination across the 10 compared populations. The observed higher frequency of Met homozygotes at codon 129 does not necessarily suggest that these populations are at increased risk of developing CJD. PMID:16547836

Saetta, Angelica A; Michalopoulos, Nikolaos V; Malamis, George; Papanastasiou, Polyanthi I; Mazmanian, Niki; Karlou, Maria; Kouzoupis, Anastasios; Korkolopoulou, Penelope; Patsouris, Efstratios

2006-01-01

290

Codon-based phylogenetics introduces novel flagellar gene markers to oomycete systematics.  

PubMed

Oomycete systematics has traditionally been reliant on ribosomal RNA and mitochondrial cytochrome oxidase sequences. Here we report the use of two single-copy protein-coding flagellar genes, PF16 and OCM1, in oomycete systematics, showing their utility in phylogenetic reconstruction and species identification. Applying a recently proposed mutation-selection model of codon substitution, the phylogenetic relationships inferred by flagellar genes are largely in agreement with the current views of oomycete evolution, whereas nucleotide- and amino acid-level models produce biologically implausible reconstructions. Interesting parallels exist between the phylogeny inferred from the flagellar genes and zoospore ontology, providing external support for the tree obtained using the codon model. The resolution achieved for species identification is ample using PF16, and quite robust using OCM1, and the described PCR primers are able to amplify both genes for a range of oomycete genera. Altogether, when analyzed with a rich codon substitution model, these flagellar genes provide useful markers for the oomycete molecular toolbox. PMID:24747002

Robideau, Gregg P; Rodrigue, Nicolas; André Lévesque, C

2014-10-01

291

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses  

PubMed Central

Several codon-based methods are available for detecting adaptive evolution in protein-coding sequences, but to date none specifically identify sites that are selected differentially in two populations, although such comparisons between populations have been historically useful in identifying the action of natural selection. We have developed two fixed effects maximum likelihood methods: one for identifying codon positions showing selection patterns that persist in a population and another for detecting whether selection is operating differentially on individual codons of a gene sampled from two different populations. Applying these methods to two HIV populations infecting genetically distinct human hosts, we have found that few of the positively selected amino acid sites persist in the population; the other changes are detected only at the tips of the phylogenetic tree and appear deleterious in the long term. Additionally, we have identified seven amino acid sites in protease and reverse transcriptase that are selected differentially in the two samples, demonstrating specific population-level adaptation of HIV to human populations. PMID:16789820

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

2006-01-01

292

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

PubMed Central

The aim of the present study was to determine the relationship between p53 gene codon-72 polymorphisms and hypertrophic scar formation following caesarean section (CS). Blood samples from 260 female patients were collected one week following a CS for the detection of p53 gene polymorphisms using a molecular beacon-coupled quantitative polymerase chain reaction technique. Patients had follow-ups for 12–18 months to observe the scar formation. From these observations, the relationship between the p53 codon-72 polymorphisms and hypertrophic scar formation occurrence was investigated. Among the patients with the CCC/CCC genotype, nine patients had hypertrophic scars and 46 patients showed normal healing, which is a ratio of 0.19. However, the follow-up investigations indicated that the presence of a homozygous or heterozygous C-to-G alteration at the codon-72 site in gene p53 resulted in 13 patients with hypertrophic scars and 192 patients with normal healing, which is a ratio of 0.07. Therefore, these results indicate that patients with the CCC/CCC genotype had a higher risk of developing hypertrophic scars compared with that for patients with the CCC/CGC or CGC/CGC genotypes. PMID:24940419

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

2014-01-01

293

How to start up a start-up  

NASA Astrophysics Data System (ADS)

Researchers are increasingly toying with the idea of taking their ideas out of universities and into the marketplace. Starting your own company can be extremely rewarding, but it requires perseverance and a great deal of hard work.

Wyant, James C.

2007-06-01

294

Experimentally increased codon bias in the Drosophila Adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity.  

PubMed

Although most amino acids can be encoded by more than one codon, the synonymous codons are not used with equal frequency. This phenomenon is known as codon bias and appears to be a universal feature of genomes. The translational selection hypothesis posits that the use of optimal codons, which match the most abundant species of isoaccepting tRNAs, results in increased translational efficiency and accuracy. Previous work demonstrated that the experimental reduction of codon bias in the Drosophila alcohol dehydrogenase (Adh) gene led to a significant decrease in ADH protein expression. In this study we performed the converse experiment: we replaced seven suboptimal leucine codons that occur naturally in the Drosophila melanogaster Adh gene with the optimal codon. We then compared the in vivo ADH activities imparted by the wild-type and mutant alleles. The introduction of optimal leucine codons led to an increase in ADH activity in third-instar larvae. In adult flies, however, the introduction of optimal codons led to a decrease in ADH activity. There is no evidence that other selectively constrained features of the Adh gene, or its rate of transcription, were altered by the synonymous replacements. These results are consistent with translational selection for codon bias being stronger in the larval stage and suggest that there may be a selective conflict over optimal codon usage between different developmental stages. PMID:19966063

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

2010-02-01

295

Tackling group-level traits by starting at the start.  

PubMed

We agree that emergent group-level properties are important; however, we disagree that current approaches, especially culture-gene coevolutionary (CGC) approaches, have neglected them. We explain how CGC helps demystify the tumult of humans' group-level complexity by "starting at the start," and why (a) assuming undifferentiated individuals and (b) focusing on cooperation are actually powerful tools to this end. PMID:24970402

Chudek, Maciej; Henrich, Joseph

2014-06-01

296

Hydrazine engine start system air start performance and controls sizing  

SciTech Connect

Hydrazine has been used as an energy source in many applications to fuel in-flight main engine starting. In a current application, an existing hydrazine engine start system (ESS) design was adapted to meet new fuel control requirements. This paper presents a brief system description, historical context, and the motivating factors for the hydrazine controls changes and three case studies of controls design and analysis from the ESS program. 4 refs.

Johnson, A.T.

1992-01-01

297

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

PubMed Central

PrP genotypes at codons 136 and 171 in 120 Iranian Ghezel sheep breeds were studied using allele-specific PCR amplification and compared with the well-known sheep breeds in North America, the United States and Europe. The frequency of V allele and VV genotype at codon 136 of Ghezel sheep breed was significantly lower than AA and AV. At codon 171, the frequency of allele H was significantly lower than Q and R. Despite the similarities of PrP genotypes at codons 136 and 171 between Iranian Ghezel sheep breeds and some of the studied breeds, significant differences were found with others. Planning of effective breeding control and successful eradication of susceptible genotypes in Iranian Ghezel sheep breeds will not be possible unless the susceptibility of various genotypes in Ghezel sheep breeds to natural or experimental scrapie has been elucidated. PMID:21778818

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

2011-01-01

298

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

PubMed

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

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

2011-01-01

299

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

PubMed Central

Over 300 amino acids are found in proteins in nature, yet typically only 20 are genetically encoded. Reassigning stop codons and use of quadruplet codons emerged as the main avenues for genetically encoding non-canonical amino acids (NCAAs). Canonical aminoacyl-tRNAs with near-cognate anticodons also read these codons to some extent. This background suppression leads to ‘statistical protein’ that contains some natural amino acid(s) at a site intended for NCAA. We characterize near-cognate suppression of amber, opal and a quadruplet codon in common Escherichia coli laboratory strains and find that the PylRS/tRNAPyl orthogonal pair cannot completely outcompete contamination by natural amino acids. PMID:23036644

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

2012-01-01

300

The START III bargaining space  

SciTech Connect

The declining state of the Russian military and precarious Russian economic condition will give the US considerable advantages at the START III bargaining table. Taking the US-RF asymmetries into account, this paper discusses a menu of START III measures the US could ask for, and measures it could offer in return, in attempting to negotiate an equitable treaty. Measures the US might seek in a START III treaty include: further reductions in deployed strategic nuclear warheads, irreversibility of reductions through warhead dismantlement; beginning to bring theater nuclear weapons under mutual control, and increased transparency into the Russian nuclear weapons complex. The US may, however, wish to apply its bargaining advantages to attempting to achieve the first steps toward two long-range goals that would enhance US security: bringing theater nuclear weapons into the US-RF arms control arena, and increasing transparency into the Russian nuclear weapons complex. In exchange for measures relating to these objectives, the US might consider offering to Russia: Further strategic weapons reductions approaching levels at which the Russians believe they could maintain a degree of parity with the US; Measures to decrease the large disparities in potential deliver-system uploading capabilities that appear likely under current START II/START III scenarios; and Financial assistance in achieving START II/START III reductions as rapidly as is technically possible.

Karas, T.H.

1998-08-01

301

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

302

Upstream traffic multiplexing in photonic ATM access networks  

NASA Astrophysics Data System (ADS)

For the future development of residential broadband telecommunication services the present access infrastructure must be upgraded. Fiber-To-The-Home (FTTH) optical networks, though still expensive today, appear to be a future-proof solution. FTTH networks based on passive optical Remote Nodes (RN) and supporting ATM switching (ATM-PONs) have been demonstrated and are going to be standardized. In these networks the optical hardware in the RN is very simple, but a multiple access protocol is needed for upstream traffic control. In most protocols proposed in literature the control is performed electronically in a centralized way by the Central Office. In this paper we study multiple access schemes for FTTH networks which perform upstream traffic control in a distributed way with the intervention of the user Optical Network Terminations (ONTs) and of the RN only. We will also consider the case, based on recent research in photonic packet switching, in which the RN is able to perform all-optical ATM-multiplexing. We will employ ONT-RN signalling to make the relatively expensive RN optical buffer co-operate with the electronic buffers located in the ONTs. The different solutions presented will be compared by simulating the network behavior under various traffic conditions. In conclusion, in this work we evaluate performance advantages achievable in FTTH networks by increasing the optical complexity of the RN and by introducing control schemes which allow a distributed upstream traffic management and, in the case of an RN able to perform all-optical ATM-multiplexing, the co-operation of the RN buffer with the ONT buffers.

Girola, Giovanna; Maier, Guido A.; Martinelli, Mario; Pattavina, Achille

1998-10-01

303

Increased risk of oesophageal adenocarcinoma among upstream petroleum workers  

PubMed Central

Objectives To investigate cancer risk, particularly oesophageal cancer, among male upstream petroleum workers offshore potentially exposed to various carcinogenic agents. Methods Using the Norwegian Registry of Employers and Employees, 24 765 male offshore workers registered from 1981 to 2003 was compared with 283 002 male referents from the general working population matched by age and community of residence. The historical cohort was linked to the Cancer Registry of Norway and the Norwegian Cause of Death Registry. Results Male offshore workers had excess risk of oesophageal cancer (RR 2.6, 95% CI 1.4 to 4.8) compared with the reference population. Only the adenocarcinoma type had a significantly increased risk (RR 2.7, 95% CI 1.0 to 7.0), mainly because of an increased risk among upstream operators (RR 4.3, 95% CI 1.3 to 14.5). Upstream operators did not have significant excess of respiratory system or colon cancer or mortality from any other lifestyle-related diseases investigated. Conclusion We found a fourfold excess risk of oesophageal adenocarcinoma among male workers assumed to have had the most extensive contact with crude oil. Due to the small number of cases, and a lack of detailed data on occupational exposure and lifestyle factors associated with oesophageal adenocarcinoma, the results must be interpreted with caution. Nevertheless, given the low risk of lifestyle-related cancers and causes of death in this working group, the results add to the observations in other low-powered studies on oesophageal cancer, further suggesting that factors related to the petroleum stream or carcinogenic agents used in the production process might be associated with risk of oesophageal adenocarcinoma. PMID:19858535

Kirkeleit, Jorunn; Riise, Trond; Bj?rge, Tone; Moen, Bente E; Bratveit, Magne; Christiani, David C

2013-01-01

304

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

305

Decoding system for the AUA codon by tRNAIle with the UAU anticodon in Mycoplasma mobile  

PubMed Central

Deciphering the genetic code is a fundamental process in all living organisms. In many bacteria, AUA codons are deciphered by tRNAIle2 bearing lysidine (L) at the wobble position. L is a modified cytidine introduced post-transcriptionally by tRNAIle-lysidine synthetase (TilS). Some bacteria, including Mycoplasma mobile, do not carry the tilS gene, indicating that they have established a different system to decode AUA codons. In this study, tRNAIle2 has been isolated from M. mobile and was found to contain a UAU anticodon without any modification. Mycoplasma mobile isoleucyl-tRNA synthetase (IleRS) recognized the UAU anticodon, whereas Escherichia coli IleRS did not efficiently aminoacylate tRNAIle2UAU. In M. mobile IleRS, a single Arg residue at position 865 was critical for specificity for the UAU anticodon and, when the corresponding site (W905) in E. coli IleRS was substituted with Arg, the W905R mutant efficiently aminoacylated tRNA with UAU anticodon. Mycoplasma mobile tRNAIle2 cannot distinguish between AUA and AUG codon on E. coli ribosome. However, on M. mobile ribosome, M. mobile tRNAIle2UAU specifically recognized AUA codon, and not AUG codon, suggesting M. mobile ribosome has a property that prevents misreading of AUG codon. These findings provide an insight into the evolutionary reorganization of the AUA decoding system. PMID:23295668

Taniguchi, Takaaki; Miyauchi, Kenjyo; Nakane, Daisuke; Miyata, Makoto; Muto, Akira; Nishimura, Susumu; Suzuki, Tsutomu

2013-01-01

306

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

PubMed Central

Class 1 release factor in eukaryotes (eRF1) recognizes stop codons and promotes peptide release from the ribosome. The ‘molecular mimicry’ hypothesis suggests that domain 1 of eRF1 is analogous to the tRNA anticodon stem–loop. Recent studies strongly support this hypothesis and several models for specific interactions between stop codons and residues in domain 1 have been proposed. In this study we have sequenced and identified novel eRF1 sequences across a wide diversity of eukaryotes and re-evaluated the codon-binding site by bioinformatic analyses of a large eRF1 dataset. Analyses of the eRF1 structure combined with estimates of evolutionary rates at amino acid sites allow us to define the residues that are under structural (i.e. those involved in intramolecular interactions) versus non-structural selective constraints. Furthermore, we have re-assessed convergent substitutions in the ciliate variant code eRF1s using maximum likelihood-based phylogenetic approaches. Our results favor the model proposed by Bertram et al. that stop codons bind to three ‘cavities’ on the protein surface, although we suggest that the stop codon may bind in the opposite orientation to the original model. We assess the feasibility of this alternative binding orientation with a triplet stop codon and the eRF1 domain 1 structures using molecular modeling techniques. PMID:11788716

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

2002-01-01

307

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

PubMed

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

2015-01-01

308

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

309

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

310

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

311

Quantum Espresso Quick Start Introduction  

E-print Network

Quantum Espresso Quick Start Introduction Quantum Espresso (http://www.quantum properties eg., phonon dispersion, NMR shifts and band structure to name a few. Quantum Espresso is available. Matter 21, 395502 (2009). Online Guide for QE : http://www.quantum

Bjørnstad, Ottar Nordal

312

A Large Eddy Simulation Study for upstream wind energy conditioning  

NASA Astrophysics Data System (ADS)

The wind energy industry is increasingly focusing on optimal power extraction strategies based on layout design of wind farms and yaw alignment algorithms. Recent field studies by Mikkelsen et al. (Wind Energy, 2013) have explored the possibility of using wind lidar technology installed at hub height to anticipate incoming wind direction and strength for optimizing yaw alignment. In this work we study the benefits of using remote sensing technology for predicting the incoming flow by using large eddy simulations of a wind farm. The wind turbines are modeled using the classic actuator disk concept with rotation, together with a new algorithm that permits the turbines to adapt to varying flow directions. This allows for simulations of a more realistic atmospheric boundary layer driven by a time-varying geostrophic wind. Various simulations are performed to investigate possible improvement in power generation by utilizing upstream data. Specifically, yaw-correction of the wind-turbine is based on spatio-temporally averaged wind values at selected upstream locations. Velocity and turbulence intensity are also considered at those locations. A base case scenario with the yaw alignment varying according to wind data measured at the wind turbine's hub is also used for comparison. This reproduces the present state of the art where wind vanes and cup anemometers installed behind the rotor blades are used for alignment control.

Sharma, V.; Calaf, M.; Parlange, M. B.

2013-12-01

313

Flow Directs Surface-Attached Bacteria to Twitch Upstream  

PubMed Central

Bacteria inhabit a wide variety of environments in which fluid flow is present, including healthcare and food processing settings and the vasculature of animals and plants. The motility of bacteria on surfaces in the presence of flow has not been well characterized. Here we focus on Pseudomonas aeruginosa, an opportunistic human pathogen that thrives in flow conditions such as in catheters and respiratory tracts. We investigate the effects of flow on P. aeruginosa cells and describe a mechanism in which surface shear stress orients surface-attached P. aeruginosa cells along the flow direction, causing cells to migrate against the flow direction while pivoting in a zig-zag motion. This upstream movement is due to the retraction of type IV pili by the ATPase motors PilT and PilU and results from the effects of flow on the polar localization of type IV pili. This directed upstream motility could be beneficial in environments where flow is present, allowing bacteria to colonize environments that cannot be reached by other surface-attached bacteria. PMID:22828341

Shen, Yi; Siryaporn, Albert; Lecuyer, Sigolene; Gitai, Zemer; Stone, Howard A.

2012-01-01

314

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

315

Context-dependent codon partition models provide significant increases in model fit in atpB and rbcL protein-coding genes  

PubMed Central

Background Accurate modelling of substitution processes in protein-coding sequences 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 at a low computational cost. Such codon partition models however impose independent evolution of the different codon positions, which is overly restrictive from a biological point of view. Given that empirical research has provided indications of context-dependent substitution patterns at four-fold degenerate sites, we take those indications into account in this paper. Results We present so-called context-dependent codon partition models to assess previous empirical claims that the evolution of four-fold degenerate sites is strongly dependent on the composition of its two flanking bases. To this end, we have estimated and compared various existing independent models, codon models, codon partition models and context-dependent codon partition models for the atpB and rbcL genes of the chloroplast genome, which are frequently used in plant systematics. Such context-dependent codon partition models employ a full dependency scheme for four-fold degenerate sites, whilst maintaining the independence assumption for the first and second codon positions. Conclusions We show that, both in the atpB and rbcL alignments of a collection of land plants, these context-dependent codon partition models significantly improve model fit over existing codon partition models. Using Bayes factors based on thermodynamic integration, we show that in both datasets the same context-dependent codon partition model yields the largest increase in model fit compared to an independent evolutionary model. Context-dependent codon partition models hence perform closer to codon models, which remain the best performing models at a drastically increased computational cost, compared to codon partition models, but remain computationally interesting alternatives to codon models. Finally, we observe that the substitution patterns in both datasets are drastically different, leading to the conclusion that combined analysis of these two genes using a single model may not be advisable from a context-dependent point of view. PMID:21619569

2011-01-01

316

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

PubMed Central

Background Human cadavers are crucial to numerous aspects of health care, including initial and continuing training of medical doctors and advancement of medical research. Concerns have periodically been raised about the limited number of whole body donations. Little is known, however, about a unique form of donation, namely co-donations or instances when married individuals decide to register at the same time as their spouse as whole body donors. Our study aims to determine the extent of whole body co-donation and individual factors that might influence co-donation. Methods and Findings We reviewed all records of registrants to the University of Hawaii Medical School’s whole body donation program from 1967 through 2006 to identify married registrants. We then examined the 806 married individuals’ characteristics to understand their decision to register alone or with their spouse. We found that married individuals who registered at the same time as their spouse accounted for 38.2 percent of married registrants. Sex differences provided an initial lens to understand co-donation. Wives were more likely to co-donate than to register alone (p?=?0.002). Moreover, registrants’ main occupational background had a significant effect on co-donations (p?=?0.001). Married registrants (regardless of sex) in female-gendered occupations were more likely to co-donate than to donate alone (p?=?0.014). Female-gendered occupations were defined as ones in which women represented more than 55 percent of the workforce (e.g., preschool teachers). Thus, variations in donors’ occupational backgrounds explained co-donation above and beyond sex differences. Conclusions Efforts to secure whole body donations have historically focused on individual donations regardless of donors’ marital status. More attention needs to be paid, however, to co-donations since they represent a non-trivial number of total donations. Also, targeted outreach efforts to male and female members of female-gendered occupations might prove a successful way to increase donations through co-donations. PMID:22880077

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

2012-01-01

317

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

PubMed

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

Michel, C J

1989-12-01

318

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

PubMed

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

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

2012-01-01

319

Parents Should Start Talking Before They Start Drinking  

Microsoft Academic Search

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

Donnis Reese

320

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

321

Attenuation of human respiratory syncytial virus by genome-scale codon-pair deoptimization.  

PubMed

Human respiratory syncytial virus (RSV) is the most important viral agent of serious pediatric respiratory-tract disease worldwide. A vaccine or generally effective antiviral drug is not yet available. We designed new live attenuated RSV vaccine candidates by codon-pair deoptimization (CPD). Specifically, viral ORFs were recoded by rearranging existing synonymous codons to increase the content of underrepresented codon pairs. Amino acid coding was completely unchanged. Four CPD RSV genomes were designed in which the indicated ORFs were recoded: Min A (NS1, NS2, N, P, M, and SH), Min B (G and F), Min L (L), and Min FLC (all ORFs except M2-1 and M2-2). Surprisingly, the recombinant CPD viruses were temperature-sensitive for replication in vitro (level of sensitivity: Min FLC > Min L > Min B > Min A). All of the CPD mutants grew less efficiently in vitro than recombinant wild-type (WT) RSV, even at the typically permissive temperature of 32 °C (growth efficiency: WT > Min L > Min A > Min FLC > Min B). CPD of the ORFs for the G and F surface glycoproteins provided the greatest restrictive effect. The CPD viruses exhibited a range of restriction in mice and African green monkeys comparable with that of two attenuated RSV strains presently in clinical trials. This study provided a new type of attenuated RSV and showed that CPD can rapidly generate vaccine candidates against nonsegmented negative-strand RNA viruses, a large and expanding group that includes numerous pathogens of humans and animals. PMID:25157129

Le Nouën, Cyril; Brock, Linda G; Luongo, Cindy; McCarty, Thomas; Yang, Lijuan; Mehedi, Masfique; Wimmer, Eckard; Mueller, Steffen; Collins, Peter L; Buchholz, Ursula J; DiNapoli, Joshua M

2014-09-01

322

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

PubMed

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 (IC(50) = 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

2009-03-01

323

EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas.  

PubMed

Mutations at codon 641 of EZH2 are recurrent in germinal center B cell lymphomas, and the most common variants lead to altered EZH2 enzymatic activity and enhanced tri-methylation of histone H3 at lysine 27, a repressive chromatin modification. As an initial step toward screening patients for cancer genotype-directed therapy, we developed a screening assay for EZH2 codon 641 mutations amenable for testing formalin-fixed clinical specimens, based on the sensitive SNaPshot single nucleotide extension technology. We detected EZH2 mutations in 12/55 (22%) follicular lymphomas (FL), 5/35 (14%) diffuse large B cell lymphomas with a germinal center immunophenotype (GCB-DLBCL), and 2/11 (18%) high grade B cell lymphomas with concurrent rearrangements of BCL2 and MYC. No EZH2 mutations were detected in cases of Burkitt lymphoma (0/23). EZH2 mutations were frequently associated with the presence of BCL2 rearrangement (BCL2-R) in both the FL (28% of BCL-R cases versus 0% of BCL2-WT cases, p<0.05) and GCB-DLBCL groups (33% of BCL2-R cases versus 4% of BCL2-WT cases, p<0.04), and across all lymphoma types excluding BL (27% of BCL2-R cases versus 3% of BCL2-WT cases, p<0.003). We confirmed gain-of-function activity for all previously reported EZH2 codon 641 mutation variants. Our findings suggest that EZH2 mutations constitute an additional genetic "hit" in many BCL2-rearranged germinal center B cell lymphomas. Our work may be helpful in the selection of lymphoma patients for future trials of pharmacologic agents targeting EZH2 and EZH2-regulated pathways. PMID:22194861

Ryan, Russell J H; Nitta, Mai; Borger, Darrell; Zukerberg, Lawrence R; Ferry, Judith A; Harris, Nancy Lee; Iafrate, A John; Bernstein, Bradley E; Sohani, Aliyah R; Le, Long Phi

2011-01-01

324

EZH2 Codon 641 Mutations are Common in BCL2-Rearranged Germinal Center B Cell Lymphomas  

PubMed Central

Mutations at codon 641 of EZH2 are recurrent in germinal center B cell lymphomas, and the most common variants lead to altered EZH2 enzymatic activity and enhanced tri-methylation of histone H3 at lysine 27, a repressive chromatin modification. As an initial step toward screening patients for cancer genotype-directed therapy, we developed a screening assay for EZH2 codon 641 mutations amenable for testing formalin-fixed clinical specimens, based on the sensitive SNaPshot single nucleotide extension technology. We detected EZH2 mutations in 12/55 (22%) follicular lymphomas (FL), 5/35 (14%) diffuse large B cell lymphomas with a germinal center immunophenotype (GCB-DLBCL), and 2/11 (18%) high grade B cell lymphomas with concurrent rearrangements of BCL2 and MYC. No EZH2 mutations were detected in cases of Burkitt lymphoma (0/23). EZH2 mutations were frequently associated with the presence of BCL2 rearrangement (BCL2-R) in both the FL (28% of BCL-R cases versus 0% of BCL2-WT cases, p<0.05) and GCB-DLBCL groups (33% of BCL2-R cases versus 4% of BCL2-WT cases, p<0.04), and across all lymphoma types excluding BL (27% of BCL2-R cases versus 3% of BCL2-WT cases, p<0.003). We confirmed gain-of-function activity for all previously reported EZH2 codon 641 mutation variants. Our findings suggest that EZH2 mutations constitute an additional genetic “hit” in many BCL2-rearranged germinal center B cell lymphomas. Our work may be helpful in the selection of lymphoma patients for future trials of pharmacologic agents targeting EZH2 and EZH2-regulated pathways. PMID:22194861

Ryan, Russell J. H.; Nitta, Mai; Borger, Darrell; Zukerberg, Lawrence R.; Ferry, Judith A.; Harris, Nancy Lee; Iafrate, A. John; Bernstein, Bradley E.

2011-01-01

325

The p53 Codon 72 Polymorphism Modifies the Cellular Response to Inflammatory Challenge in the Liver  

PubMed Central

The p53 protein is a critical stress-response mediator and signal coordinator in cellular metabolism and environmental exposure to deleterious agents. In human populations, the p53 gene contains a common single nucleotide polymorphism (SNP) affecting codon 72 that determines whether a proline (P72) or an arginine (R72) is present at this amino acid position of the polypeptide. Previous studies carried out using human populations, mouse models, and cell culture analyses have provided evidence that this amino acid difference can alter p53 functional activities, and potentially also can affect clinical presentation of disease. The clinical presentation associated with many forms of liver disease is variable, but few of the responsible underlying genetic factors or molecular pathways have been identified. The aim of the present study was to investigate whether the p53 codon 72 polymorphism influences the cellular response to hepatic stresses. A humanized p53 knock-in (Hupki) mouse model was used to address this issue. Mice expressing either the P72 or R72 normal variation of p53 were given an acute-, intermittent- or a chronic challenge, associated with exposure to lipopolysaccharide, D-galactosamine, or a high-fat diet. The results reveal that the livers of the P72 and R72 mice exhibit notable differences in inflammatory and apoptotic response to these distinct forms of stress. Interestingly the influence of this polymorphism on the response to stress is context dependent, with P72 showing increased response to liver toxins (lipopolysaccharide and D-galactosamine), but R72 showing increased response to metabolic stress (high fat diet). When taken together, these data point to the p53 codon 72 polymorphism as an important molecular mediator of events contributing to hepatic inflammation and metabolic homeostasis. PMID:23991369

Leu, Julia I-Ju; Murphy, Maureen E; George, Donna L

2013-01-01

326

E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI)  

PubMed Central

Background The Codon Adaptation Index (CAI) is a measure of the synonymous codon usage bias for a DNA or RNA sequence. It quantifies the similarity between the synonymous codon usage of a gene and the synonymous codon frequency of a reference set. Extreme values in the nucleotide or in the amino acid composition have a large impact on differential preference for synonymous codons. It is thence essential to define the limits for the expected value of CAI on the basis of sequence composition in order to properly interpret the CAI and provide statistical support to CAI analyses. Though several freely available programs calculate the CAI for a given DNA sequence, none of them corrects for compositional biases or provides confidence intervals for CAI values. Results The E-CAI server, available at , is a web-application that calculates an expected value of CAI for a set of query sequences by generating random sequences with G+C and amino acid content similar to those of the input. An executable file, a tutorial, a Frequently Asked Questions (FAQ) section and several examples are also available. To exemplify the use of the E-CAI server, we have analysed the codon adaptation of human mitochondrial genes that codify a subunit of the mitochondrial respiratory chain (excluding those genes that lack a prokaryotic orthologue) and are encoded in the nuclear genome. It is assumed that these genes were transferred from the proto-mitochondrial to the nuclear genome and that its codon usage was then ameliorated. Conclusion The E-CAI server provides a direct threshold value for discerning whether the differences in CAI are statistically significant or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences. PMID:18230160

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

2008-01-01

327

Evolution of the vesicular stomatitis viruses: Divergence and codon usage bias.  

PubMed

Four Vesiculovirus species causing vesicular stomatitis in the Americas, together with two closely related insect isolates, can be phyletically classified into two major groups: New Jersey (NJ) and Indiana (IN). Here, Bayesian coalescent analyses were conducted to the time-stamped entire coding sequences of the G gene of these vesiculoviruses, with emphasis on their divergence scenario. The primary bifurcation was a much ancient event that might have taken place around 1.8 million years ago between NJ and IN, which shared a similar high mean rate. Interestingly, the overall codon usage bias pattern of these viruses resembled that of the insect vectors rather than the livestock hosts. PMID:25172582

Liang, Yang; He, Mei; Teng, Chun-Bo

2014-11-01

328

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

329

Hot, diamagnetic cavities upstream from the earth's bow shock  

NASA Technical Reports Server (NTRS)

On eight occasions the ISEE 1 and 2 spacecraft registered peculiar plasma structures upstream of the earth's bow shock. The events exhibit a temporary, strong reduction in the magnitude of the magnetic field and strong enhancements of the field strength bordering the reduction zone. The low field strength regions featured temperatures from 1-10 million k and pressure an order of magnitude greater than the solar wind. The pressure gradients exceeded the magnetic tension around the structures, although the field of the cavities may be a closed structure. A model is proposed of hot, expanding diamagnetic plasma cavities with scales on the order of a few earth radii. Speculations on the interaction and origin or impetus for the cavities within the bow shock, foreshock, the magnetosphere and the solar wind are discussed. Similarities between the phenomena detected and signatures obtained with the AMPTE releases of chemicals in the solar wind are noted.

Thomsen, M. F.; Gosling, J. T.; Fuselier, S. A.; Bame, S. J.; Russell, C. T.

1986-01-01

330

5. Looking west upstream, towards the location of the erstwhile ...  

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

5. Looking west upstream, towards the location of the erstwhile intake flume into canal from the upper reaches of the Potomac River above the Great Falls, on the old Potowmack Canal built by George Washington. The plan contemplated canal navigation around the Great Falls of the Potomac River, located on the Virginia side of the Potomac, about 15 miles above Washington, D.C. The Company was organized in 1785, and by 1802, this and three or four smaller canals were substantially completed and raft-like boats began operation with materials from the west to the city of Georgetown. 'Although the canals and locks of the Potomac Canal were considered a great engineering accomplishment, the improvements to the river channel were inadequate. Disappointment ... - Potowmack Company: Great Falls Canal & Locks, Great Falls, Fairfax County, VA

331

High-fidelity modeling of airfoil interaction with upstream turbulence  

NASA Astrophysics Data System (ADS)

To supplement past research on low speed unsteady airfoil responses to upstream disturbances, this work proposes and investigates a method to generate a turbulent momentum source to be convected downstream and interact with an SD7003 airfoil in a high-fidelity numerical simulation. A perturbation velocity field is generated from a summation of Fourier harmonics and applied to the forcing function in the momentum terms of the Navier Stokes Equations. The result is a three-dimensional, divergence-free, convected turbulent gust with applied statistical parameters. A parametric study has been done in 2D and 3D comparing the resultant flow fields and airfoil interactions for various numerical and physical parameters.

Brodnick, Jacob

332

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

333

Upstream and downstream strategies to economize biodiesel production.  

PubMed

In recent years biodiesel has drawn considerable amount of attention as a clean and renewable fuel. Biodiesel is produced from renewable sources such as vegetable oils and animal fat mainly through catalytic or non-catalytic transesterification method as well as supercritical method. However, as a consequence of disadvantages of these methods, the production cost increases dramatically. This article summarizes different biodiesel production methods with a focus on their advantages and disadvantages. The downstream and upstream strategies such as using waste cooking oils, application of non-edible plant oils, plant genetic engineering, using membrane separation technology for biodiesel production, separation and purification, application of crude glycerin as an energy supplement for ruminants, glycerin ultra-purification and their consequent roles in economizing the production process are fully discussed in this article. PMID:20974530

Hasheminejad, Meisam; Tabatabaei, Meisam; Mansourpanah, Yaghoub; Khatami far, Mahdi; Javani, Azita

2011-01-01

334

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

335

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

336

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

337

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

338

Explosion Clad for Upstream Oil and Gas Equipment  

SciTech Connect

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 CO{sub 2} and/or H{sub 2}S 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. [Dynamic Materials Corp., 5405 Spine Rd., Boulder, CO 80301 (United States); Massarello, Jack [Global Metallix, Consultant to DMC, 5405 Spine Rd., Boulder, CO 80301 (United States); Pauly, Stephane [DMC., Nobelclad Business Unit, 1 Allee Alfred NOBEL, 66600 Rivesaltes (France)

2011-01-17

339

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

340

Rigor Made Easy: Getting Started  

ERIC Educational Resources Information Center

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

Blackburn, Barbara R.

2012-01-01

341

Start with Breakfast Snack Right  

E-print Network

, disability, genetic information or veteran status. #12;Educational programs of the Texas A&M Agri, disability, genetic information or veteran status. Three Easy Bites Date Instructor Location Name & Phone, national origin, age, disability, genetic information or veteran status. Name & Phone Number Start

342

HANDBOOK FOR PROJECT HEAD START.  

ERIC Educational Resources Information Center

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

GRAHAM, JORY

343

Starting with the Business Basics.  

ERIC Educational Resources Information Center

A nonprofit community action agency, BusinesStart, provides business training and small loans to entrepreneurs in 18 rural counties in southwestern Virginia and northeastern Tennessee. The entrepreneurs, many with no previous business experience, cite the agency's basic business training as key to their success. (SV)

Hoffman, Carl

1999-01-01

344

Getting Started with Mathematica Introduction  

E-print Network

Getting Started with Mathematica Introduction What is Mathematica? Mathematica is a computer. Mathematica is extraordinary well-rounded. It is suitable for both numeric and symbolic work, and it has from within Mathematica. Its weaknesses include a somewhat steep learning curve, an interface

Barkana, Rennan

345

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

346

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.

347

Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals  

PubMed Central

Translation of mRNA into a polypeptide chain is a highly accurate process. Many prokaryotic and eukaryotic viruses, however, use leaky termination of translation to optimize their coding capacity. Although growing evidence indicates the occurrence of ribosomal readthrough also in higher organisms, a biological function for the resulting extended proteins has been elucidated only in very few cases. Here, we report that in human cells programmed stop codon readthrough is used to generate peroxisomal isoforms of cytosolic enzymes. We could show for NAD-dependent lactate dehydrogenase B (LDHB) and NAD-dependent malate dehydrogenase 1 (MDH1) that translational readthrough results in C-terminally extended protein variants containing a peroxisomal targeting signal 1 (PTS1). Efficient readthrough occurs at a short sequence motif consisting of a UGA termination codon followed by the dinucleotide CU. Leaky termination at this stop codon context was observed in fungi and mammals. Comparative genome analysis allowed us to identify further readthrough-derived peroxisomal isoforms of metabolic enzymes in diverse model organisms. Overall, our study highlights that a defined stop codon context can trigger efficient ribosomal readthrough to generate dually targeted protein isoforms. We speculate that beyond peroxisomal targeting stop codon readthrough may have also other important biological functions, which remain to be elucidated. PMID:25340584

Schink, Kay O.; Stehlik, Thorsten; Tillmann, Britta A. M.; Ast, Julia; Bolker, Michael

2014-01-01

348

Ribosomal Readthrough at a Short UGA Stop Codon Context Triggers Dual Localization of Metabolic Enzymes in Fungi and Animals.  

PubMed

Translation of mRNA into a polypeptide chain is a highly accurate process. Many prokaryotic and eukaryotic viruses, however, use leaky termination of translation to optimize their coding capacity. Although growing evidence indicates the occurrence of ribosomal readthrough also in higher organisms, a biological function for the resulting extended proteins has been elucidated only in very few cases. Here, we report that in human cells programmed stop codon readthrough is used to generate peroxisomal isoforms of cytosolic enzymes. We could show for NAD-dependent lactate dehydrogenase B (LDHB) and NAD-dependent malate dehydrogenase 1 (MDH1) that translational readthrough results in C-terminally extended protein variants containing a peroxisomal targeting signal 1 (PTS1). Efficient readthrough occurs at a short sequence motif consisting of a UGA termination codon followed by the dinucleotide CU. Leaky termination at this stop codon context was observed in fungi and mammals. Comparative genome analysis allowed us to identify further readthrough-derived peroxisomal isoforms of metabolic enzymes in diverse model organisms. Overall, our study highlights that a defined stop codon context can trigger efficient ribosomal readthrough to generate dually targeted protein isoforms. We speculate that beyond peroxisomal targeting stop codon readthrough may have also other important biological functions, which remain to be elucidated. PMID:25340584

Stiebler, Alina C; Freitag, Johannes; Schink, Kay O; Stehlik, Thorsten; Tillmann, Britta A M; Ast, Julia; Bölker, Michael

2014-10-01

349

On the Importance of Oxidative Folding in the Evolution of Conotoxins: Cysteine Codon Preservation through Gene Duplication and Adaptation  

PubMed Central

Conotoxin genes are among the most rapidly evolving genes currently known; however, despite the well-established hypervariability of the intercysteine loops, the cysteines demonstrate significant conservation, with a site-specific codon bias for each cysteine in a family of conotoxins. Herein we present a novel rationale behind the codon-level conservation of the cysteines that comprise the disulfide scaffold. We analyze cysteine codon conservation using an internal reference and phylogenetic tools; our results suggest that the established codon conservation can be explained as the result of selective pressures linked to the production efficiency and folding of conotoxins, driving the conservation of cysteine at the amino-acid level. The preservation of cysteine has resulted in maintenance of the ancestral codon in most of the daughter lineages, despite the hypervariability of adjacent residues. We propose that the selective pressures acting on the venom components of cone snails involve an interplay of biosynthetic efficiency, activity at the target receptor and the importance of that activity to effective prey immobilization. Functional redundancy in the venom can thus serve as a buffer for the energy expenditure of venom production. PMID:24244311

Steiner, Andrew M.; Bulaj, Grzegorz; Puillandre, Nicolas

2013-01-01

350

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

PubMed Central

Fatal familial insomnia (FFI) is a rare, hereditary prion-protein disease. Methionine-valine polymorphism at codon 129 of the prion-protein gene (PRNP) determines the phenotype in other hereditary prion-protein diseases, but association with the clinical phenotype in FFI remains uncertain. Early clinical findings in FFI comprise disturbances of the sleep-wake cycle and mild neuropsychiatric changes which typically emerge during middle to late adulthood. Here we describe an unusually early onset and rapid progression of FFI associated with dorsal midbrain involvement in a female patient with PRNP mutation at codon 178 and homozygote methionine polymorphism at codon 129. Early dorsal midbrain involvement became apparent by total loss of REM sleep and isolated bilateral trochlear nerve palsy. Early onset and rapid progression disease type associated with dorsal midbrain involvement may indicate a different spatiotemporal distribution of the neurodegenerative process in FFI patients with PRNP mutation and codon 129 methionine homozygosity compared to methioninevaline heterozygosity. Citation: Rupprecht S; Grimm A; Schultze T; Zinke J; Karvouniari P; Axer H; Witte OW; Schwab M. Does the clinical phenotype of fatal familial insomnia depend on PRNP codon 129 methionine-valine polymorphism? J Clin Sleep Med 2013;9(12):1343-1345. PMID:24340298

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

2013-01-01

351

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

352

Characterization of codon-optimized recombinant candida rugosa lipase 5 (LIP5).  

PubMed

Recombinant Candida rugosa lipase 5 (LIP5) has been functionally expressed along with other isoforms in our laboratory. However, the characterization and codon optimization of LIP5 have not been done. In this work, we characterized, codon-optimized and compared LIP5 with commercial lipase. LIP5 activity on hydrolysis of p-nitrophenyl (p-NP) butyrate was optimal at 55 °C as compared with 37 °C of the commercial lipase. Several assays were also performed to determine the substrate specificity of LIP5. p-NP butyrate (C(4)), butyryl-CoA (C(4)), cholesteryl laurate (C(12)), and N-carbobenzoxy-l-tyrosine-p-nitrophenyl ester (l-NBTNPE) were found as preferred substrates of LIP5. Interestingly, LIP5 specificity on hydrolysis of amino acid-derivative substrates was shown to be the highest among any lipase isoforms, but it had very weak preference on hydrolyzing triacylglycerol substrates. LIP5 also displays a pH-dependent maximum activity of a lipase but an esterase substrate preference in general. The characterization of LIP5 along with that of LIP1-LIP4 previously identified shows that each lipase isoform has a distinct substrate preference and catalytic activity. PMID:21854055

Lee, Li-Chiun; Yen, Chih-Chung; Malmis, Conmar C; Chen, Long-Fang; Chen, Jen-Chieh; Lee, Guan-Chiun; Shaw, Jei-Fu

2011-10-12

353

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

PubMed

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

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

2012-10-17

354

Computational identification and sequence analysis of stop codon readthrough genes in Oryza sativa.  

PubMed

Using an approach based on the Readthrough Candidate Extraction System (RCES), we extracted 111 candidates from 9620 gene sequences of rice. The results of homology search and sequence analysis demonstrated that these candidates included actual readthrough genes that would be important for further investigating the mechanism of translation termination regulated by readthrough event, and could also give some useful clues for functional genome annotation. Between the candidates and non-candidates of gene sequences in rice, there exist significant base biases at the positions surrounding the stop codons. These positions, especially both -1 and +4, are referred to as part of an extended stop signal. In candidates, G at position -1, and G or C at position +4 are much more favored than that in non-candidates. Both stop sequence patterns, GUAGC and GUGAG, might drive high readthrough efficiency in rice. Secondary structure analysis revealed that the -1 and +1 amino acids around the first stop codon of candidates have a strong bias toward arginine, particularly the +1 position (20.7%), which indicated that the amino acids at the readthrough region being frequently located in the hydrophilic region of beta-turn might be a determinant for efficient translation termination or not. PMID:15527943

Liu, Qingpo; Xue, Qingzhong

2004-11-01

355

Codon optimisation improves the expression of Trichoderma viride sp. endochitinase in Pichia pastoris  

PubMed Central

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)2 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

356

Kras gene codon 12 mutation detection enabled by gold nanoparticles conducted in a nanobioarray chip.  

PubMed

This study employs a nanobioarray (NBA) chip for multiple biodetection of single base pair mutations at the Kras gene codon 12. To distinguish between the mutant and wild-type target DNAs, current bioarray methods use high-temperature hybridization of the targets to the allele-specific probes. However, these techniques need prior temperature optimization and become harder to implement in the case of the detection of multiple mutations. We aimed to detect these mutations at a single temperature (room temperature), enabled by the use of gold nanoparticles (AuNPs) on the bioarray created within nanofluidic channels. In this method, a low amount of target oligonucleotides (5fmol) and polymerase chain reaction (PCR) products (300pg) were first loaded on the AuNP surface, and then these AuNP-bound targets were introduced into the channels of a polydimethylsiloxane (PDMS) glass chip. The targets hybridized to their complementary probes at the intersection of the target channels to the pre-printed oligonucleotide probe lines on the glass surface, creating a bioarray. Using this technique, fast and high-throughput multiple discrimination of the Kras gene codon 12 were achieved at room temperature using the NBA chip, and the specificity of the method was proved to be as high as that with the temperature stringency method. PMID:24291640

Sedighi, Abootaleb; Li, Paul C H

2014-03-01

357

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

Allner, Olof; Nilsson, Lennart

2011-01-01

358

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster  

PubMed Central

Ribosomes can read through stop codons in a regulated manner, elongating rather than terminating the nascent peptide. Stop codon readthrough is essential to diverse viruses, and phylogenetically predicted to occur in a few hundred genes in Drosophila melanogaster, but the importance of regulated readthrough in eukaryotes remains largely unexplored. Here, we present a ribosome profiling assay (deep sequencing of ribosome-protected mRNA fragments) for Drosophila melanogaster, and provide the first genome-wide experimental analysis of readthrough. Readthrough is far more pervasive than expected: the vast majority of readthrough events evolved within D. melanogaster and were not predicted phylogenetically. The resulting C-terminal protein extensions show evidence of selection, contain functional subcellular localization signals, and their readthrough is regulated, arguing for their importance. We further demonstrate that readthrough occurs in yeast and humans. Readthrough thus provides general mechanisms both to regulate gene expression and function, and to add plasticity to the proteome during evolution. DOI: http://dx.doi.org/10.7554/eLife.01179.001 PMID:24302569

Dunn, Joshua G; Foo, Catherine K; Belletier, Nicolette G; Gavis, Elizabeth R; Weissman, Jonathan S

2013-01-01

359

Angelman syndrome due to a termination codon mutation of the UBE3A gene.  

PubMed

Angelman syndrome is a neurodevelopmental disorder characterized by global developmental delay, mental retardation, seizures, microcephaly, and severe speech delay. It may be caused by deletion of chromosome region 15q11.2 of the maternally inherited chromosome, mutations in the UBE3A gene, uniparental disomy, or imprinting defects. Most patients with this diagnosis have a severe phenotype, and a few have a mild form of the disease. We report a patient with a novel mutation in the UBE3A gene that consists of a deletion of the termination codon (c.2556-*+6del GTAAAACAAA) and results in an elongated protein E3 ubiquitin-protein ligase. Our patient has a mild phenotype compared with other patients in general and specifically to patients with UBE3A mutations. He has mild developmental delay, moderate speech delay, and no seizures. Recognition of this genotype-phenotype correlation will allow better genetic counseling to other patients with similar stop codon mutations. PMID:22566713

Al-Maawali, Almundher; Machado, Jerry; Fang, Ping; Dupuis, Lucie; Faghfoury, Hannaneh; Mendoza-Londono, Roberto

2013-03-01

360

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

361

Reduced Efficacy of Natural Selection on Codon Usage Bias in Selfing Arabidopsis and Capsella Species  

PubMed Central

Population genetic theory predicts that the efficacy of natural selection in a self-fertilizing species should be lower than its outcrossing relatives because of the reduction in the effective population size (Ne) in the former brought about by inbreeding. However, previous analyses comparing Arabidopsis thaliana (selfer) with A. lyrata (outcrosser) have not found conclusive support for this prediction. In this study, we addressed this issue by examining silent site polymorphisms (synonymous and intronic), which are expected to be informative about changes in Ne. Two comparisons were made: A. thaliana versus A. lyrata and Capsella rubella (selfer) versus C. grandiflora (outcrosser). Extensive polymorphism data sets were obtained by compiling published data from the literature and by sequencing 354 exon loci in C. rubella and 89 additional loci in C. grandiflora. To extract information from the data effectively for studying these questions, we extended two recently developed models in order to investigate detailed selective differences between synonymous codons, mutational biases, and biased gene conversion (BGC), taking into account the effects of recent changes in population size. We found evidence that selection on synonymous codons is significantly weaker in the selfers compared with the outcrossers and that this difference cannot be fully accounted for by mutational biases or BGC. PMID:21856647

Qiu, Suo; Zeng, Kai; Slotte, Tanja; Wright, Stephen; Charlesworth, Deborah

2011-01-01

362

Expression of codon optimized genes in microbial systems: current industrial applications and perspectives  

PubMed Central

The efficient production of functional proteins in heterologous hosts is one of the major bases of modern biotechnology. Unfortunately, many genes are difficult to express outside their original context. Due to their apparent “silent” nature, synonymous codon substitutions have long been thought to be trivial. In recent years, this dogma has been refuted by evidence that codon replacement can have a significant impact on gene expression levels and protein folding. In the past decade, considerable advances in the speed and cost of gene synthesis have facilitated the complete redesign of entire gene sequences, dramatically improving the likelihood of high protein expression. This technology significantly impacts the economic feasibility of microbial-based biotechnological processes by, for example, increasing the volumetric productivities of recombinant proteins or facilitating the redesign of novel biosynthetic routes for the production of metabolites. This review discusses the current applications of this technology, particularly those regarding the production of small molecules and industrially relevant recombinant enzymes. Suggestions for future research and potential uses are provided as well. PMID:24550894

Elena, Claudia; Ravasi, Pablo; Castelli, Maria E.; Peiru, Salvador; Menzella, Hugo G.

2014-01-01

363

Compositional Constraint Is the Key Force in Shaping Codon Usage Bias in Hemagglutinin Gene in H1N1 Subtype of Influenza A Virus  

PubMed Central

It is vital to unravel the codon usage bias in order to gain insights into the evolutionary forces dictating the viral evolution process. Influenza A virus has attracted attention of many investigators over the years due to high mutation rate and being cross-specific shift operational in the viral genome. Several authors have reported that the codon usage bias is low in influenza A viruses, citing mutational pressure as the decisive force shaping up the codon usage in these viruses. In this study, complete coding sequences of hemagglutinin genes for H1N1 subtype of influenza A virus have been explored for the possible codon usage bias acting upon these genes. The results indicate overall low bias with peaking ENC values. The GC content is found to be substantially low as against AT content in the silent codon sites. Significant correlations were observed in between the compositional parameters versus AT3, implying the possible role of the latter in shaping codon usage profile in the viral hemagglutinin. The data showed conspicuously that the sequences were A redundant with most codons preferring nucleotide A over others in the third synonymous codon site. The results indicated the pivotal role of compositional pressure affecting codon usage in this virus. PMID:25140301

Chakraborty, Supriyo

2014-01-01

364

Managing Sure Start in partnership.  

PubMed

In March 2006, Sure Start programmes were mainstreamed, becoming 'Children's Centres' for which local authorities have assumed strategic responsibility. This paper describes an evaluation of a Sure Start local programme Management Board which was conducted in preparation for this transition. Focusing on practices relating to partnership working and community involvement, a distinctive trident evaluation model was used to explore outcomes, processes and multiple stakeholder perspectives through a multi-method approach (incorporating interviews, questionnaires and documentary analysis). This revealed that an effective, collaborative style of working had been fostered between board members, resulting in synergy. Furthermore, a number of governance arrangements were identified that specifically supported partnership developments, including quorum regulations and adherence to decision-making by consensus. A series of recommendations are presented that were made with the aim of strengthening the community voice on the board and preserving the most effective and empowering elements of practice following the transition. PMID:16922033

Hassan, Lamiece; Spencer, Joy; Hogard, Elaine

2006-08-01

365

Experimental reduction of codon bias in the Drosophila alcohol dehydrogenase gene results in decreased ethanol tolerance of adult flies.  

PubMed

The ethanol tolerance of adult transgenic flies of Drosophila containing between zero and ten unpreferred synonymous mutations that reduced codon bias in the alcohol dehydrogenase (Adh) gene was assayed. As the amino acid sequences of the ADH protein were identical in the four genotypes assayed, differences in ethanol tolerance were due to differences in the abundance of ADH protein, presumably driven by the effects of codon bias on translational efficiency. The ethanol tolerance of genotypes decreased with the number of unpreferred synonymous mutations, and a positive correlation between ADH protein abundance and ethanol tolerance was observed. This work confirms that the fitness effects of unpreferred synonymous mutations that reduce codon bias in a highly expressed gene are experimentally measurable in Drosophila melanogaster. PMID:15271077

Carlini, David B

2004-07-01

366

Low cytoplasmic mRNA levels of immunoglobulin kappa light chain genes containing nonsense codons correlate with inefficient splicing.  

PubMed Central

We have previously reported down-regulation of mRNA expression of some of the kappa light chain transgenes in a hybridoma derived from a secondary immune response. Of the five heavily mutated transgene copies present in that hybridoma, three included premature stop codons and were poorly represented at the mRNA level. Here we show that the nonsense mutations are the cause of the low mRNA levels. While we found no evidence that the reduction in mRNA abundance was attributable to an increased rate of cytoplasmic mRNA decay, the amount of cytoplasmic mRNA correlated with the accumulation of unspliced transcripts in the nucleus. Similar results were obtained with a chimeric immunoglobulin gene containing a premature chain termination codon in the variable gene segment. We suggest that inhibition of splicing induced by in-frame premature stop codons is an important mechanism for down-regulation of undesirable immunoglobulin transcripts. Images PMID:7925302

Lozano, F; Maertzdorf, B; Pannell, R; Milstein, C

1994-01-01

367

School start times for adolescents.  

PubMed

The American Academy of Pediatrics recognizes insufficient sleep in adolescents as an important public health issue that significantly affects the health and safety, as well as the academic success, of our nation's middle and high school students. Although a number of factors, including biological changes in sleep associated with puberty, lifestyle choices, and academic demands, negatively affect middle and high school students' ability to obtain sufficient sleep, the evidence strongly implicates earlier school start times (ie, before 8:30 am) as a key modifiable contributor to insufficient sleep, as well as circadian rhythm disruption, in this population. Furthermore, a substantial body of research has now demonstrated that delaying school start times is an effective countermeasure to chronic sleep loss and has a wide range of potential benefits to students with regard to physical and mental health, safety, and academic achievement. The American Academy of Pediatrics strongly supports the efforts of school districts to optimize sleep in students and urges high schools and middle schools to aim for start times that allow students the opportunity to achieve optimal levels of sleep (8.5-9.5 hours) and to improve physical (eg, reduced obesity risk) and mental (eg, lower rates of depression) health, safety (eg, drowsy driving crashes), academic performance, and quality of life. PMID:25156998

2014-09-01

368

Starting apparatus for internal combustion engines  

DOEpatents

This report is a patent description for a system to start an internal combustion engine. Remote starting and starting by hearing impaired persons are addressed. The system monitors the amount of current being drawn by the starter motor to determine when the engine is started. When the engine is started the system automatically deactivates the starter motor. Five figures are included.

Dyches, G.M.; Dudar, A.M.

1995-01-01

369

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

370

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

371

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

372

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

373

Mouse NGF promoter upstream sequences do not affect gene expression in mouse fibroblasts.  

PubMed

The expression of nerve growth factor (NGF) is tightly controlled in a tissue-specific manner during development and in response to injury. In fibroblasts and in other cell types, expression of NGF is regulated at the transcriptional level. In order to elucidate the mechanism of this regulation, we have undertaken the analysis of the mouse NGF promoter in a mouse fibroblast cell line (LTA), using transient transfection of NGF promoter-human growth hormone (hGH) reporter gene plasmids. We find that sequences between +8bp and +120bp, containing an AP-1 site, confer increased levels of expression from the full length and truncated NGF promoters. When this region is deleted, a significant decrease in expression is observed from both the full length promoter and truncated versions thereof. A gradual increase in expression is observed with successive 5' deletions of both the AP-1 containing and AP-1 deleted promoters; this effect results from the juxtapositioning of adjacent plasmid sequences closer to the transcription initiation site and not from deletion of promoter sequences as was previously reported. When the NGF promoter is analyzed using a luciferase reporter plasmid, these 5' promoter deletions have no significant effect on reporter gene expression in fibroblasts. Thus, sequences downstream of the transcription start site influence NGF promoter activity in fibroblasts, but sequences upstream of the TATA box fail to affect promoter activity in these cells. PMID:7877455

Cowie, A; Ivanco, T L; Fahnestock, M

1994-11-01

374

Glucocorticoids modulate human gonadotrophin releasing hormone upstream promoter activity in transfected human placental cells (JEG-3)  

Microsoft Academic Search

A human gonadotrophin releasing hormone (GnRH) upstream promoter\\/luciferase reporter gene construct (H2 construct) was generated by inserting a 1.7 kb XbaI\\/AflII fragment containing the human GnRH upstream promoter region only into a promoter-less luciferase reporter vector. When JEG-3 cells were transiently transfected with this construct and treated with cortisol or its synthetic analogue dexamethasone, a stimulatory effect on the upstream

Z. G. Chen; C. S. Chou; M. I. Hsu; K. W. Dong

1998-01-01

375

Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells.  

PubMed

Large-scale codon re-encoding represents a powerful method of attenuating viruses to generate safe and cost-effective vaccines. In contrast to specific approaches of codon re-encoding which modify genome-scale properties, we evaluated the effects of random codon re-encoding on the re-emerging human pathogen Chikungunya virus (CHIKV), and assessed the stability of the resultant viruses during serial in cellulo passage. Using different combinations of three 1.4 kb randomly re-encoded regions located throughout the CHIKV genome six codon re-encoded viruses were obtained. Introducing a large number of slightly deleterious synonymous mutations reduced the replicative fitness of CHIKV in both primate and arthropod cells, demonstrating the impact of synonymous mutations on fitness. Decrease of replicative fitness correlated with the extent of re-encoding, an observation that may assist in the modulation of viral attenuation. The wild-type and two re-encoded viruses were passaged 50 times either in primate or insect cells, or in each cell line alternately. These viruses were analyzed using detailed fitness assays, complete genome sequences and the analysis of intra-population genetic diversity. The response to codon re-encoding and adaptation to culture conditions occurred simultaneously, resulting in significant replicative fitness increases for both re-encoded and wild type viruses. Importantly, however, the most re-encoded virus failed to recover its replicative fitness. Evolution of these viruses in response to codon re-encoding was largely characterized by the emergence of both synonymous and non-synonymous mutations, sometimes located in genomic regions other than those involving re-encoding, and multiple convergent and compensatory mutations. However, there was a striking absence of codon reversion (<0.4%). Finally, multiple mutations were rapidly fixed in primate cells, whereas mosquito cells acted as a brake on evolution. In conclusion, random codon re-encoding provides important information on the evolution and genetic stability of CHIKV viruses and could be exploited to develop a safe, live attenuated CHIKV vaccine. PMID:23436995

Nougairede, Antoine; De Fabritus, Lauriane; Aubry, Fabien; Gould, Ernest A; Holmes, Edward C; de Lamballerie, Xavier

2013-02-01

376

ANALYSIS OF K-RAS GENE CODON 12 MUTATION IN PANCREATIC TISSUE OF PATIENTS WITH PANCREATIC CANCER  

E-print Network

Abstract — The aim of this study was to analyze K-ras codon 12 mutation in the pancreatic tissue of Serbian patients with pancreatic cancer and assess whether the given mutation can be used as a molecular marker for this disease. The study was performed on pancreatic tissue samples obtained from 40 patients with clinical diagnosis of pancreatic cancer. The presence of K-ras codon 12 mutation was analyzed by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Our study showed that K-ras mutation is present with a high frequency (66%) in the pancreatic tissue of patients with pancretic cancer.

Aleksandra Nikoli?; S. Kneževi?; Mila Krsmanovi?; M. Micev; M. Ristanovi?; Dragica Radojkovi?

377

Energetic-ion acceleration and transport in the upstream region of Jupiter: Voyager 1 and 2  

SciTech Connect

Long-lived upstream energetic ion events at Jupiter appear to be very similar in nearly all respects to upstream ion events at earth. A notable difference between the two planetary systems is the enhanced heavy ion compositional signature reported for the Jovian events. This compositional feature has suggested that ions escaping from the Jovian magnetosphere play an important role in forming upstream ion populations at Jupiter. In contrast, models of energetic upstream ions at earth emphasize in situ acceleration of reflected solar wind ions within the upstream region itself. Using Voyager 1 and 2 energetic (>approx. 30 keV) ion measurements near the magnetopause, in the magnetosheath, and immediately upstream of the bow shock, we examine the compositional patterns together with typical energy spectra in each of these regions. We find characteristic spectral changes late in ion events observed upstream of the bow shock at the same time that heavy ion fluxes are enhanced and energetic electrons are present. A model involving upstream Fermi acceleration early in events and emphasizing energetic particle escape in the prenoon part of the Jovian magnetosphere late in events is presented to explain many of the features in the upstream region of Jupiter.

Baker, D.N.; Zwickl, R.D.; Carbary, J.F.; Krimigis, S.M.; Lepping, R.P.

1982-01-01

378

An Upstream Truncation of the furA-katG Operon Confers High-Level Isoniazid Resistance in a Mycobacterium tuberculosis Clinical Isolate with No Known Resistance-Associated Mutations.  

PubMed

Although the major causes of isoniazid (INH) resistance in Mycobacterium tuberculosis are confined to structural mutations in katG and promoter mutations in the mabA-inhA operon, a significant proportion of INH-resistant strains have unknown resistance mechanisms. Recently, we identified a high-level INH-resistant M. tuberculosis clinical isolate, GB005, with no known resistance-associated mutations. A comprehensive study was performed to investigate the molecular basis of drug resistance in this strain. Although no mutations were found throughout the katG and furA-katG intergenic region, the katG expression and the catalase activity were greatly diminished compared to those in H37Rv (P < 0.01). Northern blotting revealed that the katG transcript from the isolate was smaller than that of H37Rv. Sequencing analysis of furA and upstream genes discovered a 7.2-kb truncation extended from the 96th base preceding the initiation codon of katG. Complementation of the M. tuberculosis ?(furA-katG) strain with katG and different portions of the truncated region identified a 134-bp upstream fragment of furA that was essential for full catalase activity and INH susceptibility in M. tuberculosis. The promoter activity of this fragment was also shown to be stronger than that of the furA-katG intergenic region (P < 0.01). Collectively, these findings demonstrate that deletion of the 134-bp furA upstream fragment is responsible for the reduction in katG expression, resulting in INH resistance in GB005. To our knowledge, this is the first report showing that deletion of the upstream region preceding the furA-katG operon causes high-level INH resistance in a clinical isolate of M. tuberculosis. PMID:25092698

Siu, Gilman Kit Hang; Yam, Wing Cheong; Zhang, Ying; Kao, Richard Y T

2014-10-01

379

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

PubMed Central

Background Out-of-frame stop codons (OSCs) occur naturally in coding sequences of all organisms, providing a mechanism of early termination of translation in incorrect reading frame so that the metabolic cost associated with frameshift events can be reduced. Given such a functional significance, we expect statistically overrepresented OSCs in coding sequences as a result of a widespread selection. Accordingly, we examined available prokaryotic genomes to look for evidence of this selection. Results The complete genome sequences of 990 prokaryotes were obtained from NCBI GenBank. We found that low G+C content coding sequences contain significantly more OSCs and G+C content at specific codon positions were the principal determinants of OSC usage bias in the different reading frames. To investigate if there is overrepresentation of OSCs, we modeled the trinucleotide and hexanucleotide biases of the coding sequences using Markov models, and calculated the expected OSC frequencies for each organism using a Monte Carlo approach. More than 93% of 342 phylogenetically representative prokaryotic genomes contain excess OSCs. Interestingly the degree of OSC overrepresentation correlates positively with G+C content, which may represent a compensatory mechanism for the negative correlation of OSC frequency with G+C content. We extended the analysis using additional compositional bias models and showed that lower-order bias like codon usage and dipeptide bias could not explain the OSC overrepresentation. The degree of OSC overrepresentation was found to correlate negatively with the optimal growth temperature of the organism after correcting for the G+C% and AT skew of the coding sequence. Conclusions The present study uses approaches with statistical rigor to show that OSC overrepresentation is a widespread phenomenon among prokaryotes. Our results support the hypothesis that OSCs carry functional significance and have been selected in the course of genome evolution to act against unintended frameshift occurrences. Some results also hint that OSC overrepresentation being a compensatory mechanism to make up for the decrease in OSCs in high G+C organisms, thus revealing the interplay between two different determinants of OSC frequency. PMID:20828396

2010-01-01

380

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

381

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

382

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

383

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

384

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

385

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

PubMed

This new bioinformatics research bridges Genomics and Mathematics. We propose a universal "Fractal Genome Code Law": The frequency of each of the 64 codons across the entire human genome is controlled by the codon's position in the Universal Genetic Code table. We analyze the frequency of distribution of the 64 codons (codon usage) within single-stranded DNA sequences. Concatenating 24 Human chromosomes, we show that the entire human genome employs the well known universal genetic code table as a macro structural model. The position of each codon within this table precisely dictates its population. So the Universal Genetic Code Table not only maps codons to amino acids, but serves as a global checksum matrix. Frequencies of the 64 codons in the whole human genome scale are a self-similar fractal expansion of the universal genetic code. The original genetic code kernel governs not only the micro scale but the macro scale as well. Particularly, the 6 folding steps of codon populations modeled by the binary divisions of the "Dragon fractal paper folding curve" show evidence of 2 attractors. The numerical relationship between the attractors is derived from the Golden Ratio. We demonstrate that: (i) The whole Human Genome Structure uses the Universal Genetic Code Table as a tuning model. It predetermines global codons proportions and populations. The Universal Genetic Code Table governs both micro and macro behavior of the genome. (ii) We extend the Chargaff's second rule from the domain of single TCAG nucleotides to the larger domain of codon triplets. (iii) Codon frequencies in the human genome are clustered around 2 fractal-like attractors, strongly linked to the golden ratio 1.618. PMID:20658335

Perez, Jean-Claude

2010-09-01

386

Electron distributions upstream and downstream of ICME driven IP shocks  

NASA Astrophysics Data System (ADS)

We study suprathermal electron distributions (E > 80 eV) in regions adjacent to interplanetary (IP) shocks driven by interplanetary coronal mass ejections (ICMEs). The shocks were observed by the two STEREO spacecraft during the years 2007-2010, hence during the minimum and at the beginning of the rising phase of the current solar cycle. All the ICMEs were isolated events, meaning that the shocks were produced only due to interactions of the ICMEs with the solar wind. We find that suprathermal electron pitch angle distributions (PADs) in regions adjacent to ICME driven IP shocks vary from shock to shock. At some shocks, these electrons show the "usual" isotropic halo and a narrow, field-aligned strahl. The PADs upstream and downstream of these shocks differ only in the width of the strahl, with the later being wider in the downstream regions. In other cases we observe unusual downstream conical distributions at intermediate angles (between 0 and 90 or 90 and 180° PA), counterstreaming electrons at the shock transitions and downstream PADs without the strahl component. Here we present two shocks from our sample with such unusual electrons distributions, not reported in the literature.

Kajdi?, P.; Blanco-Cano, X.; Opitz, A.; Sauvaud, J.-A.; Aguilar-Rodriguez, E.; Russell, C. T.; Luhmann, J. G.; Jian, L. K.; Rouillard, A. P.; Lavraud, B.

2013-06-01

387

Large amplitude MHD waves upstream of the Jovian bow shock  

NASA Technical Reports Server (NTRS)

Observations of large amplitude magnetohydrodynamics (MHD) waves upstream of Jupiter's bow shock are analyzed. The waves are found to be right circularly polarized in the solar wind frame which suggests that they are propagating in the fast magnetosonic mode. A complete spectral and minimum variance eigenvalue analysis of the data was performed. The power spectrum of the magnetic fluctuations contains several peaks. The fluctuations at 2.3 mHz have a direction of minimum variance along the direction of the average magnetic field. The direction of minimum variance of these fluctuations lies at approximately 40 deg. to the magnetic field and is parallel to the radial direction. We argue that these fluctuations are waves excited by protons reflected off the Jovian bow shock. The inferred speed of the reflected protons is about two times the solar wind speed in the plasma rest frame. A linear instability analysis is presented which suggests an explanation for many of the observed features of the observations.

Goldstein, M. L.; Smith, C. W.; Matthaeus, W. H.

1983-01-01

388

Long conserved fragments upstream of Mammalian polyadenylation sites.  

PubMed

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

Ho, Eric S; Gunderson, Samuel I

2011-01-01

389

Rheotaxis facilitates upstream navigation of mammalian sperm cells  

PubMed Central

A major puzzle in biology is how mammalian sperm maintain the correct swimming direction during various phases of the sexual reproduction process. Whilst chemotaxis may dominate near the ovum, it is unclear which cues guide spermatozoa on their long journey towards the egg. Hypothesized mechanisms range from peristaltic pumping to temperature sensing and response to fluid flow variations (rheotaxis), but little is known quantitatively about them. We report the first quantitative study of mammalian sperm rheotaxis, using microfluidic devices to investigate systematically swimming of human and bull sperm over a 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 stable upstream spiralling motion of sperm cells, thus providing a generic and robust rectification mechanism to support mammalian fertilisation. A minimal mathematical model is presented that accounts quantitatively for the experimental observations. DOI: http://dx.doi.org/10.7554/eLife.02403.001 PMID:24867640

Kantsler, Vasily; Dunkel, Jorn; Blayney, Martyn; Goldstein, Raymond E

2014-01-01

390

Second generation codon optimized minicircle (CoMiC) for nonviral reprogramming of human adult fibroblasts.  

PubMed

The ability to induce pluripotency in somatic cells is one of the most important scientific achievements in the fields of stem cell research and regenerative medicine. This technique allows researchers to obtain pluripotent stem cells without the controversial use of embryos, providing a novel and powerful tool for disease modeling and drug screening approaches. However, using viruses for the delivery of reprogramming genes and transcription factors may result in integration into the host genome and cause random mutations within the target cell, thus limiting the use of these cells for downstream applications. To overcome this limitation, various non-integrating techniques, including Sendai virus, mRNA, minicircle, and plasmid-based methods, have recently been developed. Utilizing a newly developed codon optimized 4-in-1 minicircle (CoMiC), we were able to reprogram human adult fibroblasts using chemically defined media and without the need for feeder cells. PMID:25070322

Diecke, Sebastian; Lisowski, Leszek; Kooreman, Nigel G; Wu, Joseph C

2014-01-01

391

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS  

PubMed Central

The ratio of divergence at nonsynonymous and synonymous sites, dN/dS, is a widely used measure in evolutionary genetic studies to investigate the extent to which selection modulates gene sequence evolution. Originally tailored to codon sequences of distantly related lineages, dN/dS represents the ratio of fixed nonsynonymous to synonymous differences. The impact of ancestral and lineage-specific polymorphisms on dN/dS, which we here show to be substantial for closely related lineages, is generally neglected in estimation techniques of dN/dS. To address this issue, we formulate a codon model that is firmly anchored in population genetic theory, derive analytical expressions for the dN/dS measure by Poisson random field approximation in a Markovian framework and validate the derivations by simulations. In good agreement, simulations and analytical derivations demonstrate that dN/dS is biased by polymorphisms at short time scales and that it can take substantial time for the expected value to settle at its time limit where only fixed differences are considered. We further show that in any attempt to estimate the dN/dS ratio from empirical data the effect of the intrinsic fluctuations of a ratio of stochastic variables, can even under neutrality yield extreme values of dN/dS at short time scales or in regions of low mutation rate. Taken together, our results have significant implications for the interpretation of dN/dS estimates, the McDonald–Kreitman test and other related statistics, in particular for closely related lineages. PMID:24129904

Mugal, Carina F.; Wolf, Jochen B.W.; Kaj, Ingemar

2014-01-01

392

Non-random base composition in codons of mitochondrial cytochrome b gene in vertebrates.  

PubMed

Cytochrome b is the central catalytic subunit of the quinol:cytochrome c oxidoreductase of complex III of the mitochondrial oxidative phosphorylation system and is essential to the viability of most eukaryotic cells. Partial cytochrome b gene sequences of 14 species representing mammals, birds, reptiles and amphibians are presented here including some species typical for Poland. For the analysed species a comparative analysis of the natural variation in the gene was performed. This information has been used to discuss some aspects of gene sequence - protein function relationships. Review of relevant literature indicates that similar comparisons have been made only for basic mammalian species. Moreover, there is little information about the Polish-specific species. We observed that there is a strong non-random distribution of nucleotides in the cytochrome b sequence in all tested species with the highest differences at the third codon position. This is also the codon position of the strongest compositional bias. Some tested species, representing distant systematic groups, showed unique base composition differing from the others. The quail, frog, python and elk prefer C over A in the light DNA strand. Species belonging to the artiodactyls stand out from the remaining ones and contain fewer pyrimidines. The observed overall rate of amino acid identity is about 61%. The region covering Q(o) center as well as histidines 82 and 96 (heme ligands) are totally conserved in all tested species. Additionally, the applied method and the sequences can also be used for diagnostic species identification by veterinary and conservation agencies. PMID:15625561

Prusak, Beata; Grzybowski, Tomasz

2004-01-01

393

Starting a nursing consultation practice.  

PubMed

Because the clinical nurse specialist (CNS) role has been changed or eliminated in many hospital organizations, many CNSs in career transition are considering establishing collaborative or independent nursing consultation practices. Opportunities for consultants exist in diverse practice settings and specialties. Before starting a consultation practice, the CNS should carefully examine goals, identify resources, and begin contacting potential referral sources. He or she must also decide what form of business organization to establish and write a business plan to solidify ideas and prepare for the unexpected. Most CNS consultants rely on personal savings to cover initial business and personal expenses, and many continue working as a CNS until the consultation practice is established. Fees can be set based on community standards, what the market will bear, desired projected income, or a third-party payor's fee schedule. The consultation practice can be marketed by word of mouth, inexpensive advertising techniques such as distributing flyers and business cards, direct mall, and media advertising. In today's healthcare marketplace, opportunities abound for the CNS risk-taker interested in starting a nursing consultation practice. PMID:10382408

Schulmeister, L

1999-03-01

394

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

395

The muscle creatine kinase gene is regulated by multiple upstream elements, including a muscle-specific enhancer  

SciTech Connect

Muscle creatine kinase (MCK) is induced to high levels during skeletal muscle differentiation. The authors examined the upstream regulatory elements of the mouse MCK gene which specify its activation during myogenesis in culture. Fusion genes containing up to 3,300 nucleotides (nt) of MCK 5' flanking DNA in various positions and orientations relative to the bacterial chloramphenicol acetyltransferase (CAT) structural gene were transfected into cultured cells. Transient expression of CAT was compared between proliferating and differentiated MM14 mouse myoblasts and with nonmyogenic mouse L cells. The major effector of high-level expression was found to have the properties of a transcriptional enhancer. This element, located between 1,050 and 1,256 nt upstream of the transcription start site, was also found to have a major influence on the tissue and differentiation specificity of MCK expression; it activated either the MCK promoter or heterologous promoters only in differentiated muscle cells. Comparisons of viral and cellular enhancer sequences with the MCK enhancer revealed some similarities to essential regions of the simian virus 40 enhancer as well as to a region of the immunoglobulin heavy-chain enhancer, which has been implicated in tissue-specific protein binding. Even in the absence of the enhancer, low-level expression from a 776-nt MCK promoter retained differentiation specificity. In addition to positive regulatory elements, our data provide some evidence for negative regulatory elements with activity in myoblasts. These may contribute to the cell type and differentiation specificity of MCK expression.

Jaynes, J.B.; Johnson, J.E.; Buskin, J.N.; Gartside, C.L.; Hauschka, S.D.

1988-01-01

396

Life without tRNA[superscript Ile]-lysidine synthetase: translation of the isoleucine codon AUA in Bacillus subtilis lacking the canonical tRNA[Ile over 2  

E-print Network

Translation of the isoleucine codon AUA in most prokaryotes requires a modified C (lysidine or agmatidine) at the wobble position of tRNA[Ile over 2] to base pair specifically with the A of the AUA codon but not with the ...

Koehrer, Caroline

397

Codon usage bias and tRNA over-expression in Buchnera aphidicola after aromatic amino acid nutritional stress on its host Acyrthosiphon pisum  

PubMed Central

Codon usage bias and relative abundances of tRNA isoacceptors were analysed in the obligate intracellular symbiotic bacterium, Buchnera aphidicola from the aphid Acyrthosiphon pisum, using a dedicated 35mer oligonucleotide microarray. Buchnera is archetypal of organisms living with minimal metabolic requirements and presents a reduced genome with high-evolutionary rate. Codonusage in Buchnera has been overcome by the high mutational bias towards AT bases. However, several lines of evidence for codon usage selection are given here. A significant correlation was found between tRNA relative abundances and codon composition of Buchnera genes. A significant codon usage bias was found for the choice of rare codons in Buchnera: C-ending codons are preferred in highly expressed genes, whereas G-ending codons are avoided. This bias is not explained by GC skew in the bacteria and might correspond to a selection for perfect matching between codon–anticodon pairs for some essential amino acids in Buchnera proteins. Nutritional stress applied to the aphid host induced a significant overexpression of most of the tRNA isoacceptors in bacteria. Although, molecular regulation of the tRNA operons in Buchnera was not investigated, a correlation between relative expression levels and organization in transcription unit was found in the genome of Buchnera. PMID:16963497

Charles, Hubert; Calevro, Federica; Vinuelas, Jose; Fayard, Jean-Michel; Rahbe, Yvan

2006-01-01

398

Placing the RPL32 Promoter Upstream of a Second Promoter Results in a Strongly Increased Number of Stably Transfected Mammalian Cell Lines That Display High Protein Expression Levels.  

PubMed

The use of high stringency selection systems commonly results in a strongly diminished number of stably transfected mammalian cell lines. Here we placed twelve different promoters upstream of an adjacent primary promoter and tested whether this might result in an increased number of colonies; this is in the context of a stringent selection system. We found that only the promoter of the human ribosomal protein, RPL32, induced a high number of colonies in CHO-DG44 cells. This phenomenon was observed when the RPL32 promoter was combined with the CMV, SV40, EF1-?, and the ?-actin promoters. In addition, these colonies displayed high protein expression levels. The RPL32 promoter had to be functionally intact, since the deletion of a small region upstream of the transcription start site demolished its positive action. We conclude that adding the RPL32 promoter to an expression cassette in cis may be a powerful tool to augment gene expression levels. PMID:21350661

Hoeksema, F; Hamer, K; Siep, M; Verhees, J A; Otte, A P

2011-01-01

399

Placing the RPL32 Promoter Upstream of a Second Promoter Results in a Strongly Increased Number of Stably Transfected Mammalian Cell Lines That Display High Protein Expression Levels  

PubMed Central

The use of high stringency selection systems commonly results in a strongly diminished number of stably transfected mammalian cell lines. Here we placed twelve different promoters upstream of an adjacent primary promoter and tested whether this might result in an increased number of colonies; this is in the context of a stringent selection system. We found that only the promoter of the human ribosomal protein, RPL32, induced a high number of colonies in CHO-DG44 cells. This phenomenon was observed when the RPL32 promoter was combined with the CMV, SV40, EF1-?, and the ?-actin promoters. In addition, these colonies displayed high protein expression levels. The RPL32 promoter had to be functionally intact, since the deletion of a small region upstream of the transcription start site demolished its positive action. We conclude that adding the RPL32 promoter to an expression cassette in cis may be a powerful tool to augment gene expression levels. PMID:21350661

Hoeksema, F.; Hamer, K.; Siep, M.; Verhees, J. A.; Otte, A. P.

2011-01-01

400

Guanidine reduces stop codon read-through caused by missense mutations inSUP35 orSUP45  

Microsoft Academic Search

Sup35 and Sup45 are essential protein components of the Saccharomyces cerevisiae translation termination factor. Yeast cells harbouring the (PSI +) prion form of Sup35 have impaired stop codon recognition (nonsense suppression). It has long been known that the (PSI +) prion is not stably transmitted to daughter cells when yeast are grown in the presence of mM concentrations of guanidine

Michael E. Bradley; Sviatoslav Bagriantsev; Namitha Vishveshwara; Susan W. Liebman

2003-01-01

401

Different allelic effects of the codons 136 and 171 of the prion protein gene in sheep with natural scrapie.  

PubMed

Scrapie is a transmissible degenerative disease of the central nervous system occurring naturally in sheep. It belongs to the group of prion diseases also affecting man in which an abnormal isoform of the host-encoded prion protein (PrP) accumulating in the brain is responsible for neuronal death. Three main polymorphisms have been described in the sheep PrP gene, at positions 136, 154 and 171. A strong association between susceptibility/resistance to natural scrapie and a dimorphism at codon 136 of the ovine PrP gene has been reported in several breeds, including Romanov. This dimorphism, however, is not found in all scrapie-affected breeds. We have compared the PrP genotypes of Lacaune sheep obtained from enzootically affected flocks with those of apparently healthy sheep. A third variant at codon 171 was also evidenced. The results were compared with those obtained in a single experimental Romanov flock orally challenged with nematode parasites in which scrapie suddenly appeared and killed 80% of the sheep. We present evidence that, even in different epizootological circumstances, the major genetic factor controlling the susceptibility/resistance to natural scrapie in sheep, is represented by codon 171 genotype of the PrP gene. We also suggest that a modification of the allelic effects of codon 136 can occur in heavily infected animals. PMID:7636494

Clouscard, C; Beaudry, P; Elsen, J M; Milan, D; Dussaucy, M; Bounneau, C; Schelcher, F; Chatelain, J; Launay, J M; Laplanche, J L

1995-08-01

402

Differential Selective Constraints Shaping Codon Usage Pattern of Housekeeping and Tissue-specific Homologous Genes of Rice and Arabidopsis  

PubMed Central

Intra-genomic variation between housekeeping and tissue-specific genes has always been a study of interest in higher eukaryotes. To-date, however, no such investigation has been done in plants. Availability of whole genome expression data for both rice and Arabidopsis has made it possible to examine the evolutionary forces in shaping codon usage pattern in both housekeeping and tissue-specific genes in plants. In the present work, we have taken 4065 rice–Arabidopsis homologous gene pairs to study evolutionary forces responsible for codon usage divergence between housekeeping and tissue-specific genes. In both rice and Arabidopsis, it is mutational bias that regulates error minimization in highly expressed genes of both housekeeping and tissue-specific genes. Our results show that, in comparison to tissue-specific genes, housekeeping genes are under strong selective constraint in plants. However, in tissue-specific genes, lowly expressed genes are under stronger selective constraint compared with highly expressed genes. We demonstrated that constraint acting on mRNA secondary structure is responsible for modulating codon usage variations in rice tissue-specific genes. Thus, different evolutionary forces must underline the evolution of synonymous codon usage of highly expressed genes of housekeeping and tissue-specific genes in rice and Arabidopsis. PMID:18827062

Mukhopadhyay, Pamela; Basak, Surajit; Ghosh, Tapash Chandra

2008-01-01

403

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

NSDL National Science Digital Library

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

2008-10-06

404

The Roles of Serum Leptin Concentration and Polymorphism in Leptin Receptor Gene at Codon 109 in Breast Cancer  

Microsoft Academic Search

Aims: We investigated the relationship between serum leptin concentrations and polymorphism of the leptin receptor gene and breast cancer. Methods: Serum leptin concentrations were measured by enzyme-linked immunosorbent assay in 47 women with invasive breast cancer compared with 41 age-matched controls without cancer. Genomic DNA was extracted from peripheral blood leukocytes. Genotyping of the leptin receptor gene at codon 109

Chien-Liang Liu; Yuan-Ching Chang; Shih-Ping Cheng; Schu-Rern Chern; Tsen-Long Yang; Jie-Jen Lee; Ing-Cherng Guo; Chih-Ping Chen

2007-01-01

405

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

Microsoft Academic Search

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

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

2003-01-01

406

GEOTAIL observation of upstream ULF waves associated with lunar wake  

NASA Astrophysics Data System (ADS)

Left-handed, circular polarized ULF waves with frequency of 0.3-1.1 Hz were detected by GEOTAIL at 27 lunar radii upstream of the moon when the spacecraft was magnetically connected with the lunar wake. The wave was detected twice at 16:45-17:00 and 18:55-19:02 on October 25, 1994, when the spacecraft and the moon were on the dawn side of the Earth's magnetosphere. The ULF wave was propagating in a direction nearly parallel to the background magnetic field. The observed frequency and polarization are explained by reversal of polarization of right-handed, sunward-propagating electron whistler waves with frequencies above 1.4 Hz in the solar wind frame of reference, which were excited through the interaction with electron beams flowing in anti-sunward direction downstream of the lunar wake. The downstream flow of electron beam is explained by filtering effect of the potential drop at the boundary of the lunar wake. Low-energy components of electrons are reflected back by the potential drop, and the rest components, with energies higher than that of the electric potential penetrate through the wake. The velocity distribution of downstream electrons would be modified to have some bump or shoulder in energy range to form a beam, which is likely to excite whistler mode wave through cyclotron resonance. The lowest energy of the resonant electrons was calculated to be 0.96-2.5 (keV) from the lower boundary of the detected frequency. The variation in the lowest frequency suggests that there are some regions of the lunar wake where potential drop is reduced.

Nakagawa, T.; Takahashi, Y.; Iizima, M.

2003-09-01

407

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

408

Nucleotide sequence of a B1 hordein gene and the identification of possible upstream regulatory elements in endosperm storage protein genes from barley, wheat and maize.  

PubMed Central

The B-hordeins are the major group of prolamin storage proteins in barley (Hordeum vulgare L.) and they are encoded by a small multigene family that is expressed specifically in the developing endosperm. We report the complete nucleotide sequence of a clone of one B-hordein gene (pBHR184). The cloned gene contains no introns and belongs to the B1 sub-family of B-hordein genes. Comparison of the 5'-flanking sequences of pBHR184 with those of related S-rich prolamin genes from wheat shows that several short sequences within 600 bp upstream of the translation initiation codon are strongly conserved. A sequence that is conserved at around -300 bp in the S-rich prolamins is also conserved at similar locations in genes encoding the two major classes of maize prolamin (the Z19 and Z21 zeins) and appears to be unique to prolamin genes. We discuss the possible role of this '-300 element' in the control of gene expression in the developing cereal endosperm. Images PMID:4059057

Forde, B G; Heyworth, A; Pywell, J; Kreis, M

1985-01-01

409

The Benthos-Plankton Relationship Upstream and Downstream of a Blackwater Impoundment  

Microsoft Academic Search

The phytoplankton, zooplankton, and the macroinvertebrate snag communities of Black Creek, South Carolina, upstream and downstream of an impoundment were Investigated during 1982. Phytoplankton and zooplankton densities upstream of the impoundment were very low. The reservoir outflow contributed a large part of the zooplankton of all sizes to the stream immediately below the impoundment. Large copepods and cladocerans were almost

David D. Herlong; Michael A. Mallin

1985-01-01

410

Upstream urbanization exacerbates urban heat island effects Da-Lin Zhang,1  

E-print Network

Upstream urbanization exacerbates urban heat island effects Da-Lin Zhang,1 Yi-Xuan Shou,1; published 19 December 2009. [1] Urban Heat Island (UHI) effects adversely impact weather, air quality find that upstream urbanization exacerbates UHI effects and that meteorological consequences of extra-urban

Zhang, Da-Lin

411

Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational Methods  

E-print Network

Analysis of Yeast's ORF Upstream Regions by Parallel Processing, Microarrays, and Computational­ gions, gene regulation, DNA­microarrays, yeast, motifs, Markov models Abstract We use a network of workstations to compute all pairwise alignments of the 500 bp upstream regions of 6,225 yeast ORFs (Open

Kibler, Dennis F.

412

Upstream Swimming Performance of Adult White Sturgeon: Effects of Partial Baffles and a Ramp  

E-print Network

with relationship to fish ladders, is limited. Wild adult white sturgeon Acipenser transmontanus (n¼25; total length- ifornia, increased flow stimulated the upstream move- ments of prespawning adult white sturgeon Acipenser transmontanus up to 25 km/d. These fish tended to cease their upstream migration or drift downstream when flows

Anderson, Todd

413

Management background, corporate governance and industrial restructuring: the Japanese upstream petroleum industry  

Microsoft Academic Search

Japanese upstream companies have consistently underperformed private independents. A recent audit by the Ministry of International Trade and Industry (MITI) underlines the magnitude of financial losses and the necessity for sectoral restructuring. MITI's proposals involve refocusing rather than redefining upstream policy, including recognition that official intervention should be reduced in favour of greater control by the more successful local production

Gerald Pollio; Koichi Uchida

1999-01-01

414

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

415

Short Wavelength Ion Waves Upstream of the Earth’s Bow Shock  

Microsoft Academic Search

ISEE-1 wide-band electric field data, antenna interference effects have been identified in the ion waves upstream of the earth's bow shock. This identification implies that wavelengths of the upstream ion waves are shorter than the antenna length. The interference effects also provide new measurements of the direction of propagation of the ion waves. The new measurements show that the wave

S. A. Fuselier; D. A. Gurnett

1984-01-01

416

3 Draft Methodological Tool “Upstream leakage emissions associated with fossil fuel use”  

E-print Network

For the purpose of this tool, the following definitions apply: Upstream emissions stage. The segmentation of upstream emissions into stages based on distinct activities occurring within a stage. Upstream emissions stages are interdependent and lead from one to the next, typically consisting of production, processing, transmission, storage and distribution. Upstream emissions stages may be broadly generalized for types of fossil fuel. However, only some of the upstream emission stages may apply to a particular fossil fuel because of location and applicationspecific circumstances. For example, a particular natural gas may go directly from the production stage to the distribution stage, without going through any processing, transmission or storage upstream emissions stages. Upstream emissions. The greenhouse gas (GHG) emissions associated with the production, processing, transmission, storage and distribution of a fossil fuel, beginning with the extraction of raw materials from the fossil fuel origin and ending with the delivery of the fossil fuel to the site of use. Fossil fuel origin. This refers to the location and type of reservoir(s) or mine(s) from which the fossil fuel originates. The type of reservoir differentiates key characteristics which influence upstream emissions. For natural gas based fossil fuels the types of reservoirs include sweet, sour, coal-bed, shale

unknown authors

417

A meta-analysis of single base-pair substitutions in translational termination codons ('nonstop' mutations) that cause human inherited disease  

PubMed Central

'Nonstop' mutations are single base-pair substitutions that occur within translational termination (stop) codons and which can lead to the continued and inappropriate translation of the mRNA into the 3'-untranslated region. We have performed a meta-analysis of the 119 nonstop mutations (in 87 different genes) known to cause human inherited disease, examining the sequence context of the mutated stop codons and the average distance to the next alternative in-frame stop codon downstream, in comparison with their counterparts from control (non-mutated) gene sequences. A paucity of alternative in-frame stop codons was noted in the immediate vicinity (0-49 nucleotides downstream) of the mutated stop codons as compared with their control counterparts (p = 7.81 × 10-4). This implies that at least some nonstop mutations with alternative stop codons in close proximity will not have come to clinical attention, possibly because they will have given rise to stable mRNAs (not subject to nonstop mRNA decay) that are translatable into proteins of near-normal length and biological function. A significant excess of downstream in-frame stop codons was, however, noted in the range 150-199 nucleotides from the mutated stop codon (p = 8.55 × 10-4). We speculate that recruitment of an alternative stop codon at greater distance from the mutated stop codon may trigger nonstop mRNA decay, thereby decreasing the amount of protein product and yielding a readily discernible clinical phenotype. Confirmation or otherwise of this postulate must await the emergence of a clearer understanding of the mechanism of nonstop mRNA decay in mammalian cells. PMID:21712188

2011-01-01

418

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

419

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters.  

PubMed

PROMoter uPstream Transcripts (PROMPTs) were identified as a new class of human RNAs, which are heterologous in length and produced only upstream of the promoters of active protein-coding genes. Here, we show that PROMPTs carry 3'-adenosine tails and 5'-cap structures. However, unlike mRNAs, PROMPTs are largely nuclear and rapidly turned over by the RNA exosome. PROMPT-transcribing DNA is occupied by RNA polymerase II (RNAPII) complexes with serine 2 phosphorylated C-terminal domains (CTDs), mimicking that of the associated genic region. Thus, the inefficient elongation capacity of PROMPT transcription cannot solely be assigned to poor CTD phosphorylation. Conditions that reduce gene transcription increase RNAPII occupancy of the upstream PROMPT region, suggesting that they reside in a common transcription compartment. Surprisingly, gene promoters that are actively transcribed by RNAPI or RNAPIII also produce PROMPTs that are targeted by the exosome. RNAPIII PROMPTs bear hallmarks of RNAPII promoter-associated RNAs, explaining the physical presence of RNAPII upstream of many RNAPIII-transcribed genes. We propose that RNAPII activity upstream gene promoters are wide-spread and integral to the act of gene transcription. PMID:21596787

Preker, Pascal; Almvig, Kristina; Christensen, Marianne S; Valen, Eivind; Mapendano, Christophe K; Sandelin, Albin; Jensen, Torben Heick

2011-09-01

420

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters  

PubMed Central

PROMoter uPstream Transcripts (PROMPTs) were identified as a new class of human RNAs, which are heterologous in length and produced only upstream of the promoters of active protein-coding genes. Here, we show that PROMPTs carry 3?-adenosine tails and 5?-cap structures. However, unlike mRNAs, PROMPTs are largely nuclear and rapidly turned over by the RNA exosome. PROMPT-transcribing DNA is occupied by RNA polymerase II (RNAPII) complexes with serine 2 phosphorylated C-terminal domains (CTDs), mimicking that of the associated genic region. Thus, the inefficient elongation capacity of PROMPT transcription cannot solely be assigned to poor CTD phosphorylation. Conditions that reduce gene transcription increase RNAPII occupancy of the upstream PROMPT region, suggesting that they reside in a common transcription compartment. Surprisingly, gene promoters that are actively transcribed by RNAPI or RNAPIII also produce PROMPTs that are targeted by the exosome. RNAPIII PROMPTs bear hallmarks of RNAPII promoter-associated RNAs, explaining the physical presence of RNAPII upstream of many RNAPIII-transcribed genes. We propose that RNAPII activity upstream gene promoters are wide-spread and integral to the act of gene transcription. PMID:21596787

Preker, Pascal; Almvig, Kristina; Christensen, Marianne S.; Valen, Eivind; Mapendano, Christophe K.; Sandelin, Albin; Jensen, Torben Heick

2011-01-01

421

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

PubMed Central

My previous theoretical research shows that the rotating circular genetic code is a viable tool to make easier to distinguish the rules of variation applied to the amino acid exchange; it presents a precise and positional bio-mathematical balance of codons, according to the amino acids they codify. Here, I demonstrate that when using the conventional or classic circular genetic code, a clearer pattern for the human codon usage per amino acid and per genome emerges. The most used human codons per amino acid were the ones ending with the three hydrogen bond nucleotides: C for 12 amino acids and G for the remaining 8, plus one codon for arginine ending in A that was used approximately with the same frequency than the one ending in G for this same amino acid (plus *). The most used codons in man fall almost all the time at the rightmost position, clockwise, ending either in C or in G within the circular genetic code. The human codon usage per genome is compared to other organisms such as fruit flies (Drosophila melanogaster), squid (Loligo pealei), and many others. The biosemiotic codon usage of each genomic population or ‘Theme’ is equated to a ‘molecular language’. The C/U choice or difference, and the G/A difference in the third nucleotide of the most used codons per amino acid are illustrated by comparing the most used codons per genome in humans and squids. The human distribution in the third position of most used codons is a 12-8-2, C-G-A, nucleotide ending signature, while the squid distribution in the third position of most used codons was an odd, or uneven, distribution in the third position of its most used codons: 13-6-3, U-A-G, as its nucleotide ending signature. These findings may help to design computational tools to compare human genomes, to determine the exchangeability between compatible codons and amino acids, and for the early detection of incompatible changes leading to hereditary diseases. PMID:22997484

Castro-Chavez, Fernando

2011-01-01

422

Analysis of the use of codon pairs in the HE gene of the ISA virus shows a correlation between bias in HPR codon-pair use and mortality rates caused by the virus  

PubMed Central

Background Segment 6 of the ISA virus codes for hemoagglutinin-esterase (HE). This segment is highly variable, with more than 26 variants identified. The major variation is observed in what is called the high polymorphism region (HPR). The role of the different HPR zones in the viral cycle or evolution remains unknown. However viruses that present the HPR0 are avirulent, while viruses with important deletions in this region have been responsible for outbreaks with high mortality rates. In this work, using bioinformatic tools, we examined the influence of different HPRs on the adaptation of HE genes to the host translational machinery and the relationship to observed virulence. Methods Translational efficiency of HE genes and their HPR were estimated analyzing codon-pair bias (CPB), adaptation to host codon use (codon adaptation index - CAI) and the adaptation to available tRNAs (tAI). These values were correlated with reported mortality for the respective ISA virus and the ?G of RNA folding. tRNA abundance was inferred from tRNA gene numbers identified in the Salmo salar genome using tRNAScan-SE. Statistical correlation between data was performed using a non-parametric test. Results We found that HPR0 contains zones with codon pairs of low frequency and low availability of tRNA with respect to salmon codon-pair usage, suggesting that HPR modifies HE translational efficiency. Although calculating tAI was impossible because one third of tRNAs (~60.000) were tRNA-ala, translational efficiency measured by CPB shows that as HPR size increases, the CPB value of the HE gene decreases (P = 2x10-7, ? = ?0.675, n = 63) and that these values correlate positively with the mortality rates caused by the virus (? = 0.829, P = 2x10-7, n = 11). The mortality associated with different virus isolates or their corresponding HPR sizes were not related with the ?G of HPR RNA folding, suggesting that the secondary structure of HPR RNA does not modify virulence. Conclusions Our results suggest that HPR size affects the efficiency of gene translation, which modulates the virulence of the virus by a mechanism similar to that observed in production of live attenuated vaccines through deoptimization of codon-pair usage. PMID:23742749

2013-01-01

423

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

424

Cloning and in vitro function analysis of codon-optimized FatI gene.  

PubMed

Currently, n-3 polyunsaturated fatty acids (n-3 PUFAs) have attracted great attention because of their biological significance to organisms. In addition, PUFAs show an obvious impact on prevention and treatment of various diseases. Because n-3 PUFAs cannot be endogenously synthesized by mammals, mammals have to rely on a dietary supplement for sufficient supply. The finding and application of the fatty acid dehydrogenase I (FatI) gene are expected to change the current situation because it can convert n-6 polyunsaturated fatty acids (n-6 PUFAs) to n-3 PUFAs. Meanwhile, the gradual maturation of transgenic technology makes it possible to produce transgenic animals that can synthesize n-3 PUFAs by themselves. In this study, the DNA coding sequence of FatI was synthesized by a chemical method after codon optimization according to the mammal's codon bias. The synthesized DNA sequence was introduced into Boer goat fetal fibroblasts by the constructed recombinant eukaryotic expression vector pcDNA3.1(+)-FatI. Boer goat fetal fibroblasts were transfected by electroporation, and the stable transfected cell lines were obtained by G418 selection. Genomic DNA PCR and Southern blot were applied to verify that the foreign gene FatI was integrated into the genome of the Boer goat fibroblasts. RT-PCR results showed the expression of FatI gene at the mRNA level. The fatty acid profile of cells carrying the FatI gene revealed an increase in total n-3 PUFAs (from 0.61 to 0.95), but a decrease in n-6 PUFAs (from 10.34 to 9.85), resulting in a remarkable increase in the n-3:n-6 ratio (from 0.059 to 0.096). The n-3:n-6 ratio had a 63.49 percent increase, which is a precursor of the response of n-3 desaturase activity of the FatI gene. The study may provide a practical tool for producing transgenic animals that can produce n-3 PUFAs by themselves, and we hope that the application will lay the foundation for animals producing n-3 PUFAs, which will benefit human nutrition and wellness. PMID:24117953

Sun, Xiao-Feng; Sun, Xing-Hong; Teng, Mei-Li; Liu, Huan-Qi; Min, Ling-Jiang; Pan, Qing-Jie; Qin, Guo-Qing; Shen, Wei; Li, Lan

2014-01-01

425

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

426

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 July 1, 2002 through September 30, 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 in a stable form with the byproducts from the FGD system. The coprecipitated mercury does not appear to adversely affect the disposal or reuse properties of the FGD byproduct. The current project will test previously identified, effective catalyst materials at a larger, pilot scale and in a commercial form, so as to provide engineering data for future full-scale 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 fourth full reporting period for the subject Cooperative Agreement. During this period, most of the project efforts were related to completing, installing and starting up the pilot unit, completing laboratory runs to size catalysts, and procuring catalysts for the pilot unit. This technical progress report provides an update on these efforts.

Gary M. Blythe

2002-10-04

427

Heliospheric termination shock motion due to fluctuations in the solar wind upstream conditions: Spherically symmetric model  

NASA Astrophysics Data System (ADS)

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 gasdynamic model [Barnes, 1993] 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 outer 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.

1996-12-01

428

The 'upstream wake' of swimming and flying animals and its correlation with propulsive efficiency.  

PubMed

The interaction between swimming and flying animals and their fluid environments generates downstream wake structures such as vortices. In most studies, the upstream flow in front of the animal is neglected. In this study, we demonstrate the existence of upstream fluid structures even though the upstream flow is quiescent or possesses a uniform incoming velocity. Using a computational model, the flow generated by a swimmer (an oscillating flexible plate) is simulated and a new fluid mechanical analysis is applied to the flow to identify the upstream fluid structures. These upstream structures show the exact portion of fluid that is going to interact with the swimmer. A mass flow rate is then defined based on the upstream structures, and a metric for propulsive efficiency is established using the mass flow rate and the kinematics of the swimmer. We propose that the unsteady mass flow rate defined by the upstream fluid structures can be used as a metric to measure and objectively compare the efficiency of locomotion in water and air. PMID:18689420

Peng, Jifeng; Dabiri, John O

2008-08-01

429

Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics  

PubMed Central

Genomics projects have resulted in a flood of sequence data. Functional annotation currently relies almost exclusively on inter-species sequence comparison and is restricted in cases of limited data from related species and widely divergent sequences with no known homologs. Here, we demonstrate that codon composition, a fusion of codon usage bias and amino acid composition signals, can accurately discriminate, in the absence of sequence homology information, cytoplasmic ribosomal protein genes from all other genes of known function in Saccharomyces cerevisiae, Escherichia coli and Mycobacterium tuberculosis using an implementation of support vector machines, SVMlight. Analysis of these codon composition signals is instructive in determining features that confer individuality to ribosomal protein genes. Each of the sets of positively charged, negatively charged and small hydrophobic residues, as well as codon bias, contribute to their distinctive codon composition profile. The representation of all these signals is sensitively detected, combined and augmented by the SVMs to perform an accurate classification. Of special mention is an obvious outlier, yeast gene RPL22B, highly homologous to RPL22A but employing very different codon usage, perhaps indicating a non-ribosomal function. Finally, we propose that codon composition be used in combination with other attributes in gene/protein classification by supervised machine learning algorithms. PMID:12034849

Lin, Kui; Kuang, Yuyu; Joseph, Jeremiah S.; Kolatkar, Prasanna R.

2002-01-01

430

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

PubMed

Vertebrate mitochondria use stop codons UAA and UAG decoded by the release factor (RF) MTRF1L and two reassigned arginine codons, AGA and AGG. A second highly conserved RF-like factor, MTRF1, which evolved from a gene duplication of an ancestral mitochondrial RF1 and not a RF2, is a good candidate for recognizing the nonstandard codons. MTRF1 differs from other RFs by having insertions in the two external loops important for stop codon recognition (tip of helix alpha5 and recognition loop) and by having key substitutions that are involved in stop codon interactions in eubacterial RF/ribosome structures. These changes may allow recognition of the larger purine base in the first position of AGA/G and, uniquely for RFs, only of G at position 2. In contrast, residues that support A and G recognition in the third position in RF1 are conserved as would be required for recognition of AGA and AGG. Since an assay with vertebrate mitochondrial ribosomes has not been established, we modified Escherichia coli RF1 at the helix alpha5 and recognition loop regions to mimic MTRF1. There was loss of peptidyl-tRNA hydrolysis activity with standard stop codons beginning with U (e.g., UAG), but a gain of activity with codons beginning with A (AAG in particular). A lower level of activity with AGA could be enhanced by solvent modification. These observations imply that MTRF1 has the characteristics to recognize A as the first base of a stop codon as would be required to decode the nonstandard codons AGA and AGG. PMID:20421313

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

2010-06-01

431

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3' UTRs and Near Stop Codons  

PubMed Central

SUMMARY Methylation of the N6 position of adenosine (m6A) is a post-transcriptional modification of RNA whose prevalence and physiological relevance is poorly understood. The recent discovery that FTO, an obesity risk gene, encodes an m6A demethylase implicates m6A as an important regulator of physiological processes. Here we present a method for transcriptome-wide m6A localization, which combines m6A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m6A, indicating that m6A is a common base modification of mRNA. The m6A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m6A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m6A residues and microRNA binding sites within 3' UTRs. These findings provide a resource for identifying transcripts that are substrates for adenosine methylation and reveal insights into the epigenetic regulation of the mammalian transcriptome. PMID:22608085

Meyer, Kate D.; Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E.; Jaffrey, Samie R.

2012-01-01

432

Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.  

PubMed

Methylation of the N(6) position of adenosine (m(6)A) is a posttranscriptional modification of RNA with poorly understood prevalence and physiological relevance. The recent discovery that FTO, an obesity risk gene, encodes an m(6)A demethylase implicates m(6)A as an important regulator of physiological processes. Here, we present a method for transcriptome-wide m(6)A localization, which combines m(6)A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m(6)A, indicating that m(6)A is a common base modification of mRNA. The m(6)A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m(6)A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m(6)A residues and microRNA-binding sites within 3' UTRs. These findings provide a resource for identifying transcripts that are substrates for adenosine methylation and reveal insights into the epigenetic regulation of the mammalian transcriptome. PMID:22608085

Meyer, Kate D; Saletore, Yogesh; Zumbo, Paul; Elemento, Olivier; Mason, Christopher E; Jaffrey, Samie R

2012-06-22

433

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

SciTech Connect

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

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

2009-06-02