Science.gov

Sample records for 3rd codon positions

  1. Model for Codon Position Bias in RNA Editing

    NASA Astrophysics Data System (ADS)

    Liu, Tsunglin; Bundschuh, Ralf

    2005-08-01

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

  2. A model for codon position bias in RNA editing

    NASA Astrophysics Data System (ADS)

    Bundschuh, Ralf; Liu, Tsunglin

    2006-03-01

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

  3. Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons.

    PubMed

    Friedman, Robert; Hughes, Austin L

    2005-03-01

    It has been suggested that codon volatility (the proportion of the point-mutation neighbors of a codon that encode different amino acids) can be used as an index of past positive selection. We compared codon volatility with patterns of synonymous and nonsynonymous nucleotide substitution in genome-wide comparisons of orthologous genes between three pairs of related genomes: (1) the protists Plasmodium falciparum and P. yoelii, (2) the fungi Saccharomyces cerevisiae and S. paradoxus, and (3) the mammals mouse and rat. Codon volatility was not consistently associated with an elevated rate of nonsynonymous substitution, as would be expected under positive selection. Rather, the most consistent and powerful correlate of elevated codon volatility was nucleotide content at the second codon position, as expected, given the nature of the genetic code.

  4. 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 Central

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

    2001-01-01

    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

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

    NASA Astrophysics Data System (ADS)

    Mitarai, Namiko; Pedersen, Steen

    2013-10-01

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

  6. Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses.

    PubMed

    Liao, Pei-Chun; Wang, Kung-Kai; Tsai, Shinn-Shyong; Liu, Hung-Jen; Huang, Bing-Hong; Chuang, Kuo-Pin

    2015-08-01

    The capsid genes from 14 pigeon circovirus (PiCV) sequences, collected from Taiwan between 2009 and 2010, were sequenced and compared with 14 PiCV capsid gene sequences from GenBank. Based on pairwise comparison, PiCV strains from Taiwan shared 73.9-100% nucleotide identity and 72-100% amino acid identity with those of the 14 reported PiCV sequences. Phylogenetic analyses revealed that Taiwanese PiCV isolates can be grouped into two clades: clade 1 comprising isolates from Belgium, Australia, USA, Italy and China, and clade 2 showing close relation to isolates from Germany and France. Recurrent positive selection was detected in clade 1 PiCV lineages, which may contribute to the diversification of predominant PiCV sequences in Taiwan. Further observations suggest that synonymous codon usage variations between PiCV clade 1 and clade 2 may reflect the adaptive divergence on translation efficiency of capsid genes in infectious hosts. Variation in selective pressures acting on the evolutionary divergence and codon usage bias of both clades explains the regional coexistence of virus sequences congeners prevented from competitive exclusion within an island such as Taiwan. Our genotyping results also provide insight into the aetiological agents of PiCV outbreak in Taiwan and we present a comparative analysis of the central coding region of PiCV genome. From the sequence comparison results of 28 PiCVs which differs in regard to the geographical origin and columbid species, we identified conserved regions within the capsid gene that are likely to be suitable for primer selection and vaccine development.

  7. Focusing the Debate for Positive Change in Teacher Education. Proceedings of the Forum on Teacher Education (3rd, Little Rock, Arkansas, March 1987).

    ERIC Educational Resources Information Center

    Education Commission of the States, Denver, CO.

    In the third regional forum on positive change in teacher education, two themes dominated discussions: the pros and cons of the "fifth-year" plan for teacher education, and the impact and future of standardized testing. In both areas, a major emphasis on traditonally black institutions emerged. This report outlines the discussions, and presents…

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

    PubMed Central

    2013-01-01

    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

  9. Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data

    PubMed Central

    Breinholt, Jesse W.; Kawahara, Akito Y.

    2013-01-01

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

  10. Avian coronavirus spike glycoprotein ectodomain shows a low codon adaptation to Gallus gallus with virus-exclusive codons in strategic amino acids positions.

    PubMed

    Brandão, Paulo E

    2012-08-01

    This is a study on the Avian coronavirus IBV and chicken host-relationship from the codon usage point of view based on fifty-nine non-redundant IBV S1 sequences (nt 1-507) from strains detected worldwide and chicken tissue-specific protein genes sequences from IBV-replicating sites. The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. The low CAI values agree with a low S protein expression and considering that S protein is a determinant for attachment and neutralization, this could be a further mechanism besides mRNA transcription attenuation for a low expression of this protein leading to an immune camouflage.

  11. Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs

    PubMed Central

    Mandal, Debabrata; Köhrer, Caroline; Su, Dan; Babu, I. Ramesh; Chan, Clement T.Y.; Liu, Yuchen; Söll, Dieter; Blum, Paul; Kuwahara, Masayasu; Dedon, Peter C.; RajBhandary, Uttam L.

    2014-01-01

    Most archaea and bacteria use a modified C in the anticodon wobble position of isoleucine tRNA to base pair with A but not with G of the mRNA. This allows the tRNA to read the isoleucine codon AUA without also reading the methionine codon AUG. To understand why a modified C, and not U or modified U, is used to base pair with A, we mutated the C34 in the anticodon of Haloarcula marismortui isoleucine tRNA (tRNA2Ile) to U, expressed the mutant tRNA in Haloferax volcanii, and purified and analyzed the tRNA. Ribosome binding experiments show that although the wild-type tRNA2Ile binds exclusively to the isoleucine codon AUA, the mutant tRNA binds not only to AUA but also to AUU, another isoleucine codon, and to AUG, a methionine codon. The G34 to U mutant in the anticodon of another H. marismortui isoleucine tRNA species showed similar codon binding properties. Binding of the mutant tRNA to AUG could lead to misreading of the AUG codon and insertion of isoleucine in place of methionine. This result would explain why most archaea and bacteria do not normally use U or a modified U in the anticodon wobble position of isoleucine tRNA for reading the codon AUA. Biochemical and mass spectrometric analyses of the mutant tRNAs have led to the discovery of a new modified nucleoside, 5-cyanomethyl U in the anticodon wobble position of the mutant tRNAs. 5-Cyanomethyl U is present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes. PMID:24344322

  12. 2nd & 3rd Generation Vehicle Subsystems

    NASA Technical Reports Server (NTRS)

    2000-01-01

    This paper contains viewgraph presentation on the "2nd & 3rd Generation Vehicle Subsystems" project. The objective behind this project is to design, develop and test advanced avionics, power systems, power control and distribution components and subsystems for insertion into a highly reliable and low-cost system for a Reusable Launch Vehicles (RLV). The project is divided into two sections: 3rd Generation Vehicle Subsystems and 2nd Generation Vehicle Subsystems. The following topics are discussed under the first section, 3rd Generation Vehicle Subsystems: supporting the NASA RLV program; high-performance guidance & control adaptation for future RLVs; Evolvable Hardware (EHW) for 3rd generation avionics description; Scaleable, Fault-tolerant Intelligent Network or X(trans)ducers (SFINIX); advance electric actuation devices and subsystem technology; hybrid power sources and regeneration technology for electric actuators; and intelligent internal thermal control. Topics discussed in the 2nd Generation Vehicle Subsystems program include: design, development and test of a robust, low-maintenance avionics with no active cooling requirements and autonomous rendezvous and docking systems; design and development of a low maintenance, high reliability, intelligent power systems (fuel cells and battery); and design of a low cost, low maintenance high horsepower actuation systems (actuators).

  13. The ribosome prohibits the G•U wobble geometry at the first position of the codon-anticodon helix.

    PubMed

    Rozov, Alexey; Westhof, Eric; Yusupov, Marat; Yusupova, Gulnara

    2016-07-27

    Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G•U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G•C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.

  14. Structures IVHM for 3rd Generation RLVs

    NASA Technical Reports Server (NTRS)

    Rogowski, Robert S.

    2000-01-01

    The primary goal of a Structures Integrated Vehicle Health Management (IVHM) system for 3rd generation Reusable Launch Vehicles (RLV) is to provide near 100% structural sensing coverage and thus eliminate both routine, and especially unplanned, inspections which are costly and time consuming. To meet this goal, significant advances in sensing and measurement system technology, data systems architectures, and structures based analysis methodology will be required to enable the needed large numbers of sensors with little weight penalty. This program will leverage X-33, 2nd Gen RLV, Shuttle, and Aviation Safety SIVHM system development experience to address this goal.

  15. BACODINE/3rd Interplanetary Network burst localization

    SciTech Connect

    Hurley, K.; Barthelmy, S.; Butterworth, P.; Cline, T.; Sommer, M.; Boer, M.; Niel, M.; Kouveliotou, C.; Fishman, G.; Meegan, C.

    1996-08-01

    Even with only two widely separated spacecraft (Ulysses and GRO), 3rd Interplanetary Network (IPN) localizations can reduce the areas of BATSE error circles by two orders of magnitude. Therefore it is useful to disseminate them as quickly as possible following BATSE bursts. We have implemented a system which transmits the light curves of BACODINE/BATSE bursts directly by e-mail to UC Berkeley immediately after detection. An automatic e-mail parser at Berkeley watches for these notices, determines the Ulysses crossing time window, and initiates a search for the burst data on the JPL computer as they are received. In ideal cases, it is possible to retrieve the Ulysses data within a few hours of a burst, generate an annulus of arrival directions, and e-mail it out to the astronomical community by local nightfall. Human operators remain in this loop, but we are developing a fully automated routine which should remove them, at least for intense events, and reduce turn-around times to an absolute minimum. We explain the current operations, the data types used, and the speed/accuracy tradeoffs.

  16. Mutations to Less-Preferred Synonymous Codons in a Highly Expressed Gene of Escherichia coli: Fitness and Epistatic Interactions

    PubMed Central

    Hauber, David J.; Grogan, Dennis W.; DeBry, Ronald W.

    2016-01-01

    Codon-tRNA coevolution to maximize protein production has been, until recently, the dominant hypothesis to explain codon-usage bias in highly expressed bacterial genes. Two predictions of this hypothesis are 1) selection is weak; and 2) similar silent replacements at different codons should have similar fitness consequence. We used an allele-replacement strategy to change five specific 3rd-codon-position (silent) sites in the highly expressed Escherichia coli ribosomal protein gene rplQ from the wild type to a less-preferred alternative. We introduced the five mutations within a 10-codon region. Four of the silent sites were chosen to test the second prediction, with a CTG to CTA mutation being introduced at two closely linked leucine codons and an AAA to AAG mutation being introduced at two closely linked lysine codons. We also introduced a fifth silent mutation, a GTG to GTA mutation at a valine codon in the same genic region. We measured the fitness effect of the individual mutations by competing each single-mutant strain against the parental wild-type strain, using a disrupted form of the araA gene as a selectively neutral phenotypic marker to distinguish between strains in direct competition experiments. Three of the silent mutations had a fitness effect of |s| > 0.02, which is contradictory to the prediction that selection will be weak. The two leucine mutations had significantly different fitness effects, as did the two lysine mutations, contradictory to the prediction that similar mutations at different codons should have similar fitness effects. We also constructed a strain carrying all five silent mutations in combination. Its fitness effect was greater than that predicted from the individual fitness values, suggesting that negative synergistic epistasis acts on the combination allele. PMID:26727272

  17. TGA cysteine codons and intron sequences in conserved and nonconserved positions are found in macronuclear RNA polymerase genes of Euplotes octocarinatus.

    PubMed Central

    Kaufmann, J; Florian, V; Klein, A

    1992-01-01

    The gene sequences of the second largest subunits of RNA polymerases I and II of Euplotes octocarinatus, RPA2 and RPB2, were determined and compared to the respective known sequences of Saccharomyces cerevisiae. The similarity of the derived polypeptide sequences permitted their assignment to the respective polymerases and allowed the comparison of the zinc binding regions. In frame TGA codons were detected, which are likely to encode conserved cysteinyl residues in the putative zinc-finger region of the RPA2 gene. They were also found in other positions in both the RPA2 and RPB2 genes. The RPB2 gene contains a 30 bp intron close to the 5'-end of its coding region. The 5'-ends of the coding regions of all three genes encoding the largest subunits of the three different polymerases were also analyzed. The zinc finger structures again show the use of TGA codons for conserved cysteinyl residues in two of the genes. An N-terminal intron is located in the RPB1 gene at a conserved position as compared to the respective genes of several other eucarya. Images PMID:1461731

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

    PubMed

    Levitin, Anastasia; Yanofsky, Charles

    2010-03-01

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

  19. AT2-AT3-profiling: a new look at synonymous codon usage.

    PubMed

    Pluhar, Wolfgang

    2006-12-01

    The teleology of synonymous codon usage (SCU) still awaits a unifying concept. Here the 2nd codon letter of human mRNA-codons was graphically, aided by a computer program, put in relation to the 3rd codon letter, the carrier of SCU: AT2, the density of A+T in 2nd codon position, behaves to AT3, the analogous density of the 3rd codon position, mostly in an inverse fashion that can be expressed as typical figures: mRNAs with an overall AT-density below 50% have a tendency to produce bulky figures called "red dragons" (when redness is attributed to graph-areas, where AT3< AT2), while mRNAs with an AT-density above 50% produce a pattern called "harlequin" consisting of alternating red and blue (blueness, in analogy, when AT3>AT2) diamonds. With more diversion of AT3 from AT2, the harlequin patterns can assume the pattern of a "blue dragon". By analysing the mRNA of known proteins, these patterns can be correlated with certain functional regions: proteins with multiple transmembrane passages show bulky "red dragons", structural proteins with a high glycine- and proline content such as collagen result in "blue dragons". Non-coding mRNAs tend to show a balance between AT2 and AT3 and hence "harlequin patterns". Signal peptides usually code red due to a low AT3 with an AT2-density at the expectance level. With this technique DNA-sequences of as yet unknown functional meaning were scanned. When stretches of harlequin patterns appear interrupted by red or blue dragons, closer scrutiny of these stretches can reveal ORFs which deserve to be looked at more closely for their protein-informational content. At least in humans, SCU appears to follow protein-dependent AT2-density in a reciprocal fashion and does not seem to serve the purpose of influencing mRNA secondary structure which is discussed in depth. PMID:16930630

  20. Presenting the 3rd edition of WRB

    NASA Astrophysics Data System (ADS)

    Schad, Peter

    2014-05-01

    The third edition of the international soil classification system "World Reference Base for Soil Resources" (WRB) will be presented during der 20th World Congress of Soil Science, Jeju, Korea, June 9-12. The second edition was published in 2006 and the first in 1998, which, in turn, was based on the Legends of the FAO Soil Map of the World. Now, after eight years of experience with the second edition, time was due for a revision. The major changes are: 1. The second edition had two different qualifier sequences for naming soils (IUSS Working Group WRB, 2006, update 2007) and for creating map legends (Guidelines for creating small-scale map legends using the WRB; IUSS Working Group WRB, 2010). The third edition has one sequence for both. The qualifiers for every Reference Soil Group are subdivided into a small number of main qualifiers that are ranked and a larger number of additional qualifiers that are not ranked and given in an alphabetical order. The name of a pedon must comprise all applying qualifiers. The name of a map unit comprises a specified small number of main qualifiers, depending on scale, whereas all other qualifiers are optional. 2. For some soils, problems have been reported. Albeluvisols are difficult to detect in the field and cover only small surfaces. They have been replaced by Retisols, which have a broader definition that is easier to identify in the field. 3. The use of some diagnostics was difficult. Examples are: The argic horizon had too low limit values, so we had much more soils with argic horizons than justified. The definitions of the cambic horizon and the gleyic and stagnic properties were not precise enough. Organic material, mollic and umbric horizons had an unnecessary complicated definition. 4. Some changes in the key to the Reference Soil Groups seemed to be justified. Fluvisols were moved further down, Durisols and Gypsisols switched their position, also Arenosols and Cambisols. The soils with an argic horizon were brought

  1. PREFACE: 3rd International Congress on Mechanical Metrology (CIMMEC2014)

    NASA Astrophysics Data System (ADS)

    2015-10-01

    From October 14th to 16th 2014, The Brazilian National Institute of Metrology, Quality, and Technology (Inmetro) and the Brazilian Society of Metrology (SBM) organized the 3rd International Congress on Mechanical Metrology (3rd CIMMEC). The 3rd CIMMEC was held in the city of Gramado, Rio Grande do Sul, Brazil. Anticipating the interest and enthusiasm of the technical-scientific community, the Organizing Institutions invite people and organizations to participate in this important congress, reiterating the commitment to organize an event according to highest international standards. This event has been conceived to integrate people and organizations from Brazil and abroad in the discussion of advanced themes in metrology. Manufacturers and dealers of measuring equipment and standards, as well as of auxiliary accessories and bibliographic material, had the chance to promote their products and services in stands at the Fair, which has taken place alongside the Congress. The 3rd CIMMEC consisted of five Keynote Speeches and 116 regular papers. Among the regular papers, the 25 most outstanding ones, comprising a high quality content on Mechanical Metrology, were selected to be published in this issue of Journal of Physics: Conference Series. It is our great pleasure to present this volume of Journal of Physics: Conference Series to the scientific community to promote further research in Mechanical Metrology and related areas. We believe that this volume will be both an excellent source of scientific material in the fast evolving fields that were covered by CIMMEC 2014.

  2. The Ups and Downs of 3rd Grade

    ERIC Educational Resources Information Center

    Felton, Kelsey Augst; Akos, Patrick

    2011-01-01

    The transition from 2nd to 3rd grade has received little notice in education research--yet the authors' experience in elementary school counseling convinced them that most students undergo a seismic shift during this period. Third grade is not only the first year students will encounter standardized end-of-grade tests, but also a year in which…

  3. 75 FR 55313 - Record of Decision (ROD) for Conversion of the 3rd Armored Cavalry Regiment (3rd ACR) to a...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-10

    ... 3rd ACR at Fort Hood is being selected because the unit will have maximum time to convert and train... required for an SBCT, and has adequate maneuver space to accommodate SBCT training. The 3rd ACR will...

  4. The 3rd Annual Controlled Structures Technology Symposium

    NASA Technical Reports Server (NTRS)

    1991-01-01

    Viewgraphs of presentations at the Controlled Structures Technology (CST) MIT Space Engineering Research Center 3rd Annual Symposium are included. Topics covered include optical interferometer testbed; active impedence matching of complex structural systems; application of CST to adaptive optics; middeck 0-G dynamics Experiment (MODE); inhibiting multiple mode vibration in controlled flexible systems; the middeck active control experiment (MACE); robust control for uncertain structures; cost averaging techniques for robust structural control; and intelligent structures technology.

  5. Precipitation Model Validation in 3rd Generation Aeroturbine Disc Alloys

    NASA Technical Reports Server (NTRS)

    Olson, G. B.; Jou, H.-J.; Jung, J.; Sebastian, J. T.; Misra, A.; Locci, I.; Hull, D.

    2008-01-01

    In support of application of the DARPA-AIM methodology to the accelerated hybrid thermal process optimization of 3rd generation aeroturbine disc alloys with quantified uncertainty, equilibrium and diffusion couple experiments have identified available fundamental thermodynamic and mobility databases of sufficient accuracy. Using coherent interfacial energies quantified by Single-Sensor DTA nucleation undercooling measurements, PrecipiCalc(TM) simulations of nonisothermal precipitation in both supersolvus and subsolvus treated samples show good agreement with measured gamma particle sizes and compositions. Observed longterm isothermal coarsening behavior defines requirements for further refinement of elastic misfit energy and treatment of the parallel evolution of incoherent precipitation at grain boundaries.

  6. Microstructure Modeling of 3rd Generation Disk Alloys

    NASA Technical Reports Server (NTRS)

    Jou, Herng-Jeng

    2010-01-01

    The objective of this program is to model, validate, and predict the precipitation microstructure evolution, using PrecipiCalc (QuesTek Innovations LLC) software, for 3rd generation Ni-based gas turbine disc superalloys during processing and service, with a set of logical and consistent experiments and characterizations. Furthermore, within this program, the originally research-oriented microstructure simulation tool will be further improved and implemented to be a useful and user-friendly engineering tool. In this report, the key accomplishment achieved during the second year (2008) of the program is summarized. The activities of this year include final selection of multicomponent thermodynamics and mobility databases, precipitate surface energy determination from nucleation experiment, multiscale comparison of predicted versus measured intragrain precipitation microstructure in quench samples showing good agreement, isothermal coarsening experiment and interaction of grain boundary and intergrain precipitates, primary microstructure of subsolvus treatment, and finally the software implementation plan for the third year of the project. In the following year, the calibrated models and simulation tools will be validated against an independently developed experimental data set, with actual disc heat treatment process conditions. Furthermore, software integration and implementation will be developed to provide material engineers valuable information in order to optimize the processing of the 3rd generation gas turbine disc alloys.

  7. Designing a 3rd generation, authenticatable attribute measurement system

    SciTech Connect

    Thron, Jonathan; Karpius, Peter; Santi, Peter; Smith, Morag; Vo, Duc; Williams, Richard

    2009-01-01

    Attribute measurement systems (AMS) are designed to measure potentially sensitive items containing Special Nuclear Materials to determine if the items possess attributes which fall within an agreed-upon range. Such systems could be used in a treaty to inspect and verify the identity of items in storage without revealing any sensitive information associated with the item. An AMS needs to satisfy two constraints: the host party needs to be sure that none of their sensitive information is released, while the inspecting party wants to have confidence that the limited amount of information they see accurately reflects the properties of the item being measured. The former involves 'certifying' the system and the latter 'authenticating' it. Previous work into designing and building AMS systems have focused more on the questions of certifiability than on the questions of authentication - although a few approaches have been investigated. The next step is to build a 3rd generation AMS which (1) makes the appropriate measurements, (2) can be certified, and (3) can be authenticated (the three generations). This paper will discuss the ideas, options, and process of producing a design for a 3rd generation AMS.

  8. The development of 3rd generation IR detectors at AIM

    NASA Astrophysics Data System (ADS)

    Ziegler, J.; Eich, D.; Mahlein, M.; Schallenberg, T.; Scheibner, R.; Wendler, J.; Wenisch, J.; Wollrab, R.; Daumer, V.; Rehm, R.; Rutz, F.; Walther, M.

    2011-06-01

    3rd generation IR modules - dual-color (DC), dual-band (DB), and large format two-dimensional arrays - require sophisticated production technologies such as molecular beam epitaxy (MBE) as well as new array processing techniques, which can satisfy the rising demand for increasingly complex device structures and low cost detectors. AIM will extend its future portfolio by high performance devices which make use of these techniques. The DC MW / MW detectors are based on antimonide type-II superlattices (produced by MBE at Fraunhofer IAF, Freiburg) in the 384x288 format with a 40 μm pitch. For AIM, the technology of choice for MW / LW DB FPAs is MCT MBE on CdZnTe substrates, which has been developed in cooperation with IAF, Freiburg. 640x512, 20 μm pitch Focal Plane Arrays (FPAs) have been processed at AIM. The growth of MW MCT MBE layers on alternate substrates is challenging, but essential for competitive fabrication of large two-dimensional arrays such as megapixel (MW 1280x1024, 15 μm pitch) FPAs. This paper will present the development status and latest results of the above-mentioned 3rd Gen FPAs and Integrated Detector Cooler Assemblies (IDCAs).

  9. 3rd grade English language learners making sense of sound

    NASA Astrophysics Data System (ADS)

    Suarez, Enrique; Otero, Valerie

    2013-01-01

    Despite the extensive body of research that supports scientific inquiry and argumentation as cornerstones of physics learning, these strategies continue to be virtually absent in most classrooms, especially those that involve students who are learning English as a second language. This study presents results from an investigation of 3rd grade students' discourse about how length and tension affect the sound produced by a string. These students came from a variety of language backgrounds, and all were learning English as a second language. Our results demonstrate varying levels, and uses, of experiential, imaginative, and mechanistic reasoning strategies. Using specific examples from students' discourse, we will demonstrate some of the productive aspects of working within multiple language frameworks for making sense of physics. Conjectures will be made about how to utilize physics as a context for English Language Learners to further conceptual understanding, while developing their competence in the English language.

  10. 3rd annual symposium of chemical and pharmaceutical structure analysis.

    PubMed

    Weng, Naidong; Zheng, Jenny; Lee, Mike

    2012-08-01

    The 3rd Annual Symposium on Chemical and Pharmaceutical Structure Analysis was once again held in Shanghai, where a rich history of 'East meets West' continued. This meeting is dedicated to bringing together scientists from pharmaceutical companies, academic institutes, CROs and instrument vendors to discuss current challenges and opportunities on the forefront of pharmaceutical research and development. The diversified symposia and roundtables are highly interactive events where scientists share their experiences and visions in a collegial setting. The symposium highlighted speakers and sessions that provided first-hand experiences as well as the latest guidance and industrial/regulatory thinking, which was reflected by the theme of this year's meeting 'From Bench to Decision Making - from Basics to Application.' In addition to the highly successful Young Scientist Excellence Award, new events were featured at this year's meeting, such as the Executive Roundtable and the inaugural Innovator Award.

  11. Results from the UK 3rd generation programme: Albion

    NASA Astrophysics Data System (ADS)

    McEwen, R. K.; Axcell, C.; Knowles, P.; Hoade, K. P.; Wilson, M.; Dennis, P. N. J.; Backhouse, P.; Gordon, N. T.

    2008-10-01

    Following the development of 1st Generation systems in the 1970s, thermal imaging has been in service with the UK armed forces for over 25 years and has proven itself to be a battle winning technology. More recently the wider accessibility to similar technologies within opposing forces has reduced the military advantage provided by these 1st Generation systems and a clear requirement has been identified by the UK MOD for thermal imaging sensors providing increased detection, recognition and identification (DRI) ranges together with a simplified logistical deployment burden and reduced through-life costs. In late 2005, the UK MOD initiated a programme known as "Albion" to develop high performance 3rd Generation single waveband infrared detectors to meet this requirement. At the same time, under a separate programme supporting higher risk technology, a dual waveband infrared detector was also developed. The development phase of the Albion programme has now been completed and prototype detectors are now available and have been integrated into demonstration thermal imaging cameras. The Albion programme has now progressed into the second phase, incorporating both single and dual waveband devices, focussing on low rate initial production (LRIP) and qualification of the devices for military applications. All of the detectors have been fabricated using cadmium mercury telluride material (CMT), grown by metal organic vapour phase epitaxy (MOVPE) on low cost, gallium arsenide (GaAs) substrates and bump bonded to the silicon read out circuit (ROIC). This paper discusses the design features of the 3rd Generation detectors developed in the UK together with the results obtained from the prototype devices both in the laboratory and when integrated into field deployable thermal imaging cameras.

  12. Beyond 3rd generation MCT: SXGA QWIP (Invited Paper)

    NASA Astrophysics Data System (ADS)

    Crawford, Stewart; Skivington, Tracey; Craig, Robert; Haining, Andrew; Costard, Eric; Belhaire, Eric; Bois, Philippe

    2005-05-01

    Successful past experience of implementing long wave MCT 1st and 2nd Generation thermal imagers has demonstrated to THALES Optronics that MCT presents difficult challenges when correcting non-uniformity errors caused by rapidly changing detector element gain and offset drifts. These problems become even more demanding when the move is made from long linear arrays to focal plane arrays due to the significantly larger number of detector elements. Relaxation of these demands would make a significant impact on the price/performance trade which inevitably occurs in a camera development. In recognition of the need to offer UK MOD best value, THALES Optronics has initiated a programme to achieve a SXGA resolution camera and is working with UK MOD, over a two year period, to investigate whether an alternative technology can maintain the high resolution required whilst achieving a downward step change in price. The selected technology is 3rd Generation Gallium Arsenide long wave Quantum Well Infra-red Photodiode (QWIP) chosen because initial indications are that drift rates are orders of magnitude slower than MCT. The programme involves studies to determine effects of defect clusters, bimodalism, non-uniformity correction levels and higher than normal operating temperatures on achieving acceptable performance, including logistics, in user scenarios whilst maximising detector yield. Development of demonstrator IR camera hardware (technology readiness level 6/7) based on a THALES Research & Technology QWIP array is also part of the programme.

  13. Development of the 3rd Generation ECR ion source

    SciTech Connect

    Lyneis, C.M.; Xie, Z.Q.; Taylor, C.E.

    1997-09-01

    The LBNL 3rd Generation ECR ion source has progressed from a concept to the fabrication of a full scale prototype superconducting magnet structure. This new ECR ion source will combine the recent ECR ion source techniques that significantly enhance the production of high charge state ions. The design includes a plasma chamber made from aluminum to provide additional cold electrons, three separate microwave feeds to allow multiple-frequency plasma heating (at 10, 14 and 18 GHz or at 6, 10 and 14 GHz) and very high magnetic mirror fields. The design calls for mirror fields of 4 T at injection and 3 T at extraction and for a radial field strength at the wall of 2.4 T. The prototype superconducting magnet structure which consists of three solenoid coils and six race track coils with iron poles forming the sextupole has been tested in a vertical dewar. After training, the sextupole magnet reached 105% of its design current with the solenoids off. With the solenoids operating at approximately 70% of their full design field, the sextuple coils operated at 95% of the design value which corresponds to a sextupole field strength at the plasma wall of more than 2.1 T.

  14. 80. GENERAL VIEW TO NORTH ON 3RD AVENUE EL AT ...

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

    80. GENERAL VIEW TO NORTH ON 3RD AVENUE EL AT GUN HILL STATION. 7TH AVENUE EL EXPRESS IS VISIBLE ABOVE THE 3RD AVENUE EL WHICH JOINED ONTO THE SAME STRUCTURE AT GUN HILL ROAD. NOTE: GUN HILL ROAD IS THE NORTH TERMINUS OF THE 3RD AVENUE ELEVATED. TRAINS DID NOT CARRY PASSENGERS BEYOND THIS POINT, ALTHOUGH THE 3RD AVENUE TRACK DID EXTEND FURTHER NORTH FOR SWITCHING PURPOSES AND INTO THE YARDS. - Interborough Rapid Transit Company, Third Avenue Elevated Line, Borough of the Bronx, New York County, NY

  15. Design of the 3rd generation ECR ion source

    SciTech Connect

    Lyneis, C.M.; Xie, Z.Q.; Taylor, C.E.

    1997-02-01

    Development of the 3rd Generation ECR ion source has progressed from a concept described in the last ECR Ion Source Workshop to the fabrication of a full scale prototype superconducting magnet structure. The prototype consists of three solenoid coils and six race track coils with iron poles forming the sextupole. The design calls for mirror fields of 4 T at injection and 3 T at extraction and for a radial field strength at the wall of 2.4 T. The prototype magnet will be tested this spring in an existing vertical cryostat to determine its operating characteristics including maximum operating values, training characteristics and to study the interaction between the solenoid and sextupole coils. Design of the ECR plasma chamber includes aluminum walls to provide an enhanced source of cold electrons, up to three separate microwave feeds to allow simultaneous heating of the plasma electrons at 10, 14 and 18 GHz or at 6, 10 and 14 GHz. Water cooling of the plasma chamber walls and the injection and extraction plates is planned so that up to 10 kW of microwave power can be used without excessive heating of the chamber components. Experience with the AECR-U at LBNL shows that increasing the magnetic fields and using two frequency heating allows operation at lower neutral pressures and higher microwave power density. Both of these conditions are needed to produce very high charge states from elements with masses greater than xenon and the resulting higher energy, more intense heavy beams from the 88-Inch Cyclotron would provide new research opportunities.

  16. A common periodic table of codons and amino acids.

    PubMed

    Biro, J C; Benyó, B; Sansom, C; Szlávecz, A; Fördös, G; Micsik, T; Benyó, Z

    2003-06-27

    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 main codons (and amino acids) of the fields. They were connected to each other by six axes. The resulting nucleic acid periodic table showed perfect axial symmetry for codons. The corresponding amino acid table also displaced periodicity regarding the biochemical properties (charge and hydropathy) of the 20 amino acids and the position of the stop signals. The table emphasizes the importance of the central nucleotide in the codons and predicts that purines control the charge while pyrimidines determine the polarity of the amino acids. This prediction was experimentally tested.

  17. PREFACE: 3rd International Symposium ''Optics and its Applications''

    NASA Astrophysics Data System (ADS)

    Calvo, M. L.; Dolganova, I. N.; Gevorgyan, N.; Guzman, A.; Papoyan, A.; Sarkisyan, H.; Yurchenko, S.

    2016-01-01

    The SPIE.FOCUS Armenia: 3rd International Symposium ''Optics and its Applications'' (OPTICS-2015) http://rau.am/optics2015/ was held in Yerevan, Armenia, in the period October 1 - 5, 2015. The symposium was organized by the International Society for Optics and Photonics (SPIE), the Armenian SPIE student chapter with collaboration of the Armenian TC of ICO, the Russian-Armenian University (RAU), the Institute for Physical Research of National Academy of Sciences of Armenia (IPR of NAS), the Greek-Armenian industrial company LT-PYRKAL, and the Yerevan State University (YSU). The Symposium was co-organized by the SPIE & OSA student chapters of BMSTU, the Armenian OSA student chapter, and the SPIE student chapters of Lund University and Wroclaw University of Technology. The symposium OPTICS-2015 was dedicated to the International Year of Light and Light-Based Technologies. OPTICS-2015 was devoted to modern topics and optical technologies such as: optical properties of nanostructures, silicon photonics, quantum optics, singular optics & its applications, laser spectroscopy, strong field optics, biomedical optics, nonlinear & ultrafast optics, photonics & fiber optics, and mathematical methods in optics. OPTICS-2015 was attended by 100 scientists and students representing 17 countries: Armenia, China, Czech Republic, France, Georgia, Germany, India, Iran, Italy, Latvia, Mexico, Poland, Russia, Saudi Arabia, Sweden, Ukraine, and USA. Such a broad international community confirmed the important mission of science to be a uniting force between different countries, religions, and nations. We hope that OPTICS-2015 inspired and motivated students and young scientists to work in optics and in science in general. The present volume of Journal of Physics: Conference Series includes proceedings of the symposium covering various aspects of modern problems in optics. We are grateful to all people who were involved in the organization process. We gratefully acknowledge support from

  18. PREFACE: 3rd International Congress on Ceramics (ICC3)

    NASA Astrophysics Data System (ADS)

    Niihara, Koichi; Ohji, Tatsuki; Sakka, Yoshio

    2011-10-01

    Early in 2005, the American Ceramic Society, the European Ceramic Society and the Ceramic Society of Japan announced a collaborative effort to provide leadership for the global ceramics community that would facilitate the use of ceramic and glass materials. That effort resulted in an agreement to organize a new biennial series of the International Congress on Ceramics, convened by the International Ceramic Federation (ICF). In order to share ideas and visions of the future for ceramic and glass materials, the 1st International Congress on Ceramics (ICC1) was held in Canada, 2006, under the organization of the American Ceramic Society, and the 2nd Congress (ICC2) was held in Italy, 2008, hosted by the European Ceramic Society. Organized by the Ceramic Society of Japan, the 3rd Congress (ICC3) was held in Osaka, Japan, 14-18 November 2010. Incorporating the 23rd Fall Meeting of the Ceramic Society of Japan and the 20th Iketani Conference, ICC3 was also co-organized by the Iketani Science and Technology Foundation, and was endorsed and supported by ICF, Asia-Oceania Ceramic Federation (AOCF) as well as many other organizations. Following the style of the previous two successful Congresses, the program was designed to advance ceramic and glass technologies to the next generation through discussion of the most recent advances and future perspectives, and to engage the worldwide ceramics community in a collective effort to expand the use of these materials in both conventional as well as new and exciting applications. ICC3 consisted of 22 voluntarily organized symposia in the most topical and essential themes of ceramic and glass materials, including Characterization, design and processing technologies Electro, magnetic and optical ceramics and devices Energy and environment related ceramics and systems Bio-ceramics and bio-technologies Ceramics for advanced industry and safety society Innovation in traditional ceramics It also contained the Plenary Session and the

  19. Codon Adaptation of Plastid Genes

    PubMed Central

    Suzuki, Haruo; Morton, Brian R.

    2016-01-01

    Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes. PMID:27196606

  20. Codon Adaptation of Plastid Genes.

    PubMed

    Suzuki, Haruo; Morton, Brian R

    2016-01-01

    Codon adaptation is codon usage bias that results from selective pressure to increase the translation efficiency of a gene. Codon adaptation has been studied across a wide range of genomes and some early analyses of plastids have shown evidence for codon adaptation in a limited set of highly expressed plastid genes. Here we study codon usage bias across all fully sequenced plastid genomes which includes representatives of the Rhodophyta, Alveolata, Cryptophyta, Euglenozoa, Glaucocystophyceae, Rhizaria, Stramenopiles and numerous lineages within the Viridiplantae, including Chlorophyta and Embryophyta. We show evidence that codon adaptation occurs in all genomes except for two, Theileria parva and Heicosporidium sp., both of which have highly reduced gene contents and no photosynthesis genes. We also show evidence that selection for codon adaptation increases the representation of the same set of codons, which we refer to as the adaptive codons, across this wide range of taxa, which is probably due to common features descended from the initial endosymbiont. We use various measures to estimate the relative strength of selection in the different lineages and show that it appears to be fairly strong in certain Stramenopiles and Chlorophyta lineages but relatively weak in many members of the Rhodophyta, Euglenozoa and Embryophyta. Given these results we propose that codon adaptation in plastids is widespread and displays the same general features as adaptation in eubacterial genomes. PMID:27196606

  1. Measurement and correction of the 3rd order resonance in the Tevatron

    SciTech Connect

    Schmidt, F.; Alexahin, Y.; Lebedev, V.; Still, D.; Valishev, A.; /Fermilab

    2006-06-01

    At Fermilab Tevatron BPM system has been recently upgraded resulting much better accuracy of beam position measurements and improvements of data acquisition for turn-by-turn measurements. That allows one to record the beam position at each turn for 8000 turns for all BPMs (118 in each plane) with accuracy of about 10-20 {micro}m. In the last decade a harmonic analysis tool has been developed at CERN that allows relating each FFT line derived from the BPM data with a particular non-linear resonance in the machine. In fact, one can even detect the longitudinal position of the sources of these resonances. Experiments have been performed at the Tevatron in which beams have been kicked to various amplitudes to analyze the 3rd order resonance. It was possible to address this rather large resonance to some regular machine sextupoles. An alternative sextupole scheme allowed the suppression of this resonance by a good factor of 2. Lastly, the experimental data are compared with model calculations.

  2. 1. WEST SIDE AND ENTRY, FROM ACROSS 3RD STREET, LOOKING ...

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

    1. WEST SIDE AND ENTRY, FROM ACROSS 3RD STREET, LOOKING EAST. - Oakland Naval Supply Center, Administration Building-Dental Annex-Dispensary, Between E & F Streets, East of Third Street, Oakland, Alameda County, CA

  3. Codon usage in plant genes.

    PubMed Central

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

    1989-01-01

    We have examined codon bias in 207 plant gene sequences collected from Genbank and the literature. When this sample was further divided into 53 monocot and 154 dicot genes, the pattern of relative use of synonymous codons was shown to differ between these taxonomic groups, primarily in the use of G + C in the degenerate third base. Maize and soybean codon bias were examined separately and followed the monocot and dicot codon usage patterns respectively. Codon preference in ribulose 1,5 bisphosphate and chlorophyll a/b binding protein, two of the most abundant proteins in leaves was investigated. These highly expressed are more restricted in their codon usage than plant genes in general. PMID:2644621

  4. The outcomes of therapeutic decision in lower 3rd rectal cancer patients.

    PubMed

    Chen, Chien-Hsin; Wei, Po-Li; Hsieh, Mao-Chih; Lin, En-Kwang; Chiou, Jeng-Fong; Lu, Yen-Jung; Wu, Szu-Yuan

    2016-09-01

    To investigate the outcomes of the selective neoadjuvant concurrent chemoradiotherapy (CCRT) in lower 3rd rectal cancer patients in different groups (with or without neoadjuvant CCRT), especially in survival rate, local recurrence rate, and sphincter preservation rate.From January 1999 to December 2012, 69 consecutive patients who had histologically proven adenocarcinoma of lower 3rd rectum, defined preoperatively as lower tumor margin within 7 cm from the anal verge as measured by rigid sigmoidoscopy, received total mesorectum excision (TME). Our inclusion criteria of neoadjuvant CCRT are lower 3rd rectal cancer, stage II/III, and large (diameter >5 cm or >1/2 of circumference). Neoadjuvant concurrent CCRT had begun to apply lower 3rd rectal cancer patients or not. The radiation techniques of neoadjuvant CCRT for lower 3rd rectal cancer patients were all conventional fraction intensity modulated radiotherapy (IMRT) and concurrent fluoropyrimidine chemotherapy.Five-year overall survival rate, disease-free survival rate, and local recurrence rate for lower 3rd rectal cancer patients in group I were 51%, 45%, and 25%, respectively. On the contrary, 5-year overall survival rate, disease-free survival rate, and local recurrence rate for lower rectal cancer patients in group II were 70%, 70%, and 3%, respectively. The 5-year sphincter sparing rate was increased from 38.2% to 100% after the beginning of neoadjuvant CCRT. Analyzing local recurrence, overall survival rate, disease-specific survival rate, and sphincter sparing rate in group II were statistically significant superior to group I.Five-year overall survival rate, disease-free survival rate, and sphincter sparing rate for lower 3rd rectal cancer patients were improved after the addition of neoadjuvant CCRT. No unacceptable toxicity was noted after conventional fraction IMRT and concurrent fluoropyrimidine chemotherapy. Our study showed neoadjuvant CCRT could be valuable for lower 3rd rectal cancer patients

  5. Survey of K-3rd-Grade Teachers' Knowledge of Ear Infections and Willingness to Participate in Prevention Programs

    ERIC Educational Resources Information Center

    Danhauer, Jeffrey L.; Johnson, Carole E.; Caudle, Abby T.

    2011-01-01

    Purpose: Ear infections are prevalent in kindergarten through 3rd-grade (K-3rd) children and can affect their performance at school. Chewing gum, when administered by parents and teachers, can help prevent ear infections in children. This pilot study surveyed K-3rd-grade teachers in the Santa Barbara School Districts to assess their knowledge…

  6. Elements of Effective Practice for Mentoring [TM]. 3rd Edition

    ERIC Educational Resources Information Center

    MENTOR, 2009

    2009-01-01

    As a strategy for helping young people succeed in school, work and life, mentoring works. It helps give young people the confidence, resources and support they need to achieve their potential. The fact is this: these positive outcomes are only possible when young people are engaged in high-quality mentoring relationships. The "Elements of…

  7. [3rd Hungarian Breast Cancer Consensus Conference - Radiotherapy Guidelines].

    PubMed

    Polgár, Csaba; Kahán, Zsuzsanna; Csejtei, András; Gábor, Gabriella; Landherr, László; Mangel, László; Mayer, Árpád; Fodor, János

    2016-09-01

    The radiotherapy expert panel revised and updated the radiotherapy (RT) guidelines accepted in 2009 at the 2nd Hungarian Breast Cancer Consensus Conference based on new scientific evidence. Radiotherapy of the conserved breast is indicated in ductal carcinoma in situ (St. 0), as RT decreases the risk of local recurrence by 60%. In early stage (St. I-II) invasive breast cancer RT remains a standard treatment following breast conserving surgery. However, in elderly (≥70 years) patients with stage I, hormone receptor positive tumour hormonal therapy without RT can be considered. Hypofractionated (15×2.67 Gy) whole breast irradiation and for selected cases accelerated partial breast irradiation are validated treatment alternatives of conventional (25×2 Gy) whole breast irradiation. Following mastectomy RT significantly decreases the risk of locoregional recurrence and improves overall survival of patients having 1 to 3 (pN1a) or ≥4 (pN2a, pN3a) positive axillary lymph nodes. In selected cases of patients with 1 to 2 positive sentinel lymph nodes axillary dissection can be omitted and substituted with axillary RT. After neoadjuvant chemotherapy (NAC) followed by breast conserving surgery whole breast irradiation is mandatory, while after NAC followed by mastectomy locoregional RT should be given in cases of initial stage III-IV and ypN1 axillary status. PMID:27579722

  8. Explanatory Supplement to the Astronomical Almanac (3rd Edition)

    NASA Astrophysics Data System (ADS)

    Urban, Sean E.; Seidelmann, P. K.

    2014-01-01

    Publications and software from the the Astronomical Applications Department of the US Naval Observatory (USNO) are used throughout the world, not only in the Department of Defense for safe navigation, but by many people including other navigators, astronomers, aerospace engineers, and geodesists. Products such as The Nautical Almanac, The Astronomical Almanac, and the Multiyear Interactive Computer Almanac (MICA) are regarded as international standards. To maintain credibility, it is imperative that the methodologies employed and the data used are well documented. "The Explanatory Supplement to the Astronomical Almanac" (hereafter, "The ES") is a major source of such documentation. It is a comprehensive reference book on positional astronomy, covering the theories and algorithms used to produce The Astronomical Almanac, an annual publication produced jointly by the Nautical Almanac Office of USNO and Her Majesty's Nautical Almanac Office (HMNAO). The first edition of The ES appeared in 1961, and the second followed in 1992. Several major changes have taken place in fundamental astronomy since the second edition was published. Advances in radio observations allowed the celestial reference frame to be tied to extragalactic radio sources, thus the International Celestial Reference System replaced the FK5 system. The success of ESA's Hipparcos satellite dramatically altered observational astrometry. Improvements in Earth orientation observations lead to new precession and nutation theories. Additionally, a new positional paradigm, no longer tied to the ecliptic and equinox, was accepted. Largely because of these changes, staff at USNO and HMNAO decided the time was right for the next edition of The ES. The third edition is now available; it is a complete revision of the 1992 book. Along with subjects covered in the previous two editions, the book also contains descriptions of the major advancements in positional astronomy over the last 20 years, some of which are

  9. Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum

    PubMed Central

    Heaphy, Stephen M.; Mariotti, Marco; Gladyshev, Vadim N.; Atkins, John F.; Baranov, Pavel V.

    2016-01-01

    mRNA translation in many ciliates utilizes variant genetic codes where stop codons are reassigned to specify amino acids. To characterize the repertoire of ciliate genetic codes, we analyzed ciliate transcriptomes from marine environments. Using codon substitution frequencies in ciliate protein-coding genes and their orthologs, we inferred the genetic codes of 24 ciliate species. Nine did not match genetic code tables currently assigned by NCBI. Surprisingly, we identified a novel genetic code where all three standard stop codons (TAA, TAG, and TGA) specify amino acids in Condylostoma magnum. We provide evidence suggesting that the functions of these codons in C. magnum depend on their location within mRNA. They are decoded as amino acids at internal positions, but specify translation termination when in close proximity to an mRNA 3′ end. The frequency of stop codons in protein coding sequences of closely related Climacostomum virens suggests that it may represent a transitory state. PMID:27501944

  10. Fluctuations in Student Understanding of Newton's 3rd Law

    NASA Astrophysics Data System (ADS)

    Clark, Jessica W.; Sayre, Eleanor C.; Franklin, Scott V.

    2010-10-01

    We present data from a between-student study on student response to questions on Newton's Third Law given throughout the academic year. The study, conducted at Rochester Institute of Technology, involved students from the first and third of a three-quarter sequence. Construction of a response curve reveals subtle dynamics in student learning not captured by simple pre/post testing. We find a a significant positive effect from direct instruction, peaking at the end of instruction on forces, that diminishes by the end of the quarter. Two quarters later, in physics III, a significant dip in correct response occurs when instruction changes from the vector quantities of electric forces and fields to the scalar quantity of electric potential. Student response rebounds to its initial values, however, once instruction returns to the vector-based topics involving magnetic fields.

  11. Codon Bias Patterns of E. coli’s Interacting Proteins

    PubMed Central

    Dilucca, Maddalena; Cimini, Giulio; Semmoloni, Andrea; Deiana, Antonio; Giansanti, Andrea

    2015-01-01

    Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, CompAI, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for E.coli, comparing CompAI with other widely used indices: tAI, CAI, and Nc. We show that CompAI and tAI capture similar information by being positively correlated with gene conservation, measured by the Evolutionary Retention Index (ERI), and essentiality, whereas, CAI and Nc appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of tAI and CompAI with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in E.coli. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by CompAI and tAI). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, CompAI turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation. Notably, CompAI may potentially correlate with translation speed measurements, by accounting for the specific delay induced by wobble-pairing between codons and anticodons. PMID:26566157

  12. Structural basis for stop codon recognition in eukaryotes

    PubMed Central

    Murray, Jason; Hegde, Ramanujan S.; Ramakrishnan, V.

    2015-01-01

    Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UGA, UAA, or UAG. Release factors recognise stop codons in the ribosomal A site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases1. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognise all three stop codons2. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here, we present electron cryo-microscopy (cryo-EM) structures at 3.5 – 3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A site. Binding of eRF1 flips nucleotide A1825 of 18S rRNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A site, where it is stabilised by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during tRNA selection to drive mRNA compaction. Stop codons are favoured in this compacted mRNA conformation by a hydrogen-bonding network with essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination3,4. PMID:26245381

  13. Structural basis for stop codon recognition in eukaryotes.

    PubMed

    Brown, Alan; Shao, Sichen; Murray, Jason; Hegde, Ramanujan S; Ramakrishnan, V

    2015-08-27

    Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination.

  14. Collaborative study for the establishment of the 3rd international standard for neomycin.

    PubMed

    Rautmann, G; Daas, A; Buchheit, K-H

    2013-01-01

    An international collaborative study was organised to establish the World Health Organization (WHO) 3(rd) International Standard (IS) for neomycin. Ten laboratories from different countries participated in the collaborative study. The potency of the candidate material, a freeze-dried preparation, was estimated by microbiological assays with sensitive micro-organisms. To ensure continuity between consecutive batches, the 2(nd) IS for neomycin was used as a standard. Based on the results of the study, the 3(rd) IS for neomycin was adopted at the meeting of the WHO Expert Committee on Biological Standardization (ECBS) in 2012 with an assigned potency of 19,050 IU per vial. The 3(rd) IS for neomycin is available from the European Directorate for the Quality of Medicines & HealthCare (EDQM).

  15. Radiographic findings on 3rd molars removed in 20-year-old men.

    PubMed

    Rajasuo, Ari; Peltola, Jaakko; Ventä, Irja; Murtomaa, Heikki

    2003-10-01

    In this study we assess radiographic findings characteristic of mandibular 3rd molars that had required either routine or surgical extraction. X-ray findings relating to acute pericoronitis were also examined. The material was collected by investigating patient records and rotational panoramic radiographs of 20-year-old Finnish male conscripts (n = 738) treated during military service because of 3rd-molar-related problems. The follicle around the crown of mandibular 3rd molars with acute pericoronitis was enlarged in 19% of cases and in 13% of chronic symptom-free pericoronitis cases (not statistically significant difference). Mandibular 3rd molars extracted surgically were more often mesially inclined than those extracted routinely (61% vs. 23%; P < 0.001), partially or totally intrabony impacted (92% vs. 66%; P < 0.001) and deep situated (on average 4.2 mm vs. 2.5 mm under the occlusal plane). Surgical extraction was also associated with the roots completely developed [92% vs. 84% of the teeth routinely extracted, odds ratio (OR) 2.6, 95% confidence interval (CI) 1.2-5.5] and with the absence of radiographic pericoronitis [around 27% vs. 39% of the teeth routinely extracted (OR 0.5, 95% CI 0.3-0.8)]. In 86% of cases the space between 2nd molar and ramus of the mandible was narrower than the 3rd molar extracted surgically, whereas this was 62% in routine extraction cases (P < 0.001). We conclude that there are some typical 3rd-molar findings in rotational panoramic radiographs that show a need for surgical extraction.

  16. Radiographic findings on 3rd molars removed in 20-year-old men.

    PubMed

    Rajasuo, Ari; Peltola, Jaakko; Ventä, Irja; Murtomaa, Heikki

    2003-10-01

    In this study we assess radiographic findings characteristic of mandibular 3rd molars that had required either routine or surgical extraction. X-ray findings relating to acute pericoronitis were also examined. The material was collected by investigating patient records and rotational panoramic radiographs of 20-year-old Finnish male conscripts (n = 738) treated during military service because of 3rd-molar-related problems. The follicle around the crown of mandibular 3rd molars with acute pericoronitis was enlarged in 19% of cases and in 13% of chronic symptom-free pericoronitis cases (not statistically significant difference). Mandibular 3rd molars extracted surgically were more often mesially inclined than those extracted routinely (61% vs. 23%; P < 0.001), partially or totally intrabony impacted (92% vs. 66%; P < 0.001) and deep situated (on average 4.2 mm vs. 2.5 mm under the occlusal plane). Surgical extraction was also associated with the roots completely developed [92% vs. 84% of the teeth routinely extracted, odds ratio (OR) 2.6, 95% confidence interval (CI) 1.2-5.5] and with the absence of radiographic pericoronitis [around 27% vs. 39% of the teeth routinely extracted (OR 0.5, 95% CI 0.3-0.8)]. In 86% of cases the space between 2nd molar and ramus of the mandible was narrower than the 3rd molar extracted surgically, whereas this was 62% in routine extraction cases (P < 0.001). We conclude that there are some typical 3rd-molar findings in rotational panoramic radiographs that show a need for surgical extraction. PMID:14763776

  17. 3rd International Conference on Turbulent Mixing and Beyond

    NASA Astrophysics Data System (ADS)

    Abarzhi, Snezhana I.; Gauthier, Serge; Keane, Christopher J.; Niemela, Joseph J.

    2013-07-01

    , technology and mathematics; (iii) TMB participants conduct highly innovative research and their interactions strengthen the community's might. Based on the success of the first and second conferences and on the recommendations of the conference round table discussions, and in response to the inquiry of the community, the Third International Conference on Turbulent Mixing and Beyond was organized. The Third International Conference on Turbulent Mixing and Beyond, TMB-2011, was held on 21-28 August 2011 at the Abdus Salam International Centre for Theoretical Physics (ICTP), Trieste, Italy. This was a highly informative and exciting meeting, and it strengthened and reaffirmed the success of TMB-2009 and 2007. The objectives of the Third International Conference on Turbulent Mixing and Beyond were to: (i) focus the integration of theory, experiments, large-scale numerical simulations and state-of-the-art technologies on the exploration of physical mechanisms of non-equilibrium dynamics, from micro to macro-scales, in both high and low energy density regimes; (ii) foster the application of innovative approaches for tackling the fundamental aspects of turbulent mixing problems and for understanding and further extending the range of applicability of canonical considerations; (iii) encourage the development of new approaches and stimulate the application of advanced data analysis techniques for unified characterization of experimental and numerical data sets, for estimation of their quality and information capacity, and for transforming data to knowledge; (iv) further develop the 'Turbulent Mixing and Beyond' community via organizing a positive and constructive collaborative environment, maintaining the quality of information flux in the community and sharing research methodologies, tools and data among the community members. The objectives were accomplished at TMB-2011. 4. Programme of TMB-2011 TMB-2011 brought together 150 participants, ranging from students to members of

  18. Codon usage bias in phylum Actinobacteria: relevance to environmental adaptation and host pathogenicity.

    PubMed

    Lal, Devi; Verma, Mansi; Behura, Susanta K; Lal, Rup

    2016-10-01

    Actinobacteria are Gram-positive bacteria commonly found in soil, freshwater and marine ecosystems. In this investigation, bias in codon usages of ninety actinobacterial genomes was analyzed by estimating different indices of codon bias such as Nc (effective number of codons), SCUO (synonymous codon usage order), RSCU (relative synonymous codon usage), as well as sequence patterns of codon contexts. The results revealed several characteristic features of codon usage in Actinobacteria, as follows: 1) C- or G-ending codons are used frequently in comparison with A- and U ending codons; 2) there is a direct relationship of GC content with use of specific amino acids such as alanine, proline and glycine; 3) there is an inverse relationship between GC content and Nc estimates, 4) there is low SCUO value (<0.5) for most genes; and 5) GCC-GCC, GCC-GGC, GCC-GAG and CUC-GAC are the frequent context sequences among codons. This study highlights the fact that: 1) in Actinobacteria, extreme GC content and codon bias are driven by mutation rather than natural selection; (2) traits like aerobicity are associated with effective natural selection and therefore low GC content and low codon bias, demonstrating the role of both mutational bias and translational selection in shaping the habitat and phenotype of actinobacterial species.

  19. 16. 3RD FLOOR, J.M. LEHMANN CO. FIVEROLL TOILET SOAP MILL ...

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

    16. 3RD FLOOR, J.M. LEHMANN CO. FIVE-ROLL TOILET SOAP MILL INSTALLED 1950, TO WEST; BUCKET CONVEYOR AT RIGHT MOVED WASTE FROM 2ND FLOOR SOAP PRESSES TO 5TH FLOOR RE-MANUFACTURE - Colgate & Company Jersey City Plant, Building No. B-14, 54-58 Grand Street, Jersey City, Hudson County, NJ

  20. 75 FR 34450 - Filing Dates for the Indiana Special Election in the 3rd Congressional District

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-17

    ... From the Federal Register Online via the Government Publishing Office FEDERAL ELECTION COMMISSION Filing Dates for the Indiana Special Election in the 3rd Congressional District AGENCY: Federal Election Commission. ACTION: Notice of filing dates for special election. SUMMARY: Indiana has scheduled a...

  1. Colorectal cancer in inflammatory bowel disease: results of the 3rd ECCO pathogenesis scientific workshop (I).

    PubMed

    Sebastian, Shaji; Hernández, Vincent; Myrelid, Pär; Kariv, Revital; Tsianos, Epameinondas; Toruner, Murat; Marti-Gallostra, Marc; Spinelli, Antonino; van der Meulen-de Jong, Andrea E; Yuksel, Elif Sarıtas; Gasche, Christoph; Ardizzone, Sandro; Danese, Silvio

    2014-01-01

    Epidemiological studies demonstrate an increased risk of colorectal cancer in patients with inflammatory bowel disease (IBD). A detailed literature review was conducted on epidemiology, risk factors, pathophysiology, chemoprevention and outcomes of colorectal cancer (CRC) in IBD as part of the 3rd ECCO scientific pathogenesis workshop.

  2. PreK-3rd: What Is the Price Tag? Policy to Action Brief. No. 2

    ERIC Educational Resources Information Center

    Shore, Rima

    2009-01-01

    In an era of intense fiscal pressures, educators are focusing on those investments most likely to lift student achievement. They are also trying to make more strategic use of existing resources. To achieve these goals, a growing number of policymakers are considering integrated PreK-3rd approaches. Increasingly, they are recognizing that the first…

  3. Evaluation of the "Respect Not Risk" Firearm Safety Lesson for 3rd-Graders

    ERIC Educational Resources Information Center

    Liller, Karen D.; Perrin, Karen; Nearns, Jodi; Pesce, Karen; Crane, Nancy B.; Gonzalez, Robin R.

    2003-01-01

    The purpose of this study was to evaluate the MORE HEALTH "Respect Not Risk" Firearm Safety Lesson for 3rd-graders in Pinellas County, Florida. Six schools representative of various socioeconomic levels were selected as the test sites. Qualitative and quantitative data were collected. A total of 433 matched pretests/posttests were used to…

  4. Prediction of High School Dropout or Graduation from 3rd Grade Data.

    ERIC Educational Resources Information Center

    Lloyd, Dee Norman; Bleach, Gail

    Measures of background characteristics, school performance, and tested achievement were analyzed for four race-by-sex samples of 3rd graders who were known to have later become high school dropouts or graduates. Results showed that as early as five to eight years before leaving school, dropouts differed significantly from graduates in age, tested…

  5. Using Food as a Tool to Teach Science to 3rd Grade Students in Appalachian Ohio

    ERIC Educational Resources Information Center

    Duffrin, Melani W.; Hovland, Jana; Carraway-Stage, Virginia; McLeod, Sara; Duffrin, Christopher; Phillips, Sharon; Rivera, David; Saum, Diana; Johanson, George; Graham, Annette; Lee, Tammy; Bosse, Michael; Berryman, Darlene

    2010-01-01

    The Food, Math, and Science Teaching Enhancement Resource (FoodMASTER) Initiative is a compilation of programs aimed at using food as a tool to teach mathematics and science. In 2007 to 2008, a foods curriculum developed by professionals in nutrition and education was implemented in 10 3rd-grade classrooms in Appalachian Ohio; teachers in these…

  6. The Effect of Book Blogging on the Motivation of 3rd-Grade Students

    ERIC Educational Resources Information Center

    Swanson, Kristen N.; Legutko, Robert S.

    2008-01-01

    A Web 2.0 technology was implemented during reading instruction in one 3rd-grade classroom in suburban southeastern Pennsylvania. Trained preservice teachers provided feedback to students via the World Wide Web to enhance their performance and social connections. Motivation scores were measured before and after the intervention was implemented. A…

  7. Synonymous codon usage, accuracy of translation, and gene length in Caenorhabditis elegans.

    PubMed

    Marais, G; Duret, L

    2001-03-01

    In many unicellular organisms, invertebrates, and plants, synonymous codon usage biases result from a coadaptation between codon usage and tRNAs abundance to optimize the efficiency of protein synthesis. However, it remains unclear whether natural selection acts at the level of the speed or the accuracy of mRNAs translation. Here we show that codon usage can improve the fidelity of protein synthesis in multicellular species. As predicted by the model of selection for translational accuracy, we find that the frequency of codons optimal for translation is significantly higher at codons encoding for conserved amino acids than at codons encoding for nonconserved amino acids in 548 genes compared between Caenorhabditis elegans and Homo sapiens. Although this model predicts that codon bias correlates positively with gene length, a negative correlation between codon bias and gene length has been observed in eukaryotes. This suggests that selection for fidelity of protein synthesis is not the main factor responsible for codon biases. The relationship between codon bias and gene length remains unexplained. Exploring the differences in gene expression process in eukaryotes and prokaryotes should provide new insights to understand this key question of codon usage. PMID:11428464

  8. Foundational Skills to Support Reading for Understanding in Kindergarten through 3rd Grade. Educator's Practice Guide. NCEE 2016-4008

    ERIC Educational Resources Information Center

    Foorman, Barbara; Beyler, Nicholas; Borradaile, Kelley; Coyne, Michael; Denton, Carolyn A.; Dimino, Joseph; Furgeson, Joshua; Hayes, Lynda; Henke, Juliette; Justice, Laura; Keating, Betsy; Lewis, Warnick; Sattar, Samina; Streke, Andrei; Wagner, Richard; Wissel, Sarah

    2016-01-01

    The goal of this practice guide is to offer educators specific, evidence-based recommendations for teaching foundational reading skills to students in kindergarten through 3rd grade. This guide is a companion to the existing practice guide, "Improving Reading Comprehension in Kindergarten Through 3rd Grade", and as a set, these guides…

  9. Conference report: the 3rd Global CRO Council for Bioanalysis at the International Reid Bioanalytical Forum.

    PubMed

    Breda, Massimo; Garofolo, Fabio; Caturla, Maria Cruz; Couerbe, Philippe; Maltas, John; White, Peter; Struwe, Petra; Sangster, Timothy; Riches, Suzanne; Hillier, Jim; Garofolo, Wei; Zimmerman, Thomas; Pawula, Maria; Collins, Eileen; Schoutsen, Dick; Wieling, Jaap; Green, Rachel; Houghton, Richard; Jeanbaptiste, Bernard; Claassen, Quinton; Harter, Tammy; Seymour, Mark

    2011-12-01

    The 3rd Global CRO Council Closed Forum was held on the 3rd and 4th July 2011 in Guildford, United Kingdom, in conjunction with the 19th International Reid Bioanalytical Forum. In attendance were 21 senior-level representatives from 19 CROs on behalf of nine European countries and, for many of the attendees, this occasion was the first time that they had participated in a GCC meeting. Therefore, this closed forum was an opportunity to increase awareness of the aim of the GCC and how it works, share information about bioanalytical regulations and audit findings from different agencies, their policies and procedures and also to discuss some topics of interest and aim to develop ideas and provide recommendations for bioanalytical practices at future GCC meetings in Europe.

  10. 3rd Workshop on Semantic Ambient Media Experience (SAME) - In Conjunction with AmI-2010

    NASA Astrophysics Data System (ADS)

    Lugmayr, Artur; Stockleben, Bjoern; Kaario, Juha; Pogorelc, Bogdan; Risse, Thomas

    The SAME workshop takes place for the 3rd time in 2010, and it's theme in this year was creating the business value-creation, vision, media theories and technology for ambient media. SAME differs from other workshops due to its interactive and creative touch and going beyond simple powerpoint presentations. Several results will be published by AMEA - the AMbient Media Association (www.ambientmediaassociation.org.

  11. Higher order modes of a 3rd harmonic cavity with an increased end-cup iris

    SciTech Connect

    T. Khabibouline; N. Solyak; R. Wanzenberg

    2003-05-19

    The cavity design for a 3rd harmonic cavity for the TTF 2 photoinjector has been revised to increase the coupling between the main coupler and the cavity cells. The iris radius of the end cup of the cavity has been increased to accomplish a better coupling. The basic rf-parameters and the higher order modes of the modified design are summarized in this report.

  12. Insights from the 3rd World Congress on Integrated Computational Materials Engineering

    NASA Astrophysics Data System (ADS)

    Howe, D.; Goodlet, B.; Weaver, J.; Spanos, G.

    2016-05-01

    The 3rd World Congress on Integrated Computational Materials Engineering (ICME) was a forum for presenting the "state-of-the-art" in the ICME discipline, as well as for charting a path for future community efforts. The event concluded with in an interactive panel-led discussion that addressed such topics as integrating efforts between experimental and computational scientists, uncertainty quantification, and identifying the greatest challenges for future workforce preparation. This article is a summary of this discussion and the thoughts presented.

  13. 13. Photocopy of 1920 drawing titled: BUILDING 78, 3RD FLOOR ...

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

    13. Photocopy of 1920 drawing titled: BUILDING 78, 3RD FLOOR BALCONY AND FIRE ESCAPES, including plans for skylight and North Elevation. HABS photograph is an 8x10' contact print made from a high contrast negative of an enlargement made from microfiche. Original is in the collection of Department of Public Works, Puget Sound Naval Shipyard, Bremerton, WA. - Puget Sound Naval Shipyard, Administration Building, Farragut Avenue, Bremerton, Kitsap County, WA

  14. Analysis of synonymous codon usage patterns in seven different citrus species.

    PubMed

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

    2013-01-01

    We used large samples of expressed sequence tags to characterize the patterns of codon usage bias (CUB) in seven different Citrus species and to analyze their evolutionary effect on selection and base composition. We found that A- and T-ending codons are predominant in Citrus species. Next, we identified 21 codons for 18 different amino acids that were considered preferred codons in all seven species. We then performed correspondence analysis and constructed plots for the effective number of codons (ENCs) to analyze synonymous codon usage. Multiple regression analysis showed that gene expression in each species had a constant influence on the frequency of optional codons (FOP). Base composition differences between the proportions were large. Finally, positive selection was detected during the evolutionary process of the different Citrus species. Overall, our results suggest that codon usages were the result of positive selection. Codon usage variation among Citrus genes is influenced by translational selection, mutational bias, and gene length. CUB is strongly affected by selection pressure at the translational level, and gene length plays only a minor role. One possible explanation for this is that the selection-mediated codon bias is consistently strong in Citrus, which is one of the most widely cultivated fruit trees. PMID:23761955

  15. The Goodrich 3rd generation DB-110 system: successful flight test on the F-16 aircraft

    NASA Astrophysics Data System (ADS)

    Lange, Davis; Iyengar, Mrinal; Maver, Larry; Dyer, Gavin; Francis, John

    2007-04-01

    The 3rd Generation Goodrich DB-110 system provides users with a three (3) field-of-view high performance Airborne Reconnaissance capability that incorporates a dual-band day and nighttime imaging sensor, a real time recording and a real time data transmission capability to support long range, medium range, and short range standoff and over-flight mission scenarios, all within a single pod. Goodrich developed their 3rd Generation Airborne Reconnaissance Pod for operation on a range of aircraft types including F-16, F-15, F-18, Euro-fighter and older aircraft such as the F-4, F-111, Mirage and Tornado. This system upgrades the existing, operationally proven, 2nd generation DB-110 design with enhancements in sensor resolution, flight envelope and other performance improvements. Goodrich recently flight tested their 3rd Generation Reconnaissance System on a Block 52 F-16 aircraft with first flight success and excellent results. This paper presents key highlights of the system and presents imaging results from flight test.

  16. Using Photographs to Probe Students' Understanding of Physical Concepts: The Case of Newton's 3rd Law

    NASA Astrophysics Data System (ADS)

    Eshach, Haim

    2010-08-01

    The starting point of the present research is the following question: since we live in an age that makes increasing use of visual representations of all sorts, is not the visual representation a learner constructs a window into his/her understanding of what is or is not being learned? Following this direction of inquiry, the present preliminary study introduces and evaluates a novel technique for pinpointing learners’ misconceptions, namely, one that has learners create and interpret their own photographs (CIP). 27 high-school students and 26 pre-service teacher trainees were asked to assume the role of textbook designers and create a display—photograph plus attached verbal explanation—which, in their opinion, best depicted Newton’s 3rd law. Subsequent analysis of the participants’ photographs yielded the following six misconception categories: 3rd law not depicted; 3rd law depicts a sequence of events; tendency to introduce irrelevant entities in explanations; the word ‘reaction’ used colloquially; tendency to restrict the application of the third law to dynamic situations; and informal explanations in which the word “force” is absent. The findings indicate that, indeed, the CIP method can be effectively employed to elicit, detect, and investigate learners’ misconceptions. The CIP method joins the growing efforts to utilize the yet relatively untapped potential of visual tools for science education purposes.

  17. Asc1, homolog of human RACK1, prevents frameshifting in yeast by ribosomes stalled at CGA codon repeats.

    PubMed

    Wolf, Andrew S; Grayhack, Elizabeth J

    2015-05-01

    Quality control systems monitor and stop translation at some ribosomal stalls, but it is unknown if halting translation at such stalls actually prevents synthesis of abnormal polypeptides. In yeast, ribosome stalling occurs at Arg CGA codon repeats, with even two consecutive CGA codons able to reduce translation by up to 50%. The conserved eukaryotic Asc1 protein limits translation through internal Arg CGA codon repeats. We show that, in the absence of Asc1 protein, ribosomes continue translating at CGA codons, but undergo substantial frameshifting with dramatically higher levels of frameshifting occurring with additional repeats of CGA codons. Frameshifting depends upon the slow or inefficient decoding of these codons, since frameshifting is suppressed by increased expression of the native tRNA(Arg(ICG)) that decodes CGA codons by wobble decoding. Moreover, the extent of frameshifting is modulated by the position of the CGA codon repeat relative to the translation start site. Thus, translation fidelity depends upon Asc1-mediated quality control.

  18. Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

    PubMed

    Wohlin, Åsa

    2015-03-21

    The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system.

  19. Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code.

    PubMed

    Wohlin, Åsa

    2015-03-21

    The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system. PMID:25623487

  20. Characterization of Codon usage bias in the newly identified DEV UL18 gene

    NASA Astrophysics Data System (ADS)

    Chen, Xiwen; Cheng, Anchun; Wang, Mingshu; Xiang, Jun

    2011-10-01

    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.

  1. A detailed comparative analysis of codon usage bias in Zika virus.

    PubMed

    Cristina, Juan; Fajardo, Alvaro; Soñora, Martín; Moratorio, Gonzalo; Musto, Héctor

    2016-09-01

    Zika virus (ZIKV) is a member of the family Flaviviridae and its genome consists of a single-stranded positive sense RNA molecule with 10,794 nucleotides. Clinical manifestations of disease caused by ZIKV infection range from asymptomatic cases to an influenza-like syndrome. There is an increasing concern about the possible relation among microcephaly and ZIKV infection. To get insight into the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness, evasion from host's immune system and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of ZIKV. The overall codon usage among ZIKV strains is similar and slightly biased. Different codon preferences in ZIKV genes in relation to codon usage of human, Aedes aegypti and Aedes albopictus genes were found. Most of the highly frequent codons are A-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. G+C compositional constraint as well as dinucleotide composition also influence the codon usage of ZIKV. The results of these studies suggest that the emergence of ZIKV outside Africa, in the Pacific and the Americas may also be reflected in ZIKV codon usage. No significant differences were found in codon usage among strains isolated from microcephaly cases and the rest of strains from the Asian cluster enrolled in these studies.

  2. A detailed comparative analysis of codon usage bias in Zika virus.

    PubMed

    Cristina, Juan; Fajardo, Alvaro; Soñora, Martín; Moratorio, Gonzalo; Musto, Héctor

    2016-09-01

    Zika virus (ZIKV) is a member of the family Flaviviridae and its genome consists of a single-stranded positive sense RNA molecule with 10,794 nucleotides. Clinical manifestations of disease caused by ZIKV infection range from asymptomatic cases to an influenza-like syndrome. There is an increasing concern about the possible relation among microcephaly and ZIKV infection. To get insight into the relation of codon usage among viruses and their hosts is extremely important to understand virus survival, fitness, evasion from host's immune system and evolution. In this study, we performed a comprehensive analysis of codon usage and composition of ZIKV. The overall codon usage among ZIKV strains is similar and slightly biased. Different codon preferences in ZIKV genes in relation to codon usage of human, Aedes aegypti and Aedes albopictus genes were found. Most of the highly frequent codons are A-ending, which strongly suggests that mutational bias is the main force shaping codon usage in this virus. G+C compositional constraint as well as dinucleotide composition also influence the codon usage of ZIKV. The results of these studies suggest that the emergence of ZIKV outside Africa, in the Pacific and the Americas may also be reflected in ZIKV codon usage. No significant differences were found in codon usage among strains isolated from microcephaly cases and the rest of strains from the Asian cluster enrolled in these studies. PMID:27449601

  3. Are synonymous codons indeed synonymous?

    PubMed

    Venetianer, Pál

    2012-02-01

    Abstract It has long been known that the distribution and frequency of occurence of synonymous codons can vary greatly among different species, and that the abundance of isoaccepting tRNA species could also be very different. The interaction of these two factors may influence the rate and efficiency of protein synthesis and therefore synonymous mutations might influence the fitness of the organism and cannot be treated generally as 'neutral' in an evolutionary sense. These general effects of synonymous mutations, and their possible role in evolution, have been discussed in several recent papers. This review, however, will only deal with the influence of synonymous codon replacements on the expression of individual genes. It will describe the possible mechanisms of such effects and will present examples demonstrating the existence and effects of each of these mechanisms.

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

    PubMed

    Nabiyouni, Maryam; Prakash, Ashwin; Fedorov, Alexei

    2013-04-25

    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

  5. [Modern surgical treatment of breast cancer. 3rd Breast Cancer Consensus Conference].

    PubMed

    Lázár, György; Bursics, Attila; Farsang, Zoltán; Harsányi, László; Kósa, Csaba; Maráz, Róbert; Mátrai, Zoltán; Paszt, Attila; Pavlovics, Gábor; Tamás, Róbert

    2016-09-01

    Therapy for breast cancer today is characterised by ever more precise diagnostic methods and ever more effective oncological treatments, a trend which will certainly continue into the future. Breast preservation and the application of oncoplastic principles are increasingly popular. A sentinel lymph node biopsy in the surgical treatment of the axilla is primary, with the indication for axillary block dissection (ABD) narrowing and radiation therapy becoming an alternative to ABD in certain cases. This publication summarises our recommendations on the surgical treatment of breast cancer based on the content of the 3rd Breast Cancer Consensus Conference and considering the latest international studies and professional recommendations. PMID:27644928

  6. Preface to Special Topic: Invited Papers of the 3rd International Conference on Ultrafast Structural Dynamics

    PubMed Central

    Johnson, S. L.

    2016-01-01

    The ability to visualize the real-time dynamics of atomic, magnetic, and electronic structure is widely recognized in many fields as a key element underpinning many important processes in chemistry, materials science, and biology. The need for an improved understanding of such processes becomes acute as energy conversion processes on fast time scales become increasingly relevant to problems in science and technology. This special issue, containing invited papers from participants at the 3rd International Conference on Ultrafast Structural Dynamics held June 10–12, 2015 in Zurich, Switzerland, discusses several recent developments in this area. PMID:27191008

  7. NURSING EMERGING. ANA Nursing: Scope and Standards of Practice, (2015) 3rd Edition.

    PubMed

    Mariano, Carla

    2016-04-01

    AHNA Past-President Carla Mariano recently had the privilege of serving on the American Nurses Association's (ANA) Nursing Scope and Standards Revision Workgroup. Representing the specialty practice of holistic nursing, Carla's presence within this workgroup contributed greatly to the inclusion of holistic principles and values throughout the new 2015 Nursing: Scope and Standards of Practice, 3rd edition, the foundational document that informs and guides professional nursing practice within the United States. This is a significant step forward for holistic nursing and an indicator of our growing influence as specialty practice. PMID:27305802

  8. Preface to Special Topic: Invited Papers of the 3rd International Conference on Ultrafast Structural Dynamics.

    PubMed

    Johnson, S L

    2016-03-01

    The ability to visualize the real-time dynamics of atomic, magnetic, and electronic structure is widely recognized in many fields as a key element underpinning many important processes in chemistry, materials science, and biology. The need for an improved understanding of such processes becomes acute as energy conversion processes on fast time scales become increasingly relevant to problems in science and technology. This special issue, containing invited papers from participants at the 3rd International Conference on Ultrafast Structural Dynamics held June 10-12, 2015 in Zurich, Switzerland, discusses several recent developments in this area. PMID:27191008

  9. Overview of the 3rd isirv-Antiviral Group Conference – advances in clinical management

    PubMed Central

    Hurt, Aeron C; Hui, David S; Hay, Alan; Hayden, Frederick G

    2015-01-01

    This review highlights the main points which emerged from the presentations and discussions at the 3rd isirv-Antiviral Group Conference - advances in clinical management. The conference covered emerging and potentially pandemic influenza viruses and discussed novel/pre-licensure therapeutics and currently approved antivirals and vaccines for the control of influenza. Current data on approved and novel treatments for non-influenza respiratory viruses such as MERS-CoV, respiratory syncytial virus (RSV) and rhinoviruses and the challenges of treating immunocompromised patients with respiratory infections was highlighted. PMID:25399715

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

    PubMed Central

    Behura, Susanta K.; Severson, David W.

    2012-01-01

    Background Codon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene. Although genome sequencing of multiple species of dipteran and hymenopteran insects have been completed only a few of these species have been analyzed for codon usage bias. Methods and Principal Findings Here, we use bioinformatics approaches to analyze codon usage bias and codon context patterns in a genome-wide manner among 15 dipteran and 7 hymenopteran insect species. Results show that GAA is the most frequent codon in the dipteran species whereas GAG is the most frequent codon in the hymenopteran species. Data reveals that codons ending with C or G are frequently used in the dipteran genomes whereas codons ending with A or T are frequently used in the hymenopteran genomes. Synonymous codon usage orders (SCUO) vary within genomes in a pattern that seems to be distinct for each species. Based on comparison of 30 one-to-one orthologous genes among 17 species, the fruit fly Drosophila willistoni shows the least codon usage bias whereas the honey bee (Apis mellifera) shows the highest bias. Analysis of codon context patterns of these insects shows that specific codons are frequently used as the 3′- and 5′-context of start and stop codons, respectively. Conclusions Codon bias pattern is distinct between dipteran and hymenopteran insects. While codon bias is favored by high GC content of dipteran genomes, high AT content of genes favors biased usage of synonymous codons in the hymenopteran insects. Also, codon context patterns vary among these species largely according to their phylogeny. PMID:22912801

  11. Codon Optimizing for Increased Membrane Protein Production: A Minimalist Approach.

    PubMed

    Mirzadeh, Kiavash; Toddo, Stephen; Nørholm, Morten H H; Daley, Daniel O

    2016-01-01

    Reengineering a gene with synonymous codons is a popular approach for increasing production levels of recombinant proteins. Here we present a minimalist alternative to this method, which samples synonymous codons only at the second and third positions rather than the entire coding sequence. As demonstrated with two membrane-embedded transporters in Escherichia coli, the method was more effective than optimizing the entire coding sequence. The method we present is PCR based and requires three simple steps: (1) the design of two PCR primers, one of which is degenerate; (2) the amplification of a mini-library by PCR; and (3) screening for high-expressing clones. PMID:27485329

  12. Extreme and Local 3rd Harmonic Response of Niobium (Nb) Superconductor

    NASA Astrophysics Data System (ADS)

    Oripov, Bakhrom; Tai, Tamin; Anlage, Steven

    Superconducting Radio Frequency (SRF) cavities are being widely used in new generation particle accelerators. These SRF cavities are based on bulk Nb. Based on the needs of the SRF community to identify defects on Nb surfaces, a novel near-field magnetic microwave microscope was successfully built using a magnetic writer from a conventional magnetic recording hard-disk drive1. This magnetic writer can create an RF magnetic field, localized and strong enough to drive Nb into the vortex state. This probe enables us to locate defects through scanning and mapping of the local electrodynamic response in the multi-GHz frequency range. Recent measurements have shown that 3rd harmonic nonlinear response is far more sensitive to variations in input power and temperature then linear response, thus we mainly study the 3rd harmonic response. Moreover, the superconductor is usually the only source for nonlinear response in our setup, thus there is less chance of having noise or background signal. Understanding the mechanism responsible for this non-linear response is important for improving the performance of SRF cavities. Besides Nb we also study various other superconductors such as MgB2 and the cuprate Bi-Sr-Ca-Cu-O (BSCCO) for potential applications in SRF cavities. This work is funded by US Department of Energy through Grant # DE-SC0012036T and CNAM.

  13. Treatment of 3rd molar-induced periodontal defects with guided tissue regeneration.

    PubMed

    Oxford, G E; Quintero, G; Stuller, C B; Gher, M E

    1997-07-01

    Recent reports provide evidence of increased attachment levels when using guided tissue regeneration (GTR) techniques for the treatment of periodontal defects. Periodontal defects frequently occur at the distal aspect of mandibular 2nd molars which are next to mesioangular impacted 3rd molars that have oral communication. The purpose of this study was to determine whether the use of GTR can enhance probing attachment levels (PALs) following extraction of mesioangular impacted third molars. 12 patients with bilateral soft tissue impacted mandibular 3rd molars entered this split mouth study. After extractions, the previously exposed distal root surface of the 2nd molars were debrided. The defects on the randomly selected experimental sites were covered with expanded polytetraflouro-ethylene (e-PTFE) membrane and the tissue was replaced to cover the membrane. Membranes were removed after 6 weeks. Control sites were treated identically except no membrane was placed. GI, P1I, PD, PAL and BOP records were obtained at 0, 3 and 6 months. The use of barrier material did not provide statistically-significant differences in PAL when comparing experimental versus control sites. Nevertheless, PAL gain was consistently greater at 3 and 6 months when GTR techniques were used in sites with deep impactions. PMID:9226386

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

    PubMed Central

    2011-01-01

    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

  15. PREFACE: 3rd International Conference of Mechanical Engineering Research (ICMER 2015)

    NASA Astrophysics Data System (ADS)

    Mamat, Riazalman; Rahman, Mustafizur; Mohd. Zuki Nik Mohamed, Nik; Che Ghani, Saiful Anwar; Harun, Wan Sharuzi Wan

    2015-12-01

    The 3rd ICMER2015 is the continuity of the NCMER2010. The year 2010 represents a significant milestone in the history for Faculty of Mechanical Engineering, Universiti Malaysia Pahang (UMP) Malaysia with the organization of the first and second national level conferences (1st and 2nd NCMER) at UMP on May 26-27 and Dec 3-4 2010. The Faculty then changed the name from National Conference on Mechanical Engineering Research (NCMER) to International Conference on Mechanical Engineering Research (ICMER) in 2011 and this year, 2015 is our 3rd ICMER. These proceedings contain the selected scientific manuscripts submitted to the conference. It is with great pleasure to welcome you to the "International Conference on Mechanical Engineering Research (ICMER2015)" that is held at Zenith Hotel, Kuantan, Malaysia. The call for papers attracted submissions of over two hundred abstracts from twelve different countries including Japan, Iran, China, Kuwait, Indonesia, Norway, Philippines, Morocco, Germany, UAE and more. The scientific papers published in these proceedings have been revised and approved by the technical committee of the 3rd ICMER2015. All of the papers exhibit clear, concise, and precise expositions that appeal to a broad international readership interested in mechanical engineering, combustion, metallurgy, materials science as well as in manufacturing and biomechanics. The reports present original ideas or results of general significance supported by clear reasoning and compelling evidence, and employ methods, theories and practices relevant to the research. The authors clearly state the questions and the significance of their research to theory and practice, describe how the research contributes to new knowledge, and provide tables and figures that meaningfully add to the narrative. In this edition of ICMER representatives attending are from academia, industry, governmental and private sectors. The plenary and invited speakers will present, discuss, promote and

  16. Malaria and Fetal Growth Alterations in the 3rd Trimester of Pregnancy: A Longitudinal Ultrasound Study

    PubMed Central

    Schmiegelow, Christentze; Minja, Daniel; Oesterholt, Mayke; Pehrson, Caroline; Suhrs, Hannah Elena; Boström, Stéphanie; Lemnge, Martha; Magistrado, Pamela; Rasch, Vibeke; Nielsen, Birgitte Bruun; Lusingu, John; Theander, Thor G.

    2013-01-01

    Background Pregnancy associated malaria is associated with decreased birth weight, but in-utero evaluation of fetal growth alterations is rarely performed. The objective of this study was to investigate malaria induced changes in fetal growth during the 3rd trimester using trans-abdominal ultrasound. Methods An observational study of 876 pregnant women (398 primi- and secundigravidae and 478 multigravidae) was conducted in Tanzania. Fetal growth was monitored with ultrasound and screening for malaria was performed regularly. Birth weight and fetal weight were converted to z-scores, and fetal growth evaluated as fetal weight gain from the 26th week of pregnancy. Results Malaria infection only affected birth weight and fetal growth among primi- and secundigravid women. Forty-eight of the 398 primi- and secundigravid women had malaria during pregnancy causing a reduction in the newborns z-score of −0.50 (95% CI: −0.86, −0.13, P = 0.008, multiple linear regression). Fifty-eight percent (28/48) of the primi- and secundigravidae had malaria in the first half of pregnancy, but an effect on fetal growth was observed in the 3rd trimester with an OR of 4.89 for the fetal growth rate belonging to the lowest 25% in the population (95%CI: 2.03–11.79, P<0.001, multiple logistic regression). At an individual level, among the primi- and secundigravidae, 27% experienced alterations of fetal growth immediately after exposure but only for a short interval, 27% only late in pregnancy, 16.2% persistently from exposure until the end of pregnancy, and 29.7% had no alterations of fetal growth. Conclusions The effect of malaria infections was observed during the 3rd trimester, despite infections occurring much earlier in pregnancy, and different mechanisms might operate leading to different patterns of growth alterations. This study highlights the need for protection against malaria throughout pregnancy and the recognition that observed changes in fetal growth might be a

  17. To keep the catch – that is the question: a personal account of the 3rd Annual EULAR Congress, Stockholm

    PubMed Central

    Wollheim, Frank A

    2002-01-01

    The 3rd Annual EULAR Congress, held in Stockholm on 12–15 June 2002, had a turnout of 8300 delegates, almost identical to last year's record attendance level in Prague. The venue was close to ideal, allowing ample space for poster sessions in the exhibition hall. The manned poster sessions were well attended, even on the last day of the Congress. The numerous invited speakers represented the world's elite, allowing the staging of excellent state-of-the-art podium sessions. The aim of attracting the young scientific community was partly achieved, but individual delegates' dependence on industry sponsorship poses potential problems. The organization was a big improvement compared to that of the two previous congresses. Approximately 1800 abstracts were submitted, an increase of 50%, resulting in a higher quality of accepted abstracts. The satellite symposia held every morning and late afternoon were well attended; thus, industry exposure of new products, both in podium sessions and at the exhibitions, was well accommodated. The Annual EULAR Congress consolidates its position as one of the two most important annual congresses of rheumatology, but EULAR economy and commercial aspects are still too dominant in relation to science. PMID:12223107

  18. Codon compression algorithms for saturation mutagenesis.

    PubMed

    Pines, Gur; Pines, Assaf; Garst, Andrew D; Zeitoun, Ramsey I; Lynch, Sean A; Gill, Ryan T

    2015-05-15

    Saturation mutagenesis is employed in protein engineering and genome-editing efforts to generate libraries that span amino acid design space. Traditionally, this is accomplished by using degenerate/compressed codons such as NNK (N = A/C/G/T, K = G/T), which covers all amino acids and one stop codon. These solutions suffer from two types of redundancy: (a) different codons for the same amino acid lead to bias, and (b) wild type amino acid is included within the library. These redundancies increase library size and downstream screening efforts. Here, we present a dynamic approach to compress codons for any desired list of amino acids, taking into account codon usage. This results in a unique codon collection for every amino acid to be mutated, with the desired redundancy level. Finally, we demonstrate that this approach can be used to design precise oligo libraries amendable to recombineering and CRISPR-based genome editing to obtain a diverse population with high efficiency.

  19. Codon usage in Tetrahymena and other ciliates.

    PubMed

    Martindale, D W

    1989-01-01

    Codon usage in ciliates was examined by analyzing the coding regions of 22 ciliate genes corresponding to a total of 26,142 nucleotides (8,714 codons). It was found that Tetrahymena, Paramecium and the hypotrichs (Oxytricha and Stylonychia) differed in which synonymous codons were used most frequently by their genes. In fact, the codon choices in highly expressed Tetrahymena genes were more similar to those of yeast genes than those of Paramecium genes. The ciliates do not appear to have unusually strong biases in codon usage frequency when compared to other protists such as yeast. The analysis of the Tetrahymena genes indicated that genes which are highly expressed during normal cell growth have a stronger bias towards using the "preferred" codons than those expressed at lower levels during growth or for brief periods during processes such as conjugation. This conforms to what is found in other protists.

  20. Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias.

    PubMed

    Pan, A; Dutta, C; Das, J

    1998-07-30

    Biases in the codon usage and base compositions at three codon sites in different genes of A+T-rich Gram-negative bacterium Haemophillus influenzae and G+C-rich Gram-positive bacterium Mycobacterium tuberculosis have been examined to address the following questions: (1) whether the synonymous codon usage in organisms having highly skewed base compositions is totally dictated by the mutational bias as reported previously (Sharp, P.M., Devine, K.M., 1989. Codon usage and gene expression level in Dictyostelium discoideum: highly expressed genes do 'prefer' optimal codons. Nucleic Acids Res. 17, 5029-5039), or is also controlled by translational selection; (2) whether preference of G in the first codon positions by highly expressed genes, as reported in Escherichia coli (Gutierrez, G., Marquez, L., Marin, A., 1996. Preference for guanosine at first codon position in highly expressed Escherichia coli genes. A relationship with translational efficiency. Nucleic Acids Res. 24, 2525-2527), is true in other bacteria; and (3) whether the usage of bases in three codon positions is species-specific. Result presented here show that even in organisms with high mutational bias, translational selection plays an important role in dictating the synonymous codon usage, though the set of optimal codons is chosen in accordance with the mutational pressure. The frequencies of G-starting codons are positively correlated to the level of expression of genes, as estimated by their Codon Adaptation Index (CAI) values, in M. tuberculosis as well as in H. influenzae in spite of having an A+T-rich genome. The present study on the codon preferences of two organisms with oppositely skewed base compositions thus suggests that the preference of G-starting codons by highly expressed genes might be a general feature of bacteria, irrespective of their overall G+C contents. The ranges of variations in the frequencies of individual bases at the first and second codon positions of genes of both H

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

    PubMed

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

    2012-12-01

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

  2. Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation.

    PubMed

    Liu, Guiming; Wu, Jinyu; Yang, Huanming; Bao, Qiyu

    2010-01-01

    The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak. PMID:20445740

  3. Codon Usage Patterns in Corynebacterium glutamicum: Mutational Bias, Natural Selection and Amino Acid Conservation.

    PubMed

    Liu, Guiming; Wu, Jinyu; Yang, Huanming; Bao, Qiyu

    2010-01-01

    The alternative synonymous codons in Corynebacterium glutamicum, a well-known bacterium used in industry for the production of amino acid, have been investigated by multivariate analysis. As C. glutamicum is a GC-rich organism, G and C are expected to predominate at the third position of codons. Indeed, overall codon usage analyses have indicated that C and/or G ending codons are predominant in this organism. Through multivariate statistical analysis, apart from mutational selection, we identified three other trends of codon usage variation among the genes. Firstly, the majority of highly expressed genes are scattered towards the positive end of the first axis, whereas the majority of lowly expressed genes are clustered towards the other end of the first axis. Furthermore, the distinct difference in the two sets of genes was that the C ending codons are predominate in putatively highly expressed genes, suggesting that the C ending codons are translationally optimal in this organism. Secondly, the majority of the putatively highly expressed genes have a tendency to locate on the leading strand, which indicates that replicational and transciptional selection might be invoked. Thirdly, highly expressed genes are more conserved than lowly expressed genes by synonymous and nonsynonymous substitutions among orthologous genes fromthe genomes of C. glutamicum and C. diphtheriae. We also analyzed other factors such as the length of genes and hydrophobicity that might influence codon usage and found their contributions to be weak.

  4. Meeting Report: 3rd International Workshop on Insulin & Cancer Heidelberg, Germany, October 30-31, 2010

    PubMed Central

    2010-01-01

    The 3rd International Workshop on Insulin & Cancer was held on October 30-31, 2010 at the German Cancer Research Centre in Heidelberg/Germany. The topics followed-up the discussions of the previous workshops: possible differences in mitogenicity between natural insulin and genetically engineered insulin derivatives (insulin analogues), as shown by laboratory studies and epidemiologic studies alike; molecular studies on the links between metabolic and mitogenic effects of insulin, and of hyperinsulinaemia in particular; epidemiologic evidence of interferences between insulin and other hormones, particularly sex hormones, and obesity-associated cancer; the involvement of inflammatory cytokines produced by fat tissue in obesity-associated cancer; aspects of drug-design (binding drugs to albumin) and, last but not least, detection and investigation of circulating cancer cells. PMID:21176129

  5. Meeting report: 3rd international workshop on insulin & cancer heidelberg, Germany, october 30-31, 2010.

    PubMed

    Chantelau, Ernst; Mayer, Doris

    2010-01-01

    The 3rd International Workshop on Insulin & Cancer was held on October 30-31, 2010 at the German Cancer Research Centre in Heidelberg/Germany. The topics followed-up the discussions of the previous workshops: possible differences in mitogenicity between natural insulin and genetically engineered insulin derivatives (insulin analogues), as shown by laboratory studies and epidemiologic studies alike; molecular studies on the links between metabolic and mitogenic effects of insulin, and of hyperinsulinaemia in particular; epidemiologic evidence of interferences between insulin and other hormones, particularly sex hormones, and obesity-associated cancer; the involvement of inflammatory cytokines produced by fat tissue in obesity-associated cancer; aspects of drug-design (binding drugs to albumin) and, last but not least, detection and investigation of circulating cancer cells.

  6. Passive solar progress: a simplified guide to the 3rd national passive solar conference

    SciTech Connect

    Miller, H.; Howell, Y.; Richards, D.

    1980-10-01

    Some of the concepts and practices that have come to be known as passive solar heating and cooling are introduced, and a current picture of the field is presented. Much of the material presented is derived from papers given at the 3rd National Passive Solar Conference held in San Jose, California in January 1979 and sponsored by the US Department of Energy. Extracts and data from these papers have been integrated in the text with explanatory and descriptive material. In this way, it is attempted to present technical information in an introductory context. Topics include design considerations, passive and hybrid systems and applications, sizing methods and performance prediction, and implementation issues. A glossary is included. (WHK)

  7. Dental health in antique population of Vinkovci - Cibalae in Croatia (3rd-5th century).

    PubMed

    Peko, Dunja; Vodanović, Marin

    2016-08-01

    Roman city Cibalae (Vinkovci) - the birthplace of Roman emperors Valentinian I and Valens was a very well developed urban ares in the late antique what was evidenced by numerous archaeological findings. The aim of this paper is to get insight in dental health of antique population of Cibalae. One hundred individuals with 2041 teeth dated to 3rd - 5th century AD have been analyzed for caries, antemortem tooth loss, periapical diseases and tooth wear. Prevalence of antemortem tooth loss was 4.3% in males, 5.2% in females. Prevalence of caries per tooth was 8.4% in males, 7.0% in females. Compared to other Croatian antique sites, ancient inhabitants of Roman Cibalae had rather good dental health with low caries prevalence and no gender differences. Statistically significant difference was found between males in females in the prevalence of periapical lesions and degree of tooth wear. Periapical lesions were found only in males. PMID:27598951

  8. John D. Rockefeller 3rd, statesman and founder of the Population Council.

    PubMed

    Dunlop, J

    2000-01-01

    This article presents a profile of John D. Rockefeller 3rd, statesman and founder of the Population Council. It is noted that Rockefeller took a broad view of population control as a means to address poverty and economic development rather than as an end in itself. In 1952 he initiated the convocation of the Conference on Population Problems held in Williamsburg, Virginia. The discussion focused on food supply, industrial development, depletion of natural resources, and political instability resulting from unchecked population growth. In 1967, Rockefeller initiated, lobbied for, and finally achieved a World Leaders' Statement signed by 30 heads of state including US President Lyndon Johnson. The document drew attention to population growth as a world problem and engendered political support for family planning as a solution. After 3 years the Commission on Population Growth and the American Future was established, and Rockefeller was made its chairman. Several issues were debated, including more safer fertility control and the legalization of abortion.

  9. Food: The Chemistry of Its Components, 3rd Edition (by T. P. Coultate)

    NASA Astrophysics Data System (ADS)

    Carandang, Rachelle; Ziegler, Greg

    1998-02-01

    Food: The Chemistry of Its Components, 3rd edition, by T. P. Coultate, is an excellent textbook in food chemistry for undergraduates. It is a concise version of the very detailed Food Chemistry by Fennema and similar to, but with advantages over, Mechanism and Theory in Food Chemistry by Wong and Principles of Food Chemistry by Deman. The book assumes knowledge of biochemistry and basic principles in organic chemistry, but presents very practical examples that allow the student to see the obvious link between theory and practice. The examples are described almost as if the author is performing a demonstration in a classvery vivid to the imagination. This is important because students are expected in the future to perform and put into practice their knowledge of food chemistry.

  10. PREFACE: 3rd International Symposium on Functional Materials 2009 (ISFM 2009) 3rd International Symposium on Functional Materials 2009 (ISFM 2009)

    NASA Astrophysics Data System (ADS)

    Kiwon, Kim; Li, Lu; Taehyun, Nam; Jouhyeon, Ahn

    2010-05-01

    The 3rd International Symposium on Functional Materials 2009 (ISFM 2009) and its preconference, Advances in Functional Materials 2009 (AFM 2009), were successfully held in the Republic of Korea from 15-18 June 2009 and in the People's Republic of China from 8-12 June 2009, respectively. The two conferences attracted over 300 oral and poster presentations from over 12 countries including Australia, Canada, China, Germany, Japan, India, Israel, Korea, The Netherlands, Thailand, the UK and the USA. In the two conferences, eight keynote lectures were delivered by S Miyazaki, S A Akbar, D J Singh, C Suryanarayana, M~Greenblatt, H Zhang, T Sato and J Ding. This topical issue of Physica Scripta contains papers presented at the ISFM 2009 and AFM 2009. Keyan Li from Dalian University, People's Republic of China, presents some empirical formulae to estimate the elastic moduli of rocksalt-, zincblende- and chalcopyrite-structured crystals, on the basis of electronegativities of bonded atoms in the crystallographic frame. Min-Jung Kim from Hanyang University, Korea, reports on the preparation and characterization of carboxyl functionalization of magnetite nanoparticles for oligonucleotide immobilization. F Yan from the National University of Singapore studies the fabrication of Bi(Fe0.5Sc0.5)O3-PbTiO3 (BSF-PT) thin films by pulsed laser deposition, and the enhanced magnetic moment with respect to BiFeO3-PbTiO3. Dong-Gil Lee from Pusan National University, Korea, reports on the sterilization of enteropathogenic Escherichia coli using nanofiber TiO2 films prepared by the electrostatic spray method. Sang-Eun Park from the Korea Institute of Science and Technology reports on the study of encapsulated Fe3O4 nanoparticles with a silica thin layer with a reversible capacity of about 363 mAhg-1. Other researchers report on many other exiting achievements in the fields of ferromagnetic materials, magneto-optical materials, thermoelectric materials, shape memory materials, fuel-cell and

  11. Effect of non-erupted 3rd molars on distal roots and supporting structures of approximal teeth. A radiographic survey of 202 cases.

    PubMed

    Nemcovsky, C E; Libfeld, H; Zubery, Y

    1996-09-01

    Root resorption of 2nd molars in proximity to non-erupted 3rd molars has been widely reported. The purpose of this study was to determine the prevalence of root resorption in second molars adjacent to non-erupted third molars. Its association to age and gender of the patient, location and inclination of the non-erupted third molar and to distal bone support of the 2nd molars was analyzed. A radiographic survey of 202 periapical radiographs taken in patients with clinically missing third molars was conducted. 3 examiners independently evaluated the radiographs and only those cases where at least 2 observers agreed were included in this report. Statistical analysis was performed on 186 radiographs. Associations were analyzed with the Pearson chi 2 test. Radiographic evidence of root resorption was found in 45 2nd molars (24.2%) of which 12 (6.5%) showed moderate to complete root resorption. Non-erupted tooth apical position and mesio-inclination of 60 degrees or more relative to the distal root of the second molar were significantly associated with root resorption (p = 0.01368 and p = 0.0194, respectively). Resorption was positively associated with age of patient (p = 0.00606). These results may support early extraction of impacted 3rd molars especially in cases with a mesio-angulation of 60 degrees or more and an apical location in proximity to the distal root of the 2nd molar. PMID:8891930

  12. Simulation of robustness of a new e-beam column with the 3 rd-order imaging technique

    NASA Astrophysics Data System (ADS)

    Takeya, K.; Fuse, T.; Kinoshita, H.; Parker, N. William

    2008-03-01

    We are now investigating a new concept column with the 3 rd-order imaging technique, in order to obtain fine resolution and high current density beams for electron beam direct writing (EBDW) suitable for below 32nm technology nodes. From the first experimental verification, it is found that the 3 rd-order imaging has a benefit of increasing the beam current compared with conventional Gaussian beam without any beam blurring. However, in order to realize such a column which can work stably in the sub 32nm technology node generations, it is important to clarify how robust the 3 rd-order imaging is against the mechanical tolerances in column manufacturing. This paper describes the tolerance analysis for errors of column manufacturing by simulation. The column has an electron gun with small virtual source and two (Gun and Main) lenses. A patterned beam defining aperture, which enables the 3 rd-order imaging, is set between the 1 st and the 2 nd lenses. The influences of errors such as concentricity, offset and tilt between optical parts on the beam shape, beam current density distribution, and beam edge acuity on a wafer is analyzed for this column. According to these results, the 3 rd-order imaging appears to have sufficiently large allowance compared to the error budget for column manufacturing required in the sub 32nm technology node patterning.

  13. Codes in the codons: construction of a codon/amino acid periodic table and a study of the nature of specific nucleic acid-protein interactions.

    PubMed

    Benyo, B; Biro, J C; Benyo, Z

    2004-01-01

    The theory of "codon-amino acid coevolution" was first proposed by Woese in 1967. It suggests that there is a stereochemical matching - that is, affinity - between amino acids and certain of the base triplet sequences that code for those amino acids. We have constructed a common periodic table of codons and amino acids, where the nucleic acid table showed perfect axial symmetry for codons and the corresponding amino acid table also displayed periodicity regarding the biochemical properties (charge and hydrophobicity) of the 20 amino acids and the position of the stop signals. The table indicates that the middle (2/sup nd/) amino acid in the codon has a prominent role in determining some of the structural features of the amino acids. The possibility that physical contact between codons and amino acids might exist was tested on restriction enzymes. Many recognition site-like sequences were found in the coding sequences of these enzymes and as many as 73 examples of codon-amino acid co-location were observed in the 7 known 3D structures (December 2003) of endonuclease-nucleic acid complexes. These results indicate that the smallest possible units of specific nucleic acid-protein interaction are indeed the stereochemically compatible codons and amino acids.

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

    PubMed Central

    Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

    2014-01-01

    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

  15. The effect of mutation and selection on codon adaptation in Escherichia coli bacteriophage.

    PubMed

    Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

    2014-05-01

    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

  16. Studying Codon Usage: From sequence to function

    NASA Astrophysics Data System (ADS)

    Hwa, Terry; Klumpp, Stefan; Dong, Jiajia

    2007-03-01

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

  17. A Web Interface for Codon Compression.

    PubMed

    Halweg-Edwards, Andrea L; Pines, Gur; Winkler, James D; Pines, Assaf; Gill, Ryan T

    2016-09-16

    Saturation mutagenesis is widely used in protein engineering and other experiments. A common practice is to utilize the single degenerate codon NNK. However, this approach suffers from amino acid bias and the presence of a stop codon and of the wild type amino acid. These extra features needlessly increase library size and consequently downstream screening load. Recently, we developed the DYNAMCC algorithms for codon compression that find the minimal set of degenerate codons, covering any defined set of amino acids, with no off-target codons and with redundancy control. Additionally, we experimentally demonstrated the advantages of this approach over the standard NNK method. While the code is freely available from our Web site, we have now made this method more accessible to a broader audience without any computational background by building a user-friendly web-based interface for those algorithms. The Web site can be accessed through: www.dynamcc.com .

  18. A Web Interface for Codon Compression.

    PubMed

    Halweg-Edwards, Andrea L; Pines, Gur; Winkler, James D; Pines, Assaf; Gill, Ryan T

    2016-09-16

    Saturation mutagenesis is widely used in protein engineering and other experiments. A common practice is to utilize the single degenerate codon NNK. However, this approach suffers from amino acid bias and the presence of a stop codon and of the wild type amino acid. These extra features needlessly increase library size and consequently downstream screening load. Recently, we developed the DYNAMCC algorithms for codon compression that find the minimal set of degenerate codons, covering any defined set of amino acids, with no off-target codons and with redundancy control. Additionally, we experimentally demonstrated the advantages of this approach over the standard NNK method. While the code is freely available from our Web site, we have now made this method more accessible to a broader audience without any computational background by building a user-friendly web-based interface for those algorithms. The Web site can be accessed through: www.dynamcc.com . PMID:27169595

  19. TEC obtained from 3rd Stokes parameter for improved quality of SMOS salinity retrieval

    NASA Astrophysics Data System (ADS)

    Vergely, Jean-Luc; Waldteufel, Philippe; Boutin, Jacqueline; Yin, Xiaobin; Spurgeon, Paul

    2014-05-01

    While SMOS was designed with full polarimetric capability, the 3rd Stokes parameter information has not been introduced so far in the data processing. The analysis reported in the present contribution proposes to estimate from this information the total ionospheric electron content (TEC). Indeed the Faraday effect generated by the ionospheric electrons on the path from Earth to satellite is believed to be responsible for large uncertainties in the evening half-orbits (circa 06 PM local time) when the ionospheric content is close to its diurnal maximum. It is shown that the 3rd Stokes parameter exhibits a maximal sensitivity to TEC in a restricted area located at the front of the SMOS 2D field of view. However, since the Faraday angle depends on the scalar product between line-of-sight and magnetic field vectors, a latitudinal zone is found where this sensitivity vanishes. This zone occurs around 15° N a latitude nearly invariant with longitude around the Earth. Accordingly it is possible, when carrying out the TEC estimation over a descending half-orbit, to isolate over this "blind zone" the so-called "Ocean Target Transformation" parameter, which aims at correcting for pixel dependent biases. TEC maps obtained in this way compare favorably with maps built from GPS measurements, which have been introduced so far in the SMOS processing chain as auxiliary data. The space resolution is somewhat improved, allowing a better selection of the relevant electron content in zones exhibiting large horizontal TEC gradients. In a latter step, based on the TEC maps, it becomes possible to recompute the OTT correction for those brightness temperature components to be used as input in the salinity retrieval. Then the additional information impacts the salinity retrieval both directly (as the quality of the TEC auxiliary data is improved) and indirectly (as the empirical OTT correction is no longer contaminated by spurious Faraday rotation effects). The respective contributions of

  20. Codon information value and codon transition-probability distributions in short-term evolution

    NASA Astrophysics Data System (ADS)

    Jiménez-Montaño, M. A.; Coronel-Brizio, H. F.; Hernández-Montoya, A. R.; Ramos-Fernández, A.

    2016-07-01

    To understand the way the Genetic Code and the physical-chemical properties of coded amino acids affect accepted amino acid substitutions in short-term protein evolution, taking into account only overall amino acid conservation, we consider an underlying codon-level model. This model employs codon pair-substitution frequencies from an empirical matrix in the literature, modified for single-base mutations only. Ordering the degenerated codons according to their codon information value (Volkenstein, 1979), we found that three-fold and most of four-fold degenerated codons, which have low codon values, were best fitted to rank-frequency distributions with constant failure rate (exponentials). In contrast, almost all two-fold degenerated codons, which have high codon values, were best fitted to rank-frequency distributions with variable failure rate (inverse power-laws). Six-fold degenerated codons are considered to be doubly assigned. The exceptional behavior of some codons, including non-degenerate codons, is discussed.

  1. The Power of PreK-3rd: How a Small Foundation Helped Push Washington State to the Forefront of the PreK-3rd Movement. FCD Case Study

    ERIC Educational Resources Information Center

    Nyhan, Paul

    2011-01-01

    The New School Foundation was not born from a commission, legislative mandate, research project, think tank, or even the mind of a leading education scholar. One of Washington state's pioneering PreK-3rd initiatives began as the brainchild of a wealthy Seattle businessman, Stuart Sloan, 20 years ago. The New School Foundation and its ideas were…

  2. Effects of notetaking instruction on 3rd grade student's science learning and notetaking behavior

    NASA Astrophysics Data System (ADS)

    Lee, Pai-Lin

    The research examined effects of notetaking instruction on elementary-aged students' ability to recall science information and notetaking behavior. Classes of 3rd grade students were randomly assigned to three treatment conditions, strategic notetaking, partial strategic notetaking, and control, for 4 training sessions. The effects of the notetaking instruction were measured by their performances on a test on science information taught during the training, a long-term free recall of the information, and number of information units recalled with or without cues. Students' prior science achievement was used to group students into two levels (high vs. low) and functioned as another independent variable in analysis. Results indicated significant treatment effect on cued and non-cued recall of the information units in favor of the strategy instruction groups. Students with higher prior achievement in science performed better on cued recall and long-term free recall of information. The results suggest that students as young as at the third grade can be instructed to develop the ability of notetaking that promotes their learning.

  3. The 3^rd International Conference on Women in Physics: Global Perspectives, Common Concerns, Worldwide Views

    NASA Astrophysics Data System (ADS)

    Zastavker, Yevgeniya V.

    2009-03-01

    The 3^rd International Conference on Women in Physics (ICWIP), held in Seoul, Korea, in October 2008, brought together 300 participants from 57 countries, including a diverse 22-member U.S. Delegation, for a 3-day summit of stimulating discussions, thought-provoking presentations, inspirational posters, and networking. Held under the auspices of the Working Group on Women in Physics of the International Union of Pure and Applied Physics (IUPAP), this meeting built on the successes of the 1^st (Paris, 2002) and 2^nd (Rio de Janeiro, 2005) Conferences and further clarified the importance of diversifying the field of physics worldwide. Although considerable progress has been made since 2002, it was clear that the global scientific workforce is still under-utilizing a large percentage of the available female talent pool. If human society is to benefit to its fullest from various contributions that the field of physics can offer in addressing global issues of economic crisis, energy, environment, water, health, poverty, and hunger, women of all races and nationalities need to become fully included and engaged in the national and international physical community. To address these and many other issues, the ICWIP unanimously approved a five-part resolution to IUPAP recommending actions to promote the recruitment, retention, and advancement of women in physics and related fields.

  4. Measuring the cascade rate in anisotropic turbulence through 3rd order structure functions.

    NASA Astrophysics Data System (ADS)

    Verdini, Andrea; Landi, Simone; Hellinger, Petr

    2014-05-01

    We employ the Von-Karman-Howart-Yaglom-Politano-Poquet (KHYPP)law, to compute the cascade rate by means of 3rd order structure functions in homogeneous, forced, DNS at high resolution. We consider first the isotropic case (no guide field) and verify that the cascade rate is consistent with the dissipation rate. Then we consider an anisotropic case (with guide field) for which the isotropic KHYPP law does not apply. We compute the parallel and perpendicular cascade rates and find that the latter basically accounts for the total dissipation rate, as expected for anisotropic turbulence. Also, the cascade rate derived from the isotropic law is found to be a good approximation for the total cascade rate. Recent works have shown that the hypothesis of stationary turbulence must be probably relaxed in the solar wind. We present preliminary results on the measure of the cascade rate in the expanding solar wind, obtained with DNS of MHD turbulence in the expanding box model. Such model incorporates the basic physic of expansion thus inducing anisotropies driven by both the magnetic field and expansion, along with an energy decrease due to the conservation of linear invariants (angular momentum and magnetic flux). The correction due to non-stationary conditions is found to be important and to become negligible only at small scales, thus suggesting that solar wind measurements over- estimate the actual cascade rate.

  5. SESAME-A 3rd Generation Synchrotron Light Source for the Middle East

    NASA Astrophysics Data System (ADS)

    Winick, Herman

    2010-02-01

    Developed under the auspices of UNESCO and modeled on CERN, SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East) is an international research center in construction in Jordan. It will enable world class research by scientists from the region, reversing the brain drain. It will also build bridges between diverse societies, contributing to a culture of peace through international cooperation in science. The centerpiece is a synchrotron light source originating from BESSY I, a gift by Germany. The upgraded machine, a 2.5 GeV 3rd Generation Light Source (133m circumference, 26nm-rad emittance and 12 places for insertion devices), will provide light from infra-red to hard X-rays, offering excellent opportunities to train local scientists and attract those working abroad to return. The SESAME Council meets twice each year and presently has nine Members (Bahrain, Cyprus, Egypt, Iran, Israel, Jordan, Pakistan, Palestinian Authority, Turkey). Members have responsibility for the project and provide the annual operations budget (1.5M US dollars in 2009, expected to rise to about 5M when operation starts in 2012-13). Jordan provided the site, building, and infrastructure. A staff of 20 is installing the 0.8 GeV BESSY I injection system. The facility will have the capacity to serve 30 or more experiments operating simultaneously. See www.sesame.org.jo )

  6. Geysers Characteristics before and after Landslide of June 3-rd, 2007 (Geysers Valley, Kamchatka, Russia)

    NASA Astrophysics Data System (ADS)

    Droznin, V. A.; Kiryukhin, A. V.; Muraviev, J. D.

    2007-12-01

    Since 1990 cycling characteristics of five geysers (Maly, Bolshoy, Shel, Velican, Troynoy) were contentiously monitoring using automatic telemetric system (V A Drosnin, http://www.ch0103.emsd.iks.ru/ ). The most powerful geyser Velikan erupted steam clouds at 300 m height. 1:20 UTC June 3-rd, 2007 lower basin of the Geysers Valley was in a few minutes buried under 10 mln m3 of mud, debris, and blocks of rocks. Some indications were found, that landslide triggered by steam eruption in the upstream area of Vodopadny creek. As a result of this three famous geysers (Pervenets, Sakharny,Troynoy) located at lower elevations were sealed under 10-30 m thick caprock as well as Vodopadny hot creek, a rock dumb trap Geysernaya river and lifted water into 20 m deep lake, which flooded three famous geysers (Conus, Bolshoy and Maly) terminating their cycling activity. Nevertheless Bolshoy and Maly activity continues in a form of discharge of water circulated in the former geysers channels and a clear plume at a lake surface above exits observed. Shortly after landslide continuous monitoring of the cycling characteristics of the upper basin geysers, including Velikan and lake level, accomplished by temperature loggers - restarted. There are some indications time periods of the geysers cycling decrease.

  7. Visual, Critical, and Scientific Thinking Dispositions in a 3rd Grade Science Classroom

    NASA Astrophysics Data System (ADS)

    Foss, Stacy

    Many American students leave school without the required 21st century critical thinking skills. This qualitative case study, based on the theoretical concepts of Facione, Arheim, and Vygotsky, explored the development of thinking dispositions through the arts in science on the development of scientific thinking skills when used as a conceptual thinking routine in a rural 3rd grade classroom. Research questions examined the disposition to think critically through the arts in science and focused on the perceptions and experiences of 25 students with the Visual Thinking Strategy (VTS) process. Data were collected from classroom observations (n = 10), student interviews (n = 25), teacher interviews ( n = 1), a focus group discussion (n = 3), and artifacts of student work (n = 25); these data included perceptions of VTS, school culture, and classroom characteristics. An inductive analysis of qualitative data resulted in several emergent themes regarding disposition development and students generating questions while increasing affective motivation. The most prevalent dispositions were open-mindedness, the truth-seeking disposition, the analytical disposition, and the systematicity disposition. The findings about the teachers indicated that VTS questions in science supported "gradual release of responsibility", the internalization of process skills and vocabulary, and argumentation. This case study offers descriptive research that links visual arts inquiry and the development of critical thinking dispositions in science at the elementary level. A science curriculum could be developed, that emphasizes the development of thinking dispositions through the arts in science, which in turn, could impact the professional development of teachers and learning outcomes for students.

  8. Resurgence of duckweed research and applications: report from the 3rd International Duckweed Conference.

    PubMed

    Appenroth, Klaus-J; Sree, K Sowjanya; Fakhoorian, Tamra; Lam, Eric

    2015-12-01

    Duckweed, flowering plants in the Lemnaceae family, comprises the smallest angiosperms in the plant kingdom. They have some of the fastest biomass accumulation rates reported to date for plants and have the demonstrated ability to thrive on wastewater rich in dissolved organic compounds and thus could help to remediated polluted water resources and prevents eutrophication. With a high quality genome sequence now available and increased commercial interest worldwide to develop duckweed biomass for renewables such as protein and fuel, the 3rd International Duckweed Conference convened at Kyoto, Japan, in July of 2015, to update the community of duckweed researchers and developers on the progress in the field. In addition to sharing results and ideas, the conference also provided ample opportunities for new-comers as well as established workers in the field to network and create new aliances. We hope this meeting summary will also help to disseminate the key advances and observations that have been presented in this conference to the broader plant biology community in order to encourage increased cross-fertilization of ideas and technologies. PMID:26506824

  9. Resurgence of duckweed research and applications: report from the 3rd International Duckweed Conference.

    PubMed

    Appenroth, Klaus-J; Sree, K Sowjanya; Fakhoorian, Tamra; Lam, Eric

    2015-12-01

    Duckweed, flowering plants in the Lemnaceae family, comprises the smallest angiosperms in the plant kingdom. They have some of the fastest biomass accumulation rates reported to date for plants and have the demonstrated ability to thrive on wastewater rich in dissolved organic compounds and thus could help to remediated polluted water resources and prevents eutrophication. With a high quality genome sequence now available and increased commercial interest worldwide to develop duckweed biomass for renewables such as protein and fuel, the 3rd International Duckweed Conference convened at Kyoto, Japan, in July of 2015, to update the community of duckweed researchers and developers on the progress in the field. In addition to sharing results and ideas, the conference also provided ample opportunities for new-comers as well as established workers in the field to network and create new aliances. We hope this meeting summary will also help to disseminate the key advances and observations that have been presented in this conference to the broader plant biology community in order to encourage increased cross-fertilization of ideas and technologies.

  10. PREFACE: 3rd International Conference on Manufacturing, Optimization, Industrial and Material Engineering (MOIME 2015)

    NASA Astrophysics Data System (ADS)

    Lumban Gaol, Ford; Webb, Jeff; Ding, Jun

    2015-05-01

    The 3rd International Conference on Manufacturing, Optimization, Industrial and Material Engineering (MOIME 2015) was held at the Sheraton Kuta, Bali, Indonesia, from 28 - 29 March 2015. The MOIME 2015 conference is aimed to bring together researchers, engineers and scientists in the domain of interest from around the world. MOIME 2015 is placed on promoting interaction between the theoretical, experimental, and applied communities, so that a high level exchange is achieved in new and emerging areas within Material Engineering, Industrial Engineering and all areas that relate to Optimization. We would like to express our sincere gratitude to all in the Technical Program Committee who have reviewed the papers and developed a very interesting Conference Program, as well as the invited and plenary speakers. This year, we received 99 papers and after rigorous review, 24 papers were accepted. The participants come from eight countries. There were four parallel sessions and two invited speakers. It is an honour to present this volume of IOP Conference Series: Materials Science and Engineering (MSE) and we deeply thank the authors for their enthusiastic and high-grade contributions. Finally, we would like to thank the conference chairmen, the members of the steering committee, the organizing committee, the organizing secretariat and the financial support from the conference sponsors that allowed the success of MOIME 2015. The Editors of the MOIME 2015 Proceedings Dr. Ford Lumban Gaol Jeff Webb, Ph.D Prof. Jun DING, Ph.D

  11. Exploiting stem cell therapy: the 3rd meeting of stem cell research Italy.

    PubMed

    Di Bernardo, Giovanni; Piva, Roberta; Giordano, Antonio; Galderisi, Umberto

    2013-04-01

    The study of stem cells is one of the most exciting areas of contemporary biomedical research. During the 3rd Joint Meeting of Stem Cell Research Italy (June 2012, Ferrara, Italy), scientists from different multidisciplinary areas explored new frontiers of basic and applied stem cell research with key lectures and oral presentations. There was a public debate on ethics during the opening ceremony, specifically on the limits and potentialities of adult and embryonic stem cells. Some scientists presented basic research data showing evolutionary aspects, which could be of interest in understanding specific biological phenomena. Others focused on "dangerous liaisons" between gene transfer vectors and the human genome. Some speakers provided insight into current stem cell therapies, such as those involving human epithelial stem cells for treatment of skin diseases. Other researchers presented data on close-to-therapy findings, such as the use of mesenchymal stem cells in brain repair. Of note, during the meeting, spotlights were focused on major issues that have to be considered for GMP stem cell production for cell therapy. In "Meet the Expert" sessions, specialists presented innovative technologies such as a next-generation sequencing system. Finally, the meeting provided an excellent opportunity for young scientists to show their findings, and to discuss with each other and with internationally recognized experts.

  12. Evolutionary characterization of Tembusu virus infection through identification of codon usage patterns.

    PubMed

    Zhou, Hao; Yan, Bing; Chen, Shun; Wang, Mingshu; Jia, Renyong; Cheng, Anchun

    2015-10-01

    Tembusu virus (TMUV) is a single-stranded, positive-sense RNA virus. As reported, TMUV infection has resulted in significant poultry losses, and the virus may also pose a threat to public health. To characterize TMUV evolutionarily and to understand the factors accounting for codon usage properties, we performed, for the first time, a comprehensive analysis of codon usage bias for the genomes of 60 TMUV strains. The most recently published TMUV strains were found to be widely distributed in coastal cities of southeastern China. Codon preference among TMUV genomes exhibits a low bias (effective number of codons (ENC)=53.287) and is maintained at a stable level. ENC-GC3 plots and the high correlation between composition constraints and principal component factor analysis of codon usage demonstrated that mutation pressure dominates over natural selection pressure in shaping the TMUV coding sequence composition. The high correlation between the major components of the codon usage pattern and hydrophobicity (Gravy) or aromaticity (Aromo) was obvious, indicating that properties of viral proteins also account for the observed variation in TMUV codon usage. Principal component analysis (PCA) showed that CQW1 isolated from Chongqing may have evolved from GX2013H or GX2013G isolated from Guangxi, thus indicating that TMUV likely disseminated from southeastern China to the mainland. Moreover, the preferred codons encoding eight amino acids were consistent with the optimal codons for human cells, indicating that TMUV may pose a threat to public health due to possible cross-species transmission (birds to birds or birds to humans). The results of this study not only have theoretical value for uncovering the characteristics of synonymous codon usage patterns in TMUV genomes but also have significant meaning with regard to the molecular evolutionary tendencies of TMUV. PMID:26205688

  13. Mutation and Selection Cause Codon Usage and Bias in Mitochondrial Genomes of Ribbon Worms (Nemertea)

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  15. Codon usage and tRNA content in unicellular and multicellular organisms.

    PubMed

    Ikemura, T

    1985-01-01

    Choices of synonymous codons in unicellular organisms are here reviewed, and differences in synonymous codon usages between Escherichia coli and the yeast Saccharomyces cerevisiae are attributed to differences in the actual populations of isoaccepting tRNAs. There exists a strong positive correlation between codon usage and tRNA content in both organisms, and the extent of this correlation relates to the protein production levels of individual genes. Codon-choice patterns are believed to have been well conserved during the course of evolution. Examination of silent substitutions and tRNA populations in Enterobacteriaceae revealed that the evolutionary constraint imposed by tRNA content on codon usage decelerated rather than accelerated the silent-substitution rate, at least insofar as pairs of taxonomically related organisms were examined. Codon-choice patterns of multicellular organisms are briefly reviewed, and diversity in G+C percentage at the third position of codons in vertebrate genes--as well as a possible causative factor in the production of this diversity--is discussed. PMID:3916708

  16. Constancy and Variability: Dialogic Literacy Events as Sites for Improvisation in Two 3rd-Grade Classrooms

    ERIC Educational Resources Information Center

    Jordan, Michelle E.; Santori, Diane

    2015-01-01

    This multisite study investigates dialogic literacy events that revolved around narrative and informational texts in two 3rd-grade classrooms. The authors offer a metaphor of musical improvisation to contemplate dialogic literacy events as part of the repertoire of teaching and learning experiences. In literacy learning, where there is much…

  17. Test Review: C. Keith Conners "Conners 3rd Edition" Toronto, Ontario, Canada--Multi-Health Systems, 2008

    ERIC Educational Resources Information Center

    Kao, Grace S.; Thomas, Hillary M.

    2010-01-01

    "Conners 3rd Edition" is the most updated version of a series of measures for assessing attention deficit hyperactivity disorder (ADHD) and common comorbid problems/disorders in children and adolescents ranging from 6 to 18 years of age. Related problems that the test helps assess include executive dysfunction, learning problems, aggression, and…

  18. Predicting 3rd Grade and 10th Grade FCAT Success for 2006-07. Research Brief. Volume 0601

    ERIC Educational Resources Information Center

    Froman, Terry; Rubiera, Vilma

    2006-01-01

    For the past few years the Florida School Code has set the Florida Comprehensive Assessment Test (FCAT) performance requirements for promotion of 3rd graders and graduation for 10th graders. Grade 3 students who do not score at level 2 or higher on the FCAT SSS Reading must be retained unless exempted for special circumstances. Grade 10 students…

  19. Predicting 3rd Grade and 10th Grade FCAT Success for 2007-08. Research Brief. Volume 0702

    ERIC Educational Resources Information Center

    Froman, Terry; Rubiera, Vilma

    2008-01-01

    For the past few years the Florida School Code has set the Florida Comprehensive Assessment Test (FCAT) performance requirements for promotion of 3rd graders and graduation for 10 graders. Grade 3 students who do not score at level 2 or higher on the FCAT SSS Reading must be retained unless exempted for special circumstances. Grade 10 students…

  20. The Lived Experiences of 3rd Generation and beyond U.S.-Born Mexican Heritage College Students: A Qualitative Study

    ERIC Educational Resources Information Center

    Galvan, Richard

    2011-01-01

    The purpose of this study was to describe the psychosocial and identity challenges of 3rd generation and beyond U.S.-born (3GAB-USB) Mexican heritage college students. Alvarez (1973) has written about the psychosocial impact "hybridity" can have on a U.S.- born (USB) Mexican individual who incorporates two distinct cultures (American and Mexican)…

  1. Iron metabolism in African American women during the 2nd and 3rd trimester of a high-risk pregnancy

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Objective: To examine iron metabolism during the 2nd and 3rd trimester in African American women classified as a high-risk pregnancy. Design: Longitudinal. Setting: Large, university-based, urban Midwestern medical center. Participants: Convenience sample of 47 African American women classified a...

  2. Iowa Acceleration Scale Manual: A Guide for Whole-Grade Acceleration K-8. (3rd Edition, Manual)

    ERIC Educational Resources Information Center

    Assouline, Susan G.; Colangelo, Nicholas; Lupkowski-Shoplik, Ann; Forstadt, Leslie; Lipscomb, Jonathon

    2009-01-01

    Feedback from years of nationwide use has resulted in a 3rd Edition of this unique, systematic, and objective guide to considering and implementing academic acceleration. Developed and tested by the Belin-Blank Center at the University of Iowa, the IAS ensures that acceleration decisions are systematic, thoughtful, well reasoned, and defensible.…

  3. A Program Evaluation of ClassScape Used in 3rd Grade Classes in a Rural County in North Carolina

    ERIC Educational Resources Information Center

    Rogers, Misha Neely

    2012-01-01

    The research study will examine the impact of using the ClassScape program and targeted interventions on 3rd grade reading levels of performance. The conceptual and theoretical framework for the study suggests the need to connect formative, benchmark, and summative assessments in North Carolina. Furthermore, the review of the literature will…

  4. 3rd Annual PIALA Conference Saipan--Collecting, Preserving & Sharing Information in Micronesia. Conference Proceedings. October 13-15, 1993.

    ERIC Educational Resources Information Center

    Edmundson, Margaret, Ed.

    1993-01-01

    This PIALA 1993 Proceedings contains many of the papers presented at the 3rd annual conference of the Pacific Islands Association of Libraries and Archives. This publication is the first time papers from this Micronesian regional library and archives conference have ever been published. The conference addressed various topics of interest to…

  5. Molecular Phylogeny of Sequenced Saccharomycetes Reveals Polyphyly of the Alternative Yeast Codon Usage

    PubMed Central

    Mühlhausen, Stefanie; Kollmar, Martin

    2014-01-01

    The universal genetic code defines the translation of nucleotide triplets, called codons, into amino acids. In many Saccharomycetes a unique alteration of this code affects the translation of the CUG codon, which is normally translated as leucine. Most of the species encoding CUG alternatively as serine belong to the Candida genus and were grouped into a so-called CTG clade. However, the “Candida genus” is not a monophyletic group and several Candida species are known to use the standard CUG translation. The codon identity could have been changed in a single branch, the ancestor of the Candida, or to several branches independently leading to a polyphyletic alternative yeast codon usage (AYCU). In order to resolve the monophyly or polyphyly of the AYCU, we performed a phylogenomics analysis of 26 motor and cytoskeletal proteins from 60 sequenced yeast species. By investigating the CUG codon positions with respect to sequence conservation at the respective alignment positions, we were able to unambiguously assign the standard code or AYCU. Quantitative analysis of the highly conserved leucine and serine alignment positions showed that 61.1% and 17% of the CUG codons coding for leucine and serine, respectively, are at highly conserved positions, whereas only 0.6% and 2.3% of the CUG codons, respectively, are at positions conserved in the respective other amino acid. Plotting the codon usage onto the phylogenetic tree revealed the polyphyly of the AYCU with Pachysolen tannophilus and the CTG clade branching independently within a time span of 30–100 Ma. PMID:25646540

  6. PREFACE: 3rd International Youth Conference "Interdisciplinary Problems of Nanotechnology, Biomedicine and Nanotoxicology" (Nanobiotech 2015)

    NASA Astrophysics Data System (ADS)

    Refsnes, Magne, Prof; Gusev, Alexander, Dr; Godymchuk, Anna, Dr; Bogdan, Anna

    2015-11-01

    The 3rd International Youth Conference "Interdisciplinary Problems of Nanotechnology, Biomedicine and Nanotoxicology" (Nanobiotech2015) was held on 21-22 May 2015 in Tambov, Russia, and was jointly organized by Tambov Derzhavin State University (Russia), the Norwegian Institute of Public Health (Norway), the National University of Science and Technology MISiS (Russia), Tomsk Polytechnic University (Russia) and Tomsk State University. The conference gathered experienced and young researchers, post-docs and students, working in the fieldof nanotechnologies, nanomedicine, nano(eco)toxicology and risk assessment of nanomaterials, in order to facilitate the aggregation and sharing of interests and results for better collaboration and visibility of activity. The goal of Nanobiotech2015 was to bring researchers and practitioners together to share the latest knowledge on nanotechnology-specific risks to occupational and environmental health and assessing how to reduce these potential risks. The main objective of the conference is to identify, systematize and solve current scientific problems inthe sphere of nanobiotechnologies, nanomedicine and nanotoxicology, in order to join forces todetermine prospective areas and compose working groups of interested co-workers for carrying out interdisciplinary research projects. The topics of Nanobiotech2015 were: (1) Nanotechnologies in pharmaceutics and medicine; (2) Sources and mechanisms of nanoparticle release into the environment; (3) Ecological and biological effects of nanoparticles; (4) (Eco)toxicology of nanomaterials; (5) Methods for detection of nanoparticles in the environment and in biological objects; and (6) Physico-chemical properties of nanoparticles in the environment. We want to thank the Organizing Committee, the universities and sponsors supporting the conference,and everyone who contributed to the organization of this meeting, for their contribution towards the conference and for their contributions to these

  7. 3rd hand smoking; heterogeneous oxidation of nicotine and secondary aerosol formation in the indoor environment

    NASA Astrophysics Data System (ADS)

    Petrick, Lauren; Dubowski, Yael

    2010-05-01

    Tobacco smoking is well known as a significant source of primary indoor air pollutants. However, only recently has it been recognized that the impact of Tobacco smoking may continue even after the cigarette has been extinguished (i.e., third hand smoke) due to the effect of indoor surfaces. These surfaces may affect the fate of tobacco smoke in the form of secondary reactions and pollutants, including secondary organic aerosol (SOA) formation. Fourier Transform Infrared spectrometry with Attenuated Total Reflection (FTIR-ATR) in tandem with a Scanning Mobility Particle Sizing (SMPS) system was used to monitor the ozonation of cellulose sorbed nicotine and resulting SOA formation. SOA formation began at onset of ozone introduction ([O3] = 60 ± 5 ppb) with a size distribution of dp ≤ 25 nm, and was determined to be a result of heterogeneous reaction (opposed to homogeneous). SOA yield from reacted surface nicotine was on the order of 10 %. Simultaneous to SOA monitoring, FTIR-ATR spectra showed surface changes in the nicotine film as the reaction progressed, revealing a pseudo first-order surface reaction rate of 0.0026 ± 0.0008 min-1. Identified surface oxidation products included: cotinine, myosmine, methylnicotinamide and nicotyrine. Surface reaction rate was found to be partially inhibited at high relative humidity. Given the toxicity of some of the identified products (e.g., cotinine has shown potential mutagenicity and teratogenicity) and that small particles may contribute to adverse health effects, the present study indicates that exposure to 3rd hand smoke ozonation products may pose additional health risks.

  8. Analysis of Codon Usage Patterns in Herbaceous Peony (Paeonia lactiflora Pall.) Based on Transcriptome Data.

    PubMed

    Wu, Yanqing; Zhao, Daqiu; Tao, Jun

    2015-10-22

    Codon usage bias, which exists in many genomes, is mainly determined by mutation and selection. To elucidate the genetic features and evolutionary history of herbaceous peony (Paeonia lactiflora), a well-known symbol of prosperity in China, we examined synonymous codon usage in 24,216 reconstructed genes from the P. lactiflora transcriptome. The mean GC content was 44.4%, indicating that the nucleotide content of P. lactiflora genes is slightly AT rich and GC poor. The P. lactiflora genome has a wide range of GC3 (GC content at the third synonymous codon position) distribution, with a significant correlation between GC12 and GC3. ENC (effective number of codons) analysis suggested that mutational bias played a major role in shaping codon usage. Parity Rule 2 (PR2) analysis revealed that GC and AU were not used proportionally. We identified 22 "optimal codons", most ending with an A or U. Our results suggested that nucleotide composition mutation bias and translational selection were the main driving factors of codon usage bias in P. lactiflora. These results lay the foundation for exploring the evolutionary mechanisms and heterologous expression of functionally-important proteins in P. lactiflora.

  9. Analysis of Codon Usage Patterns in Herbaceous Peony (Paeonia lactiflora Pall.) Based on Transcriptome Data.

    PubMed

    Wu, Yanqing; Zhao, Daqiu; Tao, Jun

    2015-01-01

    Codon usage bias, which exists in many genomes, is mainly determined by mutation and selection. To elucidate the genetic features and evolutionary history of herbaceous peony (Paeonia lactiflora), a well-known symbol of prosperity in China, we examined synonymous codon usage in 24,216 reconstructed genes from the P. lactiflora transcriptome. The mean GC content was 44.4%, indicating that the nucleotide content of P. lactiflora genes is slightly AT rich and GC poor. The P. lactiflora genome has a wide range of GC3 (GC content at the third synonymous codon position) distribution, with a significant correlation between GC12 and GC3. ENC (effective number of codons) analysis suggested that mutational bias played a major role in shaping codon usage. Parity Rule 2 (PR2) analysis revealed that GC and AU were not used proportionally. We identified 22 "optimal codons", most ending with an A or U. Our results suggested that nucleotide composition mutation bias and translational selection were the main driving factors of codon usage bias in P. lactiflora. These results lay the foundation for exploring the evolutionary mechanisms and heterologous expression of functionally-important proteins in P. lactiflora. PMID:26506393

  10. Codon compression algorithms for saturation mutagenesis.

    PubMed

    Pines, Gur; Pines, Assaf; Garst, Andrew D; Zeitoun, Ramsey I; Lynch, Sean A; Gill, Ryan T

    2015-05-15

    Saturation mutagenesis is employed in protein engineering and genome-editing efforts to generate libraries that span amino acid design space. Traditionally, this is accomplished by using degenerate/compressed codons such as NNK (N = A/C/G/T, K = G/T), which covers all amino acids and one stop codon. These solutions suffer from two types of redundancy: (a) different codons for the same amino acid lead to bias, and (b) wild type amino acid is included within the library. These redundancies increase library size and downstream screening efforts. Here, we present a dynamic approach to compress codons for any desired list of amino acids, taking into account codon usage. This results in a unique codon collection for every amino acid to be mutated, with the desired redundancy level. Finally, we demonstrate that this approach can be used to design precise oligo libraries amendable to recombineering and CRISPR-based genome editing to obtain a diverse population with high efficiency. PMID:25303315

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

    PubMed Central

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

    2001-01-01

    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

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

    SciTech Connect

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

    1987-05-01

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

  13. Translation initiation factor eIF3 promotes programmed stop codon readthrough

    PubMed Central

    Beznosková, Petra; Wagner, Susan; Jansen, Myrte Esmeralda; von der Haar, Tobias; Valášek, Leoš Shivaya

    2015-01-01

    Programmed stop codon readthrough is a post-transcription regulatory mechanism specifically increasing proteome diversity by creating a pool of C-terminally extended proteins. During this process, the stop codon is decoded as a sense codon by a near-cognate tRNA, which programs the ribosome to continue elongation. The efficiency of competition for the stop codon between release factors (eRFs) and near-cognate tRNAs is largely dependent on its nucleotide context; however, the molecular mechanism underlying this process is unknown. Here, we show that it is the translation initiation (not termination) factor, namely eIF3, which critically promotes programmed readthrough on all three stop codons. In order to do so, eIF3 must associate with pre-termination complexes where it interferes with the eRF1 decoding of the third/wobble position of the stop codon set in the unfavorable termination context, thus allowing incorporation of near-cognate tRNAs with a mismatch at the same position. We clearly demonstrate that efficient readthrough is enabled by near-cognate tRNAs with a mismatch only at the third/wobble position. Importantly, the eIF3 role in programmed readthrough is conserved between yeast and humans. PMID:25925566

  14. Efficient Reassignment of a Frequent Serine Codon in Wild-Type Escherichia coli.

    PubMed

    Ho, Joanne M; Reynolds, Noah M; Rivera, Keith; Connolly, Morgan; Guo, Li-Tao; Ling, Jiqiang; Pappin, Darryl J; Church, George M; Söll, Dieter

    2016-02-19

    Expansion of the genetic code through engineering the translation machinery has greatly increased the chemical repertoire of the proteome. This has been accomplished mainly by read-through of UAG or UGA stop codons by the noncanonical aminoacyl-tRNA of choice. While stop codon read-through involves competition with the translation release factors, sense codon reassignment entails competition with a large pool of endogenous tRNAs. We used an engineered pyrrolysyl-tRNA synthetase to incorporate 3-iodo-l-phenylalanine (3-I-Phe) at a number of different serine and leucine codons in wild-type Escherichia coli. Quantitative LC-MS/MS measurements of amino acid incorporation yields carried out in a selected reaction monitoring experiment revealed that the 3-I-Phe abundance at the Ser208AGU codon in superfolder GFP was 65 ± 17%. This method also allowed quantification of other amino acids (serine, 33 ± 17%; phenylalanine, 1 ± 1%; threonine, 1 ± 1%) that compete with 3-I-Phe at both the aminoacylation and decoding steps of translation for incorporation at the same codon position. Reassignments of different serine (AGU, AGC, UCG) and leucine (CUG) codons with the matching tRNA(Pyl) anticodon variants were met with varying success, and our findings provide a guideline for the choice of sense codons to be reassigned. Our results indicate that the 3-iodo-l-phenylalanyl-tRNA synthetase (IFRS)/tRNA(Pyl) pair can efficiently outcompete the cellular machinery to reassign select sense codons in wild-type E. coli.

  15. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.

    PubMed

    Napolitano, Michael G; Landon, Matthieu; Gregg, Christopher J; Lajoie, Marc J; Govindarajan, Lakshmi; Mosberg, Joshua A; Kuznetsov, Gleb; Goodman, Daniel B; Vargas-Rodriguez, Oscar; Isaacs, Farren J; Söll, Dieter; Church, George M

    2016-09-20

    The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 "recalcitrant" AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional "safe replacement zone" (SRZ) within which alternative codons are more likely to be viable. To evaluate synonymous and nonsynonymous alternatives to essential AGRs further, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild-type allele, allowing us to evaluate exhaustively the fitness impact of all 64 codon alternatives. Using this method, we confirmed the relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes.

  16. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.

    PubMed

    Napolitano, Michael G; Landon, Matthieu; Gregg, Christopher J; Lajoie, Marc J; Govindarajan, Lakshmi; Mosberg, Joshua A; Kuznetsov, Gleb; Goodman, Daniel B; Vargas-Rodriguez, Oscar; Isaacs, Farren J; Söll, Dieter; Church, George M

    2016-09-20

    The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 "recalcitrant" AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional "safe replacement zone" (SRZ) within which alternative codons are more likely to be viable. To evaluate synonymous and nonsynonymous alternatives to essential AGRs further, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild-type allele, allowing us to evaluate exhaustively the fitness impact of all 64 codon alternatives. Using this method, we confirmed the relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes. PMID:27601680

  17. Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli

    PubMed Central

    Napolitano, Michael G.; Landon, Matthieu; Gregg, Christopher J.; Lajoie, Marc J.; Govindarajan, Lakshmi; Mosberg, Joshua A.; Kuznetsov, Gleb; Goodman, Daniel B.; Vargas-Rodriguez, Oscar; Isaacs, Farren J.; Söll, Dieter; Church, George M.

    2016-01-01

    The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 “recalcitrant” AGRs required diversification to identify viable alternatives. Successful replacement codons tended to conserve local ribosomal binding site-like motifs and local mRNA secondary structure, sometimes at the expense of amino acid identity. Based on these observations, we empirically defined metrics for a multidimensional “safe replacement zone” (SRZ) within which alternative codons are more likely to be viable. To evaluate synonymous and nonsynonymous alternatives to essential AGRs further, we implemented a CRISPR/Cas9-based method to deplete a diversified population of a wild-type allele, allowing us to evaluate exhaustively the fitness impact of all 64 codon alternatives. Using this method, we confirmed the relevance of the SRZ by tracking codon fitness over time in 14 different genes, finding that codons that fall outside the SRZ are rapidly depleted from a growing population. Our unbiased and systematic strategy for identifying unpredicted design flaws in synthetic genomes and for elucidating rules governing codon choice will be crucial for designing genomes exhibiting radically altered genetic codes. PMID:27601680

  18. ic-cmtp3: 3rd International Conference on Competitive Materials and Technology Processes

    NASA Astrophysics Data System (ADS)

    2016-04-01

    Competitiveness is one of the most important factors in our lives and it plays a key role in the efficiency both of organizations and societies. The more scientifically advanced and prepared organizations develop more competitive materials with better physical, chemical, and biological properties, and the leading companies apply more competitive equipment and technological processes. The aims of the 3rd International Conference on Competitive Materials and Technology Processes (ic-cmtp3), and the 1st International Symposium on Innovative Carbons and Carbon Based Materials (is-icbm1) and the 1st International Symposium on Innovative Construction Materials (is-icm1) organized alongside are the following: —Promote new methods and results of scientific research in the fields of material, biological, environmental and technological sciences; —Exchange information between the theoretical and applied sciences as well as technical and technological implementations; —Promote communication and collaboration between the scientists, researchers and engineers of different nations, countries and continents. Among the major fields of interest are advanced and innovative materials with competitive characteristics, including mechanical, physical, chemical, biological, medical and thermal, properties and extreme dynamic strength. Their crystalline, nano - and micro-structures, phase transformations as well as details of their technological processes, tests and measurements are also in the focus of the ic-cmtp3 conference and the is-scbm1 and is-icm1 symposia. Multidisciplinary applications of material science and the technological problems encountered in sectors like ceramics, glasses, thin films, aerospace, automotive and marine industries, electronics, energy, construction materials, medicine, biosciences and environmental sciences are of particular interest. In accordance with the program of the ic-cmtp3 conference and is-icbm1 and is-icm1 symposia we have received more

  19. PREFACE: 3rd International Workshop on "State of the Art in Nuclear Cluster Physics"

    NASA Astrophysics Data System (ADS)

    Yamada, Taiichi; Kanada-En'yo, Yoshiko

    2014-12-01

    The 3rd International Workshop on "State of the Art in Nuclear Cluster Physics"(SOTANCP3) was held at KGU Kannai Media Center, Kanto Gakuin University, Yokohama, Japan, from May 26 to 30, 2014. Yokohama is the second largest city in Japan, about 25 km southeast of Tokyo. The first workshop of the series was held in Strasbourg, France, in 2008 and the second one was in Brussels, Belgium, in 2010. The purpose of SOTANCP3 was to discuss the present status and future perspectives of the nuclear cluster physics. The following nine topics were selected in order to cover most of the scientific programme and highlight an area where new ideas have emerged over recent years: (1) Cluster structures and many-body correlations in stable and unstable nuclei (2) Clustering aspects of nuclear reactions and resonances (3) Alpha condensates and analogy with condensed matter approaches (4) Role of tensor force in cluster physics and ab initio approaches (5) Clustering in hypernuclei (6) Nuclear fission, superheavy nuclei, and cluster decay (7) Cluster physics and nuclear astrophysics (8) Clustering in nuclear matter and neutron stars (9) Clustering in hadron and atomic physics There were 122 participants, including 53 from 17 foreign countries. In addition to invited talks, we had many talks selected from contributed papers. There were plenary, parallel, and poster sessions. Poster contributions were also presented as four-minute talks in parallel sessions. This proceedings contains the papers presented in invited and selected talks together with those presented in poster sessions. We would like to express our gratitude to the members of the International Advisory Committee and those of the Organizing Committee for their efforts which made this workshop successful. In particular we would like to present our great thanks to Drs. Y. Funaki, W. Horiuchi, N. Itagaki, M. Kimura, T. Myo, and T. Yoshida. We would like also to thank the following organizations for their sponsors: RCNP

  20. PREFACE: 3rd International Workshop on Statistical Physics and Mathematics for Complex Systems (SPMCS 2012)

    NASA Astrophysics Data System (ADS)

    Tayurskii, Dmitrii; Abe, Sumiyoshi; Alexandre Wang, Q.

    2012-11-01

    The 3rd International Workshop on Statistical Physics and Mathematics for Complex Systems (SPMCS2012) was held between 25-30 August at Kazan (Volga Region) Federal University, Kazan, Russian Federation. This workshop was jointly organized by Kazan Federal University and Institut Supérieur des Matériaux et Mécaniques Avancées (ISMANS), France. The series of SPMCS workshops was created in 2008 with the aim to be an interdisciplinary incubator for the worldwide exchange of innovative ideas and information about the latest results. The first workshop was held at ISMANS, Le Mans (France) in 2008, and the third at Huazhong Normal University, Wuhan (China) in 2010. At SPMCS2012, we wished to bring together a broad community of researchers from the different branches of the rapidly developing complexity science to discuss the fundamental theoretical challenges (geometry/topology, number theory, statistical physics, dynamical systems, etc) as well as experimental and applied aspects of many practical problems (condensed matter, disordered systems, financial markets, chemistry, biology, geoscience, etc). The program of SPMCS2012 was prepared based on three categories: (i) physical and mathematical studies (quantum mechanics, generalized nonequilibrium thermodynamics, nonlinear dynamics, condensed matter physics, nanoscience); (ii) natural complex systems (physical, geophysical, chemical and biological); (iii) social, economical, political agent systems and man-made complex systems. The conference attracted 64 participants from 10 countries. There were 10 invited lectures, 12 invited talks and 28 regular oral talks in the morning and afternoon sessions. The book of Abstracts is available from the conference website (http://www.ksu.ru/conf/spmcs2012/?id=3). A round table was also held, the topic of which was 'Recent and Anticipated Future Progress in Science of Complexity', discussing a variety of questions and opinions important for the understanding of the concept of

  1. SESAME - A 3rd Generation Synchrotron Light Source for the Middle East

    SciTech Connect

    Ulkue, Dincer; Rahighi, Javad; Winick, Herman

    2007-01-19

    SESAME (Synchrotron-light for Experimental Science and Applications in the Middle East) will be the Middle East's first international research center. It is a cooperative venture by the scientists and governments of the region with founding members Bahrain, Egypt, Israel, Jordan, Pakistan, Palestine Authority, and Turkey. Iran is in the process of finalizing its formal membership. Other countries (Cyprus, Morocco, and the United Arab Emirates) are also expected to join. The permanent Council of member states has full responsibility for the project. Members provide the annual operating budget. Observer countries are Germany, Greece, Italy, Kuwait, Portugal, Russian Federation, Sweden, the UK, and the US. SESAME is being developed under the umbrella of UNESCO. Jordan was selected as the building site. SESAME will offer excellent opportunities for training of Middle East scientists and attract those working abroad to consider returning. SESAME will be a 2.5GeV 3rd Generation light source (emittance 26nm-rad, circumference {approx}133m), providing excellent performance for structural molecular biology, molecular environmental science, surface and interface science, microelectromechanical devices, x-ray imaging, archaeological microanalysis, and materials characterization. It will cover a broad spectral range from the infrared to hard x-rays and will have 12 straight sections for insertion devices (average length 2.75m). The injector will be the BESSY I 0.8 GeV booster synchrotron which has been given as a gift from Germany. Four committees advise the Council and assist in developing the technical design, beam lines, user community, and scientific Program. The SESAME building, now in construction with funds and a site provided by Jordan, is scheduled for completion in late 2006 after which the BESSY I injector will be installed. First stored beam in the new 2.5 GeV ring is planned for 2009 with six initial beamlines planned. Some beamlines will be built by member

  2. Building monument materials during the 3rd-4rd millennium (Portugal)

    NASA Astrophysics Data System (ADS)

    Moita, Patricia; Pedro, Jorge; Boaventura, Rui; Mataloto, Rui; Maximo, Jaime; Almeida, Luís; Nogueira, Pedro

    2014-05-01

    Dolmens are the most conspicuous remains of the populations of the 4th and first half of 3rd millennia BCE. These tombs are impressive not only for their monumentality, but also because of the socioeconomic investment they represent for those Neolithic communities, namely from the Central-South of Portugal, who built them. Although dolmens have been studied for their funerary content and typologies, an interdisciplinary approach toward the geological characterization and sourcing of stones used in these constructions has not received enough attention from researchers. With MEGAGEO project a multidisciplinary group of geologist and archaeologists intends to assess the relationship between the distribution of dolmens in Central-South Portugal, their source materials, and the geological landscape. GIS will map the information gathered and will be used to analyse these relationships. The selection of the areas, with distinctive geologies (limestone vs granite), will allow to verify if human patterns of behaviour regarding the selection of megaliths are similar or different regionally. Geologically the first target area (Freixo, Alentejo) is dominated by a small intrusion of gabbro mingled/mixed within a granodioritic intrusion both related with variscan orogeny. Granodiorite exhibit several enclaves of igneous and metamorphic nature attesting the interaction between both igneous rocks as well with enclosing gneisses. Despite Alentejo region have a reduced number of outcrops the granodiorite provides rounded to tabular metric blocks. The gabbro is very coarse grained, sometimes with a cumulate texture, and their fracturing and weathering provide very fresh tabular blocks. The five studied dolmens (Quinta do Freixo #1 to #5) are implanted in a large granodioritic intrusion, around the gabbroic rocks, within an area of approximately 9km2. The medium grained granodiorite is ubiquity in all the dolmens slabs and occasionally it can be observed features of mixing and

  3. OmniChange: The Sequence Independent Method for Simultaneous Site-Saturation of Five Codons

    PubMed Central

    Marienhagen, Jan; Schwaneberg, Ulrich

    2011-01-01

    Focused mutant library generation methods have been developed to improve mainly “localizable” enzyme properties such as activity and selectivity. Current multi-site saturation methods are restricted by the gene sequence, require subsequent PCR steps and/or additional enzymatic modifications. Here we report, a multiple site saturation mutagenesis method, OmniChange, which simultaneously and efficiently saturates five independent codons. As proof of principle, five chemically cleaved DNA fragments, each carrying one NNK-degenerated codon, were generated and assembled to full gene length in a one-pot-reaction without additional PCR-amplification or use of restriction enzymes or ligases. Sequencing revealed the presence of up to 27 different codons at individual positions, corresponding to 84.4% of the theoretical diversity offered by NNK-degeneration. OmniChange is absolutely sequence independent, does not require a minimal distance between mutated codons and can be accomplished within a day. PMID:22039444

  4. Additional circular intercostal space created by bifurcation of the left 3rd rib and its costal cartilage: a case report

    PubMed Central

    2013-01-01

    Introduction In the thorax there are normally 11 pairs of intercostal spaces: the spaces between adjacent ribs. The intercostal spaces contain intercostal muscles, intercostal nerves and vessels. Case presentation During a routine dissection for undergraduate medical students, we observed a variation involving the left 3rd rib and 3rd costal cartilage in the cadaver of a man of Indian ethnicity aged about 65 years. The left 3rd rib and its costal cartilage were bifurcated at their costochondral junction enclosing a small circular additional intercostal space. Muscle tissue covered by deep fascia was present in this circular intercostal space. The muscle in the circular intercostal space received its nerve supply from a branch of the 2nd intercostal nerve. Conclusions Knowledge of such variations is helpful to surgeons operating on the anterior thoracic wall involving ribs and intercostal spaces. Knowing the possibility of the presence of an additional space between normal intercostal spaces can guide a surgeon through to a successful surgery. PMID:23298541

  5. The effect of surgical technique on lingual nerve damage during lower 3rd molar removal by dental students.

    PubMed

    Robinson, P P; Loescher, A R; Smith, K G

    1999-05-01

    We have previously shown that avoidance of lingual flap retraction with a Howarth periosteal elevator during lower 3rd molar removal, reduces the incidence of lingual nerve damage. In that study, the surgery was undertaken by qualified staff and we have now assessed the effect of revising the method taught to our junior undergraduate dental students. We evaluated the outcome of surgery undertaken by 2 consecutive years of students, each group being taught 1 of the 2 methods. A total of 200 patients requiring lower 3rd molar removal under local anaesthesia were included in the study. In year 1, the surgery included elevation of a lingual flap and insertion of a Howarth elevator adjacent to the lingual plate; in year 2 this part of the procedure was avoided by using a purely buccal approach. There were no significant differences between the levels of tooth eruption and types of impaction of the teeth removed in each year. Lingual sensory disturbance occurred in 3 patients in the 'flap' group (3.3%) and in 1 patient (0.9%) in the 'no flap' group. As this incidence is not significantly different in the 2 groups (P < 0.4), we conclude that avoidance of lingual retraction by students undertaking lower 3rd molar removal does not appear to place the lingual nerve at greater risk. In view of the results of our previous study, we therefore advocate this method for use in undergraduate dental education. PMID:10530161

  6. Nucleotide sequence conservation in paramyxoviruses; the concept of codon constellation.

    PubMed

    Rima, Bert K

    2015-05-01

    The stability and conservation of the sequences of RNA viruses in the field and the high error rates measured in vitro are paradoxical. The field stability indicates that there are very strong selective constraints on sequence diversity. The nature of these constraints is discussed. Apart from constraints on variation in cis-acting RNA and the amino acid sequences of viral proteins, there are other ones relating to the presence of specific dinucleotides such CpG and UpA as well as the importance of RNA secondary structures and RNA degradation rates. Recent other constraints identified in other RNA viruses, such as effects of secondary RNA structure on protein folding or modification of cellular tRNA complements, are also discussed. Using the family Paramyxoviridae, I show that the codon usage pattern (CUP) is (i) specific for each virus species and (ii) that it is markedly different from the host - it does not vary even in vaccine viruses that have been derived by passage in a number of inappropriate host cells. The CUP might thus be an additional constraint on variation, and I propose the concept of codon constellation to indicate the informational content of the sequences of RNA molecules relating not only to stability and structure but also to the efficiency of translation of a viral mRNA resulting from the CUP and the numbers and position of rare codons.

  7. SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage

    PubMed Central

    Pouyet, Fanny; Bailly-Bechet, Marc; Mouchiroud, Dominique; Guéguen, Laurent

    2016-01-01

    Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences. PMID:27401173

  8. SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage.

    PubMed

    Pouyet, Fanny; Bailly-Bechet, Marc; Mouchiroud, Dominique; Guéguen, Laurent

    2016-01-01

    Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences.

  9. SENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage.

    PubMed

    Pouyet, Fanny; Bailly-Bechet, Marc; Mouchiroud, Dominique; Guéguen, Laurent

    2016-01-01

    Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences. PMID:27401173

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

    PubMed Central

    Xia, Xuhua

    2015-01-01

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

  11. Does 3rd Age + 3rd World = 3rd Class?

    ERIC Educational Resources Information Center

    Tout, Ken

    1992-01-01

    Demographic changes, migration, and industrialization are having drastic effects on older adults in developing nations. Local programs such as Pro Vida in Colombia, supported by Help Age International, rely on the support of volunteers to improve the quality of life for elderly people. (SK)

  12. CodonExplorer: an interactive online database for the analysis of codon usage and sequence composition.

    PubMed

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

    2009-01-01

    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.

  13. Experimentally Increased Codon Bias in the Drosophila Adh Gene Leads to an Increase in Larval, But Not Adult, Alcohol Dehydrogenase Activity

    PubMed Central

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

    2010-01-01

    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

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

    PubMed

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

    2010-02-01

    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.

  15. PREFACE: 3rd International Workshop on Materials Analysis and Processing in Magnetic Fields (MAP3)

    NASA Astrophysics Data System (ADS)

    Sakka, Yoshio; Hirota, Noriyuki; Horii, Shigeru; Ando, Tsutomu

    2009-07-01

    The 3rd International Workshop on Materials Analysis and Processing in Materials Fields (MAP3) was held on 14-16 May 2008 at the University of Tokyo, Japan. The first was held in March 2004 at the National High Magnetic Field Laboratory in Tallahassee, USA. Two years later the second took place in Grenoble, France. MAP3 was held at The University of Tokyo International Symposium, and jointly with MANA Workshop on Materials Processing by External Stimulation, and JSPS CORE Program of Construction of the World Center on Electromagnetic Processing of Materials. At the end of MAP3 it was decided that the next MAP4 will be held in Atlanta, USA in 2010. Processing in magnetic fields is a rapidly expanding research area with a wide range of promising applications in materials science. MAP3 focused on the magnetic field interactions involved in the study and processing of materials in all disciplines ranging from physics to chemistry and biology: Magnetic field effects on chemical, physical, and biological phenomena Magnetic field effects on electrochemical phenomena Magnetic field effects on thermodynamic phenomena Magnetic field effects on hydrodynamic phenomena Magnetic field effects on crystal growth Magnetic processing of materials Diamagnetic levitation Magneto-Archimedes effect Spin chemistry Application of magnetic fields to analytical chemistry Magnetic orientation Control of structure by magnetic fields Magnetic separation and purification Magnetic field-induced phase transitions Materials properties in high magnetic fields Development of NMR and MRI Medical application of magnetic fields Novel magnetic phenomena Physical property measurement by Magnetic fields High magnetic field generation> MAP3 consisted of 84 presentations including 16 invited talks. This volume of Journal of Physics: Conference Series contains the proceeding of MAP3 with 34 papers that provide a scientific record of the topics covered by the conference with the special topics (13 papers) in

  16. FOREWORD: 3rd International Workshop on New Computational Methods for Inverse Problems (NCMIP 2013)

    NASA Astrophysics Data System (ADS)

    Blanc-Féraud, Laure; Joubert, Pierre-Yves

    2013-10-01

    Conference logo This volume of Journal of Physics: Conference Series is dedicated to the scientific contributions presented during the 3rd International Workshop on New Computational Methods for Inverse Problems, NCMIP 2013 (http://www.farman.ens-cachan.fr/NCMIP_2013.html). This workshop took place at Ecole Normale Supérieure de Cachan, in Cachan, France, on 22 May 2013, at the initiative of Institut Farman. The prior editions of NCMIP also took place in Cachan, France, firstly within the scope of the ValueTools Conference, in May 2011 (http://www.ncmip.org/2011/), and secondly at the initiative of Institut Farman, in May 2012 (http://www.farman.ens-cachan.fr/NCMIP_2012.html). The NCMIP Workshop focused on recent advances in the resolution of inverse problems. Indeed inverse problems appear in numerous scientific areas such as geophysics, biological and medical imaging, material and structure characterization, electrical, mechanical and civil engineering, and finances. The resolution of inverse problems consists of estimating the parameters of the observed system or structure from data collected by an instrumental sensing or imaging device. Its success firstly requires the collection of relevant observation data. It also requires accurate models describing the physical interactions between the instrumental device and the observed system, as well as the intrinsic properties of the solution itself. Finally, it requires the design of robust, accurate and efficient inversion algorithms. Advanced sensor arrays and imaging devices provide high rate and high volume data; in this context, the efficient resolution of the inverse problem requires the joint development of new models and inversion methods, taking computational and implementation aspects into account. During this one-day workshop, researchers had the opportunity to bring to light and share new techniques and results in the field of inverse problems. The topics of the workshop were: algorithms and computational

  17. PREFACE: 3rd Workshop on Theory, Modelling and Computational Methods for Semiconductors (TMCSIII)

    NASA Astrophysics Data System (ADS)

    Califano, Marco; Migliorato, Max; Probert, Matt

    2012-05-01

    These conference proceedings contain the written papers of the contributions presented at the 3rd International Conference on Theory, Modelling and Computational Methods for Semiconductor materials and nanostructures. The conference was held at the School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK on 18-20 January 2012. The previous conferences in this series took place in 2010 at St William's College, York and in 2008 at the University of Manchester, UK. The development of high-speed computer architectures is finally allowing the routine use of accurate methods for calculating the structural, thermodynamic, vibrational, optical and electronic properties of semiconductors and their hetero- and nano-structures. The scope of this conference embraces modelling, theory and the use of sophisticated computational tools in semiconductor science and technology, where there is substantial potential for time-saving in R&D. Theoretical approaches represented in this meeting included: Density Functional Theory, Tight Binding, Semiempirical Pseudopotential Methods, Effective Mass Models, Empirical Potential Methods and Multiscale Approaches. Topics included, but were not limited to: Optical and Transport Properties of Quantum Nanostructures including Colloids and Nanotubes, Plasmonics, Magnetic Semiconductors, Graphene, Lasers, Photonic Structures, Photovoltaic and Electronic Devices. This workshop ran for three days, with the objective of bringing together UK and international leading experts in the theoretical modelling of Group IV, III-V and II-VI semiconductors, as well as students, postdocs and early-career researchers. The first day focused on providing an introduction and overview of this vast field, aimed particularly at students, with several lectures given by recognised experts in various theoretical approaches. The following two days showcased some of the best theoretical research carried out in the UK in this field, with several

  18. Hand gesture recognition by analysis of codons

    NASA Astrophysics Data System (ADS)

    Ramachandra, Poornima; Shrikhande, Neelima

    2007-09-01

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

  19. An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes

    PubMed Central

    Nielsen, Henrik; Wernersson, Rasmus

    2006-01-01

    Background A knowledge of the positions of introns in eukaryotic genes is important for understanding the evolution of introns. Despite this, there has been relatively little focus on the distribution of intron positions in genes. Results In proteins with signal peptides, there is an overabundance of phase 1 introns around the region of the signal peptide cleavage site. This has been described before. But in proteins without signal peptides, a novel phenomenon is observed: There is a sharp peak of phase 0 intron positions immediately following the start codon, i.e. between codons 1 and 2. This effect is seen in a wide range of eukaryotes: Vertebrates, arthropods, fungi, and flowering plants. Proteins carrying this start codon intron are found to comprise a special class of relatively short, lysine-rich and conserved proteins with an overrepresentation of ribosomal proteins. In addition, there is a peak of phase 0 introns at position 5 in Drosophila genes with signal peptides, predominantly representing cuticle proteins. Conclusion There is an overabundance of phase 0 introns immediately after the start codon in eukaryotic genes, which has been described before only for human ribosomal proteins. We give a detailed description of these start codon introns and the proteins that contain them. PMID:17034638

  20. Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria

    PubMed Central

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

    2016-01-01

    The different triplets encoding the same amino acid, termed as synonymous codons, are not equally abundant in a genome. Factors such as G + C% and tRNA are known to influence their abundance in a genome. However, the order of the nucleotide in each codon per se might also be another factor impacting on its abundance values. Of the synonymous codons for specific amino acids, some are preferentially used in the high expression genes that are referred to as the ‘optimal codons’ (OCs). In this study, we compared OCs of the 18 amino acids in 221 species of bacteria. It is observed that there is amino acid specific influence for the selection of OCs. There is also influence of phylogeny in the choice of OCs for some amino acids such as Glu, Gln, Lys and Leu. The phenomenon of codon bias is also supported by the comparative studies of the abundance values of the synonymous codons with same G + C. It is likely that the order of the nucleotides in the triplet codon is also perhaps involved in the phenomenon of codon usage bias in organisms. PMID:27426467

  1. DHX29 reduces leaky scanning through an upstream AUG codon regardless of its nucleotide context

    PubMed Central

    Pisareva, Vera P.; Pisarev, Andrey V.

    2016-01-01

    During eukaryotic translation initiation, the 43S preinitiation complex (43S PIC), consisting of the 40S ribosomal subunit, eukaryotic initiation factors (eIFs) and initiator tRNA scans mRNA to find an appropriate start codon. Key roles in the accuracy of initiation codon selection belong to eIF1 and eIF1A, whereas the mammalian-specific DHX29 helicase substantially contributes to ribosomal scanning of structured mRNAs. Here, we show that DHX29 stimulates the recognition of the AUG codon but not the near-cognate CUG codon regardless of its nucleotide context during ribosomal scanning. The stimulatory effect depends on the contact between DHX29 and eIF1A. The unique DHX29 N-terminal domain binds to the ribosomal site near the mRNA entrance, where it contacts the eIF1A OB domain. UV crosslinking assays revealed that DHX29 may rearrange eIF1A and eIF2α in key nucleotide context positions of ribosomal complexes. Interestingly, DHX29 impedes the 48S initiation complex formation in the absence of eIF1A perhaps due to forming a physical barrier that prevents the 43S PIC from loading onto mRNA. Mutational analysis allowed us to split the mRNA unwinding and codon selection activities of DHX29. Thus, DHX29 is another example of an initiation factor contributing to start codon selection. PMID:27067542

  2. Analysis of Codon Usage Patterns in Herbaceous Peony (Paeonia lactiflora Pall.) Based on Transcriptome Data

    PubMed Central

    Wu, Yanqing; Zhao, Daqiu; Tao, Jun

    2015-01-01

    Codon usage bias, which exists in many genomes, is mainly determined by mutation and selection. To elucidate the genetic features and evolutionary history of herbaceous peony (Paeonia lactiflora), a well-known symbol of prosperity in China, we examined synonymous codon usage in 24,216 reconstructed genes from the P. lactiflora transcriptome. The mean GC content was 44.4%, indicating that the nucleotide content of P. lactiflora genes is slightly AT rich and GC poor. The P. lactiflora genome has a wide range of GC3 (GC content at the third synonymous codon position) distribution, with a significant correlation between GC12 and GC3. ENC (effective number of codons) analysis suggested that mutational bias played a major role in shaping codon usage. Parity Rule 2 (PR2) analysis revealed that GC and AU were not used proportionally. We identified 22 “optimal codons”, most ending with an A or U. Our results suggested that nucleotide composition mutation bias and translational selection were the main driving factors of codon usage bias in P. lactiflora. These results lay the foundation for exploring the evolutionary mechanisms and heterologous expression of functionally-important proteins in P. lactiflora. PMID:26506393

  3. Codon usage biases of transposable elements and host nuclear genes in Arabidopsis thaliana and Oryza sativa.

    PubMed

    Jia, Jia; Xue, Qingzhong

    2009-12-01

    Transposable elements (TEs) are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of Oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa (r=0.944 and 0.839, respectively, P<0.0001) but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species. PMID:20172490

  4. Codon usage biases of transposable elements and host nuclear genes in Arabidopsis thaliana and Oryza sativa.

    PubMed

    Jia, Jia; Xue, Qingzhong

    2009-12-01

    Transposable elements (TEs) are mobile genetic entities ubiquitously distributed in nearly all genomes. High frequency of codons ending in A/T in TEs has been previously observed in some species. In this study, the biases in nucleotide composition and codon usage of TE transposases and host nuclear genes were investigated in the AT-rich genome of Arabidopsis thaliana and the GC-rich genome of Oryza sativa. Codons ending in A/T are more frequently used by TEs compared with their host nuclear genes. A remarkable positive correlation between highly expressed nuclear genes and C/G-ending codons were detected in O. sativa (r=0.944 and 0.839, respectively, P<0.0001) but not in A. thaliana, indicating a close association between the GC content and gene expression level in monocot species. In both species, TE codon usage biases are similar to that of weakly expressed genes. The expression and activity of TEs may be strictly controlled in plant genomes. Mutation bias and selection pressure have simultaneously acted on the TE evolution in A. thaliana and O. sativa. The consistently observed biases of nucleotide composition and codon usage of TEs may also provide a useful clue to accurately detect TE sequences in different species.

  5. Optimal codons in Tremella fuciformis end in C/G, a strong difference with known Tremella species.

    PubMed

    Deng, Youjin; Huang, Xiaoxing; Ruan, Banzhan; Xie, Baogui; van Peer, Arend Frans; Jiang, Yuji

    2015-11-01

    Tremella fuciformis is a popular edible fungus with fruiting bodies that can be produced in large quantities at low costs, while it is easy to transform and cultivate as yeast. This makes it an attractive potential bioreactor. Enhanced heterologous gene expression through codon optimization would be useful, but until now codon usage preferences in T. fuciformis remain unknown. To precisely determine the preferred codon usage of T. fuciformis we sequenced the genome of strain Tr26 resulting in a 24.2 Mb draft genome with 10,040 predicted genes. 3288 of the derived predicted proteins matched the UniProtKB/Swiss-Prot databases with 40% or more similarity. Corresponding gene models of this subset were subsequently optimized through repetitive comparison of alternative start codons and selection of best length matching gene models. For experimental confirmation of gene models, 96 random clones from an existing T. fuciformis cDNA library were sequenced, generating 80 complete CDSs. Calculated optimal codons for the 3288 predicted and the 80 cloned CDSs were highly similar, indicating sufficient accuracy of predicted gene models for codon usage analysis. T. fuciformis showed a strong preference for C and then G at the third base pair position of used codons, while average GC content of predicted genes was slightly higher than the total genome sequence average. Most optimal codons ended in C or G except for one, and an increased frequency of C ending codons was observed in genes with higher expression levels. Surprisingly, the preferred codon usage in T. fuciformis strongly differed from T. mesenterica and C. neoformans. Instead, optimal codon usage was similar to more distant related species such as Ustilago maydis and Neurospora crassa. Despite much higher overall sequence homology between T. fuciformis and T. mesenterica, only 7 out of 21 optimal codons were equal, whereas T. fuciformis shared up to 20 out of 21 optimal codons with other species. Clearly, codon usage in

  6. Preparation of an ochre suppressor tRNA recognizing exclusively UAA codon by using the molecular surgery technique.

    PubMed

    Yokogawa, Takashi; Hassan, Hanim Munirah Binti Che; Yokota, Yukiko; Ohno, Satoshi; Nishikawa, Kazuya

    2009-01-01

    In order to create an ochre suppressor tRNA which exclusively recognizes UAA codon, we replaced the G34 at the first position of yeast tRNA(Tyr)[GPsiA] anticodon with pseudouridine34 (Psi34) by using the molecular surgery technique. This tRNA(Tyr)[PsiPsiA] recognized only the UAA codon as expectedly, but tRNA(Tyr)[UPsiA] made as a control also behaved similarly. This result may suggest that U34 must be somehow modified to facilitate the wobble-pairing to G at the third position of codon. PMID:19749377

  7. FOREWORD: 3rd International Workshop on New Computational Methods for Inverse Problems (NCMIP 2013)

    NASA Astrophysics Data System (ADS)

    Blanc-Féraud, Laure; Joubert, Pierre-Yves

    2013-10-01

    Conference logo This volume of Journal of Physics: Conference Series is dedicated to the scientific contributions presented during the 3rd International Workshop on New Computational Methods for Inverse Problems, NCMIP 2013 (http://www.farman.ens-cachan.fr/NCMIP_2013.html). This workshop took place at Ecole Normale Supérieure de Cachan, in Cachan, France, on 22 May 2013, at the initiative of Institut Farman. The prior editions of NCMIP also took place in Cachan, France, firstly within the scope of the ValueTools Conference, in May 2011 (http://www.ncmip.org/2011/), and secondly at the initiative of Institut Farman, in May 2012 (http://www.farman.ens-cachan.fr/NCMIP_2012.html). The NCMIP Workshop focused on recent advances in the resolution of inverse problems. Indeed inverse problems appear in numerous scientific areas such as geophysics, biological and medical imaging, material and structure characterization, electrical, mechanical and civil engineering, and finances. The resolution of inverse problems consists of estimating the parameters of the observed system or structure from data collected by an instrumental sensing or imaging device. Its success firstly requires the collection of relevant observation data. It also requires accurate models describing the physical interactions between the instrumental device and the observed system, as well as the intrinsic properties of the solution itself. Finally, it requires the design of robust, accurate and efficient inversion algorithms. Advanced sensor arrays and imaging devices provide high rate and high volume data; in this context, the efficient resolution of the inverse problem requires the joint development of new models and inversion methods, taking computational and implementation aspects into account. During this one-day workshop, researchers had the opportunity to bring to light and share new techniques and results in the field of inverse problems. The topics of the workshop were: algorithms and computational

  8. Tunnelling of the 3rd kind: A test of the effective non-locality of quantum field theory

    NASA Astrophysics Data System (ADS)

    Gardiner, Simon A.; Gies, Holger; Jaeckel, Joerg; Wallace, Chris J.

    2013-03-01

    Integrating out virtual quantum fluctuations in an originally local quantum field theory results in an effective theory which is non-local. In this letter we argue that tunnelling of the 3rd kind —where particles traverse a barrier by splitting into a pair of virtual particles which recombine only after a finite distance— provides a direct test of this non-locality. We sketch a quantum-optical setup to test this effect, and investigate observable effects in a simple toy model.

  9. Synthetic Gene Design Using Codon Optimization On-Line (COOL).

    PubMed

    Yu, Kai; Ang, Kok Siong; Lee, Dong-Yup

    2017-01-01

    Codon optimization has been widely used for designing native or synthetic genes to enhance their expression in heterologous host organisms. We recently developed Codon Optimization On-Line (COOL) which is a web-based tool to provide multi-objective codon optimization functionality for synthetic gene design. COOL provides a simple and flexible interface for customizing codon optimization based on several design parameters such as individual codon usage, codon pairing, and codon adaptation index. User-defined sequences can also be compared against the COOL optimized ones to show the extent by which the user's sequences can be evaluated and further improved. The utility of COOL is demonstrated via a case study where the codon optimized sequence of an invertase enzyme is generated for the enhanced expression in E. coli. PMID:27671929

  10. VizieR Online Data Catalog: Catalog of Infrared observations, 3rd Edition (Gezari+ 1993)

    NASA Astrophysics Data System (ADS)

    Gezari, D. Y.; Schmitz, M.; Pitts, P. S.; Mead, J. M.

    1994-03-01

    The Catalog of Infrared Observations and its associated data base comprise a summary of infrared astronomical observations published in the scientific literature from 1965 through 1990 in the wavelength range 1 micrometer - 1 mm. The database contains infrared observational data for sources outside the Solar System, constructed through a search of the most active scientific journals, IR surveys and catalogs. To date, about 4500 journal articles and 10 major survey catalogs have been included in the data base, which contains more than 205000 individual observations of about 11500 different infrared sources. More than 8000 of these sources are identifiable with visible objects. The bibliographical files link observations in the catalog with the original articles published in the literature. References give the standard information plus full titles. The Index of Infrared Source Positions is ordered alphabetically by source name and can be used to quickly locate sources in the position-ordered catalog. For sources with no published IR source position, a nominal position may have been given based on other sources. Nominal positions are usually the best available, but not necessarily the true IR positions. Nominal position references are indicated in the index. (6 data files).

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

    PubMed

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

    2014-08-10

    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 α and β 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 α and β 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.

  12. Poly(2-oxazoline) based micelles with high capacity for 3rd generation taxoids: preparation, in vitro and in vivo evaluation.

    PubMed

    He, Zhijian; Schulz, Anita; Wan, Xiaomeng; Seitz, Joshua; Bludau, Herdis; Alakhova, Daria Y; Darr, David B; Perou, Charles M; Jordan, Rainer; Ojima, Iwao; Kabanov, Alexander V; Luxenhofer, Robert

    2015-06-28

    The clinically and commercially successful taxanes, paclitaxel and docetaxel suffer from two major drawbacks, namely their very low aqueous solubility and the risk of developing resistance. Here, we present a method that overcomes both drawbacks in a very simple manner. We formulated 3rd generation taxoids, able to avoid common drug resistance mechanisms with doubly amphiphilic poly(2-oxazoline)s (POx), a safe and highly efficient polymer for the formulation of extremely hydrophobic drugs. We found excellent solubilization of different 3rd generation taxoids irrespective of the drug's chemical structures with essentially quantitative drug loading and final drug to polymer ratios around unity. The small, highly loaded micelles with a hydrodynamic diameter of less than 100nm are excellently suited for parenteral administration. Moreover, a selected formulation with the taxoid SB-T-1214 is about one to two orders of magnitude more active in vitro than paclitaxel in the multidrug resistant breast cancer cell line LCC6-MDR. In contrast, in wild-type LCC6, no difference was observed. Using a q4d×4 dosing regimen, we also found that POx/SB-T-1214 significantly inhibits the growth of LCC6-MDR orthotropic tumors, outperforming commercial paclitaxel drug Taxol and Cremophor EL formulated SB-T-1214.

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

    NASA Astrophysics Data System (ADS)

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

    1985-06-01

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

  14. Stop Codon Reassignment in the Wild

    SciTech Connect

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

    2014-03-21

    Since the discovery of the genetic code and protein translation mechanisms (1), a limited number of variations of the standard assignment between unique base triplets (codons) and their encoded amino acids and translational stop signals have been found in bacteria and phages (2-3). Given the apparent ubiquity of the canonical genetic code, the design of genomically recoded organisms with non-canonical codes has been suggested as a means to prevent horizontal gene transfer between laboratory and environmental organisms (4). It is also predicted that genomically recoded organisms are immune to infection by viruses, under the assumption that phages and their hosts must share a common genetic code (5). This paradigm is supported by the observation of increased resistance of genomically recoded bacteria to phages with a canonical code (4). Despite these assumptions and accompanying lines of evidence, it remains unclear whether differential and non-canonical codon usage represents an absolute barrier to phage infection and genetic exchange between organisms. Our knowledge of the diversity of genetic codes and their use by viruses and their hosts is primarily derived from the analysis of cultivated organisms. Advances in single-cell sequencing and metagenome assembly technologies have enabled the reconstruction of genomes of uncultivated bacterial and archaeal lineages (6). These initial findings suggest that large scale systematic studies of uncultivated microorganisms and viruses may reveal the extent and modes of divergence from the canonical genetic code operating in nature. To explore alternative genetic codes, we carried out a systematic analysis of stop codon reassignments from the canonical TAG amber, TGA opal, and TAA ochre codons in assembled metagenomes from environmental and host-associated samples, single-cell genomes of uncultivated bacteria and archaea, and a collection of phage sequences

  15. Earth's Volcanoes and their Eruptions; the 3rd edition of the Smithsonian Institution's Volcanoes of the World

    NASA Astrophysics Data System (ADS)

    Siebert, L.; Simkin, T.; Kimberly, P.

    2010-12-01

    The 3rd edition of the Smithsonian Institution’s Volcanoes of the World incorporates data on the world’s volcanoes and their eruptions compiled since 1968 by the Institution’s Global Volcanism Program (GVP). Published this Fall jointly by the Smithsonian and the University of California Press, it supplements data from the 1994 2nd edition and includes new data on the number of people living in proximity to volcanoes, the dominant rock lithologies at each volcano, Holocene caldera-forming eruptions, and preliminary lists of Pleistocene volcanoes and large-volume Pleistocene eruptions. The 3rd edition contains data on nearly 1550 volcanoes of known or possible Holocene age, including chronologies, characteristics, and magnitudes for >10,400 Holocene eruptions. The standard 20 eruptive characteristics of the IAVCEI volcano catalog series have been modified to include dated vertical edifice collapse events due to magma chamber evacuation following large-volume explosive eruptions or mafic lava effusion, and lateral sector collapse. Data from previous editions of Volcanoes of the World are also supplemented by listings of up to the 5 most dominant lithologies at each volcano, along with data on population living within 5, 10, 30, and 100 km radii of each volcano or volcanic field. Population data indicate that the most populated regions also contain the most frequently active volcanoes. Eruption data document lava and tephra volumes and Volcanic Explosivity Index (VEI) assignments for >7800 eruptions. Interpretation of VRF data has led to documentation of global eruption rates and the power law relationship between magnitude and frequency of volcanic eruptions. Data with volcanic hazards implications include those on fatalities and evacuations and the rate at which eruptions reach their climax. In recognition of the hazards implications of potential resumption of activity at pre-Holocene volcanoes, the 3rd edition includes very preliminary lists of Pleistocene

  16. Sunphotometric Measurement of Columnar H2O and Aerosol Optical Depth During the 3rd Water Vapor IOP in Fall 2000 at the SGP ARM Site

    NASA Technical Reports Server (NTRS)

    Schmid, B; Eilers, J. A.; McIntosh, D. M.; Longo, K.; Livingston, J. M.; Redemann, J.; Russell, P. B.; Braun, J.; Rocken, C.; Hipskind, R. Stephen (Technical Monitor)

    2001-01-01

    We conducted ground-based measurements with the Ames Airborne Tracking 6-channel Sunphotometer (AATS-6) during the 3rd Water Vapor IOP (WVIOP3), September 18 - October 8, 2000 at the SGP ARM site. For this deployment our primary result was columnar water vapor (CWV) obtained from continuous solar transmittance measurements in the 0.94-micron band. In addition, we simultaneously measured aerosol optical depth (AOD) at 380, 450, 525, 864 and 1020 nm. During the IOP, preliminary results of CWV and AOD were displayed in real-time. The result files were made available to other investigators by noon of the next day. During WVIOP3 those data were shown on the daily intercomparison plots on the IOP web-site. Our preliminary results for CWV fell within the spread of values obtained from other techniques. After conclusion of WVIOP3, AATS-6 was shipped directly to Mauna Loa, Hawaii for post-mission calibration. The updated calibration, a cloud screening technique for AOD, along with other mostly cosmetic changes were applied to the WVIOP3 data set and released as version 0.1. The resulting changes in CWV are small, the changes in AOD and Angstrom parameter are more noticeable. Data version 0.1 was successfully submitted to the ARM External Data Center. In the poster we will show data examples for both CWV and AOD. We will also compare our CWV results with those obtained from a GPS (Global Positioning System) slant path method.

  17. A critical analysis of codon optimization in human therapeutics.

    PubMed

    Mauro, Vincent P; Chappell, Stephen A

    2014-11-01

    Codon optimization describes gene engineering approaches that use synonymous codon changes to increase protein production. Applications for codon optimization include recombinant protein drugs and nucleic acid therapies, including gene therapy, mRNA therapy, and DNA/RNA vaccines. However, recent reports indicate that codon optimization can affect protein conformation and function, increase immunogenicity, and reduce efficacy. We critically review this subject, identifying additional potential hazards including some unique to nucleic acid therapies. This analysis highlights the evolved complexity of codon usage and challenges the scientific bases for codon optimization. Consequently, codon optimization may not provide the optimal strategy for increasing protein production and may decrease the safety and efficacy of biotech therapeutics. We suggest that the use of this approach is reconsidered, particularly for in vivo applications.

  18. Sequence Architecture Downstream of the Initiator Codon Enhances Gene Expression and Protein Stability in Plants1

    PubMed Central

    Sawant, Samir V.; Kiran, Kanti; Singh, Pradhyumna K.; Tuli, Rakesh

    2001-01-01

    Nucleotide positions conserved on the 3′ side of the initiator codon ATG and the corresponding N-terminal amino acid residues in a number of highly abundant plant proteins were identified by computational analysis of a dataset of highly expressed plant genes. The reporter genes uidA and gfp were modified to introduce these features. Insertion of GCT TCC TCC after the initiator codon ATG augmented expression for both the reporter genes. The insertion of each successive codon improved the expression of β-glucuronidase (GUS) in an incremental fashion in transient transformation of tobacco (Nicotiana tabacum) leaves. The insertion of alanine-serine (Ser)-Ser resulted in about a 2-fold increase in the stability of GUS. However, this did not account for the 30- to 40-fold increase in GUS activity between the constructs coding for methionine-alanine-Ser-Ser-GUS and the native enzyme. Substitution of the codon for Ser at the third amino acid residue with synonymous codons reduced GUS expression. The results suggest a role for the conserved nucleotides in the +4 to +11 region in augmenting posttranscriptional events in the expression of genes in plants. PMID:11500561

  19. Premature termination codon at the sterol 27-hydroxylase gene causes cerebrotendinous xanthomatosis in a French family.

    PubMed

    Segev, H; Reshef, A; Clavey, V; Delbart, C; Routier, G; Leitersdorf, E

    1995-02-01

    Cerebrotendinous xanthomatosis (CTX) is an autosomal recessive lipid-storage disease caused by mutations in the sterol 27-hydroxylase gene (CYP27). So far several mutations causing CTX have been identified and characterized. A new mutation creating an insertion of cytosine at position 6 in the cDNA, which is expected to result in a frameshift and a premature termination codon at codon 179, has been identified in a French family. The mutation creates a new site for the restriction endonuclease HaeIII.

  20. 3rd Tech DeltaSphere-3000 Laser 3D Scene Digitizer infrared laser scanner hazard analysis.

    SciTech Connect

    Augustoni, Arnold L.

    2005-02-01

    A laser hazard analysis and safety assessment was performed for the 3rd Tech model DeltaSphere-3000{reg_sign} Laser 3D Scene Digitizer, infrared laser scanner model based on the 2000 version of the American National Standard Institute's Standard Z136.1, for the Safe Use of Lasers. The portable scanner system is used in the Robotic Manufacturing Science and Engineering Laboratory (RMSEL). This scanning system had been proposed to be a demonstrator for a new application. The manufacture lists the Nominal Ocular Hazard Distance (NOHD) as less than 2 meters. It was necessary that SNL validate this NOHD prior to its use as a demonstrator involving the general public. A formal laser hazard analysis is presented for the typical mode of operation for the current configuration as well as a possible modified mode and alternative configuration.

  1. THE 3rd SCHIZOPHRENIA INTERNATIONAL RESEARCH SOCIETY CONFERENCE, 14-18 APRIL 2012, FLORENCE, ITALY: SUMMARIES OF ORAL SESSIONS

    PubMed Central

    Abbs, Brandon; Achalia, Rashmin M; Adelufosi, Adegoke O; Aktener, Ahmet Yiğit; Beveridge, Natalie J; Bhakta, Savita G; Blackman, Rachael K; Bora, Emre; Byun, MS; Cabanis, Maurice; Carrion, Ricardo; Castellani, Christina A; Chow, Tze Jen; Dmitrzak-Weglarz, M; Gayer-Anderson, Charlotte; Gomes, Felipe V; Haut, Kristen; Hori, Hiroaki; Kantrowitz, Joshua T; Kishimoto, Taishiro; Lee, Frankie HF; Lin, Ashleigh; Palaniyappan, Lena; Quan, Meina; Rubio, Maria D; Ruiz de Azúa, Sonia; Sahoo, Saddichha; Strauss, Gregory P; Szczepankiewicz, Aleksandra; Thompson, Andrew D; Trotta, Antonella; Tully, Laura M; Uchida, Hiroyuki; Velthorst, Eva; Young, Jared W; O’Shea, Anne; DeLisi, Lynn E.

    2013-01-01

    The 3rd Schizophrenia International Research Society Conference was held in Florence, Italy, April 14-18, 2012.and this year had as its emphasis, “The Globalization of Research”. Student travel awardees served as rapporteurs for each oral session and focused their summaries on the most significant findings that emerged and the discussions that followed. The following report is a composite of these summaries. We hope that it will provide an overview for those who were present, but could not participate in all sessions, and those who did not have the opportunity to attend, but who would be interested in an update on current investigations ongoing in the field of schizophrenia research. PMID:22910407

  2. Use of 2nd and 3rd Level Correlation Analysis for Studying Degradation in Polycrystalline Thin-Film Solar Cells

    SciTech Connect

    Albin, D. S.; del Cueto, J. A.; Demtsu, S. H.; Bansal, S.

    2011-03-01

    The correlation of stress-induced changes in the performance of laboratory-made CdTe solar cells with various 2nd and 3rd level metrics is discussed. The overall behavior of aggregated data showing how cell efficiency changes as a function of open-circuit voltage (Voc), short-circuit current density (Jsc), and fill factor (FF) is explained using a two-diode, PSpice model in which degradation is simulated by systematically changing model parameters. FF shows the highest correlation with performance during stress, and is subsequently shown to be most affected by shunt resistance, recombination and in some cases voltage-dependent collection. Large decreases in Jsc as well as increasing rates of Voc degradation are related to voltage-dependent collection effects and catastrophic shunting respectively. Large decreases in Voc in the absence of catastrophic shunting are attributed to increased recombination. The relevance of capacitance-derived data correlated with both Voc and FF is discussed.

  3. ANT: Software for Generating and Evaluating Degenerate Codons for Natural and Expanded Genetic Codes.

    PubMed

    Engqvist, Martin K M; Nielsen, Jens

    2015-08-21

    The Ambiguous Nucleotide Tool (ANT) is a desktop application that generates and evaluates degenerate codons. Degenerate codons are used to represent DNA positions that have multiple possible nucleotide alternatives. This is useful for protein engineering and directed evolution, where primers specified with degenerate codons are used as a basis for generating libraries of protein sequences. ANT is intuitive and can be used in a graphical user interface or by interacting with the code through a defined application programming interface. ANT comes with full support for nonstandard, user-defined, or expanded genetic codes (translation tables), which is important because synthetic biology is being applied to an ever widening range of natural and engineered organisms. The Python source code for ANT is freely distributed so that it may be used without restriction, modified, and incorporated in other software or custom data pipelines.

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

    PubMed Central

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

    2012-01-01

    Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation. PMID:22581775

  5. Codon optimization of genes for efficient protein expression in mammalian cells by selection of only preferred human codons.

    PubMed

    Inouye, Satoshi; Sahara-Miura, Yuiko; Sato, Jun-ichi; Suzuki, Takahiro

    2015-05-01

    A simple design method for codon optimization of genes to express a heterologous protein in mammalian cells is described. Codon optimization was performed by choosing only codons preferentially used in humans and with over 60% GC content, and the method was named the "preferred human codon-optimized method." To test our simple rule for codon optimization, the preferred human codon-optimized genes for six proteins containing photoproteins (aequorin and clytin II) and luciferases (Gaussia luciferase, Renilla luciferase, and firefly luciferases from Photinus pyralis and Luciola cruciata) were chemically synthesized and transiently expressed in Chinese hamster ovary-K1 cells. All preferred human codon-optimized genes showed higher luminescence activity than the corresponding wild-type genes. Our simple design method could be used to improve protein expression in mammalian cells efficiently.

  6. Optimization protein productivity of human interleukin-2 through codon usage, gene copy number and intracellular tRNA concentration in CHO cells.

    PubMed

    Ou, Kua-Chun; Wang, Chih-Yang; Liu, Kuan-Ting; Chen, Yi-Ling; Chen, Yi-Chen; Lai, Ming-Derg; Yen, Meng-Chi

    2014-11-14

    Transfer RNA (tRNA) abundance is one of the critical factors for the enhancement of protein productivity in prokaryotic and eukaryotic hosts. Gene copy number of tRNA and tRNA codon usage bias are generally used to match tRNA abundance of protein-expressing hosts and to optimize the codons of recombinant proteins. Because sufficient concentration of intracellular tRNA and optimized codons of recombinant proteins enhanced translation efficiency, we hypothesized that sufficient supplement of host's tRNA improved protein productivity in mammalian cells. First, the small tRNA sequencing results of CHO-K1 cells showed moderate positive correlation with gene copy number and codon usage bias. Modification of human interleukin-2 (IL-2) through codons with high gene copy number and high codon usage bias (IL-2 HH, modified on Leu, Thr, Glu) significantly increased protein productivity in CHO-K1 cells. In contrast, modification through codons with relatively high gene copy number and low codon usage bias (IL-2 HL, modified on Ala, Thr, Val), or relatively low gene copy number and low codon usage bias (IL-2 LH, modified on Ala, Thr, Val) did not increase IL-2 productivity significantly. Furthermore, supplement of the alanine tRNA or threonine tRNA increased IL-2 productivity of IL-2 HL. In summary, we revealed a potential strategy to enhance productivity of recombinant proteins, which may be applied in production of protein drug or design of DNA vaccine.

  7. Does stereo-endoscopy improve neurosurgical targeting in 3rd ventriculostomy?

    NASA Astrophysics Data System (ADS)

    Abhari, Kamyar; de Ribaupierre, Sandrine; Peters, Terry; Eagleson, Roy

    2011-03-01

    Endoscopic third ventriculostomy is a minimally invasive surgical technique to treat hydrocephalus; a condition where patients suffer from excessive amounts of cerebrospinal fluid (CSF) in the ventricular system of their brain. This technique involves using a monocular endoscope to locate the third ventricle, where a hole can be made to drain excessive fluid. Since a monocular endoscope provides only a 2D view, it is difficult to make this perforation due to the lack of monocular cues and depth perception. In a previous study, we had investigated the use of a stereo-endoscope to allow neurosurgeons to locate and avoid hazardous areas on the surface of the third ventricle. In this paper, we extend our previous study by developing a new methodology to evaluate the targeting performance in piercing the hole in the membrane. We consider the accuracy of this surgical task and derive an index of performance for a task which does not have a well-defined position or width of target. Our performance metric is sensitive and can distinguish between experts and novices. We make use of this metric to demonstrate an objective learning curve on this task for each subject.

  8. The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

    PubMed Central

    Sengupta, Supratim; Yang, Xiaoguang

    2007-01-01

    Many cases of nonstandard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The “gain” represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The “loss” represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is codon disappearance (CD), where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the unassigned codon mechanism, the loss occurs first, whereas in the ambiguous intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. CD is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense-to-sense reassignments cannot be explained by CD. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the unassigned codon and the ambiguous intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully. Electronic supplementary material The online version of this article (doi:10.1007/s00239-006-0284-7) contains supplementary material, which is available to authorized users. PMID:17541678

  9. Innovative Strategies for Enhancing Geoscience: Lesson Plans from the 3rd Millennium B.C.E.

    NASA Astrophysics Data System (ADS)

    Romani, P. N.; Bartholomew, I.; Frank, M.; Hackett, K.; Jackson, T.; Melzer, S.; 6th Grade,

    2002-05-01

    Each year the fifth and sixth grade students at Glenarden Woods Elementary Magnet School for Talented and Gifted (TAG) Students, in Glenarden, Maryland study an ancient culture to provide a unifying theme to their studies. The thematic unit is year-long and involves language arts, social studies, and art. Originally, the curriculum did not include any math or science, but for the past seven years we have been working to integrate the technology of the ancient culture into the program. Our goals are to keep the science as hands on as possible and to have the students learn by solving problems. This year's culture was ancient Egypt and the math and science components had a distinctive geoscience flavor to them. The initial problem for the students was to how to lay out a pyramid so that the four sides were aligned with the four cardinal directions as the pyramids are in Egypt. In keeping with the spirit of their studies they had to do so as the Egyptians did, i.e. without a pole star and without the use of any "modern" conveniences such as compasses, global positioning systems, etc. The problem was solved by measurements and observations of a gnomon's shadow. This work then provided a nice springboard for their next problem, duplicating Eratosthenes's measurement of the circumference of the Earth. Eratosthenes was a Greek who lived and experimented in Egypt in the Ptolemaic era. His determination of the Earth's circumference was within 15% of the modern day value. For this work the students had to team with other elementary students in Amherst, Massachusetts. We will present how we did the projects and lessons learned.

  10. Accuracy of initial codon selection by aminoacyl-tRNAs on the mRNA-programmed bacterial ribosome

    PubMed Central

    Zhang, Jingji; Ieong, Ka-Weng; Johansson, Magnus; Ehrenberg, Måns

    2015-01-01

    We used a cell-free system with pure Escherichia coli components to study initial codon selection of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP on messenger RNA-programmed ribosomes. We took advantage of the universal rate-accuracy trade-off for all enzymatic selections to determine how the efficiency of initial codon readings decreased linearly toward zero as the accuracy of discrimination against near-cognate and wobble codon readings increased toward the maximal asymptote, the d value. We report data on the rate-accuracy variation for 7 cognate, 7 wobble, and 56 near-cognate codon readings comprising about 15% of the genetic code. Their d values varied about 400-fold in the 200–80,000 range depending on type of mismatch, mismatch position in the codon, and tRNA isoacceptor type. We identified error hot spots (d = 200) for U:G misreading in second and U:U or G:A misreading in third codon position by His-tRNAHis and, as also seen in vivo, Glu-tRNAGlu. We suggest that the proofreading mechanism has evolved to attenuate error hot spots in initial selection such as those found here. PMID:26195797

  11. Nonsense-codon mutations of the ornithine aminotransferase gene with decreased levels of mutant mRNA in gyrate atrophy.

    PubMed

    Mashima, Y; Murakami, A; Weleber, R G; Kennaway, N G; Clarke, L; Shiono, T; Inana, G

    1992-07-01

    A generalized deficiency of the mitochondrial matrix enzyme ornithine aminotransferase (OAT) is the inborn error in gyrate atrophy (GA), an autosomal recessive degenerative disease of the retina and choroid of the eye. Mutations in the OAT gene show a high degree of molecular heterogeneity in GA, reflecting the genetic heterogeneity in this disease. Using the combined techniques of PCR, denaturing gradient gel electrophoresis, and direct sequencing, we have identified three nonsense-codon mutations and one nonsense codon-generating mutation of the OAT gene in GA pedigrees. Three of them are single-base substitutions, and one is a 2-bp deletion resulting in a reading frameshift. A nonsense codon created at position 79 (TGA) by a frameshift and nonsense mutations at codons 209 (TAT----TAA) and 299 (TAC----TAG) result in abnormally low levels of OAT mRNA in the patient's skin fibroblasts. A nonsense mutation at codon 426 (CGA----TGA) in the last exon, however, has little effect on the mRNA level. Thus, the mRNA level can be reduced by nonsense-codon mutations, but the position of the mutation may be important, with earlier premature-translation termination having a greater effect than a later mutation.

  12. Synonymous codon usage is subject to selection in thermophilic bacteria

    PubMed Central

    Lynn, David J.; Singer, Gregory A. C.; Hickey, Donal A.

    2002-01-01

    The patterns of synonymous codon usage, both within and among genomes, have been extensively studied over the past two decades. Despite the accumulating evidence that natural selection can shape codon usage, it has not been possible to link a particular pattern of codon usage to a specific external selective force. Here, we have analyzed the patterns of synonymous codon usage in 40 completely sequenced prokaryotic genomes. By combining the genes from several genomes (more than 80 000 genes in all) into a single dataset for this analysis, we were able to investigate variations in codon usage, both within and between genomes. The results show that synonymous codon usage is affected by two major factors: (i) the overall G+C content of the genome and (ii) growth at high temperature. This study focused on the relationship between synonymous codon usage and the ability to grow at high temperature. We have been able to eliminate both phylogenetic history and lateral gene transfer as possible explanations for the characteristic pattern of codon usage among the thermophiles. Thus, these results demonstrate a clear link between a particular pattern of codon usage and an external selective force. PMID:12364606

  13. The accuracy of codon recognition by polypeptide release factors

    PubMed Central

    Freistroffer, David V.; Kwiatkowski, Marek; Buckingham, Richard H.; Ehrenberg, Måns

    2000-01-01

    The precision with which individual termination codons in mRNA are recognized by protein release factors (RFs) has been measured and compared with the decoding of sense codons by tRNA. An Escherichia coli system for protein synthesis in vitro with purified components was used to study the accuracy of termination by RF1 and RF2 in the presence or absence of RF3. The efficiency of factor-dependent termination at all sense codons differing from any of the three stop codons by a single mutation was measured and compared with the efficiency of termination at the three stop codons. RF1 and RF2 discriminate against sense codons related to stop codons by between 3 and more than 6 orders of magnitude. This high level of accuracy is obtained without energy-driven error correction (proofreading), in contrast to codon-dependent aminoacyl-tRNA recognition by ribosomes. Two codons, UAU and UGG, stand out as hotspots for RF-dependent premature termination. PMID:10681447

  14. Organizational Support for the 3rd Summer Institute on Complex Plasmas, July 30 – August 8, 2012

    SciTech Connect

    Lopez, Jose L.

    2012-07-01

    This grant provided partial funds for American graduate students to attend the 3rd Graduate Summer Institute on Complex Plasmas, which was held from July 30 to August 8, 2012 at Seton Hall University in South Orange, New Jersey. The Graduate Summer Institute is a topical series of instructional workshops held bi-annually on the emerging field of complex plasmas that is jointly organized through a collaboration between American and German-European Union plasmas researchers. This specialized program brings together many of the world's leading researchers in the specialized area of complex plasmas, who freely provide instructional lectures and tutorials on the most recent research and discoveries done in this branch of plasma science. The partial funds provided by this grant helped support the travel and accommodation expenses of the participating American students and tutorial instructors. Partial funds further supported the travel and accommodation of three renown American plasma researchers that provided educational tutorials to the thirty-eight participating students from the United States, Europe, and Asia. The organized program afforded a unique opportunity for the participating American graduate students to learn about and engage more deeply in an area of plasma science that is not studied in any of the graduate educational curriculums provided by universities in the United States of America. The educational experience offered by this program provided the necessary knowledge needed by future American plasma researchers to keep the national plasma research effort on the cutting-edge and keep the national plasma community as a global leader.

  15. Development of Partially-Coherent Wavefront Propagation Simulation Methods for 3rd and 4th Generation Synchrotron Radiation Sources.

    SciTech Connect

    Chubar O.; Berman, L; Chu, Y.S.; Fluerasu, A.; Hulbert, S.; Idir, M.; Kaznatcheev, K.; Shapiro, D.; Baltser, J.

    2012-04-04

    Partially-coherent wavefront propagation calculations have proven to be feasible and very beneficial in the design of beamlines for 3rd and 4th generation Synchrotron Radiation (SR) sources. These types of calculations use the framework of classical electrodynamics for the description, on the same accuracy level, of the emission by relativistic electrons moving in magnetic fields of accelerators, and the propagation of the emitted radiation wavefronts through beamline optical elements. This enables accurate prediction of performance characteristics for beamlines exploiting high SR brightness and/or high spectral flux. Detailed analysis of radiation degree of coherence, offered by the partially-coherent wavefront propagation method, is of paramount importance for modern storage-ring based SR sources, which, thanks to extremely small sub-nanometer-level electron beam emittances, produce substantial portions of coherent flux in X-ray spectral range. We describe the general approach to partially-coherent SR wavefront propagation simulations and present examples of such simulations performed using 'Synchrotron Radiation Workshop' (SRW) code for the parameters of hard X-ray undulator based beamlines at the National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory. These examples illustrate general characteristics of partially-coherent undulator radiation beams in low-emittance SR sources, and demonstrate advantages of applying high-accuracy physical-optics simulations to the optimization and performance prediction of X-ray optical beamlines in these new sources.

  16. The 3rd Canadian Symposium on Hepatitis C Virus: Expanding care in the interferon-free era

    PubMed Central

    MacParland, Sonya A; Bilodeau, Marc; Grebely, Jason; Bruneau, Julie; Cooper, Curtis; Klein, Marina; Sagan, Selena M; Choucha, Norma; Balfour, Louise; Bialystok, Frank; Krajden, Mel; Raven, Jennifer; Roberts, Eve; Russell, Rodney; Houghton, Michael; Tyrrell, D Lorne; Feld, Jordan J

    2014-01-01

    Hepatitis C virus (HCV) currently infects approximately 250,000 individuals in Canada and causes more years of life lost than any other infectious disease in the country. In August 2011, new therapies were approved by Health Canada that have achieved higher response rates among those treated, but are poorly tolerated. By 2014/2015, short-course, well-tolerated treatments with cure rates >95% will be available. However, treatment uptake is poor due to structural, financial, geographical, cultural and social barriers. As such, ‘Barriers to access to HCV care in Canada’ is a crucial topic that must be addressed to decrease HCV disease burden and potentially eliminate HCV in Canada. Understanding how to better care for HCV-infected individuals requires integration across multiple disciplines including researchers, clinical services and policy makers to address the major populations affected by HCV including people who inject drugs, baby boomers, immigrants and Aboriginal and/or First Nations people. In 2012, the National CIHR Research Training Program in Hepatitis C organized the 1st Canadian Symposium on Hepatitis C Virus (CSHCV) in Montreal, Quebec. The 2nd CSHCV was held in 2013 in Victoria, British Columbia. Both symposia were highly successful, attracting leading international faculty with excellent attendance leading to dialogue and knowledge translation among attendees of diverse backgrounds. The current article summarizes the 3rd CSHCV, held February 2014, in Toronto, Ontario. PMID:25314353

  17. 3rd Quarter Transportation Report FY 2014: Radioactive Waste Shipments to and from the Nevada National Security Site (NNSS)

    SciTech Connect

    Gregory, Louis

    2014-09-20

    This report satisfies the U.S. Department of Energy (DOE), National Nuclear Security Administration Nevada Field Office (NNSA/NFO) commitment to prepare a quarterly summary report of radioactive waste shipments to the Nevada National Security Site (NNSS) Radioactive Waste Management Complex (RWMC) at Area 5. There were no shipments sent for offsite treatment and returned to the NNSS this quarter. This report summarizes the 3rd quarter of Fiscal Year (FY) 2014 low-level radioactive waste (LLW) and mixed low-level radioactive waste (MLLW) shipments. This report also includes annual summaries for FY 2014 in Tables 4 and 5. Tabular summaries are provided which include the following: Sources of and carriers for LLW and MLLW shipments to and from the NNSS; Number and external volume of LLW and MLLW shipments; Highway routes used by carriers; and Incident/accident data applicable to LLW and MLLW shipments. In this report shipments are accounted for upon arrival at the NNSS, while disposal volumes are accounted for upon waste burial. The disposal volumes presented in this report do not include minor volumes of non-radioactive materials that were approved for disposal. Volume reports showing cubic feet generated using the Low-Level Waste Information System may vary slightly due to differing rounding conventions.

  18. Evaluation of a model of dissertation supervision for 3rd year B.Sc. undergraduate nursing students.

    PubMed

    Scholefield, Donna; Cox, Georgina

    2016-03-01

    All English universities now offer an all degree undergraduate nursing programme. Many currently use an individual supervision model to support final year dissertation students, but with increased numbers and limited resources new models of supervision are needed. This study evaluated a mixed (group and individual) model of dissertation supervision to determine its effectiveness for a large group of undergraduate nursing students. A sample of 3rd year students and their supervisors were selected from one large university. An evaluation survey was conducted using anonymous internet-based questionnaires and focus groups. The data was analysed using Survey Monkey, SPSS and thematic analysis. A 51% (n = 56/110) response rate (students) and 65% (n = 24/37) for supervisors was obtained. The majority of students and supervisors were satisfied with the new model. There was a mixed response to the group workshops and supervision groups. Three themes emerged from the qualitative data: engaging with the process, motivation to supervise and valuing the process. The supervision process is a struggle but both parties gained considerably from going through the process. In conclusion, a mixed model of supervision together with a range of other learning resources can be an effective approach in supporting students through the dissertation process. PMID:26700648

  19. Evaluation of a model of dissertation supervision for 3rd year B.Sc. undergraduate nursing students.

    PubMed

    Scholefield, Donna; Cox, Georgina

    2016-03-01

    All English universities now offer an all degree undergraduate nursing programme. Many currently use an individual supervision model to support final year dissertation students, but with increased numbers and limited resources new models of supervision are needed. This study evaluated a mixed (group and individual) model of dissertation supervision to determine its effectiveness for a large group of undergraduate nursing students. A sample of 3rd year students and their supervisors were selected from one large university. An evaluation survey was conducted using anonymous internet-based questionnaires and focus groups. The data was analysed using Survey Monkey, SPSS and thematic analysis. A 51% (n = 56/110) response rate (students) and 65% (n = 24/37) for supervisors was obtained. The majority of students and supervisors were satisfied with the new model. There was a mixed response to the group workshops and supervision groups. Three themes emerged from the qualitative data: engaging with the process, motivation to supervise and valuing the process. The supervision process is a struggle but both parties gained considerably from going through the process. In conclusion, a mixed model of supervision together with a range of other learning resources can be an effective approach in supporting students through the dissertation process.

  20. Effects of using relaxation breathing training to reduce music performance anxiety in 3rd to 6th graders.

    PubMed

    Su, Yu-Huei; Luh, Jer-Junn; Chen, Hsin-I; Lin, Chao-Chen; Liao, Miin-Jiun; Chen, Heng-Shuen

    2010-06-01

    The current study examined the effects of applying relaxation breathing training (RBT) as a means to reduce music performance anxiety (MPA) in young, talented musicians. A group of 59 young musicians from 3rd to 6th grade participated in this study, and all of them started RBT twice a week for 2 months prior to the examination. Four tests--2 mos, 1 mos, half an hour and 5 min before the examination--were conducted to examine the level of MPA after the application of RBT. Results show that the degree of MPA 5 min before the trial was lower than the degree of performance anxiety half an hour before the jury (t = -3.683, p < 0.01), which indicated that the RBT was associated with a decrease in MPA. Although a series of RBT exercises was applied, results indicated that when approaching the date of examination, the degree of performance anxiety still increased and reached its maximum half an hour before the jury. The recommendation for future studies is to combine the application of RBT with other methods to expand its effect in reducing MPA.

  1. Changing motor patterns of the 3rd axillary muscle activities associated with longitudinal control in freely flying hawkmoths.

    PubMed

    Ando, Noriyasu; Kanzaki, Ryohei

    2004-02-01

    The 3rd axillary muscles (3AXMs) in the mesothorax in hawkmoths are direct flight muscles and pull forewings back along to the body axis. The 3AXMs are regarded as steering muscles because of their changeable activities during turning flight under tethered conditions. We investigated activities of the upper unit of the 3AXMs during free flight with a micro-telemetry device and captured body and wing movements by high-speed cameras. The 3AXM was activated with 1 to 3 spikes per each wingbeat cycle but sometimes ceased to fire. The phase of the onset of the activities was, even though it was variable, close to the phase of the elevator muscle activities. Therefore the upper unit of the 3AXM activities would affect upstroke properties phasically including wing retractions. We focused on longitudinal flight control and identified a correlation between the phase of the 3AXM and body pitch angle, which is important kinematical parameter for longitudinal control in insect flight. The phasic changes of the 3AXM activities would support quick changes in longitudinal control. PMID:14993822

  2. InAs/GaSb type II superlattices for advanced 2nd and 3rd generation detectors

    NASA Astrophysics Data System (ADS)

    Walther, Martin; Rehm, Robert; Schmitz, Johannes; Fleissner, Joachim; Rutz, Frank; Kirste, Lutz; Scheibner, Ralf; Wendler, Joachim; Ziegler, Johann

    2010-01-01

    InAs/GaSb short-period superlattices (SL) based on GaSb, InAs and AlSb have proven their great potential for high performance infrared detectors. Lots of interest is currently focused on the development of short-period InAs/GaSb SLs for advanced 2nd and 3rd generation infrared detectors between 3 - 30 μm. For the fabrication of mono- and bispectral thermal imaging systems in the mid-wavelength infrared region (MWIR) a manufacturable technology for high responsivity thermal imaging systems has been developed. InAs/GaSb short-period superlattices can be fabricated with up to 1000 periods in the intrinsic region without revealing diffusion limited behavior. This enables the fabrication of InAs/GaSb SL camera systems with high responsivity comparable to state of the art CdHgTe and InSb detectors. The material system is also ideally suited for the fabrication of dual-color MWIR/MWIR InAs/GaSb SL camera systems with high quantum efficiency for missile approach warning systems with simultaneous and spatially coincident detection in both spectral channels.

  3. Altered differential hemocyte count in 3rd instar larvae of Drosophila melanogaster as a response to chronic exposure of Acephate

    PubMed Central

    Rajak, Prem; Dutta, Moumita

    2015-01-01

    Acephate, an organophosphate (OP) pesticide, was used to investigate the effects of its chronic exposure on hemocyte abundance in a non-target dipteran insect Drosophila melanogaster. For this purpose, six graded concentrations ranging from 1 to 6 μg/ml were selected, which are below the reported residual values (up to 14 μg/ml) of the chemical. 1st instar larvae were fed with these concentrations up to the 3rd instar stage and accordingly hemolymph smears from these larvae were prepared for differential hemocyte count. Three types of cells are found in Drosophila hemolymph, namely, plasmatocytes, lamellocytes and crystal cells. Plasmatocyte count was found to decrease with successive increase in treatment concentrations. Crystal cells showed an increasing trend in their number. Though the number of lamellocytes was very low, a bimodal response was noticed. Lamellocyte number was found to increase with the initial three concentrations, followed by a dose dependent reduction in their number. As hemocytes are directly linked to the immune system of fruit flies, fluctuations in normal titer of these cells may affect insect immunity. Hemocytes share homologies in their origin and mode of action with the immune cells of higher organisms including man. Thus the present findings suggest that immune cells of humans and other organisms may be affected adversely under chronic exposure to Acephate. PMID:27486365

  4. Stop codons in bacteria are not selectively equivalent

    PubMed Central

    2012-01-01

    Background The evolution and genomic stop codon frequencies have not been rigorously studied with the exception of coding of non-canonical amino acids. Here we study the rate of evolution and frequency distribution of stop codons in bacterial genomes. Results We show that in bacteria stop codons evolve slower than synonymous sites, suggesting the action of weak negative selection. However, the frequency of stop codons relative to genomic nucleotide content indicated that this selection regime is not straightforward. The frequency of TAA and TGA stop codons is GC-content dependent, with TAA decreasing and TGA increasing with GC-content, while TAG frequency is independent of GC-content. Applying a formal, analytical model to these data we found that the relationship between stop codon frequencies and nucleotide content cannot be explained by mutational biases or selection on nucleotide content. However, with weak nucleotide content-dependent selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates the relationship between TAG and nucleotide content. For biologically plausible rates of mutations we show that, in bacteria, TAG stop codon is universally associated with lower fitness, with TAA being the optimal for G-content < 16% while for G-content > 16% TGA has a higher fitness than TAG. Conclusions Our data indicate that TAG codon is universally suboptimal in the bacterial lineage, such that TAA is likely to be the preferred stop codon for low GC content while the TGA is the preferred stop codon for high GC content. The optimization of stop codon usage may therefore be useful in genome engineering or gene expression optimization applications. Reviewers This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev. For the full reviews, please go to the Reviewers’ Comments section. PMID:22974057

  5. Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation.

    PubMed

    Kwon, Kwang-Chul; Chan, Hui-Ting; León, Ileana R; Williams-Carrier, Rosalind; Barkan, Alice; Daniell, Henry

    2016-09-01

    Codon optimization based on psbA genes from 133 plant species eliminated 105 (human clotting factor VIII heavy chain [FVIII HC]) and 59 (polio VIRAL CAPSID PROTEIN1 [VP1]) rare codons; replacement with only the most highly preferred codons decreased transgene expression (77- to 111-fold) when compared with the codon usage hierarchy of the psbA genes. Targeted proteomic quantification by parallel reaction monitoring analysis showed 4.9- to 7.1-fold or 22.5- to 28.1-fold increase in FVIII or VP1 codon-optimized genes when normalized with stable isotope-labeled standard peptides (or housekeeping protein peptides), but quantitation using western blots showed 6.3- to 8-fold or 91- to 125-fold increase of transgene expression from the same batch of materials, due to limitations in quantitative protein transfer, denaturation, solubility, or stability. Parallel reaction monitoring, to our knowledge validated here for the first time for in planta quantitation of biopharmaceuticals, is especially useful for insoluble or multimeric proteins required for oral drug delivery. Northern blots confirmed that the increase of codon-optimized protein synthesis is at the translational level rather than any impact on transcript abundance. Ribosome footprints did not increase proportionately with VP1 translation or even decreased after FVIII codon optimization but is useful in diagnosing additional rate-limiting steps. A major ribosome pause at CTC leucine codons in the native gene of FVIII HC was eliminated upon codon optimization. Ribosome stalls observed at clusters of serine codons in the codon-optimized VP1 gene provide an opportunity for further optimization. In addition to increasing our understanding of chloroplast translation, these new tools should help to advance this concept toward human clinical studies. PMID:27465114

  6. A facile and efficient transposon mutagenesis method for generation of multi-codon deletions in protein sequences.

    PubMed

    Liu, Shu-Su; Wei, Xuan; Ji, Qun; Xin, Xiu; Jiang, Biao; Liu, Jia

    2016-06-10

    Substitutions, insertions and deletions are all important mutation events in natural and laboratory protein evolution. However, protein engineering using insertions and deletions (indels) is hindered by the lack of a convenient mutagenesis method. Here, we describe a general transposon mutagenesis method that allows for removal of up to five consecutive in-frame codons from a random position of a target protein. This method, referred to as codon deletion mutagenesis (CDM), relies on an engineered Mu transposon that carries asymmetric terminal sequences flanking the MuA transposase recognition sites. CDM requires minimal DNA manipulations, and can generate multi-codon deletions with high efficiency (>90%). As a proof of principle, we constructed five libraries of green fluorescent protein (GFP) containing one to five random codon deletions, respectively. Several variants with multi-codon deletions remained fluorescent, none of which could be easily identified using traditional mutagenesis method. CDM provides a facile and efficient approach to sampling a protein sequence with multi-codon deletions. It will not only facilitate our understanding of the effects of amino acid deletions on protein function but also expedite protein engineering using deletion mutagenesis. PMID:27071724

  7. Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags.

    PubMed

    Ahmad, Touqeer; Sablok, Gaurav; Tatarinova, Tatiana V; Xu, Qiang; Deng, Xiu-Xin; Guo, Wen-Wu

    2013-04-01

    Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid.

  8. Evaluation of codon biology in citrus and Poncirus trifoliata based on genomic features and frame corrected expressed sequence tags.

    PubMed

    Ahmad, Touqeer; Sablok, Gaurav; Tatarinova, Tatiana V; Xu, Qiang; Deng, Xiu-Xin; Guo, Wen-Wu

    2013-04-01

    Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid. PMID:23315666

  9. Evaluation of Codon Biology in Citrus and Poncirus trifoliata Based on Genomic Features and Frame Corrected Expressed Sequence Tags

    PubMed Central

    Ahmad, Touqeer; Sablok, Gaurav; Tatarinova, Tatiana V.; Xu, Qiang; Deng, Xiu-Xin; Guo, Wen-Wu

    2013-01-01

    Citrus, as one of the globally important fruit trees, has been an object of interest for understanding genetics and evolutionary process in fruit crops. Meta-analyses of 19 Citrus species, including 4 globally and economically important Citrus sinensis, Citrus clementina, Citrus reticulata, and 1 Citrus relative Poncirus trifoliata, were performed. We observed that codons ending with A- or T- at the wobble position were preferred in contrast to C- or G- ending codons, indicating a close association with AT richness of Citrus species and P. trifoliata. The present study postulates a large repertoire of a set of optimal codons for the Citrus genus and P. trifoliata and demonstrates that GCT and GGT are evolutionary conserved optimal codons. Our observation suggested that mutational bias is the dominating force in shaping the codon usage bias (CUB) in Citrus and P. trifoliata. Correspondence analysis (COA) revealed that the principal axis [axis 1; COA/relative synonymous codon usage (RSCU)] contributes only a minor portion (∼10.96%) of the recorded variance. In all analysed species, except P. trifoliata, Gravy and aromaticity played minor roles in resolving CUB. Compositional constraints were found to be strongly associated with the amino acid signatures in Citrus species and P. trifoliata. Our present analysis postulates compositional constraints in Citrus species and P. trifoliata and plausible role of the stress with GC3 and coevolution pattern of amino acid. PMID:23315666

  10. The Relationship between Perceived and Ideal Body Size and Body Mass Index in 3rd-Grade Low Socioeconomic Hispanic Children

    ERIC Educational Resources Information Center

    Fisher, Allison; Lange, Mary Anne; Young-Cureton, Virginia; Canham, Daryl

    2005-01-01

    Very little is known about body satisfaction among minority children. This study examined the relationship between perceived and actual body size and Body Mass Index among 43 low-socioeconomic Hispanic 3rd-graders. Researchers measured participants' Body Mass Index; students self-reported Perceived Ideal Self Image and Perceived Actual Self Image…

  11. "Elderly Deafblindness." Proceedings of the European Conference of Deafblind International's Acquired Deafblindness Network (3rd, Marcelli di Numana, Italy, October 2-7, 1998).

    ERIC Educational Resources Information Center

    Deafblind International, London (England).

    This text includes all of the plenary presentations from the 3rd European Conference of Deafblind International's Acquired Deafblindness Network. This international conference was the first to focus specifically on older people with dual sensory impairment. Presentations addressed the awareness of the needs of older people with deafblind or dual…

  12. Implications of Technology for Teaching and Learning. Annual Professional Education Seminar of Central States Colleges and Universities (3rd, November, 1967).

    ERIC Educational Resources Information Center

    Woodruff, Asahel; Froyen, Len

    This report of the proceedings of the 3rd Annual Professional Education Seminar of the Central States Colleges and Universities centers upon the implications of technology for teaching and learning and contains addresses delivered, including "Some Concerns Related to Technology in Education," by Len Froyen; and "Implications of Technology for…

  13. Midwest Child-Parent Center (CPC) PreK-3rd Grade School Reform Model: Impacts on Child and Family Outcomes over Time

    ERIC Educational Resources Information Center

    Gaylor, Erika; Spiker, Donna; Wei, Xin; Lease, Erin; Reynolds, Arthur

    2015-01-01

    This presentation reports on the goals and preliminary outcomes of the Child-Parent Centers (CPC) Expansion Project, which is a PreK to 3rd grade school reform model aimed at improving the short- and long-term outcomes of participating children and families. The model provides continuous education and family support services to schools serving a…

  14. 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

    Castro-Chavez, Fernando

    2011-01-01

    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

  15. Synonymous codon usage pattern in glycoprotein gene of rabies virus.

    PubMed

    Morla, Sudhir; Makhija, Aditi; Kumar, Sachin

    2016-06-10

    Rabies virus (RABV) is the causative agent of a fatal nervous system ailment. The disease is zoonotic and prevalent in many developing countries. The glycoprotein (G) of RABV is the major antigenic determinant of the virus and plays a pivotal role in its neurovirulence. Various aspects of 'G' protein biology have been explored, but the factors affecting the nucleotide choice and synonymous codon usage have never been reported. In the present study, we have analyzed the relative synonymous codon usage and effective number of codons (Nc) using 132 'G' protein genes of RABV. Corresponding analysis was used to calculate major trends in codon usage. The correlation between base composition and codon usage as well as the plot between Nc and GC3 suggest that mutational pressure is the major factor that influences the codon usage in the G gene of RABV. In addition, factors like aromaticity, aliphatic index and hydropathy have shown slight correlation suggesting that natural selection also contributes to the codon usage variations of the 'G' gene. In conclusion, codon usage bias in 'G' gene of RABV is mainly by mutational pressure and natural selection. PMID:26945626

  16. Two new beta0-thalassemic mutations: a deletion (-CC) at codon 142 or overlapping codons 142-143, and an insertion (+T) at codon 45 or overlapping codons 44-45/45-46 of the beta-globin gene.

    PubMed

    Lacan, Philippe; Aubry, Martine; Couprie, Nicole; Francina, Alain

    2007-01-01

    We report here two new beta(0)-thalassemic mutations. In the first case, a deletion of two nucleotides (-CC) at codon 142 was found in a French Caucasian woman. In the second case, an insertion of a single nucleotide (+T) at codon 45 was found in a Turkish girl. In both cases, no dominant thalassemia-like phenotype was observed.

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

    PubMed Central

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

    2011-01-01

    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

  18. A model of protein translation including codon bias, nonsense errors, and ribosome recycling.

    PubMed

    Gilchrist, Michael A; Wagner, Andreas

    2006-04-21

    We present and analyse a model of protein translation at the scale of an individual messenger RNA (mRNA) transcript. The model we develop is unique in that it incorporates the phenomena of ribosome recycling and nonsense errors. The model conceptualizes translation as a probabilistic wave of ribosome occupancy traveling down a heterogeneous medium, the mRNA transcript. Our results show that the heterogeneity of the codon translation rates along the mRNA results in short-scale spikes and dips in the wave. Nonsense errors attenuate this wave on a longer scale while ribosome recycling reinforces it. We find that the combination of nonsense errors and codon usage bias can have a large effect on the probability that a ribosome will completely translate a transcript. We also elucidate how these forces interact with ribosome recycling to determine the overall translation rate of an mRNA transcript. We derive a simple cost function for nonsense errors using our model and apply this function to the yeast (Saccharomyces cervisiae) genome. Using this function we are able to detect position dependent selection on codon bias which correlates with gene expression levels as predicted a priori. These results indirectly validate our underlying model assumptions and confirm that nonsense errors can play an important role in shaping codon usage bias. PMID:16171830

  19. [Level of smoking of 3rd and 4th grade students studying health and related factors: follow-up study].

    PubMed

    Göktalay, Tuğba; Cengiz Özyurt, Beyhan; Sakar Coşkun, Ayşin; Celik, Pinar

    2011-01-01

    The levels of smoking of 1st and 2nd year students at Faculty of Medicine and Manisa School of Health at Celal Bayar University were investigated in 2006-2007. This study is carried out in order to see if there is a change in the same students' level of smoking while they are in 3rd and 4th year. In addition, the study aimed to examine the factors affecting the level of use and attitudes towards the law effectuated in July 19, 2009. This is a follow-up study with 80.42% return rate. A 26-item structured questionnaire was administered. The participants filled out the questionnaires under supervision of the researchers in their classrooms. The University Institutional Review Board approved the study. The total of participants (263) of the follow-up study included 189 female and 74 male. The rate of experimenting with smoking was 49% with the mean age of 15.7 (SD= 4.01 years). The mean age of experimenting with smoking was the earliest on male students studying at faculty of medicine. The level of smoking was found to be the most on females, studying at faculty of medicine and staying at the dormitory, with smoking parents (p< 0.05). The most important reason to begin smoking was curiosity (55.2%) while bad breath and yellowing of teeth were the reasons to quit (91.7%). 83.3% of the students thought that the law will be effective on quit smoking. The level of both experimenting and use of smoking has been increased over time. It is suggested that medical students' awareness about the danger of smoking should be raised at earlier grades. In addition, lectures should be offered to students at School of Health and they should be encouraged to unite in order to fight with smoking.

  20. Classification of biliary tract cancers established by the Japanese Society of Hepato-Biliary-Pancreatic Surgery: 3(rd) English edition.

    PubMed

    Miyazaki, Masaru; Ohtsuka, Masayuki; Miyakawa, Shuichi; Nagino, Masato; Yamamoto, Masakazu; Kokudo, Norihiro; Sano, Keiji; Endo, Itaru; Unno, Michiaki; Chijiiwa, Kazuo; Horiguchi, Akihiko; Kinoshita, Hisafumi; Oka, Masaaki; Kubota, Keiichi; Sugiyama, Masanori; Uemoto, Shinji; Shimada, Mitsuo; Suzuki, Yasuyuki; Inui, Kazuo; Tazuma, Susumu; Furuse, Junji; Yanagisawa, Akio; Nakanuma, Yasuni; Kijima, Hiroshi; Takada, Tadahiro

    2015-03-01

    The 3(rd) English edition of the Japanese classification of biliary tract cancers was released approximately 10 years after the 5(th) Japanese edition and the 2(nd) English edition. Since the first Japanese edition was published in 1981, the Japanese classification has been in extensive use, particularly among Japanese surgeons and pathologists, because the cancer status and clinical outcomes in surgically resected cases have been the main objects of interest. However, recent advances in the diagnosis, management and research of the disease prompted the revision of the classification that can be used by not only surgeons and pathologists but also by all clinicians and researchers, for the evaluation of current disease status, the determination of current appropriate treatment, and the future development of medical practice for biliary tract cancers. Furthermore, during the past 10 years, globalization has advanced rapidly, and therefore, internationalization of the classification was an important issue to revise the Japanese original staging system, which would facilitate to compare the disease information among institutions worldwide. In order to achieve these objectives, the new Japanese classification of the biliary tract cancers principally adopted the 7(th) edition of staging system developed by the International Union Against Cancer (UICC) and the American Joint Committee on Cancer (AJCC). However, because there are some points pending in these systems, several distinctive points were also included for the purpose of collection of information for the future optimization of the staging system. Free mobile application of the new Japanese classification of the biliary tract cancers is available via http://www.jshbps.jp/en/classification/cbt15.html. PMID:25691463

  1. [Level of smoking of 3rd and 4th grade students studying health and related factors: follow-up study].

    PubMed

    Göktalay, Tuğba; Cengiz Özyurt, Beyhan; Sakar Coşkun, Ayşin; Celik, Pinar

    2011-01-01

    The levels of smoking of 1st and 2nd year students at Faculty of Medicine and Manisa School of Health at Celal Bayar University were investigated in 2006-2007. This study is carried out in order to see if there is a change in the same students' level of smoking while they are in 3rd and 4th year. In addition, the study aimed to examine the factors affecting the level of use and attitudes towards the law effectuated in July 19, 2009. This is a follow-up study with 80.42% return rate. A 26-item structured questionnaire was administered. The participants filled out the questionnaires under supervision of the researchers in their classrooms. The University Institutional Review Board approved the study. The total of participants (263) of the follow-up study included 189 female and 74 male. The rate of experimenting with smoking was 49% with the mean age of 15.7 (SD= 4.01 years). The mean age of experimenting with smoking was the earliest on male students studying at faculty of medicine. The level of smoking was found to be the most on females, studying at faculty of medicine and staying at the dormitory, with smoking parents (p< 0.05). The most important reason to begin smoking was curiosity (55.2%) while bad breath and yellowing of teeth were the reasons to quit (91.7%). 83.3% of the students thought that the law will be effective on quit smoking. The level of both experimenting and use of smoking has been increased over time. It is suggested that medical students' awareness about the danger of smoking should be raised at earlier grades. In addition, lectures should be offered to students at School of Health and they should be encouraged to unite in order to fight with smoking. PMID:22233305

  2. Electrocradiographic Qrs Axis, Q Wave and T-wave Changes in 2nd and 3rd Trimester of Normal Pregnancy

    PubMed Central

    S., Chandrasekharappa; Brid, S.V

    2014-01-01

    Background: Pregnancy although a physiological phenomena affects all the functions of the maternal body and brings about remarkable changes in the cardiovascular system. The cardiovascular changes and many of the physiological adaptations of normal pregnancy alter the physical findings thus, sometimes misleading the diagnosis of heart disease. Pregnancy also brings about various changes in the electrocardiogram, further confusing with that of heart disease. This study is undertaken to highlight the effect of normal pregnancy on the QRS axis, Q wave and T-wave of the Electrocardiogram and thereby helps us to distinguish it from that of pathological changes. Objectives: To study the effect of normal pregnancy on the QRS axis, Q wave and T-wave in the electrocardiogram and to compare with that of normal non pregnant women. Materials and Methods: Fifty normal pregnant women in 2nd and 3rd trimester each between 20– 35 y of age and 50 normal non pregnant women of the same age group were selected for the study. A 12 lead ECG was recorded by using ECG machine with special emphasis on QRS axis, Q wave and T-wave changes and all the parameters were analysed. Results: The ECG changes observed in our study include, deviation of QRS axis towards left as pregnancy advanced, significant increased incidence of occurrence of prominent Q waves in lead II, III and avF in pregnant group (p < 0.05 ) and, T-wave abnormalities like flat and inverted T-waves in lead III, V1 – V3 were more frequent in pregnant group ( p<0.05 ) than in non pregnant group. Conclusion:Normal pregnancy brings about various changes in ECG. These changes during pregnancy should be interpretated with caution by the physicians. It is necessary to understand the normal physiological changes which in turn help us in better management of those with cardiac disease. PMID:25386425

  3. Classification of biliary tract cancers established by the Japanese Society of Hepato-Biliary-Pancreatic Surgery: 3(rd) English edition.

    PubMed

    Miyazaki, Masaru; Ohtsuka, Masayuki; Miyakawa, Shuichi; Nagino, Masato; Yamamoto, Masakazu; Kokudo, Norihiro; Sano, Keiji; Endo, Itaru; Unno, Michiaki; Chijiiwa, Kazuo; Horiguchi, Akihiko; Kinoshita, Hisafumi; Oka, Masaaki; Kubota, Keiichi; Sugiyama, Masanori; Uemoto, Shinji; Shimada, Mitsuo; Suzuki, Yasuyuki; Inui, Kazuo; Tazuma, Susumu; Furuse, Junji; Yanagisawa, Akio; Nakanuma, Yasuni; Kijima, Hiroshi; Takada, Tadahiro

    2015-03-01

    The 3(rd) English edition of the Japanese classification of biliary tract cancers was released approximately 10 years after the 5(th) Japanese edition and the 2(nd) English edition. Since the first Japanese edition was published in 1981, the Japanese classification has been in extensive use, particularly among Japanese surgeons and pathologists, because the cancer status and clinical outcomes in surgically resected cases have been the main objects of interest. However, recent advances in the diagnosis, management and research of the disease prompted the revision of the classification that can be used by not only surgeons and pathologists but also by all clinicians and researchers, for the evaluation of current disease status, the determination of current appropriate treatment, and the future development of medical practice for biliary tract cancers. Furthermore, during the past 10 years, globalization has advanced rapidly, and therefore, internationalization of the classification was an important issue to revise the Japanese original staging system, which would facilitate to compare the disease information among institutions worldwide. In order to achieve these objectives, the new Japanese classification of the biliary tract cancers principally adopted the 7(th) edition of staging system developed by the International Union Against Cancer (UICC) and the American Joint Committee on Cancer (AJCC). However, because there are some points pending in these systems, several distinctive points were also included for the purpose of collection of information for the future optimization of the staging system. Free mobile application of the new Japanese classification of the biliary tract cancers is available via http://www.jshbps.jp/en/classification/cbt15.html.

  4. An Unprecedented Non-canonical Nuclear Genetic Code with All Three Termination Codons Reassigned as Sense Codons.

    PubMed

    Záhonová, Kristína; Kostygov, Alexei Y; Ševčíková, Tereza; Yurchenko, Vyacheslav; Eliáš, Marek

    2016-09-12

    A limited number of non-canonical genetic codes have been described in eukaryotic nuclear genomes. Most involve reassignment of one or two termination codons as sense ones [1-4], but no code variant is known that would have reassigned all three termination codons. Here, we describe such a variant that we discovered in a clade of trypanosomatids comprising nominal Blastocrithidia species. In these protists, UGA has been reassigned to encode tryptophan, while UAG and UAA (UAR) have become glutamate encoding. Strikingly, UAA and, less frequently, UAG also serve as bona fide termination codons. The release factor eRF1 in Blastocrithidia contains a substitution of a conserved serine residue predicted to decrease its affinity to UGA, which explains why this triplet can be read as a sense codon. However, the molecular basis for the dual interpretation of UAR codons remains elusive. Our findings expand the limits of comprehension of one of the fundamental processes in molecular biology.

  5. An Unprecedented Non-canonical Nuclear Genetic Code with All Three Termination Codons Reassigned as Sense Codons.

    PubMed

    Záhonová, Kristína; Kostygov, Alexei Y; Ševčíková, Tereza; Yurchenko, Vyacheslav; Eliáš, Marek

    2016-09-12

    A limited number of non-canonical genetic codes have been described in eukaryotic nuclear genomes. Most involve reassignment of one or two termination codons as sense ones [1-4], but no code variant is known that would have reassigned all three termination codons. Here, we describe such a variant that we discovered in a clade of trypanosomatids comprising nominal Blastocrithidia species. In these protists, UGA has been reassigned to encode tryptophan, while UAG and UAA (UAR) have become glutamate encoding. Strikingly, UAA and, less frequently, UAG also serve as bona fide termination codons. The release factor eRF1 in Blastocrithidia contains a substitution of a conserved serine residue predicted to decrease its affinity to UGA, which explains why this triplet can be read as a sense codon. However, the molecular basis for the dual interpretation of UAR codons remains elusive. Our findings expand the limits of comprehension of one of the fundamental processes in molecular biology. PMID:27593378

  6. p53 codon 72 polymorphism and human papillomavirus associated skin cancer

    PubMed Central

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

    2001-01-01

    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

  7. Structural Basis for Translation Termination on a Pseudouridylated Stop Codon.

    PubMed

    Svidritskiy, Egor; Madireddy, Rohini; Korostelev, Andrei A

    2016-05-22

    Pseudouridylation of messenger RNA emerges as an abundant modification involved in gene expression regulation. Pseudouridylation of stop codons in eukaryotic and bacterial cells results in stop-codon read through. The structural mechanism of this phenomenon is not known. Here we present a 3.1-Å crystal structure of Escherichia coli release factor 1 (RF1) bound to the 70S ribosome in response to the ΨAA codon. The structure reveals that recognition of a modified stop codon does not differ from that of a canonical stop codon. Our in vitro biochemical results support this finding by yielding nearly identical rates for peptide release from E. coli ribosomes programmed with pseudouridylated and canonical stop codons. The crystal structure also brings insight into E. coli RF1-specific interactions and suggests involvement of L27 in bacterial translation termination. Our results are consistent with a mechanism in which read through of a pseudouridylated stop codon in bacteria results from increased decoding by near-cognate tRNAs (miscoding) rather than from decreased efficiency of termination. PMID:27107638

  8. Premature termination codons in modern human genomes

    PubMed Central

    Fujikura, Kohei

    2016-01-01

    The considerable range of genetic variation in human populations may partly reflect distinctive processes of adaptation to variable environmental conditions. However, the adaptive genomic signatures remain to be completely elucidated. This research explores candidate loci under selection at the population level by characterizing recently arisen premature termination codons (PTCs), some of which indicate a human knockout. From a total of 7595 participants from two population exome projects, 246 PTCs were found where natural selection has resulted in new alleles with a high frequency (from 1% to 96%) of derived alleles and various levels of population differentiation (FST = 0.00139–0.626). The PTC genes formed protein and regulatory networks limited to 15 biological processes or gene families, of which seven categories were previously unreported. PTC mutations have a strong tendency to be introduced into members of the same gene family, even during modern human evolution, although the exact nature of the selection is not fully known. The findings here suggest the ongoing evolutionary plasticity of modern humans at the genetic level and also partly provide insights into common human knockouts. PMID:26932450

  9. Analysis of amino acid and codon usage in Paramecium bursaria.

    PubMed

    Dohra, Hideo; Fujishima, Masahiro; Suzuki, Haruo

    2015-10-01

    The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis. PMID:26341535

  10. Analysis of amino acid and codon usage in Paramecium bursaria.

    PubMed

    Dohra, Hideo; Fujishima, Masahiro; Suzuki, Haruo

    2015-10-01

    The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis.

  11. Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes.

    PubMed

    Nakagawa, So; Niimura, Yoshihito; Gojobori, Takashi; Tanaka, Hiroshi; Miura, Kin-ichiro

    2008-02-01

    Understanding regulatory mechanisms of protein synthesis in eukaryotes is essential for the accurate annotation of genome sequences. Kozak reported that the nucleotide sequence GCCGCC(A/G)CCAUGG (AUG is the initiation codon) was frequently observed in vertebrate genes and that this 'consensus' sequence enhanced translation initiation. However, later studies using invertebrate, fungal and plant genes reported different 'consensus' sequences. In this study, we conducted extensive comparative analyses of nucleotide sequences around the initiation codon by using genomic data from 47 eukaryote species including animals, fungi, plants and protists. The analyses revealed that preferred nucleotide sequences are quite diverse among different species, but differences between patterns of nucleotide bias roughly reflect the evolutionary relationships of the species. We also found strong biases of A/G at position -3, A/C at position -2 and C at position +5 that were commonly observed in all species examined. Genes with higher expression levels showed stronger signals, suggesting that these nucleotides are responsible for the regulation of translation initiation. The diversity of preferred nucleotide sequences around the initiation codon might be explained by differences in relative contributions from two distinct patterns, GCCGCCAUG and AAAAAAAUG, which implies the presence of multiple molecular mechanisms for controlling translation initiation.

  12. In vitro cultivation of Hysterothylacium aduncum (Nematoda: Anisakidae) from 3rd-stage larvae to egg-laying adults.

    PubMed

    Iglesias, L; Valero, A; Gálvez, L; Benítez, R; Adroher, F J

    2002-11-01

    This is the first demonstration of the in vitro development of the 3rd-stage larvae (L3) of Hysterothylacium aduncum to the adult. This was achieved in a semi-defined medium that is easy to prepare and to reproduce. The L3, collected from the peritoneal cavity of horse mackerel (Trachurus trachurus), were individually inoculated into RPMI-1640 medium +20% heat-inactivated fetal bovine serum (IFBS). It has been demonstrated that the optimum temperature for development is around 13 degrees C and is stimulated by the presence of 5% CO2 in the growth atmosphere, increasing the percentage moulting to the 4th larval stage (L4) by 1.9-fold (from 44 to 82%) and the average survival of the nematodes by 1.6 times (from 60 to 96 days). When the larvae were grown at different pHs, optimum development occurred at pH 4.0. Under these conditions, all the larvae moulted to the L4 and more than two-thirds transformed to the adult stage--in which 25-30% of the females laid eggs--and reached an average survival of over 4 months. When this medium was supplemented with 1% (w/v) of commercial pepsin, all the larvae reached the adult stage, at least 45% of the females oviposited, laying around 12-fold more eggs per female than in the medium without pepsin. The mean size of the eggs (non-fertilized) obtained was 56.8 x 47.6 microm. The mean length of the adult males obtained was between 3.2 and 5.2 cm and the females were between 3.0 and 6.5 cm. The adult specimens were morphologically identified as Hysterothylacium aducum aduncum. This culture medium (RPMI-1640+20% (v/v) IFBS+1 commercial pepsin, at pH 4.0, 13 degrees C and 5% CO2 in air) could facilitate the identification of at least some of the larvae of the genus Hysterothylacium--and perhaps other anisakids--for which the specific identification and the biological study of these parasites is often difficult. PMID:12458831

  13. PREFACE: 3rd International Conference on Geological, Geographical, Aerospace and Earth Science 2015 (AeroEarth 2015)

    NASA Astrophysics Data System (ADS)

    Gaol, F. L.

    2016-02-01

    The 3rd International Conferences on Geological, Geographical, Aerospaces and Earth Sciences 2015 (AeroEarth 2015), was held at The DoubleTree Hilton, Jakarta, Indonesia during 26 - 27 September 2015. The 1st AeoroEarth was held succefully in Jakarta in 2013. The success continued to The 2nd AeroEarth 2014 that was held in Kuta Bali, Indonesia. The publications were published by EES IOP in http://iopscience.iop.org/1755-1315/19/1 and http://iopscience.iop.org/1755-1315/23/1 respectively. The AeroEarth 2015 conference aims to bring together researchers, engineers and scientists from around the world. Through research and development, Earth's scientists have the power to preserve the planet's different resource domains by providing expert opinion and information about the forces which make life possible on Earth. The theme of AeroEarth 2015 is ''Earth and Aerospace Sciences : Challenges and Opportunities'' Earth provides resources and the exact conditions to make life possible. However, with the advent of technology and industrialization, the Earth's resources are being pushed to the brink of depletion. Non-sustainable industrial practices are not only endangering the supply of the Earth's natural resources, but are also putting burden on life itself by bringing about pollution and climate change. A major role of earth science scholars is to examine the delicate balance between the Earth's resources and the growing demands of industrialization. Through research and development, earth scientists have the power to preserve the planet's different resource domains by providing expert opinion and information about the forces which make life possible on Earth. We would like to express our sincere gratitude to all in the Technical Program Committee who have reviewed the papers and developed a very interesting Conference Program as well as the invited and plenary speakers. This year, we received 78 papers and after rigorous review, 18 papers were accepted. The participants

  14. Effect on Physical Activity of a Randomized Afterschool Intervention for Inner City Children in 3rd to 5th Grade

    PubMed Central

    Crouter, Scott E.; de Ferranti, Sarah D.; Whiteley, Jessica; Steltz, Sarah K.; Osganian, Stavroula K.; Feldman, Henry A.; Hayman, Laura L.

    2015-01-01

    Background Less than 45% of U.S. children meet the 60 min.d-1 physical activity (PA) guideline. Structured after-school PA programing is one approach to help increase activity levels. This study aimed to evaluate the feasibility and short-term impact of a supervised after-school PA and nutrition education program on activity levels. Methods Forty-two 3rd-5th graders from an inner-city school in Boston, MA were randomly assigned to a 10-wk after-school program of either: 1) weekly nutrition education, or 2) weekly nutrition education plus supervised PA 3 d.wk-1 at a community-based center. At baseline and follow-up, PA was measured using accelerometry and fitness (VO2max) was estimated using the PACER 15-m shuttle run. Additional measures obtained were non-fasting finger stick total cholesterol (TC) and glucose levels, waist circumference (WC), body mass index (BMI), percent body fat (%BF), and blood pressure (BP). Values are presented as mean±SE, unless noted otherwise. Results Thirty-six participants completed the study (mean±SD; age 9.7±0.9 years). Participants attended >80% of the sessions. After adjusting for accelerometer wear time and other design factors, light and moderate-to-vigorous PA (MVPA) increased in the nutrition+PA group (+21.5±14.5 and +8.6±8.0 min.d-1, respectively) and decreased in the nutrition only group (-35.2±16.3 and -16.0±9.0 min.d-1, respectively); mean difference between groups of 56.8±21.7 min.d-1 (light PA, p = 0.01) and 24.5±12.0 min.d-1 (MVPA, p = 0.04). Time spent in sedentary behaviors declined in the nutrition+PA group (-14.8±20.7 min.d-1) and increased in the nutrition only group (+55.4±23.2 min.d-1); mean difference between groups of -70.2±30.9 min.d-1 (p = 0.02). Neither group showed changes in TC, BP, WC, %BF, BMI percentile, or fitness (p>0.05). Conclusions The supervised afterschool community-based nutrition and PA program was well accepted and had high attendance. The changes in light PA and MVPA has potential

  15. PREFACE: 3rd International Conference on Science & Engineering in Mathematics, Chemistry and Physics 2015 (ScieTech 2015)

    NASA Astrophysics Data System (ADS)

    Gaol, F. L.

    2015-06-01

    The 3rd International Conference on Science & Engineering in Mathematics, Chemistry and Physics 2015 (ScieTech 2015), was held at The Westin Resort Nusa Dua, Bali on 31 January - 1 February 2015. The ScieTech 2015 conference is aimed to bring together researchers, engineers and scientists from around the world. ScieTech 2015 is placed on promoting interaction between the theoretical, experimental, and applied communities, so that a high level exchange is achieved in new and emerging areas within mathematics, chemistry and physics. As we already know that science and technology have brought tremendous benefits for human civilization. People are becoming healthier, wealthier, better educated, more peaceful, increasingly connected, and living longer. Of course, science and technology provide many answers to global challenges, but we will face more complex problems in the next decade due to increasing world population, limitation of energy, and climate change. Therefore, researchers should be more active in conducting research that enables collaboration between one and the others. Interdisciplinary cooperation is absolutely necessary in order to create a smart system for solving the global problems. We need a global and general long-term view of the future with long-range goals for solving complex problems in next decade. Therefore the conference was held to be a forum for researchers from different disciplines to start collaborating and conducting research that provides a solution to the global issues. The theme of ScieTech 2015 was ''The interdisciplinary Application between Mathematics, Chemistry and Physics to enhance the Quality of Life''. We would like to express our sincere gratitude to all in the Technical Program Committee who have reviewed the papers and developed a very interesting conference program as well as the invited and plenary speakers. This year, we received 197 papers and after rigorous review, 59 papers were accepted. The participants came from 19

  16. Effects of an Opal Termination Codon Preceding the nsP4 Gene Sequence in the O'Nyong-Nyong Virus Genome on Anopheles gambiae Infectivity

    PubMed Central

    Myles, Kevin M.; Kelly, Cindy L. H.; Ledermann, Jeremy P.; Powers, Ann M.

    2006-01-01

    The genomic RNA of an alphavirus encodes four different nonstructural proteins, nsP1, nsP2, nsP3, and nsP4. The polyprotein P123 is produced when translation terminates at an opal termination codon between nsP3 and nsP4. The polyprotein P1234 is produced when translational readthrough occurs or when the opal termination codon has been replaced by a sense codon in the alphavirus genome. Evolutionary pressures appear to have maintained genomic sequences encoding both a stop codon (opal) and an open reading frame (arginine) as a general feature of the O'nyong-nyong virus (ONNV) genome, indicating that both are required at some point. Alternate replication of ONNVs in both vertebrate and invertebrate hosts may determine predominance of a particular codon at this locus in the viral quasispecies. However, no systematic study has previously tested this hypothesis in whole animals. We report here the results of the first study to investigate in a natural mosquito host the functional significance of the opal stop codon in an alphavirus genome. We used a full-length cDNA clone of ONNV to construct a series of mutants in which the arginine between nsP3 and nsP4 was replaced with an opal, ochre, or amber stop codon. The presence of an opal stop codon upstream of nsP4 nearly doubled (75.5%) the infectivity of ONNV over that of virus possessing a codon for the amino acid arginine at the corresponding position (39.8%). Although the frequency with which the opal virus disseminated from the mosquito midgut did not differ significantly from that of the arginine virus on days 8 and 10, dissemination did began earlier in mosquitoes infected with the opal virus. Although a clear fitness advantage is provided to ONNV by the presence of an opal codon between nsP3 and nsP4 in Anopheles gambiae, sequence analysis of ONNV RNA extracted from mosquito bodies and heads indicated codon usage at this position corresponded with that of the virus administered in the blood meal. These results

  17. Effects of an opal termination codon preceding the nsP4 gene sequence in the O'Nyong-Nyong virus genome on Anopheles gambiae infectivity.

    PubMed

    Myles, Kevin M; Kelly, Cindy L H; Ledermann, Jeremy P; Powers, Ann M

    2006-05-01

    The genomic RNA of an alphavirus encodes four different nonstructural proteins, nsP1, nsP2, nsP3, and nsP4. The polyprotein P123 is produced when translation terminates at an opal termination codon between nsP3 and nsP4. The polyprotein P1234 is produced when translational readthrough occurs or when the opal termination codon has been replaced by a sense codon in the alphavirus genome. Evolutionary pressures appear to have maintained genomic sequences encoding both a stop codon (opal) and an open reading frame (arginine) as a general feature of the O'nyong-nyong virus (ONNV) genome, indicating that both are required at some point. Alternate replication of ONNVs in both vertebrate and invertebrate hosts may determine predominance of a particular codon at this locus in the viral quasispecies. However, no systematic study has previously tested this hypothesis in whole animals. We report here the results of the first study to investigate in a natural mosquito host the functional significance of the opal stop codon in an alphavirus genome. We used a full-length cDNA clone of ONNV to construct a series of mutants in which the arginine between nsP3 and nsP4 was replaced with an opal, ochre, or amber stop codon. The presence of an opal stop codon upstream of nsP4 nearly doubled (75.5%) the infectivity of ONNV over that of virus possessing a codon for the amino acid arginine at the corresponding position (39.8%). Although the frequency with which the opal virus disseminated from the mosquito midgut did not differ significantly from that of the arginine virus on days 8 and 10, dissemination did began earlier in mosquitoes infected with the opal virus. Although a clear fitness advantage is provided to ONNV by the presence of an opal codon between nsP3 and nsP4 in Anopheles gambiae, sequence analysis of ONNV RNA extracted from mosquito bodies and heads indicated codon usage at this position corresponded with that of the virus administered in the blood meal. These results

  18. Human alpha and beta papillomaviruses use different synonymous codon profiles.

    PubMed

    Cladel, Nancy M; Bertotto, Alex; Christensen, Neil D

    2010-06-01

    Human papillomaviruses use rare codons relative to their hosts. It has been theorized that this is a mechanism to allow the virus to escape immune surveillance. In the present study, we examined the codings of four major genes of 21 human alpha (mucosatropic) viruses and 16 human beta (cutaneous-tropic) viruses. We compared the codon usage of different genes from a given papillomavirus and also the same genes from different papillomaviruses. Our data showed that codon usage was not always uniform between two genes of a given papillomavirus or between the same genes of papillomaviruses from different genera. We speculate as to why this might be and conclude that codon usage in the papillomaviruses may not only play a role in facilitating escape from immune surveillance but may also underlie some of the unanswered questions in the papillomavirus field.

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

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

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

  20. α(+)-Thalassemia Due to a Frameshift Mutation of the α2-Globin Gene [codons 55/56 (+T) or HBA2: c.168dup].

    PubMed

    Waye, John S; Eng, Barry; Hanna, Meredith; Hohenadel, Betty-Ann; Nakamura, Lisa M; Walker, Lynda

    2015-01-01

    We report a case of α(+)-thalassemia (α(+)-thal) trait in a Chinese-Canadian family caused by a novel frameshift mutation of the α2-globin gene, specifically the duplication of a single nucleotide at amino acid codon 56 [HBA2: c.168dup]. The mutation results in substitution of a termination codon (TAA) for lysine (AAG) at amino acid position 56.

  1. Sequence coding for the alphavirus nonstructural proteins is interrupted by an opal termination codon.

    PubMed Central

    Strauss, E G; Rice, C M; Strauss, J H

    1983-01-01

    We have obtained the nucleotide sequence of the genomic RNAs of two alphaviruses, Sindbis virus and Middelburg virus, over an extensive region encoding the nonstructural (replicase) proteins. In both viruses in an equivalent position an opal (UGA) termination codon punctuates a long otherwise open reading frame. The nonstructural proteins are translated as polyprotein precursors that are processed by posttranslational cleavage into four polypeptide chains; the sequence data presented here indicate that the COOH-terminal polypeptide, ns72, may be produced by read-through of this opal codon. The high degree of amino acid homology between the ns72 polypeptides of the two viruses, in contrast to the lack of conserved sequence upstream from the read-through site, suggests that ns72 plays an important role in viral replication, possibly modulating the action of other replicase components. PMID:6577423

  2. Codon Usage Bias and Determining Forces in Taenia solium Genome.

    PubMed

    Yang, Xing; Ma, Xusheng; Luo, Xuenong; Ling, Houjun; Zhang, Xichen; Cai, Xuepeng

    2015-12-01

    The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome. PMID:26797435

  3. Codon Usage Bias and Determining Forces in Taenia solium Genome.

    PubMed

    Yang, Xing; Ma, Xusheng; Luo, Xuenong; Ling, Houjun; Zhang, Xichen; Cai, Xuepeng

    2015-12-01

    The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

  4. Codon Usage Bias and Determining Forces in Taenia solium Genome

    PubMed Central

    Yang, Xing; Ma, Xusheng; Luo, Xuenong; Ling, Houjun; Zhang, Xichen; Cai, Xuepeng

    2015-01-01

    The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome. PMID:26797435

  5. Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis.

    PubMed

    Jacob, Etai; Unger, Ron; Horovitz, Amnon

    2015-09-15

    Methods for analysing correlated mutations in proteins are becoming an increasingly powerful tool for predicting contacts within and between proteins. Nevertheless, limitations remain due to the requirement for large multiple sequence alignments (MSA) and the fact that, in general, only the relatively small number of top-ranking predictions are reliable. To date, methods for analysing correlated mutations have relied exclusively on amino acid MSAs as inputs. Here, we describe a new approach for analysing correlated mutations that is based on combined analysis of amino acid and codon MSAs. We show that a direct contact is more likely to be present when the correlation between the positions is strong at the amino acid level but weak at the codon level. The performance of different methods for analysing correlated mutations in predicting contacts is shown to be enhanced significantly when amino acid and codon data are combined.

  6. Codon-level information improves predictions of inter-residue contacts in proteins by correlated mutation analysis

    PubMed Central

    Jacob, Etai; Unger, Ron; Horovitz, Amnon

    2015-01-01

    Methods for analysing correlated mutations in proteins are becoming an increasingly powerful tool for predicting contacts within and between proteins. Nevertheless, limitations remain due to the requirement for large multiple sequence alignments (MSA) and the fact that, in general, only the relatively small number of top-ranking predictions are reliable. To date, methods for analysing correlated mutations have relied exclusively on amino acid MSAs as inputs. Here, we describe a new approach for analysing correlated mutations that is based on combined analysis of amino acid and codon MSAs. We show that a direct contact is more likely to be present when the correlation between the positions is strong at the amino acid level but weak at the codon level. The performance of different methods for analysing correlated mutations in predicting contacts is shown to be enhanced significantly when amino acid and codon data are combined. DOI: http://dx.doi.org/10.7554/eLife.08932.001 PMID:26371555

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

    PubMed

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

    2012-12-01

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

  8. Human alpha2-globin nonsense-mediated mRNA decay induced by a novel alpha-thalassaemia frameshift mutation at codon 22.

    PubMed

    Pereira, Francisco J C; do Céu Silva, Maria; Picanço, Isabel; Seixas, Maria T; Ferrão, Anabela; Faustino, Paula; Romão, Luísa

    2006-04-01

    We describe a novel alpha-thalassaemia determinant in a 3-year-old girl presenting a mild microcytic and hypochromic anaemia, and normal haemoglobin A2 level. Molecular studies revealed heterozygosity for a novel microdeletion (-C) at codon 22 of the alpha2-globin gene. As the frameshift mutation generates a premature translation termination codon at position 48/49, we investigated the effect of the nonsense codon on the alpha2-globin gene expression. Although it does not affect RNA splicing, the premature nonsense codon induces accelerated mRNA degradation. To our knowledge, this is the first time the nonsense-mediated mRNA decay has been reported to occur in human alpha-globin mRNA.

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

    PubMed Central

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

    2004-01-01

    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 genomic changes following symbiosis. We identified clear strand asymmetries, distribution biases (putative high-expression genes were found more often on the leading strand), and a residual slight codon bias within each strand. Amino acid usage was strongly biased in putative high-expression genes, characterized by avoidance of aromatic amino acids, but above all by greater conservation and resistance to AT enrichment. Despite the almost complete loss of codon bias and heavy mutational pressure, selective forces are still strong at nonsynonymous sites of a fraction of the genome. However, Buchnera from Baizongia pistaciae appears to have suffered a stronger symbiotic syndrome than the two other species. PMID:14672975

  10. Recognition of the amber UAG stop codon by release factor RF1

    SciTech Connect

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

    2010-08-23

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

  11. Factors impacting the aminoglycoside-induced UGA stop codon readthrough in selenoprotein translation.

    PubMed

    Martitz, Janine; Hofmann, Peter Josef; Johannes, Jörg; Köhrle, Josef; Schomburg, Lutz; Renko, Kostja

    2016-09-01

    Aminoglycosides (AG) are oligosaccharide antibiotics that interfere with the small ribosomal subunit in aerobic, Gram-negative bacteria, causing pathogen-destructing error rates in their protein biosynthesis. Aminoglycosides also induce mRNA misinterpretation in eukaryotic cells, especially of the UGA (Opal)-stop codon, albeit to a lower extent. UGA recoding is essentially required for the incorporation of selenocysteine (Sec) into growing selenoproteins during translation. Selenocysteine incorporation requires the presence of a selenoprotein-specific stem-loop structure within the 3'-untranslated region of the mRNA, the so-called Sec-insertion sequence (SECIS) element. Interestingly, selenoprotein genes differ in their SECIS-element sequence and in their UGA base context. We hypothesized that the SECIS-element and the specific codon context synergize in controlling the effects of AG on stop codon readthrough. To this end, the SECIS-elements of glutathione peroxidase 1, glutathione peroxidase 4 and selenoprotein P transcripts were cloned into a reporter system and analyzed in combination with different UGA codon contexts. Our results indicate that a cytosine in position 4 (directly downstream of UGA) confers strongest effects on both the Se- and AG-dependent readthrough. Overall selenoprotein biosynthesis rate depends on the Se-status, AG concentration and the specific SECIS-element present in the transcript. These findings help to get a better understanding for the susceptibility of different transcripts towards AG-mediated interference with the biosynthesis of functional Se-containing selenoproteins, and highlight the importance of the Se-status for successful selenoprotein biosynthesis under antibiotic therapy. PMID:27157664

  12. Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae.

    PubMed

    Li, Xiuzhang; Song, Hui; Kuang, Yu; Chen, Shuihong; Tian, Pei; Li, Chunjie; Nan, Zhibiao

    2016-01-01

    Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C. PMID:27428961

  13. Genome-Wide Analysis of Codon Usage Bias in Epichloë festucae

    PubMed Central

    Li, Xiuzhang; Song, Hui; Kuang, Yu; Chen, Shuihong; Tian, Pei; Li, Chunjie; Nan, Zhibiao

    2016-01-01

    Analysis of codon usage data has both practical and theoretical applications in understanding the basics of molecular biology. Differences in codon usage patterns among genes reflect variations in local base compositional biases and the intensity of natural selection. Recently, there have been several reports related to codon usage in fungi, but little is known about codon usage bias in Epichloë endophytes. The present study aimed to assess codon usage patterns and biases in 4870 sequences from Epichloë festucae, which may be helpful in revealing the constraint factors such as mutation or selection pressure and improving the bioreactor on the cloning, expression, and characterization of some special genes. The GC content with 56.41% is higher than the AT content (43.59%) in E. festucae. The results of neutrality and effective number of codons plot analyses showed that both mutational bias and natural selection play roles in shaping codon usage in this species. We found that gene length is strongly correlated with codon usage and may contribute to the codon usage patterns observed in genes. Nucleotide composition and gene expression levels also shape codon usage bias in E. festucae. E. festucae exhibits codon usage bias based on the relative synonymous codon usage (RSCU) values of 61 sense codons, with 25 codons showing an RSCU larger than 1. In addition, we identified 27 optimal codons that end in a G or C. PMID:27428961

  14. An Engineered Rare Codon Device for Optimization of Metabolic Pathways

    PubMed Central

    Wang, You; Li, Chunying; Khan, Md. Rezaul Islam; Wang, Yushu; Ruan, Yunfeng; Zhao, Bin; Zhang, Bo; Ma, Xiaopan; Zhang, Kaisi; Zhao, Xiwen; Ye, Guanhao; Guo, Xizhi; Feng, Guoyin; He, Lin; Ma, Gang

    2016-01-01

    Rare codons generally arrest translation due to rarity of their cognate tRNAs. This property of rare codons can be utilized to regulate protein expression. In this study, a linear relationship was found between expression levels of genes and copy numbers of rare codons inserted within them. Based on this discovery, we constructed a molecular device in Escherichia coli using the rare codon AGG, its cognate tRNA (tRNAArg (CCU)), modified tRNAAsp (GUC → CCU), and truncated aspartyl-tRNA synthetase (TDRS) to switch the expression of reporter genes on or off as well as to precisely regulate their expression to various intermediate levels. To underscore the applicability of our work, we used the rare codon device to alter the expression levels of four genes of the fatty acid synthesis II (FASII) pathway (i.e. fabZ, fabG, fabI, and tesA’) in E. coli to optimize steady-state kinetics, which produced nearly two-fold increase in fatty acid yield. Thus, the proposed method has potential applications in regulating target protein expression at desired levels and optimizing metabolic pathways by precisely tuning in vivo molar ratio of relevant enzymes. PMID:26852704

  15. Impact of rare codons and the functional coproduction of rate-limiting tRNAs on recombinant protein production in Bacillus megaterium.

    PubMed

    Finger, Constanze; Gamer, Martin; Klunkelfuß, Saskia; Bunk, Boyke; Biedendieck, Rebekka

    2015-11-01

    The Gram-positive bacterium Bacillus megaterium was systematically developed for the plasmid-based production of recombinant proteins at the gram-per-liter scale. The amount of protein produced per cell was found strongly correlated to the codon usage of the heterologous gene of interest in comparison to the codon usage of B. megaterium. For analyzing the influence of rare codons on the translational efficiency and protein production in B. megaterium, a test system using the gene for the green fluorescent protein (GFP) as reporter was established. For this purpose, four consecutive identical codons were introduced into the 5' end of gfp and the resulting variations in GFP formation were quantified. Introduction of the rare codons GCC, CGG, and ACC for alanine, arginine, and threonine reduced GFP production 2.1-, 3.3-, and 1.7-fold in comparison to the favored codons GCU, CGU, and ACA, respectively. Coexpression of the corresponding rare codon tRNA (rctRNA) genes improved GFP production 4.2-, 2.7-, and 1.7-fold, respectively. The system was applied to the production of a formate dehydrogenase (FDH) from Mycobacterium vaccae and an extracellular hydrolase (TFH) from Thermobifida fusca. Coexpression of one to three different rctRNA genes resulted in an up to 18-fold increased protein production. Interestingly, rctRNA gene coexpression also elevated the production of M. vaccae FDH and T. fusca TFH from codon optimized genes, indicating a general positive effect by rctRNA gene overexpression on the protein production in B. megaterium. Thus, the basis for a B. megaterium enhanced production strain coexpressing rctRNA genes was laid. PMID:26138251

  16. Impact of rare codons and the functional coproduction of rate-limiting tRNAs on recombinant protein production in Bacillus megaterium.

    PubMed

    Finger, Constanze; Gamer, Martin; Klunkelfuß, Saskia; Bunk, Boyke; Biedendieck, Rebekka

    2015-11-01

    The Gram-positive bacterium Bacillus megaterium was systematically developed for the plasmid-based production of recombinant proteins at the gram-per-liter scale. The amount of protein produced per cell was found strongly correlated to the codon usage of the heterologous gene of interest in comparison to the codon usage of B. megaterium. For analyzing the influence of rare codons on the translational efficiency and protein production in B. megaterium, a test system using the gene for the green fluorescent protein (GFP) as reporter was established. For this purpose, four consecutive identical codons were introduced into the 5' end of gfp and the resulting variations in GFP formation were quantified. Introduction of the rare codons GCC, CGG, and ACC for alanine, arginine, and threonine reduced GFP production 2.1-, 3.3-, and 1.7-fold in comparison to the favored codons GCU, CGU, and ACA, respectively. Coexpression of the corresponding rare codon tRNA (rctRNA) genes improved GFP production 4.2-, 2.7-, and 1.7-fold, respectively. The system was applied to the production of a formate dehydrogenase (FDH) from Mycobacterium vaccae and an extracellular hydrolase (TFH) from Thermobifida fusca. Coexpression of one to three different rctRNA genes resulted in an up to 18-fold increased protein production. Interestingly, rctRNA gene coexpression also elevated the production of M. vaccae FDH and T. fusca TFH from codon optimized genes, indicating a general positive effect by rctRNA gene overexpression on the protein production in B. megaterium. Thus, the basis for a B. megaterium enhanced production strain coexpressing rctRNA genes was laid.

  17. [Use of imaging methods in the current screening, diagnostics and treatment of breast cancer - Professional guidelines. 3rd Breast Cancer Consensus Meeting].

    PubMed

    Forrai, Gábor; Ambrózay, Éva; Bidlek, Mária; Borbély, Katalin; Kovács, Eszter; Lengyel, Zsolt; Ormándi, Katalin; Péntek, Zoltán; Riedl, Erika; Sebõ, Éva; Szabó, Éva

    2016-09-01

    Breast radiologists and nuclear medical specialists have refreshed their previous statement text during the 3rd Hungarian Breast Cancer Consensus Meeting. They suggest taking into consideration this actual protocol for the screening, diagnostics and treatment of breast tumors, from now on. This recommendation includes the description of the newest technologies, the recent results of scientific research, as well as the role of imaging methods in the therapeutic processes and the follow-up. Suggestions for improvement of the Hungarian current practice and other related issues as forensic medicine, media connections, regulations, and reimbursement are also detailed. The statement text has been cross-checked with the related medical disciplines. PMID:27579719

  18. Influence of the TP53 codon 72 polymorphism on the cellular responses to X-irradiation in fibroblasts from nonagenarians.

    PubMed

    den Reijer, P Martijn; Maier, Andrea B; Westendorp, Rudi G J; van Heemst, Diana

    2008-04-01

    In mice, genetic modification of the gene encoding p53 affects both cancer incidence and longevity. In humans, we recently found that a TP53 codon 72 Arginine (Arg) to Proline (Pro) polymorphism affected both cancer incidence and longevity as well. The TP53 codon 72 polymorphism has previously been shown to influence the apoptotic potential of human cells in response to oxidative stress. Here, we studied the influence of this polymorphism on the cellular responses to X-irradiation of fibroblasts obtained from nonagenarians. We found that the average clonogenic survival after X-irradiation was similar for the three TP53 codon 72 genotype groups. As described before, X-irradiation did not induce an appreciable degree of apoptosis in human fibroblasts. However, percentages of senescence-associated (SA)-beta-galactosidase positive cells (p < 0.001), micronucleated cells (p < 0.001) and cells displaying abnormal nuclear morphologies (p < 0.001) significantly increased with the radiation dose. Compared to Arg/Arg fibroblasts, Pro/Pro fibroblasts exhibited higher irradiation dose-dependent increases in SA-beta-galactosidase positive cells (p(interaction) = 0.018), micronucleated cells (p(interaction) = 0.005) and cells displaying abnormal nuclear morphologies (p(interaction) = 0.029) at 3 days after irradiation. Possibly, these differences in cellular responses to stress between the TP53 codon 72 genotypes contribute to the differences in cancer incidence and longevity observed earlier for these genotypes. PMID:18272203

  19. Design, synthesis, and testing toward a 57-codon genome.

    PubMed

    Ostrov, Nili; Landon, Matthieu; Guell, Marc; Kuznetsov, Gleb; Teramoto, Jun; Cervantes, Natalie; Zhou, Minerva; Singh, Kerry; Napolitano, Michael G; Moosburner, Mark; Shrock, Ellen; Pruitt, Benjamin W; Conway, Nicholas; Goodman, Daniel B; Gardner, Cameron L; Tyree, Gary; Gonzales, Alexandra; Wanner, Barry L; Norville, Julie E; Lajoie, Marc J; Church, George M

    2016-08-19

    Recoding--the repurposing of genetic codons--is a powerful strategy for enhancing genomes with functions not commonly found in nature. Here, we report computational design, synthesis, and progress toward assembly of a 3.97-megabase, 57-codon Escherichia coli genome in which all 62,214 instances of seven codons were replaced with synonymous alternatives across all protein-coding genes. We have validated 63% of recoded genes by individually testing 55 segments of 50 kilobases each. We observed that 91% of tested essential genes retained functionality with limited fitness effect. We demonstrate identification and correction of lethal design exceptions, only 13 of which were found in 2229 genes. This work underscores the feasibility of rewriting genomes and establishes a framework for large-scale design, assembly, troubleshooting, and phenotypic analysis of synthetic organisms. PMID:27540174

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

    NASA Astrophysics Data System (ADS)

    Lind, Christoffer; Sund, Johan; Åqvist, Johan

    2013-12-01

    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.

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

    PubMed Central

    Chithambaram, Shivapriya; Prabhakaran, Ramanandan; Xia, Xuhua

    2014-01-01

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

  2. A primary cardiac leiomyosarcoma with mutation at H-ras codon 12.

    PubMed

    Parissis, J; Arvanitis, D; Sourvinos, G; Spandidos, D

    1997-01-01

    The presence of activating ras mutations in a cardiac leiomyosarcoma which occurred in the right atrium of the heart of a female patient was examined. The tumor had the appearance of leiomyosarcoma in rutine histopathological examination and the definite diagnosis was confirmed by a positive immunohistochemical reaction to smooth muscle actin. Molecular analysis by polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) technique showed a point mutation of H-ras gene at codon 12. To the best of our knowledge, this is the first report describing ras gene mutation in a cardiac leiomyosarcoma implying a role for the ras oncogenes in the development of this tumor.

  3. Gene classification using codon usage and support vector machines.

    PubMed

    Ma, Jianmin; Nguyen, Minh N; Rajapakse, Jagath C

    2009-01-01

    A novel approach for gene classification, which adopts codon usage bias as input feature vector for classification by support vector machines (SVM) is proposed. The DNA sequence is first converted to a 59-dimensional feature vector where each element corresponds to the relative synonymous usage frequency of a codon. As the input to the classifier is independent of sequence length and variance, our approach is useful when the sequences to be classified are of different lengths, a condition that homology-based methods tend to fail. The method is demonstrated by using 1,841 Human Leukocyte Antigen (HLA) sequences which are classified into two major classes: HLA-I and HLA-II; each major class is further subdivided into sub-groups of HLA-I and HLA-II molecules. Using codon usage frequencies, binary SVM achieved accuracy rate of 99.3% for HLA major class classification and multi-class SVM achieved accuracy rates of 99.73% and 98.38% for sub-class classification of HLA-I and HLA-II molecules, respectively. The results show that gene classification based on codon usage bias is consistent with the molecular structures and biological functions of HLA molecules. PMID:19179707

  4. Mitochondrial gene diversity associated with the atp9 stop codon in natural populations of wild carrot (Daucus carota ssp. carota).

    PubMed

    Mandel, Jennifer R; McAssey, Edward V; Roland, Katherine M; McCauley, David E

    2012-01-01

    Mitochondrial genomes extracted from the wild populations of Daucus carota have been used as a genetic resource by breeders of cultivated carrot, yet little is known concerning the extent of their diversity in nature. Of special interest is an SNP in the putative stop codon of the mitochondrial gene atp9 that has been associated previously with male-sterile and male-fertile phenotypic variants. In this study, either the sequence or PCR/RFLP genotypes were obtained from the mitochondrial genes atp1, atp9, and cox1 found in D. carota individuals collected from 24 populations in the eastern United States. More than half of the 128 individuals surveyed had a CAA or AAA, rather than TAA, genotype at the position usually thought to function as an atp9 stop codon in this species. We also found no evidence for mitochondrial RNA editing (Cytosine to Uridine) of the CAA stop codon in either floral or leaf tissue. Evidence for intragenic recombination, as opposed to the more common intergenic recombination in plant mitochondrial genomes, in our data set is presented. Indel and SNP variants elsewhere in atp9, and in the other 2 genes surveyed, were nonrandomly associated with the 3 atp9 stop codon variants, though further analysis suggested that multilocus genotypic diversity had been enhanced by recombination. Overall the mitochondrial genetic diversity was only modestly structured among populations with an F(ST) of 0.34.

  5. Expression of a Chimeric Allergen with High Rare Codons Content in Codon Bias-Adjusted Escherichia coli: Escherichia coli BL21 (DE3)-Codon Plus RIL as an Efficient Host.

    PubMed

    Nouri, Hamid Reza; Karkhah, Ahmad; Varasteh, Abdolreza; Sankian, Mojtaba

    2016-07-01

    The expression of heterologous proteins in Escherichia coli (E. coli) is importantly affected by codon bias. Hence, the aim of the current study was to determine which codon bias-adjusted E. coli strain is sufficient for expression of a chimeric allergen coded by high rare codon content. To investigate the expression level, a chimeric protein of Chenopodium album (C. album) was used as an appropriate model. An expression construct was assembled and was transformed to four strains of codon bias-adjusted E. coli including origami, BL21 (DE3), BL21 (DE3)-codon plus RIL, and Rosetta. The level of expression and solubility of the chimeric allergen was analyzed by SDS-PAGE. In addition, the allergenicity of chimeric allergen was determined using immunoblotting. Our results showed that the chimeric allergen was expressed at high level in E. coli BL21 (DE3)-codon plus RIL and Rosetta. In detail, this recombinant allergen was isolated from soluble fraction in the codon bias-adjusted strains of E. coli BL21 (DE3)-codon plus RIL and Rosetta. Moreover, some lower molecular weight proteins were observed in Rosetta, which could be related to inappropriate expression or broken compartments of the chimeric allergen. The immunoblotting assay confirmed that the IgE-specific immune reactivity of our chimeric allergen expressed in BL21 (DE3)-codon plus RIL was significantly higher than the other strains. Our results showed that the expression of the chimeric allergen with high rare codons content in a codon bias-adjusted strain E. coli BL21 (DE3)-codon plus RIL improves the quality and solubility of the heterologous protein production. PMID:27040822

  6. Expression of a Chimeric Allergen with High Rare Codons Content in Codon Bias-Adjusted Escherichia coli: Escherichia coli BL21 (DE3)-Codon Plus RIL as an Efficient Host.

    PubMed

    Nouri, Hamid Reza; Karkhah, Ahmad; Varasteh, Abdolreza; Sankian, Mojtaba

    2016-07-01

    The expression of heterologous proteins in Escherichia coli (E. coli) is importantly affected by codon bias. Hence, the aim of the current study was to determine which codon bias-adjusted E. coli strain is sufficient for expression of a chimeric allergen coded by high rare codon content. To investigate the expression level, a chimeric protein of Chenopodium album (C. album) was used as an appropriate model. An expression construct was assembled and was transformed to four strains of codon bias-adjusted E. coli including origami, BL21 (DE3), BL21 (DE3)-codon plus RIL, and Rosetta. The level of expression and solubility of the chimeric allergen was analyzed by SDS-PAGE. In addition, the allergenicity of chimeric allergen was determined using immunoblotting. Our results showed that the chimeric allergen was expressed at high level in E. coli BL21 (DE3)-codon plus RIL and Rosetta. In detail, this recombinant allergen was isolated from soluble fraction in the codon bias-adjusted strains of E. coli BL21 (DE3)-codon plus RIL and Rosetta. Moreover, some lower molecular weight proteins were observed in Rosetta, which could be related to inappropriate expression or broken compartments of the chimeric allergen. The immunoblotting assay confirmed that the IgE-specific immune reactivity of our chimeric allergen expressed in BL21 (DE3)-codon plus RIL was significantly higher than the other strains. Our results showed that the expression of the chimeric allergen with high rare codons content in a codon bias-adjusted strain E. coli BL21 (DE3)-codon plus RIL improves the quality and solubility of the heterologous protein production.

  7. Codon-specific missense errors in vivo.

    PubMed

    Bouadloun, F; Donner, D; Kurland, C G

    1983-01-01

    We have developed a simple method for measuring the missense substitution of amino acids at specified positions in proteins synthesized in vivo. We find that the frequency of cysteine substitution for the single arginine in Escherichia coli ribosomal protein L7/L12 is close to 10(-3) for wild-type bacteria, decreases to 4 x 10(-4) in streptomycin-resistant bacteria containing mutant S12 (rpsL), and is virtually unchanged in Ram bacteria containing mutant S4 (rpsD). We have also found that the frequency of the cysteine substitution for the single tryptophan in E. coli ribosomal protein S6 is 3-4 x 10(-3) for wild-type bacteria, decreases to 6 x 10(-4) in streptomycin-resistant bacteria and is elevated to nearly 10(-2) in Ram bacteria.

  8. [Pathological diagnosis, work-up and reporting of breast cancer. Recommendations of the 3rd Hungarian Consensus Conference on Breast Cancer].

    PubMed

    Cserni, Gábor; Kulka, Janina; Francz, Monika; Járay, Balázs; Kálmán, Endre; Kovács, Ilona; Krenács, Tibor; Udvarhelyi, Nóra; Vass, László

    2016-09-01

    There have been relevant changes in the diagnosis and treatment of breast cancer to implement the updating of the 2010 recommendations made during the 2nd national consensus conference on the disease. Following a wide interdisciplinary consultation, the present recommendations have been finalized after their public discussion at the 3rd Hungarian Consensus Conference on Breast Cancer. The recommendations cover non-operative and intraoperative diagnostics, the work-up of operative specimens, the determination of prognostic and predictive markers and the content of the cytology and histology reports. Furthermore, it touches some special issues such as the current status of multigene molecular markers, the role of pathologists in clinical trials and prerequisites for their involvement, some relevant points about the future. PMID:27579721

  9. From challenges to solutions. European Bioanalysis Forum 3rd Annual Open Symposium, Hesperia Towers, Barcelona, Spain, 1-3 December 2010.

    PubMed

    Abbott, Richard W; Gordon, Ben; van Amsterdam, Peter; Lausecker, Berthold; Brudny-Kloeppel, Margarete; Smeraglia, John; Romero, Fernando; Globig, Susanne; Golob, Michaela; Knutsson, Magnus; Herling, Christian; Vieser, Eva; Timmerman, Philip

    2011-04-01

    The European Bioanalysis Forum is a bioanalytical nonprofit organization comprised of European pharmaceutical companies (27 members to date) and currently expanding to include CROs as well. The European Bioanalysis Forum provides a broad European bioanalytical network for the discussion of scientific, technological and regulatory topics of bioanalytical interest. The 3rd Annual Open Symposium was again much anticipated after the two previous successful meetings. The symposium included sessions on thinking outside the 'commodity' box, bioanalytical challenges with blood, global harmonization, assay platforms, dried blood spots, immunogenicity, matrix effects, anomalous results, biomarkers and two plenary technology sessions hosted by the Platinum sponsors. Experts and key opinion leaders were invited as guest speakers. A total of 424 delegates registered from 113 companies representing a large percentage of the European bioanalytical community. In addition to 48 oral presentations, 88 posters were presented and there was a vendor exposition of 40 companies.

  10. Reflections: Surgical Education-the Times they are a-Changin': Lessons Learned from the 3rd MAYMET-ESO Joint Meeting.

    PubMed

    Tarkowski, Radoslaw; Vetto, John T

    2015-09-01

    Technical skills are not sufficient for successful surgical care. Non-technical skills such as team work, decision-making in cancer treatment, communication with the patient, ethical challenges, situation awareness, and communication in the operating room are mandatory for favorable outcomes. Although formally taught in other high-demand disciplines, such skills were traditionally rarely discussed in surgical oncology. The 3rd MAYMET-ESO Joint Meeting "Professionalism for Breast Surgeons" held in Istanbul, Turkey, 5 October 2013 was dedicated to the development of non-technical skills in the everyday activity of breast surgeons. We briefly discuss information from this very interesting and inspiring educational event and how it relates to more recent changes in surgical oncology education. PMID:25903052

  11. Deuterium beam acceleration with 3rd harmonic ion cyclotron resonance heating in Joint European Torus: Sawtooth stabilization and Alfvén eigenmodes

    NASA Astrophysics Data System (ADS)

    Gassner, T.; Schoepf, K.; Sharapov, S. E.; Kiptily, V. G.; Pinches, S. D.; Hellesen, C.; Eriksson, J.; JET-EFDA contributors

    2012-03-01

    Experiments on accelerating NBI-produced deuterium (D) beam ions from their injection energy of ˜110 keV up to the MeV energy range with 3rd harmonic ion cyclotron resonance heating were performed on the Joint European Torus [P. H. Rebut and B. E. Keen, Fusion Technol. 11, 13 (1987)]. A renewed set of nuclear diagnostics was used for analysing fast D ions during sawtooth stabilization, monster sawtooth crashes, and during excitation of Alfvén eigenmodes (AEs) residing inside the q = 1 radius. The measurements and modeling of the fast ions with the nonlinear HAGIS code [S. D. Pinches et al., Comput. Phys. Commun. 111, 133 (1998)] show that monster sawtooth crashes are strongly facilitated by the AE-induced re-distribution of the fast D ions from inside the q = 1 radius to the plasma edge.

  12. Clustering of classical swine fever virus isolates by codon pair bias

    PubMed Central

    2011-01-01

    Background The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as well as with viruses. Reasons for these differences are not completely understood. For classical swine fever virus (CSFV), it was suggested that the synonymous codon usage does not significantly influence virulence, but the relationship between variations in codon pair usage and CSFV virulence is unknown. Virulence can be related to the fitness of a virus: Differences in codon pair usage influence genome translation efficiency, which may in turn relate to the fitness of a virus. Accordingly, the potential of the codon pair bias for clustering CSFV isolates into classes of different virulence was investigated. Results The complete genomic sequences encoding the viral polyprotein of 52 different CSFV isolates were analyzed. This included 49 sequences from the GenBank database (NCBI) and three newly sequenced genomes. The codon usage did not differ among isolates of different virulence or genotype. In contrast, a clustering of isolates based on their codon pair bias was observed, clearly discriminating highly virulent isolates and vaccine strains on one side from moderately virulent strains on the other side. However, phylogenetic trees based on the codon pair bias and on the primary nucleotide sequence resulted in a very similar genotype distribution. Conclusion Clustering of CSFV genomes based on their codon pair bias correlate with the genotype rather than with the virulence of the isolates. PMID:22126254

  13. Knowledge and institutional requirements to promote land degradation neutrality in drylands - An analysis of the outcomes of the 3rd UNCCD scientific conference

    NASA Astrophysics Data System (ADS)

    Akhtar-Schuster, Mariam; Safriel, Uriel; Abraham, Elena; de Vente, Joris; Essahli, Wafa; Escadafal, Richard; Stringer, Lindsay

    2015-04-01

    Achieving land degradation neutrality (LDN) through sustainable land management (SLM) targets the maintenance or restoration of the productivity of land, and therefore has to include decision-makers, knowledge generators and knowledge holders at the different relevant geographic scales. In order to enhance the implementation of the Convention, the Conference of the Parties (COP) of the United Nations Convention to Combat Desertification therefore decided that each future session of its Committee on Science and Technology (CST) would be organized in a predominantly scientific and technical conference-style format. This contribution will outline the major outcomes of UNCCD's 3rd scientific conference that will be held in Cancún, Mexico, from 9 to 12 March 2015, on addressing desertification, land degradation and drought issues (DLDD) for poverty reduction and sustainable development. The conference follows an exceptional new round table conference format that will allow the various stakeholders to discuss scientific as well as the contribution of traditional knowledge and practices in combating land degradation. This format should provide two-way communication and enable deeper insight into the availability and contribution of all forms of knowledge for achieving LDN through the assessment of: • the vulnerability of lands to DLDD and climate change and the adaptive capacities of socio-ecosystems; • best examples of adapted, knowledge-based practices and technologies; • monitoring and assessment methods to evaluate the effectiveness of adaptation practices and technologies. The outcomes of UNCCD's 3rd scientific conference will serve as a basis for discussing: • contributions of science to diagnose the status of land; • research gaps that need to be addressed to achieve LDN for poverty reduction; • additional institutional requirements to optimally bridge knowledge generation, knowledge maintenance and knowledge implementation at the science

  14. Limbic system development underlies the emergence of classical fear conditioning during the 3rd and 4th weeks of life in the rat

    PubMed Central

    Deal, Alex L.; Erickson, Kristen J.; Shiers, Stephanie I.; Burman, Michael A.

    2016-01-01

    Classical fear conditioning creates an association between an aversive stimulus and a neutral stimulus. Although the requisite neural circuitry is well understood in mature organisms, the development of these circuits is less well studied. The current experiments examine the ontogeny of fear conditioning and relate it to neuronal activation assessed through immediate early gene (IEG) expression in the amygdala, hippocampus, perirhinal cortex, and hypothalamus of periweanling rats. Rat pups were fear conditioned, or not, during the 3rd or 4th weeks of life. Neuronal activation was assessed by quantifying expression of FBJ osteosarcoma oncogene (FOS) using immunohistochemistry (IHC) in Experiment 1. Fos and early growth response gene-1 (EGR1) expression was assessed using qRT-PCR in Experiment 2. Behavioral data confirm that both auditory and contextual fear continue to emerge between PD 17 and 24. The IEG expression data are highly consistent with these behavioral results. IHC results demonstrate significantly more FOS protein expression in the basal amygdala of fear conditioned PD 23 subjects compared to control subjects, but no significant difference at PD 17. qRT-PCR results suggest specific activation of the amygdala only in older subjects during auditory fear expression. A similar effect of age and conditioning status was also observed in the perirhinal cortex during both contextual and auditory fear expression. Overall, the development of fear conditioning occurring between the 3rd and 4th weeks of life appears to be at least partly attributable to changes in activation of the amygdala and perirhinal cortex during fear conditioning or expression. PMID:26820587

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

    ERIC Educational Resources Information Center

    Szeberenyi, Jozsef

    2009-01-01

    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…

  16. The importance of codon context for understanding the Ig-like somatic hypermutation strand-biased patterns in TP53 mutations in breast cancer.

    PubMed

    Lindley, Robyn A

    2013-06-01

    Evidence already exists that the activation-induced deaminase (AID)/APOBEC family constitutes a set of differentially expressed enzymes capable of deaminating cytosines (C to U) in single-stranded DNA (ssDNA) and that they are potentially powerful mutagens. The mutagenic processes involved are believed to be activated in many nonlymphoid tissue types-for example, initiating some cancers and/or leading to further somatic mutagenesis. To investigate the extent that codon context might be important in influencing the likely location of TP53 mutations in breast cancer, the codon-bias patterns resulting from the ssDNA target specificities of cytidine deaminases of the AID/APOBEC family were analyzed. The data indicate that codon context strongly influences the likely location of mutations at motifs for AID/APOBEC1/APOBEC3G, and at WA sites. An unexpected finding is a highly significant preference for transitions of cytosine to occur at the first nucleotide position and for transitions of guanosine to occur at the second nucleotide position in the mutated codon (read 3' to 5'). Thus, the mechanisms involved appear to be sensitive to codon reading frames and to have an intrinsic ability to differentiate between the cytosines on the nontranscribed strand and those on the transcribed strand in the context of an open "transcription bubble."

  17. Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha

    PubMed Central

    Karumathil, Sudeesh; Dirisala, Vijaya R.; Srinadh, Uthpala; Nikhil, Valaboju; Kumar, N. Satya Sampath; Nair, Rahul R.

    2016-01-01

    Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman’s rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from

  18. Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha

    PubMed Central

    Karumathil, Sudeesh; Dirisala, Vijaya R.; Srinadh, Uthpala; Nikhil, Valaboju; Kumar, N. Satya Sampath; Nair, Rahul R.

    2016-01-01

    Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman’s rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from

  19. Evolution of Synonymous Codon Usage in the Mitogenomes of Certain Species of Bilaterian Lineage with Special Reference to Chaetognatha.

    PubMed

    Karumathil, Sudeesh; Dirisala, Vijaya R; Srinadh, Uthpala; Nikhil, Valaboju; Kumar, N Satya Sampath; Nair, Rahul R

    2016-01-01

    Chaetognatha is a minor phylum, comprising transparent marine invertebrates varying in size from 0.5 to 12 cm. The exact phylogenetic position of Chaetognatha in Metazoa has not been deciphered as some embryological characteristics place chaetognaths among deuterostomes and some morphological characteristics place these among protostomes. In this study, the major factors that drive synonymous codon usage bias (SCUB) in the mitogenomes of representative species of Chaetognatha and chosen species of other closely related phyla were analyzed. Spearman's rank correlation analyses of nucleotide contents suggested that mutational pressure and selection were acting in all examined mitogenomes but with varying intensities. The quantification of SCUB using effective number of codons vs. GC composition at the third codon position (GC3) plot suggested that mutational pressure due to GC compositional constraints might be one of the major influencing forces driving the SCUB in all chaetognaths except Sagitta enflata. However, neutrality plots revealed no significant correlation between GC3 and cumulative GC content at first and second codon positions (GC12) in all other species, except in Daphnia pulex. The parity rule 2 bias plot showed that significant compositional differences existed between C and G, as well as between A and T, contents in most of the protein-coding genes (PCGs) and, comparatively, A and T contents were used more proportionally than C and G contents in all chosen mitogenomes. Chi-square analysis revealed the presence of putative optimal codons in all species, except in S. enflata. The correspondence analysis identified that mutational pressure and selection act on the mitogenomes of the selected chaetognaths and other phyla with varying intensities. The cluster analysis based on relative synonymous codon usage (RSCU) values revealed that RSCU variations in the PCGs of mitogenomes of chaetognaths are more comparable with those of protostomes. Apart from

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

    PubMed

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

    2013-01-01

    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.

  1. Optimizing the codon usage of synthetic gene with QPSO algorithm.

    PubMed

    Cai, Yujie; Sun, Jun; Wang, Jie; Ding, Yanrui; Tian, Na; Liao, Xiangru; Xu, Wenbo

    2008-09-01

    Molecular Biology makes it possible to express foreign genes in microorganism, plants and animals. To improve the heterologous expression, it is important that the codon usage of sequence be optimized to make it adaptive to host organism. In this paper, a novel method based on Quantum-behaved Particle Swarm Optimization (QPSO) algorithm is developed to optimize the codon usage of synthetic gene. Compared to the existing probability methods, QPSO is able to generate better results when DNA/RNA sequence length is less than 6Kb which is the commonly used range. While the software or web service based on probability method may not exclude all defined restriction sites when there are many undesired sites in the sequence, our proposed method can remove the undesired site efficiently during the optimization process.

  2. Multiple Evolutionary Selections Involved in Synonymous Codon Usages in the Streptococcus agalactiae Genome

    PubMed Central

    Ma, Yan-Ping; Ke, Hao; Liang, Zhi-Ling; Liu, Zhen-Xing; Hao, Le; Ma, Jiang-Yao; Li, Yu-Gu

    2016-01-01

    Streptococcus agalactiae is an important human and animal pathogen. To better understand the genetic features and evolution of S. agalactiae, multiple factors influencing synonymous codon usage patterns in S. agalactiae were analyzed in this study. A- and U-ending rich codons were used in S. agalactiae function genes through the overall codon usage analysis, indicating that Adenine (A)/Thymine (T) compositional constraints might contribute an important role to the synonymous codon usage pattern. The GC3% against the effective number of codon (ENC) value suggested that translational selection was the important factor for codon bias in the microorganism. Principal component analysis (PCA) showed that (i) mutational pressure was the most important factor in shaping codon usage of all open reading frames (ORFs) in the S. agalactiae genome; (ii) strand specific mutational bias was not capable of influencing the codon usage bias in the leading and lagging strands; and (iii) gene length was not the important factor in synonymous codon usage pattern in this organism. Additionally, the high correlation between tRNA adaptation index (tAI) value and codon adaptation index (CAI), frequency of optimal codons (Fop) value, reinforced the role of natural selection for efficient translation in S. agalactiae. Comparison of synonymous codon usage pattern between S. agalactiae and susceptible hosts (human and tilapia) showed that synonymous codon usage of S. agalactiae was independent of the synonymous codon usage of susceptible hosts. The study of codon usage in S. agalactiae may provide evidence about the molecular evolution of the bacterium and a greater understanding of evolutionary relationships between S. agalactiae and its hosts. PMID:26927064

  3. Saving the 2nd Molar from the 3rd Is it Really the Guilt of the Tilt?

    PubMed Central

    Yadav, Pankaj; Nawal, Ruchika Roongta; Talwar, Sangeeta; Verma, Mahesh

    2016-01-01

    Introduction Clinicians often relate the distal caries in second molars to angulated third molars, which if left undetected can lead to gross decay that may further require removal of the tooth. Due to this fact, many third molars are advised for prophylactic removal to prevent decay in the second molar. But this approach would only be justified when the incidence of decay/loss of second molar due to third molar are reasonably high. We sought to determine incidence of caries experience and also sequel extraction in second molars associated with the third molars. Aim The study was conducted to answer the basic question that whether the incidence of caries and subsequent extraction of second molar due to angulated third molars is high enough to justify the prophylactic removal of third molar or not. Materials and Methods This study was conducted on radiographic records of 1187 patients. The effect of tilted third molar on the second molar was measured in relation with three parameters namely level & position of third molar with respect to second molar and the distribution among arches. Results The results indicated that out of total number of teeth examined only 5.4% of maxillary and 9.6% of mandibular second molars were affected by tilted third molars. Further, only 2.2% of mandibular and 2.9% of maxillary second molars were indicated for extraction. The data was statistically insignificant. Conclusion It was concluded that distal caries in second molars is not very common. It may be present in some cases of third molar impactions and prophylactic removal of these impacted teeth may not be considered appropriate. PMID:27437353

  4. The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons

    PubMed Central

    Simões, João; Bezerra, Ana R.; Moura, Gabriela R.; Araújo, Hugo; Gut, Ivo; Bayes, Mónica; Santos, Manuel A. S.

    2016-01-01

    The ascomycete Candida albicans is a normal resident of the gastrointestinal tract of humans and other warm-blooded animals. It occurs in a broad range of body sites and has high capacity to survive and proliferate in adverse environments with drastic changes in oxygen, carbon dioxide, pH, osmolarity, nutrients, and temperature. Its biology is unique due to flexible reassignment of the leucine CUG codon to serine and synthesis of statistical proteins. Under standard growth conditions, CUG sites incorporate leucine (3% of the times) and serine (97% of the times) on a proteome wide scale, but leucine incorporation fluctuates in response to environmental stressors and can be artificially increased up to 98%. In order to determine whether such flexibility also exists at other codons, we have constructed several serine tRNAs that decode various non-cognate codons. Expression of these tRNAs had minor effects on fitness, but growth of the mistranslating strains at different temperatures, in medium with different pH and nutrients composition was often enhanced relatively to the wild type (WT) strain, supporting our previous data on adaptive roles of CUG ambiguity in variable growth conditions. Parallel evolution of the recombinant strains (100 generations) followed by full genome resequencing identified various strain specific single nucleotide polymorphisms (SNP) and one SNP in the deneddylase (JAB1) gene in all strains. Since JAB1 is a subunit of the COP9 signalosome complex, which interacts with cullin (Cdc53p) to mediate degradation of a variety of cellular proteins, our data suggest that neddylation plays a key role in tolerance and adaptation to codon ambiguity in C. albicans. PMID:27065968

  5. Codon Distribution in Error-Detecting Circular Codes.

    PubMed

    Fimmel, Elena; Strüngmann, Lutz

    2016-03-15

    In 1957, Francis Crick et al. suggested an ingenious explanation for the process of frame maintenance. The idea was based on the notion of comma-free codes. Although Crick's hypothesis proved to be wrong, in 1996, Arquès and Michel discovered the existence of a weaker version of such codes in eukaryote and prokaryote genomes, namely the so-called circular codes. Since then, circular code theory has invariably evoked great interest and made significant progress. In this article, the codon distributions in maximal comma-free, maximal self-complementary C³ and maximal self-complementary circular codes are discussed, i.e., we investigate in how many of such codes a given codon participates. As the main (and surprising) result, it is shown that the codons can be separated into very few classes (three, or five, or six) with respect to their frequency. Moreover, the distribution classes can be hierarchically ordered as refinements from maximal comma-free codes via maximal self-complementary C(3) codes to maximal self-complementary circular codes.

  6. Codon Distribution in Error-Detecting Circular Codes.

    PubMed

    Fimmel, Elena; Strüngmann, Lutz

    2016-01-01

    In 1957, Francis Crick et al. suggested an ingenious explanation for the process of frame maintenance. The idea was based on the notion of comma-free codes. Although Crick's hypothesis proved to be wrong, in 1996, Arquès and Michel discovered the existence of a weaker version of such codes in eukaryote and prokaryote genomes, namely the so-called circular codes. Since then, circular code theory has invariably evoked great interest and made significant progress. In this article, the codon distributions in maximal comma-free, maximal self-complementary C³ and maximal self-complementary circular codes are discussed, i.e., we investigate in how many of such codes a given codon participates. As the main (and surprising) result, it is shown that the codons can be separated into very few classes (three, or five, or six) with respect to their frequency. Moreover, the distribution classes can be hierarchically ordered as refinements from maximal comma-free codes via maximal self-complementary C(3) codes to maximal self-complementary circular codes. PMID:26999215

  7. Tracing specific synonymous codon-secondary structure correlations through evolution.

    PubMed

    Oresic, Matej; Dehn, Michael; Korenblum, Daniel; Shalloway, David

    2003-04-01

    We previously showed that GAU codons are preferred (relative to synonymous GAC codons) for encoding aspartates specifically at the N-termini of alpha-helices in human, but not in E. coli, proteins. To test if this difference reflected a general difference between eucaryotes and procaryotes, we now extended the analysis to include the proteins and coding sequences of mammals, vertebrates, S. cerevisiae, and plants. We found that the GAU-alpha-helix correlation is also strong in non-human mammalian and vertebrate proteins but is much weaker or insignificant in S. cerevisiae and plants. The vertebrate correlations are of sufficient strength to enhance alpha-helix N-terminus prediction. Additional results, including the observation that the correlation is significantly enhanced when proteins that are known to be correctly expressed in recombinant procaryotic systems are excluded, suggest that the correlation is induced at the level of protein translation and folding and not at the nucleic acid level. To the best of our knowledge, it is not explicable by the canonical picture of protein expression and folding, suggesting the existence of a novel evolutionary selection mechanism. One possible explanation is that some alpha-helix N-terminal GAU codons may facilitate correct co-translational folding in vertebrates.

  8. Codon Distribution in Error-Detecting Circular Codes

    PubMed Central

    Fimmel, Elena; Strüngmann, Lutz

    2016-01-01

    In 1957, Francis Crick et al. suggested an ingenious explanation for the process of frame maintenance. The idea was based on the notion of comma-free codes. Although Crick’s hypothesis proved to be wrong, in 1996, Arquès and Michel discovered the existence of a weaker version of such codes in eukaryote and prokaryote genomes, namely the so-called circular codes. Since then, circular code theory has invariably evoked great interest and made significant progress. In this article, the codon distributions in maximal comma-free, maximal self-complementary C3 and maximal self-complementary circular codes are discussed, i.e., we investigate in how many of such codes a given codon participates. As the main (and surprising) result, it is shown that the codons can be separated into very few classes (three, or five, or six) with respect to their frequency. Moreover, the distribution classes can be hierarchically ordered as refinements from maximal comma-free codes via maximal self-complementary C3 codes to maximal self-complementary circular codes. PMID:26999215

  9. Revelation of Influencing Factors in Overall Codon Usage Bias of Equine Influenza Viruses

    PubMed Central

    Bhatia, Sandeep; Sood, Richa; Selvaraj, Pavulraj

    2016-01-01

    Equine influenza viruses (EIVs) of H3N8 subtype are culprits of severe acute respiratory infections in horses, and are still responsible for significant outbreaks worldwide. Adaptability of influenza viruses to a particular host is significantly influenced by their codon usage preference, due to an absolute dependence on the host cellular machinery for their replication. In the present study, we analyzed genome-wide codon usage patterns in 92 EIV strains, including both H3N8 and H7N7 subtypes by computing several codon usage indices and applying multivariate statistical methods. Relative synonymous codon usage (RSCU) analysis disclosed bias of preferred synonymous codons towards A/U-ended codons. The overall codon usage bias in EIVs was slightly lower, and mainly affected by the nucleotide compositional constraints as inferred from the RSCU and effective number of codon (ENc) analysis. Our data suggested that codon usage pattern in EIVs is governed by the interplay of mutation pressure, natural selection from its hosts and undefined factors. The H7N7 subtype was found less fit to its host (horse) in comparison to H3N8, by possessing higher codon bias, lower mutation pressure and much less adaptation to tRNA pool of equine cells. To the best of our knowledge, this is the first report describing the codon usage analysis of the complete genomes of EIVs. The outcome of our study is likely to enhance our understanding of factors involved in viral adaptation, evolution, and fitness towards their hosts. PMID:27119730

  10. Genome-wide analysis of synonymous codon usage in Huaiyangshan virus and other bunyaviruses.

    PubMed

    Luo, Xuelian; Liu, Qingzhen; Xiong, Yanwen; Ye, Changyun; Jin, Dong; Xu, Jianguo

    2015-12-01

    Huaiyangshan virus (HYSV) is a newly discovered bunyavirus, which is transmitted by ticks and causes hemorrhagic fever-like illness in human. The interplay of codon usage among viruses and their hosts is expected to affect viral survival, evasion from host's immune system and evolution. However, little is known about the codon usage in HYSV genome. In the present study, we analyzed synonymous codon usage in 120 available full-length HYSV sequences and performed a comparative analysis of synonymous codon usage patterns in HYSV and 42 other bunyaviruses. The relative synonymous codon usage (RSCU) analysis showed that the preferred synonymous codons were G/C-ended. A comparative analysis of RSCU between HYSV and its hosts reflected that codon usage patterns of HYSV were mostly coincident with that of its hosts. Our data suggested that although mutational bias dominated codon usage, patterns of codon usage in HYSV were also under the influence of nature selection. Phylogenetic analysis based on RSCU values across different HYSV strains and 42 other bunyaviruses suggested that codon usage pattern in HYSV was the most similar with that of Uukuniemi virus among these bunyaviruses and that viruses belonged to Phlebovirus showed a diversity of codon usage patterns. PMID:26173646

  11. Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo

    PubMed Central

    Pechmann, Sebastian; Chartron, Justin W; Frydman, Judith

    2015-01-01

    The genetic code allows most amino acids a choice of optimal and nonoptimal codons. We report that synonymous codon choice is tuned to promote interaction of nascent polypeptides with the signal recognition particle (SRP), which assists in protein translocation across membranes. Cotranslational recognition by the SRP in vivo is enhanced when mRNAs contain nonoptimal codon clusters 35–40 codons downstream of the SRP-binding site, the distance that spans the ribosomal polypeptide exit tunnel. A local translation slowdown upon ribosomal exit of SRP-binding elements in mRNAs containing these nonoptimal codon clusters is supported experimentally by ribosome profiling analyses in yeast. Modulation of local elongation rates through codon choice appears to kinetically enhance recognition by ribosome-associated factors. We propose that cotranslational regulation of nascent-chain fate may be a general constraint shaping codon usage in the genome. PMID:25420103

  12. Local slowdown of translation by nonoptimal codons promotes nascent-chain recognition by SRP in vivo.

    PubMed

    Pechmann, Sebastian; Chartron, Justin W; Frydman, Judith

    2014-12-01

    The genetic code allows most amino acids a choice of optimal and nonoptimal codons. We report that synonymous codon choice is tuned to promote interaction of nascent polypeptides with the signal recognition particle (SRP), which assists in protein translocation across membranes. Cotranslational recognition by the SRP in vivo is enhanced when mRNAs contain nonoptimal codon clusters 35-40 codons downstream of the SRP-binding site, the distance that spans the ribosomal polypeptide exit tunnel. A local translation slowdown upon ribosomal exit of SRP-binding elements in mRNAs containing these nonoptimal codon clusters is supported experimentally by ribosome profiling analyses in yeast. Modulation of local elongation rates through codon choice appears to kinetically enhance recognition by ribosome-associated factors. We propose that cotranslational regulation of nascent-chain fate may be a general constraint shaping codon usage in the genome. PMID:25420103

  13. A single amino acid change of translation termination factor eRF1 switches between bipotent and omnipotent stop-codon specificity†

    PubMed Central

    Eliseev, Boris; Kryuchkova, Polina; Alkalaeva, Elena; Frolova, Ludmila

    2011-01-01

    In eukaryotes a single class-1 translation termination factor eRF1 decodes the three stop codons: UAA, UAG and UGA. Some ciliates, like Euplotes, have a variant code, and here eRF1s exhibit UAR-only specificity, whereas UGA is reassigned as a sense codon. Since eukaryote eRF1 stop-codon recognition is associated with its N-terminal domain, structural features should exist in the N domain of ciliate eRF1s that restrict their stop-codon specificity. Using an in vitro reconstituted eukaryotic translation system we demonstrate here that a chimeric eRF1 composed of the N domain of Euplotes aediculatus eRF1 fused to the MC domains of human eRF1 exhibits UAR-only specificity. Functional analysis of eRF1 chimeras constructed by swapping Euplotes N domain sequences with the cognate regions from human eRF1 as well as site-directed mutagenesis of human eRF1 highlighted the crucial role of the alanine residue in position 70 of E. aediculatus eRF1 in restricting UGA decoding. Switching the UAR-only specificity of E. aediculatus eRF1 to omnipotent mode is due to a single point mutation. Furthermore, we examined the influence of eRF3 on the ability of chimeric and mutant eRF1s to induce peptide release in response to different stop codons. PMID:20860996

  14. The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5

    PubMed Central

    Yan, Qing; Philmus, Benjamin; Hesse, Cedar; Kohen, Max; Chang, Jeff H.; Loper, Joyce E.

    2016-01-01

    The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcriptional and post-transcriptional levels. In this study, we analyzed the genomic sequence of Pf-5 for codon usage patterns and observed that the six rarest codons in the genome are present in all seven known antibiotic biosynthesis gene clusters. In particular, there is an abundance of rare codons in pltR, which encodes a member of the LysR transcriptional regulator family that controls the expression of pyoluteorin biosynthetic genes. To test the hypothesis that rare codons in pltR influence pyoluteorin production, we generated a derivative of Pf-5 in which 23 types of rare codons in pltR were substituted with synonymous preferred codons. The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5. Accordingly, the promoter activity of the pyoluteorin biosynthetic gene pltL was 20 times higher in the codon-modified stain than in the wild-type. pltR has six AGA codons, which is the rarest codon in the Pf-5 genome. Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity. Furthermore, overexpression of tRNAUCUArg, the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5. A bias in codon usage has been linked to the regulation of many phenotypes in eukaryotes and prokaryotes but, to our knowledge, this is the first example of the role of a rare codon in the regulation of antibiotic production by a Gram-negative bacterium. PMID:27148187

  15. The Rare Codon AGA Is Involved in Regulation of Pyoluteorin Biosynthesis in Pseudomonas protegens Pf-5.

    PubMed

    Yan, Qing; Philmus, Benjamin; Hesse, Cedar; Kohen, Max; Chang, Jeff H; Loper, Joyce E

    2016-01-01

    The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcriptional and post-transcriptional levels. In this study, we analyzed the genomic sequence of Pf-5 for codon usage patterns and observed that the six rarest codons in the genome are present in all seven known antibiotic biosynthesis gene clusters. In particular, there is an abundance of rare codons in pltR, which encodes a member of the LysR transcriptional regulator family that controls the expression of pyoluteorin biosynthetic genes. To test the hypothesis that rare codons in pltR influence pyoluteorin production, we generated a derivative of Pf-5 in which 23 types of rare codons in pltR were substituted with synonymous preferred codons. The resultant mutant produced pyoluteorin at levels 15 times higher than that of the wild-type Pf-5. Accordingly, the promoter activity of the pyoluteorin biosynthetic gene pltL was 20 times higher in the codon-modified stain than in the wild-type. pltR has six AGA codons, which is the rarest codon in the Pf-5 genome. Substitution of all six AGA codons with preferred Arg codons resulted in a variant of pltR that conferred increased pyoluteorin production and pltL promoter activity. Furthermore, overexpression of tRNA[Formula: see text], the cognate tRNA for the AGA codon, significantly increased pyoluteorin production by Pf-5. A bias in codon usage has been linked to the regulation of many phenotypes in eukaryotes and prokaryotes but, to our knowledge, this is the first example of the role of a rare codon in the regulation of antibiotic production by a Gram-negative bacterium. PMID:27148187

  16. A Kinesthetic Learning Approach to Earth Science for 3rd and 4th Grade Students on the Pajarito Plateau, Los Alamos, NM

    NASA Astrophysics Data System (ADS)

    Wershow, H. N.; Green, M.; Stocker, A.; Staires, D.

    2010-12-01

    Current efforts towards Earth Science literacy in New Mexico are guided by the New Mexico Science Benchmarks [1]. We are geoscience professionals in Los Alamos, NM who believe there is an important role for non-traditional educators utilizing innovative teaching methods. We propose to further Earth Science literacy for local 3rd and 4th grade students using a kinesthetic learning approach, with the goal of fostering an interactive relationship between the students and their geologic environment. We will be working in partnership with the Pajarito Environmental Education Center (PEEC), which teaches the natural heritage of the Pajarito Plateau to 3rd and 4th grade students from the surrounding area, as well as the Family YMCA’s Adventure Programs Director. The Pajarito Plateau provides a remarkable geologic classroom because minimal structural features complicate the stratigraphy and dramatic volcanic and erosional processes are plainly on display and easily accessible. Our methodology consists of two approaches. First, we will build an interpretive display of the local geology at PEEC that will highlight prominent rock formations and geologic processes seen on a daily basis. It will include a simplified stratigraphic section with field specimens and a map linked to each specimen’s location to encourage further exploration. Second, we will develop and implement a kinesthetic curriculum for an exploratory field class. Active engagement with geologic phenomena will take place in many forms, such as a scavenger hunt for precipitated crystals in the vesicles of basalt flows and a search for progressively smaller rhyodacite clasts scattered along an actively eroding canyon. We believe students will be more receptive to origin explanations when they possess a piece of the story. Students will be provided with field books to make drawings of geologic features. This will encourage independent assessment of phenomena and introduce the skill of scientific observation. We

  17. C to U editing of the anticodon of imported mitochondrial tRNA(Trp) allows decoding of the UGA stop codon in Leishmania tarentolae.

    PubMed

    Alfonzo, J D; Blanc, V; Estévez, A M; Rubio, M A; Simpson, L

    1999-12-15

    All mitochondrial tRNAs in kinetoplastid protists are encoded in the nucleus and imported into the organelle. The tRNA(Trp)(CCA) can decode the standard UGG tryptophan codon but can not decode the mitochondrial UGA tryptophan codon. We show that the mitochondrial tRNA(Trp) undergoes a specific C to U nucleotide modification in the first position of the anticodon, which allows decoding of mitochondrial UGA codons as tryptophan. Functional evidence for the absence of a UGA suppressor tRNA in the cytosol, using a reporter gene, was also obtained, which is consistent with a mitochondrial localization of this editing event. Leishmania cells have dealt with the problem of a lack of expression within the organelle of this non-universal tRNA by compartmentalizing an editing activity that modifies the anticodon of the imported tRNA.

  18. Veterinary Microbiology, 3rd Edition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Veterinary Microbiology, Third Edition is organized into four sections and begins with an updated and expanded introductory section on infectious disease pathogenesis, diagnosis and clinical management. The second section covers bacterial and fungal pathogens, and the third section describes viral d...

  19. Stable Isotope and Trace Element Studies on Gladiators and Contemporary Romans from Ephesus (Turkey, 2nd and 3rd Ct. AD) - Implications for Differences in Diet

    PubMed Central

    Lösch, Sandra; Moghaddam, Negahnaz; Grossschmidt, Karl; Risser, Daniele U.; Kanz, Fabian

    2014-01-01

    The gladiator cemetery discovered in Ephesus (Turkey) in 1993 dates to the 2nd and 3rd century AD. The aim of this study is to reconstruct diverse diet, social stratification, and migration of the inhabitants of Roman Ephesus and the distinct group of gladiators. Stable carbon, nitrogen, and sulphur isotope analysis were applied, and inorganic bone elements (strontium, calcium) were determined. In total, 53 individuals, including 22 gladiators, were analysed. All individuals consumed C3 plants like wheat and barley as staple food. A few individuals show indication of consumption of C4 plants. The δ13C values of one female from the gladiator cemetery and one gladiator differ from all other individuals. Their δ34S values indicate that they probably migrated from another geographical region or consumed different foods. The δ15N values are relatively low in comparison to other sites from Roman times. A probable cause for the depletion of 15N in Ephesus could be the frequent consumption of legumes. The Sr/Ca-ratios of the gladiators were significantly higher than the values of the contemporary Roman inhabitants. Since the Sr/Ca-ratio reflects the main Ca-supplier in the diet, the elevated values of the gladiators might suggest a frequent use of a plant ash beverage, as mentioned in ancient texts. PMID:25333366

  20. Evidence of human-induced morphodynamic changes along the Campania coastal areas (southern Italy) since the 3rd-4th cent. AD

    NASA Astrophysics Data System (ADS)

    Russo Ermolli, Elda; Romano, Paola; Liuzza, Viviana; Amato, Vincenzo; Ruello, Maria Rosaria; Di Donato, Valentino

    2014-05-01

    Campania has always offered suitable climatic and physiographic conditions for human settlements since prehistoric times. In particular, many Graeco-Roman towns developed along its coasts starting from the 7th-6th cent. BC. In the last decade, geoarchaelogical surveys have been carried out in the archaeological excavations of Neapolis, Paestum and Elea-Velia allowing the main steps of the landscape evolution around these towns to be defined in detail. The greek town of Neapolis rose in the late 6th cent. BC [1] on a terrace overlooking a low-relief rocky coast surrounded by volcanic hills. Port activities developed in a protected bay facing the town from the 4th-2nd cent. BC up to the 4th cent. AD, as testified by the discovery of structures and shipwrecks [2, 3, 4]. Starting from the 3rd cent. AD a spit bar formed at the bay entrance causing the progressive establishment of a lagoon which was gradually filled up by alluvial inputs and completely closed in the 5th cent. AD. During the same period, episodes of increased alluvial inputs were also recorded further west along the coast, where a narrow sandy beach formed at the cliff toe. The greek town of Poseidonia, renamed Paestum by the Romans, was founded in the 540 BC on a travertine terrace facing the sandy littoral of a prograding coastal plain [5]. In front of the main town door, a coastal lagoon developed thanks to the growth of a dune ridge and was probably used for harbor activities [5]. After this period the shoreline shifted seawards, another dune ridge formed and the back-ridge depression was filled with fluvial-marshy deposits, slowly drying up. Phases of travertine deposition, which characterized the SE sector of the plain all along the Holocene, were recorded in the northern and southern quarters of the town in historical times and were connected to the abandonment of the town in the early Medieval times. The greek colony of Elea-Velia was located on top of a siliciclastic promontory where the ruins of

  1. Oxidation of methanol on 2nd and 3rd row group VIII transition metals (Pt, Ir, Os, Pd, Rh, and Ru): Application to direct methanol fuel cells

    SciTech Connect

    Kua, J.; Goddard, W.A. III

    1999-12-01

    Using first principles quantum mechanics [nonlocal density functional theory (B3LYP)], the authors calculated the 13 most likely intermediate species for methanol oxidation on clusters of all 2nd and 3rd row Group VIII transition metals for all three likely binding sites (top, bridge, and cap). This comprehensive set of binding energies and structures allows a detailed analysis of possible reaction mechanisms and how they change for different metals. This illustrates the role in which modern quantum chemical methods can be used to provide data for combinatorial strategies for discovering and designing new catalysts. Methanol dehydrogenation is most facile on Pt, with the hydrogens preferentially stripped off the carbon end. However, water dehydrogenation is most facile on Ru. These results support the bifunctional mechanism for methanol oxidation on Pt-Ru alloys in direct methanol fuel cells (DMFCs). Pure Os is capable of performing both functionalities without cocatalyst. It is suggested that pure Os be examined as a potential catalyst for low overpotential, highly dispersed catalyst DMFCs. Pathways to form the second C-O bond differ between the pure metals (Pt and Os) in which (CO){sub ads} is probably activated by (OH){sub ads} and the Pt-Ru binary system in which (COH){sub ads} is probably activated by O{sub ads}. For all cases formation of (COOH){sub ads} is an important precursor to the final dehydrogenation to desorb CO{sub 2} from the surface.

  2. Codon bias and gene ontology in holometabolous and hemimetabolous insects.

    PubMed

    Carlini, David B; Makowski, Matthew

    2015-12-01

    The relationship between preferred codon use (PCU), developmental mode, and gene ontology (GO) was investigated in a sample of nine insect species with sequenced genomes. These species were selected to represent two distinct modes of insect development, holometabolism and hemimetabolism, with an aim toward determining whether the differences in developmental timing concomitant with developmental mode would be mirrored by differences in PCU in their developmental genes. We hypothesized that the developmental genes of holometabolous insects should be under greater selective pressure for efficient translation, manifest as increased PCU, than those of hemimetabolous insects because holometabolism requires abundant protein expression over shorter time intervals than hemimetabolism, where proteins are required more uniformly in time. Preferred codon sets were defined for each species, from which the frequency of PCU for each gene was obtained. Although there were substantial differences in the genomic base composition of holometabolous and hemimetabolous insects, both groups exhibited a general preference for GC-ending codons, with the former group having higher PCU averaged across all genes. For each species, the biological process GO term for each gene was assigned that of its Drosophila homolog(s), and PCU was calculated for each GO term category. The top two GO term categories for PCU enrichment in the holometabolous insects were anatomical structure development and cell differentiation. The increased PCU in the developmental genes of holometabolous insects may reflect a general strategy to maximize the protein production of genes expressed in bursts over short time periods, e.g., heat shock proteins. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 686-698, 2015. © 2015 Wiley Periodicals, Inc. PMID:26498580

  3. Synthetic approach to stop-codon scanning mutagenesis.

    PubMed

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

    2011-04-27

    A general combinatorial mutagenesis strategy using common dimethoxytrityl-protected mononucleotide phosphoramidites and a single orthogonally protected trinucleotide phosphoramidite (Fmoc-TAG; Fmoc = 9-fluorenylmethoxycarbonyl) was developed to scan a gene with the TAG amber stop codon with complete synthetic control. In combination with stop-codon suppressors that insert natural (e.g., alanine) or unnatural (e.g., p-benzoylphenylalanine, Bpa) amino acids, a single DNA library can be used to incorporate different amino acids for diverse purposes. Here, we scanned TAG codons through part of the gene for a model four-helix bundle protein, Rop, which regulates the copy number of ColE1 plasmids. Alanine was incorporated into Rop for mapping its binding site using an in vivo activity screen, and subtle but important differences from in vitro gel-shift studies of Rop function are evident. As a test, Bpa was incorporated using a Phe14 amber mutant isolated from the scanning library. Surprisingly, Phe14Bpa-Rop is weakly active, despite the critical role of Phe14 in Rop activity. Bpa is a photoaffinity label unnatural amino acid that can form covalent bonds with adjacent molecules upon UV irradiation. Irradiation of Phe14Bpa-Rop, which is a dimer in solution like wild-type Rop, results in covalent dimers, trimers, and tetramers. This suggests that Phe14Bpa-Rop weakly associates as a tetramer in solution and highlights the use of Bpa cross-linking as a means of trapping weak and transient interactions. PMID:21452871

  4. Metabolic engineering of E.coli for the production of a precursor to artemisinin, an anti-malarial drug [Chapter 25 in Manual of Industrial Microbiology and Biotechnology, 3rd edition

    SciTech Connect

    Petzold, Christopher; Keasling, Jay

    2011-07-18

    This document is Chapter 25 in the Manual of Industrial Microbiology and Biotechnology, 3rd edition. Topics covered include: Incorporation of Amorpha-4,11-Diene Biosynthetic Pathway into E. coli; Amorpha-4,11-Diene Pathway Optimization; "-Omics" Analyses for Increased Amorpha-4,11-Diene Production; Biosynthetic Oxidation of Amorpha-4,11-Diene.

  5. Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity.

    PubMed

    Qi, Yueying; Xu, Wenjing; Xing, Tian; Zhao, Mingming; Li, Nana; Yan, Li; Xia, Guangmin; Wang, Mengcheng

    2015-01-01

    Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation-induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome.

  6. Synonymous Codon Usage Bias in the Plastid Genome is Unrelated to Gene Structure and Shows Evolutionary Heterogeneity

    PubMed Central

    Qi, Yueying; Xu, Wenjing; Xing, Tian; Zhao, Mingming; Li, Nana; Yan, Li; Xia, Guangmin; Wang, Mengcheng

    2015-01-01

    Synonymous codon usage bias (SCUB) is the nonuniform usage of codons, occurring often in nearly all organisms. Our previous study found that SCUB is correlated with intron number, is unequal among exons in the plant nuclear genome, and mirrors evolutionary specialization. However, whether this rule exists in the plastid genome has not been addressed. Here, we present an analysis of SCUB in the plastid genomes of 25 species from lower to higher plants (algae, bryophytes, pteridophytes, gymnosperms, and spermatophytes). We found NNA and NNT (A- and T-ending codons) are preferential in the plastid genomes of all plants. Interestingly, this preference is heterogeneous among taxonomies of plants, with the strongest preference in bryophytes and the weakest in pteridophytes, suggesting an association between SCUB and plant evolution. In addition, SCUB frequencies are consistent among genes with varied introns and among exons, indicating that the bias of NNA and NNT is unrelated to either intron number or exon position. Further, SCUB is associated with DNA methylation–induced conversion of cytosine to thymine in the vascular plants but not in algae or bryophytes. These data demonstrate that these SCUB profiles in the plastid genome are distinctly different compared with the nuclear genome. PMID:25922569

  7. Synonymous Codon Usage Bias in Plant Mitochondrial Genes Is Associated with Intron Number and Mirrors Species Evolution

    PubMed Central

    Zhao, Mingming; Yin, Xunhao; Xia, Guangmin; Wang, Mengcheng

    2015-01-01

    Synonymous codon usage bias (SCUB) is a common event that a non-uniform usage of codons often occurs in nearly all organisms. We previously found that SCUB is correlated with both intron number and exon position in the plant nuclear genome but not in the plastid genome; SCUB in both nuclear and plastid genome can mirror the evolutionary specialization. However, how about the rules in the mitochondrial genome has not been addressed. Here, we present an analysis of SCUB in the mitochondrial genome, based on 24 plant species ranging from algae to land plants. The frequencies of NNA and NNT (A- and T-ending codons) are higher than those of NNG and NNC, with the strongest preference in bryophytes and the weakest in land plants, suggesting an association between SCUB and plant evolution. The preference for NNA and NNT is more evident in genes harboring a greater number of introns in land plants, but the bias to NNA and NNT exhibits even among exons. The pattern of SCUB in the mitochondrial genome differs in some respects to that present in both the nuclear and plastid genomes. PMID:26110418

  8. Translational readthrough potential of natural termination codons in eucaryotes – The impact of RNA sequence

    PubMed Central

    Dabrowski, Maciej; Bukowy-Bieryllo, Zuzanna; Zietkiewicz, Ewa

    2015-01-01

    Termination of protein synthesis is not 100% efficient. A number of natural mechanisms that suppress translation termination exist. One of them is STOP codon readthrough, the process that enables the ribosome to pass through the termination codon in mRNA and continue translation to the next STOP codon in the same reading frame. The efficiency of translational readthrough depends on a variety of factors, including the identity of the termination codon, the surrounding mRNA sequence context, and the presence of stimulating compounds. Understanding the interplay between these factors provides the necessary background for the efficient application of the STOP codon suppression approach in the therapy of diseases caused by the presence of premature termination codons. PMID:26176195

  9. A new turn in codon-anticodon selection through halogen bonds.

    PubMed

    Vijay Solomon, Rajadurai; Angeline Vedha, Swaminathan; Venuvanalingam, Ponnambalam

    2014-04-28

    The halogen bond is relatively a less characterized intermolecular interaction compared to the hydrogen bond and the structure, stability and electronic structures of halogenated base pairs, particularly at the wobble junction have been investigated using DFT. Three halogens, namely Cl, Br and I, have been tested for their role in such situations with uracil as the anticodon base. Computed results reveal that when halogen atoms replace protons in the hydrogen bonding positions they induce lot of geometric changes that flip some of the observed base pairs into unobserved base pairs and vice versa. NCI, NBO and AIM analyses explain these changes at the electronic level. The new codons will have lot of impact in future applications, particularly in self assembly of biomaterials and t-RNA synthetic strategies.

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

    SciTech Connect

    Feng, Yue; Gunter, L.E.; Organ, E.L.; Cavener, D.R. )

    1991-04-01

    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.

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

    PubMed Central

    Morton, B R

    2001-01-01

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

  12. Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes.

    PubMed

    Mondal, Sunil Kanti; Kundu, Sudip; Das, Rabindranath; Roy, Sujit

    2016-08-01

    Bacteria and archaea have evolved with the ability to fix atmospheric dinitrogen in the form of ammonia, catalyzed by the nitrogenase enzyme complex which comprises three structural genes nifK, nifD and nifH. The nifK and nifD encodes for the beta and alpha subunits, respectively, of component 1, while nifH encodes for component 2 of nitrogenase. Phylogeny based on nifDHK have indicated that Cyanobacteria is closer to Proteobacteria alpha and gamma but not supported by the tree based on 16SrRNA. The evolutionary ancestor for the different trees was also different. The GC1 and GC2% analysis showed more consistency than GC3% which appeared to below for Firmicutes, Cyanobacteria and Euarchaeota while highest in Proteobacteria beta and clearly showed the proportional effect on the codon usage with a few exceptions. Few genes from Firmicutes, Euryarchaeota, Proteobacteria alpha and delta were found under mutational pressure. These nif genes with low and high GC3% from different classes of organisms showed similar expected number of codons. Distribution of the genes and codons, based on codon usage demonstrated opposite pattern for different orientation of mirror plane when compared with each other. Overall our results provide a comprehensive analysis on the evolutionary relationship of the three structural nif genes, nifK, nifD and nifH, respectively, in the context of codon usage bias, GC content relationship and amino acid composition of the encoded proteins and exploration of crucial statistical method for the analysis of positive data with non-constant variance to identify the shape factors of codon adaptation index.

  13. Exploring codon context bias for synthetic gene design of a thermostable invertase in Escherichia coli.

    PubMed

    Pek, Han Bin; Klement, Maximilian; Ang, Kok Siong; Chung, Bevan Kai-Sheng; Ow, Dave Siak-Wei; Lee, Dong-Yup

    2015-01-01

    Various isoforms of invertases from prokaryotes, fungi, and higher plants has been expressed in Escherichia coli, and codon optimisation is a widely-adopted strategy for improvement of heterologous enzyme expression. Successful synthetic gene design for recombinant protein expression can be done by matching its translational elongation rate against heterologous host organisms via codon optimization. Amongst the various design parameters considered for the gene synthesis, codon context bias has been relatively overlooked compared to individual codon usage which is commonly adopted in most of codon optimization tools. In addition, matching the rates of transcription and translation based on secondary structure may lead to enhanced protein folding. In this study, we evaluated codon context fitness as design criterion for improving the expression of thermostable invertase from Thermotoga maritima in Escherichia coli and explored the relevance of secondary structure regions for folding and expression. We designed three coding sequences by using (1) a commercial vendor optimized gene algorithm, (2) codon context for the whole gene, and (3) codon context based on the secondary structure regions. Then, the codon optimized sequences were transformed and expressed in E. coli. From the resultant enzyme activities and protein yield data, codon context fitness proved to have the highest activity as compared to the wild-type control and other criteria while secondary structure-based strategy is comparable to the control. Codon context bias was shown to be a relevant parameter for enhancing enzyme production in Escherichia coli by codon optimization. Thus, we can effectively design synthetic genes within heterologous host organisms using this criterion. PMID:26047917

  14. Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations in Human Cancers

    PubMed Central

    Wu, Xudong; Li, Guohui

    2016-01-01

    Cancer is characterized by uncontrolled cell growth, and the cause of different cancers is generally attributed to checkpoint dysregulation of cell proliferation and apoptosis. Recent studies have shown that non-optimal codons were preferentially adopted by genes to generate cell cycle-dependent oscillations in protein levels. This raises the intriguing question of how dynamic changes of codon usage modulate the cancer genome to cope with a non-controlled proliferative cell cycle. In this study, we comprehensively analyzed the somatic mutations of codons in human cancers, and found that non-optimal codons tended to be accumulated through both synonymous and non-synonymous mutations compared with other types of genomic substitution. We further demonstrated that non-optimal codons were prevalently accumulated across different types of cancers, amino acids, and chromosomes, and genes with accumulation of non-optimal codons tended to be involved in protein interaction/signaling networks and encoded important enzymes in metabolic networks that played roles in cancer-related pathways. This study provides insights into the dynamics of codons in the cancer genome and demonstrates that accumulation of non-optimal codons may be an adaptive strategy for cancerous cells to win the competition with normal cells. This deeper interpretation of the patterns and the functional characterization of somatic mutations of codons will help to broaden the current understanding of the molecular basis of cancers. PMID:27513638

  15. Analysis of synonymous codon usage in spike protein gene of infectious bronchitis virus.

    PubMed

    Makhija, Aditi; Kumar, Sachin

    2015-12-01

    Infectious bronchitis virus (IBV) is responsible for causing respiratory, renal, and urogenital diseases in poultry. IBV infection in poultry leads to high mortality rates in affected flocks and to severe economic losses due to a drop in egg production and a reduced gain in live weight of the broiler birds. IBV-encoded spike protein (S) is the major protective immunogen for the host. Although the functions of the S protein have been well studied, the factors shaping synonymous codon usage bias and nucleotide composition in the S gene have not been reported yet. In the present study, we analyzed the relative synonymous codon usage and effective number of codons (Nc) using the 53 IBV S genes. The major trend in codon usage variation was studied using correspondence analysis. The plot of Nc values against GC3 as well as the correlation between base composition and codon usage bias suggest that mutational pressure rather than natural selection is the main factor that determines the codon usage bias in the S gene. Interestingly, no association of aromaticity, degree of hydrophobicity, and aliphatic index was observed with the codon usage variation in IBV S genes. The study represents a comprehensive analysis of IBV S gene codon usage patterns and provides a basic understanding of the codon usage bias. PMID:26452019

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

    PubMed

    Liang, Han; Landweber, Laura F; Fresco, Jacques R

    2005-10-01

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

  17. Analysis of codon usage pattern evolution in avian rotaviruses and their preferred host.

    PubMed

    Kattoor, Jobin Jose; Malik, Yashpal Singh; Sasidharan, Aravind; Rajan, Vishnuraj Mangalathu; Dhama, Kuldeep; Ghosh, Souvik; Bányai, Krisztián; Kobayashi, Nobumichi; Singh, Raj Kumar

    2015-08-01

    Rotavirus infection is a worldwide problem, with occurrence of highly divergent viruses classified in 8 species (A-H). We report here the evolution assessment of codon usage patterns in virus-host system in avian rotavirus (AvRV) of species RVA, RVD, RVF and RVG (preferentially affecting birds). The nucleotide contents, codon usage bias (CUB), relative synonymous codon usage (RSCU), and effective number of codons (ENCs) values were investigated targeting overexpressing major inner capsid viral protein (VP6) of these AvRV species. The results confirm that the evolutionary characteristics influences the rotavirus (RV) genetic diversity and impact of host's natural selection on the AvRVs codons. Synonymous codon usage patterns were evaluated following multivariate statistical procedures on all available AvRV coding gene sequences. RSCU trees accommodated all AvRV species and preferred host sequences in one topology confirming greater imminence of AvRVs with the host chicken cell genes. Similarly, the codon adaptation index (CAI) results also displayed a higher adaptation of AvRVs to its chicken host. The codon preference analysis of RVs revealed that VP6 gene express more proficiently in the yeast system, whereas, codon optimization might be required for the effectual expression in Escherichia coli and Homo sapiens. The findings provide basic evidence on the dynamics of AvRV evolution and its host adaptation, which could be exploited for additional research on avian species in future. PMID:26086995

  18. Prevalent Accumulation of Non-Optimal Codons through Somatic Mutations in Human Cancers.

    PubMed

    Wu, Xudong; Li, Guohui

    2016-01-01

    Cancer is characterized by uncontrolled cell growth, and the cause of different cancers is generally attributed to checkpoint dysregulation of cell proliferation and apoptosis. Recent studies have shown that non-optimal codons were preferentially adopted by genes to generate cell cycle-dependent oscillations in protein levels. This raises the intriguing question of how dynamic changes of codon usage modulate the cancer genome to cope with a non-controlled proliferative cell cycle. In this study, we comprehensively analyzed the somatic mutations of codons in human cancers, and found that non-optimal codons tended to be accumulated through both synonymous and non-synonymous mutations compared with other types of genomic substitution. We further demonstrated that non-optimal codons were prevalently accumulated across different types of cancers, amino acids, and chromosomes, and genes with accumulation of non-optimal codons tended to be involved in protein interaction/signaling networks and encoded important enzymes in metabolic networks that played roles in cancer-related pathways. This study provides insights into the dynamics of codons in the cancer genome and demonstrates that accumulation of non-optimal codons may be an adaptive strategy for cancerous cells to win the competition with normal cells. This deeper interpretation of the patterns and the functional characterization of somatic mutations of codons will help to broaden the current understanding of the molecular basis of cancers. PMID:27513638

  19. Codon-specific and general inhibition of protein synthesis by the tRNA-sequestering minigenes.

    PubMed

    Delgado-Olivares, Luis; Zamora-Romo, Efraín; Guarneros, Gabriel; Hernandez-Sanchez, Javier

    2006-07-01

    The expression of minigenes in bacteria inhibits protein synthesis and cell growth. Presumably, the translating ribosomes, harboring the peptides as peptidyl-tRNAs, pause at the last sense codon of the minigene directed mRNAs. Eventually, the peptidyl-tRNAs drop off and, under limiting activity of peptidyl-tRNA hydrolase, accumulate in the cells reducing the concentration of specific aminoacylable tRNA. Therefore, the extent of inhibition is associated with the rate of starvation for a specific tRNA. Here, we used minigenes harboring various last sense codons that sequester specific tRNAs with different efficiency, to inhibit the translation of reporter genes containing, or not, these codons. A prompt inhibition of the protein synthesis directed by genes containing the codons starved for their cognate tRNA (hungry codons) was observed. However, a non-specific in vitro inhibition of protein synthesis, irrespective of the codon composition of the gene, was also evident. The degree of inhibition correlated directly with the number of hungry codons in the gene. Furthermore, a tRNA(Arg4)-sequestering minigene promoted the production of an incomplete beta-galactosidase polypeptide interrupted, during bacterial polypeptide chain elongation at sites where AGA codons were inserted in the lacZ gene suggesting ribosome pausing at the hungry codons.

  20. Codon optimality is a major determinant of mRNA stability

    PubMed Central

    Presnyak, Vladimir; Alhusaini, Najwa; Chen, Ying-Hsin; Martin, Sophie; Morris, Nathan; Kline, Nicholas; Olson, Sara; Weinberg, David; Baker, Kristian E.; Graveley, Brenton R.; Coller, Jeff

    2015-01-01

    Messenger RNA degradation represents a critical regulated step in gene expression. While the major pathways in turnover have been identified, accounting for disparate half-lives has been elusive. We show that codon optimality is one feature that contributes greatly to mRNA stability. Genome-wide RNA decay analysis revealed that stable mRNAs are enriched in codons designated optimal, whereas unstable mRNAs contain predominately non-optimal codons. Substitution of optimal codons with synonymous, non-optimal codons results in dramatic mRNA destabilization, while the converse substitution significantly increases stability. Further, we demonstrate that codon optimality impacts ribosome translocation, connecting the processes of translation elongation and decay through codon optimality. Finally, we show that optimal codon content accounts for the similar stabilities observed in mRNAs encoding proteins with coordinated physiological function. This work demonstrates that codon optimization exists as an mechanism to finely tune levels of mRNAs, and ultimately, proteins. PMID:25768907

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

    SciTech Connect

    Petraroli, R.; Pocchiari, M.

    1996-04-01

    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.

  2. A novel amperometric alcohol biosensor developed in a 3rd generation bioelectrode platform using peroxidase coupled ferrocene activated alcohol oxidase as biorecognition system.

    PubMed

    Chinnadayyala, Somasekhar R; Kakoti, Ankana; Santhosh, Mallesh; Goswami, Pranab

    2014-05-15

    Alcohol oxidase (AOx) with a two-fold increase in efficiency (Kcat/Km) was achieved by physical entrapment of the activator ferrocene in the protein matrix through a simple microwave based partial unfolding technique and was used to develop a 3rd generation biosensor for improved detection of alcohol in liquid samples. The ferrocene molecules were stably entrapped in the AOx protein matrix in a molar ratio of ~3:1 through electrostatic interaction with the Trp residues involved in the functional activity of the enzyme as demonstrated by advanced analytical techniques. The sensor was fabricated by immobilizing ferrocene entrapped alcohol oxidase (FcAOx) and sol-gel chitosan film coated horseradish peroxidase (HRP) on a multi-walled carbon nanotube (MWCNT) modified glassy carbon electrode through layer-by-layer technique. The bioelectrode reactions involved the formation of H2O2 by FcAOx biocatalysis of substrate alcohol followed by HRP-catalyzed reduction of the liberated H2O2 through MWCNT supported direct electron transfer mechanism. The amperometric biosensor exhibited a linear response to alcohol in the range of 5.0 × 10(-6) to 30 × 10(-4)mol L(-1) with a detection limit of 2.3 × 10(-6) mol L(-1), and a sensitivity of 150 µA mM(-1) cm(-2). The biosensor response was steady for 28 successive measurements completed in a period of 5h and retained ~90% of the original response even after four weeks when stored at 4 °C. The biosensor was successfully applied for the determination of alcohol in commercial samples and its performance was validated by comparing with the data obtained by GC analyses of the samples.

  3. Non-destructive measurement of demineralization and remineralization in the occlusal pits and fissures of extracted 3rd molars with PS-OCT

    NASA Astrophysics Data System (ADS)

    Lee, Chulsung; Hsu, Dennis J.; Le, Michael H.; Darling, Cynthia L.; Fried, Daniel

    2009-02-01

    Previous studies have demonstrated that Polarization Sensitive Optical Coherence Tomography (PS-OCT) can be used to image the remineralization of early artificial caries lesion on smooth enamel surfaces of human and bovine teeth. However, most new dental decay is found in the pits and fissures of the occlusal surfaces of posterior dentition and it is in these high risk areas where the performance of new caries imaging devices need to be investigated. The purpose of this study was to demonstrate that PS-OCT can be used to measure the subsequent remineralization of artificial lesions produced in the pits and fissures of extracted 3rd molars. A PS-OCT system operating at 1310-nm was used to acquire polarization resolved images of occlusal surfaces exposed to a demineralizing solution at pH-4.5 followed by a fluoride containing remineralizing solution at pH-7.0 containing 2-ppm fluoride. The integrated reflectivity was calculated to a depth of 200-µm in the entire lesion area using an automated image processing algorithm. Although a well-defined surface zone was clearly resolved in only a few of the samples that underwent remineralization, the PS-OCT measurements indicated a significant (p<0.05) reduction in the integrated reflectivity between the severity of the lesions that were exposed to the remineralization solution and those that were not. The lesion depth and mineral loss were also measured with polarized light microscopy and transverse microradiography after sectioning the teeth. These results show that PS-OCT can be used to non-destructively monitor the remineralization potential of anti-caries agents in the important pits and fissures of the occlusal surface.

  4. Medical school curriculum characteristics associated with intentions and frequency of tobacco dependence treatment among 3rd year U.S. medical students

    PubMed Central

    Hayes, Rashelle B.; Geller, Alan C.; Crawford, Sybil L.; Jolicoeur, Denise; Churchill, Linda C.; Okuyemi, Kola; David, Sean P.; Adams, Michael; Waugh, Jonathan; Allen, Sharon S.; Leone, Frank T.; Fauver, Randy; Leung, Katherine; Liu, Qin; Ockene, Judith K.

    2015-01-01

    Objective Physicians play a critical role in addressing tobacco dependence, yet report limited training. Tobacco dependence treatment curricula for medical students could improve performance in this area. This study identified student and medical school tobacco treatment curricula characteristics associated with intentions and use of the 5As for tobacco treatment among 3rd year U.S. medical students. Methods Third year medical students (N=1065, 49.3% male) from 10 U.S. medical schools completed a survey in 2009-2010 assessing student characteristics, including demographics, tobacco treatment knowledge, and self-efficacy. Tobacco curricula characteristics assessed included amount and type of classroom instruction, frequency of tobacco treatment observation, instruction, and perception of preceptors as role models. Results Greater tobacco treatment knowledge, self-efficacy, and curriculum-specific variables were associated with 5A intentions, while younger age, tobacco treatment self-efficacy, intentions, and each curriculum-specific variable was associated with greater 5A behaviors. When controlling for important student variables, greater frequency of receiving 5A instruction (OR = 1.07; 95%CI 1.01-1.12) and perception of preceptors as excellent role models in tobacco treatment (OR = 1.35; 95%CI 1.04-1.75) were significant curriculum predictors of 5A intentions. Greater 5A instruction (B = .06 (.03); p< .05) and observation of tobacco treatment (B= .35 (.02); p< .001) were significant curriculum predictors of greater 5A behaviors. Conclusions Greater exposure to tobacco treatment teaching during medical school is associated with both greater intentions to use and practice tobacco 5As. Clerkship preceptors, or those physicians who provide training to medical students, may be particularly influential when they personally model and instruct students in tobacco dependence treatment. PMID:25572623

  5. A psychometric study of the Bayley Scales of Infant and Toddler Development - 3rd Edition for term and preterm Taiwanese infants.

    PubMed

    Yu, Yen-Ting; Hsieh, Wu-Shiun; Hsu, Chyong-Hsin; Chen, Li-Chiou; Lee, Wang-Tso; Chiu, Nan-Chang; Wu, Ying-Chin; Jeng, Suh-Fang

    2013-11-01

    The Bayley Scales of Infant and Toddler Development - 3rd Edition (Bayley-III) was updated to enhance its usefulness for contemporary child developmental assessment. However, recent data in Western countries have implicated the overestimation of child development by the new instrument. This study aimed to investigate the psychometric features of the Bayley-III for term and preterm infants in Taiwan. Forty-seven term infants and 167 preterm infants were prospectively examined with the Bayley Scales of Infant Development - 2nd Edition (BSID-II) and the Bayley-III at 6, 12, 18, and 24 months of age (corrected for prematurity). The psychometric properties examined included reliability, construct validity, and known-group validity. The intra- and inter-rater reliabilities of the Bayley-III were good to excellent. The correlations between the BSID-II and Bayley-III raw scores were good to excellent for the cognitive and motor items and low to excellent for the language items. Term infants achieved higher composite scores than preterm infants on all of the Bayley-III scales (p<0.05). However, their rates of developmental delay were lower than the previously established prevalence estimates. The Bayley-III cut-off composite score was adjusted 10-20, 1-13, and 12-24 points higher than 70 for optimal prediction of cognitive, language, and motor delay, respectively, as defined by the BSID-II index score<70. The Bayley-III is a reliable instrument that extends its previous edition, especially in early language assessment. However, the upward adjustment of its cut-off score is recommended for the accurate identification of developmental delay in term and preterm Taiwanese infants. PMID:24029804

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

    PubMed Central

    Medori, R; Tritschler, H J

    1993-01-01

    Fatal familial insomnia (FFI) is a disease linked to a GAC(Asp)-->AAC(Asn) mutation in codon 178 of the prion protein (PrP) gene. FFI is characterized clinically by untreatable progressive insomnia, dysautonomia, and motor dysfunctions and is characterized pathologically by selective thalamic atrophy. We confirmed the 178Asn mutation in the PrP gene of a third FFI family of French ancestry. Three family members who are under 40 years of age and who inherited the mutation showed only reduced perfusion in the basal ganglia on single photon emission computerized tomography. Some FFI features differ from the clinical and neuropathologic findings associated with 178Asn reported elsewhere. However, additional intragenic mutations accounting for the phenotypic differences were not observed in two affected individuals. In other sporadic and familial forms of Creutzfeldt-Jakob disease and Gerstmann-Sträussler syndrome, Met or Val homozygosity at polymorphic codon 129 is associated with a more severe phenotype, younger age at onset, and faster progression. In FFI, young and old individuals at disease onset had 129Met/Val. Moreover, of five 178Asn individuals who are above age-at-onset range and who are well, two have 129Met and three have 129Met/Val, suggesting that polymorphic site 129 does not modulate FFI phenotypic expression. Genetic heterogeneity and environment may play an important role in inter- and intrafamilial variability of the 178Asn mutation. Images Figure 2 Figure 3 Figure 4 Figure 5 PMID:8105681

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

    SciTech Connect

    Medori, R.; Tritschler, H.J. )

    1993-10-01

    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.

  8. Codon Optimization to Enhance Expression Yields Insights into Chloroplast Translation1[OPEN

    PubMed Central

    Chan, Hui-Ting; Williams-Carrier, Rosalind; Barkan, Alice

    2016-01-01

    Codon optimization based on psbA genes from 133 plant species eliminated 105 (human clotting factor VIII heavy chain [FVIII HC]) and 59 (polio VIRAL CAPSID PROTEIN1 [VP1]) rare codons; replacement with only the most highly preferred codons decreased transgene expression (77- to 111-fold) when compared with the codon usage hierarchy of the psbA genes. Targeted proteomic quantification by parallel reaction monitoring analysis showed 4.9- to 7.1-fold or 22.5- to 28.1-fold increase in FVIII or VP1 codon-optimized genes when normalized with stable isotope-labeled standard peptides (or housekeeping protein peptides), but quantitation using western blots showed 6.3- to 8-fold or 91- to 125-fold increase of transgene expression from the same batch of materials, due to limitations in quantitative protein transfer, denaturation, solubility, or stability. Parallel reaction monitoring, to our knowledge validated here for the first time for in planta quantitation of biopharmaceuticals, is especially useful for insoluble or multimeric proteins required for oral drug delivery. Northern blots confirmed that the increase of codon-optimized protein synthesis is at the translational level rather than any impact on transcript abundance. Ribosome footprints did not increase proportionately with VP1 translation or even decreased after FVIII codon optimization but is useful in diagnosing additional rate-limiting steps. A major ribosome pause at CTC leucine codons in the native gene of FVIII HC was eliminated upon codon optimization. Ribosome stalls observed at clusters of serine codons in the codon-optimized VP1 gene provide an opportunity for further optimization. In addition to increasing our understanding of chloroplast translation, these new tools should help to advance this concept toward human clinical studies. PMID:27465114

  9. Fatal insomnia in a case of familial Creutzfeldt-Jakob disease with the codon 200(Lys) mutation.

    PubMed

    Chapman, J; Arlazoroff, A; Goldfarb, L G; Cervenakova, L; Neufeld, M Y; Werber, E; Herbert, M; Brown, P; Gajdusek, D C; Korczyn, A D

    1996-03-01

    Fatal familial insomnia (FFI) has been exclusively associated with a pathogenic mutation at codon 178 in the PRNP gene coupled with methionine (Met) at codon 129. We now describe a subject with familial Creutzfeldt-Jakob disease, heterozygous for the pathogenic lysine (Lys) mutation at codon 200 and homozygous for Met at codon 129 of the PRNP gene, who was affected by severe insomnia. At autopsy the patient had significant involvement of the thalamus, as previously described in subjects affected by FFI with the codon 178 mutation. This case demonstrates the wide variability of the clinical expressions in patients with the codon 200 mutation, that may include insomnia and thalamic pathology.

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

    PubMed Central

    Devaraj, Aishwarya; Fredrick, Kurt

    2010-01-01

    Summary Programmed frameshifting in the RF2 gene (prfB) involves an intragenic Shine-Dalgarno (SD) sequence. To investigate the role of SD-ASD pairing in the mechanism of frameshifting, we have analyzed the effect of spacing between the SD sequence and P codon on P-site tRNA binding and RF2-dependent termination. When the spacing between an extended SD sequence and the P codon is decreased from 4 to 1 nucleotides (nt), the dissociation rate (koff) for P-site tRNA increases by >100-fold. Toeprinting analysis shows that pretranslocation complexes cannot be formed when the spacer sequence is ≤ 2 nt. Instead, the tRNA added secondarily to fill the A site and its corresponding codon move spontaneously into the P site, resulting in a complex with a 3-nt longer spacer between the SD-ASD helix and the P codon. While close proximity of the SD clearly destabilizes P-site tRNA, RF2-dependent termination and EF-Tu-dependent decoding are largely unaffected in analogous complexes. These data support a model in which formation of the SD-ASD helix in ribosomes stalled at the in-frame UGA codon of prfB generates tension on the mRNA that destabilizes codon-anticodon pairing in the P site and promotes slippage of the mRNA in the 5′ direction. PMID:21143320

  11. Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness.

    PubMed

    Villanueva, Eneko; Martí-Solano, Maria; Fillat, Cristina

    2016-01-01

    Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development.

  12. Probable relationship between partitions of the set of codons and the origin of the genetic code.

    PubMed

    Salinas, Dino G; Gallardo, Mauricio O; Osorio, Manuel I

    2014-03-01

    Here we study the distribution of randomly generated partitions of the set of amino acid-coding codons. Some results are an application from a previous work, about the Stirling numbers of the second kind and triplet codes, both to the cases of triplet codes having four stop codons, as in mammalian mitochondrial genetic code, and hypothetical doublet codes. Extending previous results, in this work it is found that the most probable number of blocks of synonymous codons, in a genetic code, is similar to the number of amino acids when there are four stop codons, as well as it could be for a primigenious doublet code. Also it is studied the integer partitions associated to patterns of synonymous codons and it is shown, for the canonical code, that the standard deviation inside an integer partition is one of the most probable. We think that, in some early epoch, the genetic code might have had a maximum of the disorder or entropy, independent of the assignment between codons and amino acids, reaching a state similar to "code freeze" proposed by Francis Crick. In later stages, maybe deterministic rules have reassigned codons to amino acids, forming the natural codes, such as the canonical code, but keeping the numerical features describing the set partitions and the integer partitions, like a "fossil numbers"; both kinds of partitions about the set of amino acid-coding codons.

  13. Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness.

    PubMed

    Villanueva, Eneko; Martí-Solano, Maria; Fillat, Cristina

    2016-01-01

    Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development. PMID:27278133

  14. Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness

    PubMed Central

    Villanueva, Eneko; Martí-Solano, Maria; Fillat, Cristina

    2016-01-01

    Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development. PMID:27278133

  15. Codon optimization of the adenoviral fiber negatively impacts structural protein expression and viral fitness

    NASA Astrophysics Data System (ADS)

    Villanueva, Eneko; Martí-Solano, Maria; Fillat, Cristina

    2016-06-01

    Codon usage adaptation of lytic viruses to their hosts is determinant for viral fitness. In this work, we analyzed the codon usage of adenoviral proteins by principal component analysis and assessed their codon adaptation to the host. We observed a general clustering of adenoviral proteins according to their function. However, there was a significant variation in the codon preference between the host-interacting fiber protein and the rest of structural late phase proteins, with a non-optimal codon usage of the fiber. To understand the impact of codon bias in the fiber, we optimized the Adenovirus-5 fiber to the codon usage of the hexon structural protein. The optimized fiber displayed increased expression in a non-viral context. However, infection with adenoviruses containing the optimized fiber resulted in decreased expression of the fiber and of wild-type structural proteins. Consequently, this led to a drastic reduction in viral release. The insertion of an exogenous optimized protein as a late gene in the adenovirus with the optimized fiber further interfered with viral fitness. These results highlight the importance of balancing codon usage in viral proteins to adequately exploit cellular resources for efficient infection and open new opportunities to regulate viral fitness for virotherapy and vaccine development.

  16. Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses.

    PubMed

    Velazquez-Salinas, Lauro; Zarate, Selene; Eschbaumer, Michael; Pereira Lobo, Francisco; Gladue, Douglas P; Arzt, Jonathan; Novella, Isabel S; Rodriguez, Luis L

    2016-01-01

    Arboviruses (arthropod borne viruses) have life cycles that include both vertebrate and invertebrate hosts with substantial differences in vector and host specificity between different viruses. Most arboviruses utilize RNA for their genetic material and are completely dependent on host tRNAs for their translation, suggesting that virus codon usage could be a target for selection. In the current study we analyzed the relative synonymous codon usage (RSCU) patterns of 26 arboviruses together with 25 vectors and hosts, including 8 vertebrates and 17 invertebrates. We used hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify trends in codon usage. HCA demonstrated that the RSCU of arboviruses reflects that of their natural hosts, but not that of dead-end hosts. Of the two major components identified by PCA, the first accounted for 62.1% of the total variance, and among the 59 codons analyzed in this study, the leucine codon CTG had the highest correlation with the first principal component, however isoleucine had the highest correlation during amino acid analysis. Nucleotide and dinucleotide composition were the variables that explained most of the total codon usage variance. The results suggest that the main factors driving the evolution of codon usage in arboviruses is based on the nucleotide and dinucleotide composition present in the host. Comparing codon usage of arboviruses and potential vector hosts can help identifying potential vectors for emerging arboviruses. PMID:27455096

  17. Analysis of the synonymous codon usage bias in recently emerged enterovirus D68 strains.

    PubMed

    Karniychuk, Uladzimir U

    2016-09-01

    Understanding the codon usage pattern of a pathogen and relationship between pathogen and host's codon usage patterns has fundamental and applied interests. Enterovirus D68 (EV-D68) is an emerging pathogen with a potentially high public health significance. In the present study, the synonymous codon usage bias of 27 recently emerged, and historical EV-D68 strains was analyzed. In contrast to previously studied enteroviruses (enterovirus 71 and poliovirus), EV-D68 and human host have a high discrepancy between favored codons. Analysis of viral synonymous codon usage bias metrics, viral nucleotide/dinucleotide compositional parameters, and viral protein properties showed that mutational pressure is more involved in shaping the synonymous codon usage bias of EV-D68 than translation selection. Computation of codon adaptation indices allowed to estimate expression potential of the EV-D68 genome in several commonly used laboratory animals. This approach requires experimental validation and may provide an auxiliary tool for the rational selection of laboratory animals to model emerging viral diseases. Enterovirus D68 genome compositional and codon usage data can be useful for further pathogenesis, animal model, and vaccine design studies. PMID:27364082

  18. Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses

    PubMed Central

    Velazquez-Salinas, Lauro; Zarate, Selene; Eschbaumer, Michael; Pereira Lobo, Francisco; Gladue, Douglas P.; Arzt, Jonathan; Novella, Isabel S.; Rodriguez, Luis L.

    2016-01-01

    Arboviruses (arthropod borne viruses) have life cycles that include both vertebrate and invertebrate hosts with substantial differences in vector and host specificity between different viruses. Most arboviruses utilize RNA for their genetic material and are completely dependent on host tRNAs for their translation, suggesting that virus codon usage could be a target for selection. In the current study we analyzed the relative synonymous codon usage (RSCU) patterns of 26 arboviruses together with 25 vectors and hosts, including 8 vertebrates and 17 invertebrates. We used hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify trends in codon usage. HCA demonstrated that the RSCU of arboviruses reflects that of their natural hosts, but not that of dead-end hosts. Of the two major components identified by PCA, the first accounted for 62.1% of the total variance, and among the 59 codons analyzed in this study, the leucine codon CTG had the highest correlation with the first principal component, however isoleucine had the highest correlation during amino acid analysis. Nucleotide and dinucleotide composition were the variables that explained most of the total codon usage variance. The results suggest that the main factors driving the evolution of codon usage in arboviruses is based on the nucleotide and dinucleotide composition present in the host. Comparing codon usage of arboviruses and potential vector hosts can help identifying potential vectors for emerging arboviruses. PMID:27455096

  19. Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses.

    PubMed

    Velazquez-Salinas, Lauro; Zarate, Selene; Eschbaumer, Michael; Pereira Lobo, Francisco; Gladue, Douglas P; Arzt, Jonathan; Novella, Isabel S; Rodriguez, Luis L

    2016-01-01

    Arboviruses (arthropod borne viruses) have life cycles that include both vertebrate and invertebrate hosts with substantial differences in vector and host specificity between different viruses. Most arboviruses utilize RNA for their genetic material and are completely dependent on host tRNAs for their translation, suggesting that virus codon usage could be a target for selection. In the current study we analyzed the relative synonymous codon usage (RSCU) patterns of 26 arboviruses together with 25 vectors and hosts, including 8 vertebrates and 17 invertebrates. We used hierarchical cluster analysis (HCA) and principal component analysis (PCA) to identify trends in codon usage. HCA demonstrated that the RSCU of arboviruses reflects that of their natural hosts, but not that of dead-end hosts. Of the two major components identified by PCA, the first accounted for 62.1% of the total variance, and among the 59 codons analyzed in this study, the leucine codon CTG had the highest correlation with the first principal component, however isoleucine had the highest correlation during amino acid analysis. Nucleotide and dinucleotide composition were the variables that explained most of the total codon usage variance. The results suggest that the main factors driving the evolution of codon usage in arboviruses is based on the nucleotide and dinucleotide composition present in the host. Comparing codon usage of arboviruses and potential vector hosts can help identifying potential vectors for emerging arboviruses.

  20. Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We have previously identified the mycobacterial high G+C codon usage bias as a limiting factor in heterologous expression of MAP proteins from Lb.salivarius, and demonstrated that codon optimisation of a synthetic coding gene greatly enhances MAP protein production. Here, we effectively demonstrate ...

  1. Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD.

    PubMed

    Fu, Jingjing; Murphy, Katherine A; Zhou, Mian; Li, Ying H; Lam, Vu H; Tabuloc, Christine A; Chiu, Joanna C; Liu, Yi

    2016-08-01

    Codon usage bias is a universal feature of all genomes, but its in vivo biological functions in animal systems are not clear. To investigate the in vivo role of codon usage in animals, we took advantage of the sensitivity and robustness of the Drosophila circadian system. By codon-optimizing parts of Drosophila period (dper), a core clock gene that encodes a critical component of the circadian oscillator, we showed that dper codon usage is important for circadian clock function. Codon optimization of dper resulted in conformational changes of the dPER protein, altered dPER phosphorylation profile and stability, and impaired dPER function in the circadian negative feedback loop, which manifests into changes in molecular rhythmicity and abnormal circadian behavioral output. This study provides an in vivo example that demonstrates the role of codon usage in determining protein structure and function in an animal system. These results suggest a universal mechanism in eukaryotes that uses a codon usage "code" within genetic codons to regulate cotranslational protein folding. PMID:27542830

  2. Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding.

    PubMed

    Yu, Chien-Hung; Dang, Yunkun; Zhou, Zhipeng; Wu, Cheng; Zhao, Fangzhou; Sachs, Matthew S; Liu, Yi

    2015-09-01

    Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and has been proposed to regulate translation efficiency, accuracy, and protein folding based on the assumption that codon usage affects translation dynamics. The roles of codon usage in translation, however, are not clear and have been challenged by recent ribosome profiling studies. Here we used a Neurospora cell-free translation system to directly monitor the velocity of mRNA translation. We demonstrated that the preferred codons enhance the rate of translation elongation, whereas non-optimal codons slow elongation. Codon usage also controls ribosome traffic on mRNA. These conclusions were supported by ribosome profiling results in vitro and in vivo with template mRNAs designed to increase the signal-to-noise ratio. Finally, we demonstrate that codon usage regulates protein function by affecting co-translational protein folding. These results resolve a long-standing fundamental question and suggest the existence of a codon usage code for protein folding. PMID:26321254

  3. Synonymous codon usage and its potential link with optimal growth temperature in prokaryotes.

    PubMed

    Lobry, J R; Necşulea, A

    2006-12-30

    The relationship between codon usage in prokaryotes and their ability to grow at extreme temperatures has been given much attention over the past years. Previous studies have suggested that the difference in synonymous codon usage between (hyper)thermophiles and mesophiles is a consequence of a selective pressure linked to growth temperature. Here, we performed an updated analysis of the variation in synonymous codon usage with growth temperature; our study includes a large number of species from a wide taxonomic and growth temperature range. The presence of psychrophilic species in our study allowed us to test whether the same selective pressure acts on synonymous codon usage at very low growth temperature. Our results show that the synonymous codon usage for Arg (through the AGG, AGA and CGT codons) is the most discriminating factor between (hyper)thermophilic and non-thermophilic species, thus confirming previous studies. We report the unusual clustering of an Archaeal psychrophile with the thermophilic and hyperthermophilic species on the synonymous codon usage factorial map; the other psychrophiles in our study cluster with the mesophilic species. Our conclusion is that the difference in synonymous codon usage between (hyper)thermophilic and non-thermophilic species cannot be clearly attributed to a selective pressure linked to growth at high temperatures.

  4. ICOM2012: 3rd International Conference on the Physics of Optical Materials and Devices (Belgrade, Serbia, 2-6 September 2012)

    NASA Astrophysics Data System (ADS)

    Dramićanin, Miroslav D.; Antić, Željka; Viana, Bruno

    2013-11-01

    The 3rd International Conference on the Physics of Optical Materials and Devices (ICOM2012) was held in Belgrade (Serbia) from 2 to 6 September 2012 (figure 1). The conference was organized by the Vinča Institute of Nuclear Sciences, University of Belgrade (Serbia) and the Laboratoire de Chimie de la Matière Condensée de Paris (France), and supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia and Optical Society of America. ICOM2012 was a follow-up to the two previous, successful ICOM conferences held in Herceg Novi in 2006 and 2009. The conference aimed at providing a forum for scientists in optical materials to debate on: • Luminescent materials and nanomaterials • Hybrid optical materials (organic/inorganic) • Characterization techniques of optical materials • Luminescence mechanisms and energy transfers • Theory and modeling of optical processes • Ultrafast-laser processing of materials • Optical sensors • Medical imaging • Advanced optical materials in photovoltaics and biophotonics • Photothermal and photoacoustic spectroscopy and phenomena The conference stressed the value of a fundamental scientific understanding of optical materials. A particular accent was put on wide band-gap materials in crystalline, glass and nanocrystalline forms. The applications mainly involved lasers, scintillators and phosphors. Rare earth and transition metal ions introduced as dopants in various hosts were considered, and their impact on the optical properties were detailed in several presentations. This volume contains selected contributions of speakers and participants of the ICOM2012 conference. The conference provided a unique opportunity for about 200 scientists from 32 countries to discuss recent progress in the field of optical materials. During the three and half days, 21 invited talks and 52 contributed lectures were given, with a special event in memory of our dear colleague Professor Dr Tsoltan

  5. Importance of codon usage for the temporal regulation of viral gene expression.

    PubMed

    Shin, Young C; Bischof, Georg F; Lauer, William A; Desrosiers, Ronald C

    2015-11-10

    The glycoproteins of herpesviruses and of HIV/SIV are made late in the replication cycle and are derived from transcripts that use an unusual codon usage that is quite different from that of the host cell. Here we show that the actions of natural transinducers from these two different families of persistent viruses (Rev of SIV and ORF57 of the rhesus monkey rhadinovirus) are dependent on the nature of the skewed codon usage. In fact, the transinducibility of expression of these glycoproteins by Rev and by ORF57 can be flipped simply by changing the nature of the codon usage. Even expression of a luciferase reporter could be made Rev dependent or ORF57 dependent by distinctive changes to its codon usage. Our findings point to a new general principle in which different families of persisting viruses use a poor codon usage that is skewed in a distinctive way to temporally regulate late expression of structural gene products. PMID:26504241

  6. Importance of codon usage for the temporal regulation of viral gene expression

    PubMed Central

    Shin, Young C.; Bischof, Georg F.; Lauer, William A.; Desrosiers, Ronald C.

    2015-01-01

    The glycoproteins of herpesviruses and of HIV/SIV are made late in the replication cycle and are derived from transcripts that use an unusual codon usage that is quite different from that of the host cell. Here we show that the actions of natural transinducers from these two different families of persistent viruses (Rev of SIV and ORF57 of the rhesus monkey rhadinovirus) are dependent on the nature of the skewed codon usage. In fact, the transinducibility of expression of these glycoproteins by Rev and by ORF57 can be flipped simply by changing the nature of the codon usage. Even expression of a luciferase reporter could be made Rev dependent or ORF57 dependent by distinctive changes to its codon usage. Our findings point to a new general principle in which different families of persisting viruses use a poor codon usage that is skewed in a distinctive way to temporally regulate late expression of structural gene products. PMID:26504241

  7. Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.

    PubMed

    Pechmann, Sebastian; Frydman, Judith

    2013-02-01

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

  8. Image Quality of 3rd Generation Spiral Cranial Dual-Source CT in Combination with an Advanced Model Iterative Reconstruction Technique: A Prospective Intra-Individual Comparison Study to Standard Sequential Cranial CT Using Identical Radiation Dose

    PubMed Central

    Wenz, Holger; Maros, Máté E.; Meyer, Mathias; Förster, Alex; Haubenreisser, Holger; Kurth, Stefan; Schoenberg, Stefan O.; Flohr, Thomas; Leidecker, Christianne; Groden, Christoph; Scharf, Johann; Henzler, Thomas

    2015-01-01

    Objectives To prospectively intra-individually compare image quality of a 3rd generation Dual-Source-CT (DSCT) spiral cranial CT (cCT) to a sequential 4-slice Multi-Slice-CT (MSCT) while maintaining identical intra-individual radiation dose levels. Methods 35 patients, who had a non-contrast enhanced sequential cCT examination on a 4-slice MDCT within the past 12 months, underwent a spiral cCT scan on a 3rd generation DSCT. CTDIvol identical to initial 4-slice MDCT was applied. Data was reconstructed using filtered backward projection (FBP) and 3rd-generation iterative reconstruction (IR) algorithm at 5 different IR strength levels. Two neuroradiologists independently evaluated subjective image quality using a 4-point Likert-scale and objective image quality was assessed in white matter and nucleus caudatus with signal-to-noise ratios (SNR) being subsequently calculated. Results Subjective image quality of all spiral cCT datasets was rated significantly higher compared to the 4-slice MDCT sequential acquisitions (p<0.05). Mean SNR was significantly higher in all spiral compared to sequential cCT datasets with mean SNR improvement of 61.65% (p*Bonferroni0.05<0.0024). Subjective image quality improved with increasing IR levels. Conclusion Combination of 3rd-generation DSCT spiral cCT with an advanced model IR technique significantly improves subjective and objective image quality compared to a standard sequential cCT acquisition acquired at identical dose levels. PMID:26288186

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

    PubMed Central

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

    2014-01-01

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

  10. Joint conference of iMEC 2015 (2nd International Manufacturing Engineering Conference & APCOMS 2015 (3rd Asia-Pacific Conference on Manufacturing Systems)

    NASA Astrophysics Data System (ADS)

    2016-02-01

    The iMEC 2015 is the second International Manufacturing Engineering Conference organized by the Faculty of Manufacturing, Universiti Malaysia Pahang (UMP), held from 12-14th November 2015 in Kuala Lumpur, Malaysia, with a theme "Materials, Manufacturing and Systems for Tomorrow". For the first time, iMEC is organized together with 3rd Asia- Pacific Conference on Manufacturing System (APCOMS 2015) which owned by Fakulti Teknologi Industri, Institut Teknologi Bandung (ITB), Indonesia. This is an extended collaboration between UMP and ITB to intensify knowledge sharing and experiences between higher learning institutions. This conference (iMEC & APCOMS 2015) is a platform for knowledge exchange and the growth of ideas, particularly in manufacturing engineering. The conference aims to bring researchers, academics, scientists, students, engineers and practitioners from around the world together to present their latest findings, ideas, developments and applications related to manufacturing engineering and other related research areas. With rapid advancements in manufacturing engineering, iMEC is an appropriate medium for the associated community to keep pace with the changes. In 2015, the conference theme is “Materials, Manufacturing and Systems for Tomorrow” which reflects the acceleration of knowledge and technology in global manufacturing. The papers in these proceedings are examples of the work presented at the conference. They represent the tip of the iceberg, as the conference attracted over 200 abstracts from Malaysia, Indonesia, Japan, United Kingdom, Australia, India, Bangladesh, South Africa, Turkey and Morocco and 151 full papers were accepted in these proceedings. The conference was run in four parallel sessions with 160 presenters sharing their latest finding in the areas of manufacturing process, systems, advanced materials and automation. The first keynote presentation was given by Prof. B. S. Murthy (IIT, Madras) on "Nanomaterials with Exceptional

  11. Stages of Geoinformation Evolution Related to the Territories Described in the Bible - from the 3Rd Millennium B.C. to Modern Times

    NASA Astrophysics Data System (ADS)

    Linsenbarth, Adam

    2012-09-01

    The paper presents consecutive stages of the evolution of geoinformation related to the territories of the events described in the Bible. Two geoinformation sources are presented: the Bible and non-Bible sources. In the Bible there is much, often some highly detailed information regarding terrain topography. The oldest non-Bible sources are incorporated in the ancient documents, which were discovered in Egypt and Mesopotamia. Some of them are related to the 3rd millen- nium B.C. The further stages are related to the onomasticons and itineraries written by travellers and pilgrims to the Holy Land. The most famous onomasticons include: onomasticons prepared by bishop Eusebius from Caesarea and those pre- pared by St. Jerome. One of the oldest maps of Palestine's territory is the so-called mosaic map of Madaba dated to 565. In the 15th century several Bible maps were edited. The most rapid evolution occurred in the 16th and 17* centuries, when the world famous cartographers such as Mercator and Ortelius edited several maps of Palestine's territory. Cartographers from several European countries edited more than 6,000 maps presenting the Biblical territories and Biblical events. Modem maps, based on detailed topographical surveys, were edited m the second half of the 19* and 20th centuries. W artykule przedstawiono kolejne etapy rozwoju geoinformacji dotyczącej terenówr biblijnych. Omówiono dwa źródła informacji, a mianowicie geoinformacje biblijne i pozabiblijne. W tekstach biblijnych można znaleźć wiele, często bardzo detalicznych informacji topograficznych. Najstarsze źródła pozabiblijne, to starożytne dokumenty odnalezione na terenach Egiptu i Mezopotamii. Niektóre z nich pochodzą z trzeciego milenium przed Chr. Kolejnym etapem geoinformacji były onomastikony oraz dzienniki podróży pisane przez podróżników i pielgrzymów do Ziemi Świętej. Do najbardziej znanych należy onomastikon sporządzony przez biskupa Euzebiusza z Cezarei oraz

  12. [Cold agglutinin disease -  no response to glucocorticoids and rituximab, what treatment is best for the 3rd line of therapy? Case report and review of the literature].

    PubMed

    Adam, Z; Pejchalová, A; Chlupová, G; Ríhová, L; Pour, L; Krejčí, M; Cervinek, L; Král, Z; Mayer, J

    2013-09-01

    in about one  half of treated patients and the remission duration median after rituximab administration is 11 months. A combination of rituximab with fludarabin was more effective, though more toxic; this combination, in a clinical study, led to 75% of patients responding to treatment, including 20% experiencing complete remission. The treatment response median reached over 66 months. In a small study (10 patients) an increase in the amount of rituximab administrations from 4 to 8 led to a treatment response in 6 patients in whom administration of 4 doses of rituximab had no response. When treating Waldenström macroglobulinemia, effectiveness of the following drugs and their combinations was proven: rituximab, chlorambucil, cyclophosphamide, fludarabin, bortezomib, lenalidomid, bendamustin and alemtuzumab. The same drugs and treatment procedures are used for the treatment of the cold agglutinin disease as for Waldenström macroglobulinemia. Successful treatment with vortezomibem, combinations of rituximab + bendamustin, rituximab + cyclophosphamide or rituximab + fludarabin + cyclophosphamide, were recorded in the form of a description as regards the cold agglutinin disease treatment. An important benefit is also shown through treatment with the monoclonal antibody antiC5, eculizumab, which is otherwise used for the treatment of paroxysmal nocturnal haemoglobinuria. Eculizumab blocks the C5 element of the component and thus stops haemolysis in a patient with cold agglutinin disease. As cold agglutinin disease is very rare, there are only a few clinical studies and when treating this rare disease we have no other option than to take into account the information contained in the descriptions of the particular cases of cold agglutinin disease and the experience of Waldenström macroglobulinemia disease treatment. The discussion seeks to solve the issue regarding what 3rd line treatment option to use in the described patient. PMID:24073955

  13. Comparison of Correspondence Analysis Methods for Synonymous Codon Usage in Bacteria

    PubMed Central

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

    2008-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  15. Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer.

    PubMed

    Liu, Jibin; Zhu, Dekang; Ma, Guangpeng; Liu, Mafeng; Wang, Mingshu; Jia, Renyong; Chen, Shun; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Chen, Xiaoyue; Cheng, Anchun

    2016-01-01

    Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC₃ (p > 0.05). Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA. PMID:27517915

  16. Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States

    PubMed Central

    Villar, Diego; White, Robert J.; Marioni, John C.; Kutter, Claudia

    2016-01-01

    Whether codon usage fine-tunes mRNA translation in mammals remains controversial, with recent papers suggesting that production of proteins in specific Gene Ontological (GO) pathways can be regulated by actively modifying the codon and anticodon pools in different cellular conditions. In this work, we compared the sequence content of genes in specific GO categories with the exonic genome background. Although a substantial fraction of variability in codon usage could be explained by random sampling, almost half of GO sets showed more variability in codon usage than expected by chance. Nevertheless, by quantifying translational efficiency in healthy and cancerous tissues in human and mouse, we demonstrated that a given tRNA pool can equally well translate many different sets of mRNAs, irrespective of their cell-type specificity. This disconnect between variations in codon usage and the stability of translational efficiency is best explained by differences in GC content between gene sets. GC variation across the mammalian genome is most likely a result of the interplay between genome repair and gene duplication mechanisms, rather than selective pressures caused by codon-driven translational rates. Consequently, codon usage differences in mammalian transcriptomes are most easily explained by well-understood mutational biases acting on the underlying genome. PMID:27166679

  17. Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes

    NASA Astrophysics Data System (ADS)

    Iwane, Yoshihiko; Hitomi, Azusa; Murakami, Hiroshi; Katoh, Takayuki; Goto, Yuki; Suga, Hiroaki

    2016-04-01

    In ribosomal polypeptide synthesis the library of amino acid building blocks is limited by the manner in which codons are used. Of the proteinogenic amino acids, 18 are coded for by multiple codons and therefore many of the 61 sense codons can be considered redundant. Here we report a method to reduce the redundancy of codons by artificially dividing codon boxes to create vacant codons that can then be reassigned to non-proteinogenic amino acids and thereby expand the library of genetically encoded amino acids. To achieve this, we reconstituted a cell-free translation system with 32 in vitro transcripts of transfer RNASNN (tRNASNN) (S = G or C), assigning the initiator and 20 elongator amino acids. Reassignment of three redundant codons was achieved by replacing redundant tRNASNNs with tRNASNNs pre-charged with non-proteinogenic amino acids. As a demonstration, we expressed a 32-mer linear peptide that consists of 20 proteinogenic and three non-proteinogenic amino acids, and a 14-mer macrocyclic peptide that contains more than four non-proteinogenic amino acids.

  18. The Code of Silence: Widespread Associations Between Synonymous Codon Biases and Gene Function.

    PubMed

    Supek, Fran

    2016-01-01

    Some mutations in gene coding regions exchange one synonymous codon for another, and thus do not alter the amino acid sequence of the encoded protein. Even though they are often called 'silent,' these mutations may exhibit a plethora of effects on the living cell. Therefore, they are often selected during evolution, causing synonymous codon usage biases in genomes. Comparative analyses of bacterial, archaeal, fungal, and human cancer genomes have found many links between a gene's biological role and the accrual of synonymous mutations during evolution. In particular, highly expressed genes in certain functional categories are enriched with optimal codons, which are decoded by the abundant tRNAs, thus enhancing the speed and accuracy of the translating ribosome. The set of genes exhibiting codon adaptation differs between genomes, and these differences show robust associations to organismal phenotypes. In addition to selection for translation efficiency, other distinct codon bias patterns have been found in: amino acid starvation genes, cyclically expressed genes, tissue-specific genes in animals and plants, oxidative stress response genes, cellular differentiation genes, and oncogenes. In addition, genomes of organisms harboring tRNA modifications exhibit particular codon preferences. The evolutionary trace of codon bias patterns across orthologous genes may be examined to learn about a gene's relevance to various phenotypes, or, more generally, its function in the cell. PMID:26538122

  19. A bacterial strain with a unique quadruplet codon specifying non-native amino acids.

    PubMed

    Chatterjee, Abhishek; Lajoie, Marc J; Xiao, Han; Church, George M; Schultz, Peter G

    2014-08-18

    The addition of noncanonical amino acids to the genetic code requires unique codons not assigned to the 20 canonical amino acids. Among the 64 triplet codons, only the three nonsense "stop" codons have been used to encode non-native amino acids. Use of quadruplet "frame-shift" suppressor codons provides an abundant alternative but suffers from low suppression efficiency as a result of competing recognition of their first three bases by endogenous host tRNAs or release factors. Deletion of release factor 1 in a genomically recoded strain of E. coli (E. coli C321), in which all endogenous amber stop codons (UAG) are replaced with UAA, abolished UAG mediated translation termination. Here we show that a Methanocaldococcus jannaschii-derived frame-shift suppressor tRNA/aminoacyl-tRNA synthetase pair enhanced UAGN suppression efficiency in this recoded bacterial strain. These results demonstrate that efficient quadruplet codons for encoding non-native amino acids can be generated by eliminating competing triplet codon recognition at the ribosome.

  20. Genome-Wide Analysis of the Synonymous Codon Usage Patterns in Riemerella anatipestifer

    PubMed Central

    Liu, Jibin; Zhu, Dekang; Ma, Guangpeng; Liu, Mafeng; Wang, Mingshu; Jia, Renyong; Chen, Shun; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Chen, Xiaoyue; Cheng, Anchun

    2016-01-01

    Riemerella anatipestifer (RA) belongs to the Flavobacteriaceae family and can cause a septicemia disease in poultry. The synonymous codon usage patterns of bacteria reflect a series of evolutionary changes that enable bacteria to improve tolerance of the various environments. We detailed the codon usage patterns of RA isolates from the available 12 sequenced genomes by multiple codon and statistical analysis. Nucleotide compositions and relative synonymous codon usage (RSCU) analysis revealed that A or U ending codons are predominant in RA. Neutrality analysis found no significant correlation between GC12 and GC3 (p > 0.05). Correspondence analysis and ENc-plot results showed that natural selection dominated over mutation in the codon usage bias. The tree of cluster analysis based on RSCU was concordant with dendrogram based on genomic BLAST by neighbor-joining method. By comparative analysis, about 50 highly expressed genes that were orthologs across all 12 strains were found in the top 5% of high CAI value. Based on these CAI values, we infer that RA contains a number of predicted highly expressed coding sequences, involved in transcriptional regulation and metabolism, reflecting their requirement for dealing with diverse environmental conditions. These results provide some useful information on the mechanisms that contribute to codon usage bias and evolution of RA. PMID:27517915

  1. Switch in codon bias and increased rates of amino acid substitution in the Drosophila saltans species group.

    PubMed Central

    Rodríguez-Trelles, F; Tarrío, R; Ayala, F J

    1999-01-01

    We investigated the nucleotide composition of five genes, Xdh, Adh, Sod, Per, and 28SrRNA, in nine species of Drosophila (subgenus Sophophora) and one of Scaptodrosophila. The six species of the Drosophila saltans group markedly differ from the others in GC content and codon use bias. The GC content in the third codon position, and to a lesser extent in the first position and the introns, is higher in the D. melanogaster and D. obscura groups than in the D. saltans group (in Scaptodrosophila it is intermediate but closer to the melanogaster and obscura species). Differences are greater for Xdh than for Adh, Sod, Per, and 28SrRNA, which are functionally more constrained. We infer that rapid evolution of GC content in the saltans lineage is largely due to a shift in mutation pressure, which may have been associated with diminished natural selection due to smaller effective population numbers rather than reduced recombination rates. The rate of GC content evolution impacts the rate of protein evolution and may distort phylogenetic inferences. Previous observations suggesting that GC content evolution is very limited in Drosophila may have been distorted due to the restricted number of genes and species (mostly D. melanogaster) investigated. PMID:10471717

  2. The unfolded protein response affects readthrough of premature termination codons

    PubMed Central

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

    2014-01-01

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

  3. Suppression of Premature Termination Codons as a Therapeutic Approach

    PubMed Central

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

    2012-01-01

    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

  4. Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation.

    PubMed

    Ouellette, Scot P; Rueden, Kelsey J; Rucks, Elizabeth A

    2016-09-01

    In evolving to an obligate intracellular niche, Chlamydia has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However, Chlamydia can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-γ), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from Chlamydia Thus, how Chlamydia, a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question. We previously observed that C. pneumoniae responds to this stress by globally increasing transcription while globally decreasing translation, an unusual response. Here, we sought to understand this and hypothesized that the Trp codon content of a given gene would determine its transcription level. We quantified transcripts from C. pneumoniae genes that were either rich or poor in Trp codons and found that Trp codon-rich transcripts were increased, whereas those that lacked Trp codons were unchanged or even decreased. There were exceptions, and these involved operons or large genes with multiple Trp codons: downstream transcripts were less abundant after Trp codon-rich sequences. These data suggest that ribosome stalling on Trp codons causes a negative polar effect on downstream sequences. Finally, reassessing previous C. pneumoniae microarray data based on codon content, we found that upregulated transcripts were enriched in Trp codons, thus supporting our hypothesis. PMID:27400720

  5. SwiftLib: rapid degenerate-codon-library optimization through dynamic programming.

    PubMed

    Jacobs, Timothy M; Yumerefendi, Hayretin; Kuhlman, Brian; Leaver-Fay, Andrew

    2015-03-11

    Degenerate codon (DC) libraries efficiently address the experimental library-size limitations of directed evolution by focusing diversity toward the positions and toward the amino acids (AAs) that are most likely to generate hits; however, manually constructing DC libraries is challenging, error prone and time consuming. This paper provides a dynamic programming solution to the task of finding the best DCs while keeping the size of the library beneath some given limit, improving on the existing integer-linear programming formulation. It then extends the algorithm to consider multiple DCs at each position, a heretofore unsolved problem, while adhering to a constraint on the number of primers needed to synthesize the library. In the two library-design problems examined here, the use of multiple DCs produces libraries that very nearly cover the set of desired AAs while still staying within the experimental size limits. Surprisingly, the algorithm is able to find near-perfect libraries where the ratio of amino-acid sequences to nucleic-acid sequences approaches 1; it effectively side-steps the degeneracy of the genetic code. Our algorithm is freely available through our web server and solves most design problems in about a second.

  6. A more elaborative way to check codon quality: an open source program.

    PubMed

    Shardiwal, Rakesh Kumar; Sohrab, S S

    2010-01-01

    Relative Synonymous Codon Usage (RSCU) and Relative Adaptiveness of a Codon (RAC) table bias importance in gene expression are well documented in the literature. However, to improve the gene expression we need to figure out which codons are optimal for the expression in order to synthesise an appropriate DNA sequence. An alternative to the manual approach, which is obviously a tedious task, is to set up software on your computer to perform this. Though such kinds of programs are available on the internet, none of them are open-source libraries. Here, one can use our Perl program to do his or her task more easily and efficiently. It is free for everyone.

  7. Aminoacyl-tRNAs from Physarum polycephalum: patterns of codon recognition.

    PubMed Central

    Hatfield, D; Rice, M; Hession, C A; Melera, P W

    1982-01-01

    Isoacceptors of Physarum polycephalum Ala-, Arg-, Glu-, Gln-, Gly-, Ile-, Leu-, Lys-, Ser-, Thr-, and Val-tRNAs were resolved by reverse-phase chromatography and isolated, and their codon recognition properties were determined in a ribosomal binding assay. Codon assignments were made to most isoacceptors, and they are summarized along with those determined in other studies from Escherichia coli, yeasts, wheat germ, hymenoptera, Xenopus, and mammals. The patterns of codon recognition by isoacceptors from P. polycephalum are more similar to those of animals than to those of plants or lower fungi. PMID:7047488

  8. Comparative analysis of codon usage bias in Crenarchaea and Euryarchaea genome reveals differential preference of synonymous codons to encode highly expressed ribosomal and RNA polymerase proteins.

    PubMed

    Baruah, Vishwa Jyoti; Satapathy, Siddhartha Sankar; Powdel, Bhesh Raj; Konwarh, Rocktotpal; Buragohain, Alak Kumar; Ray, Suvendra Kumar

    2016-09-01

    The present study was undertaken to investigate the pattern of optimal codon usage in Archaea. Comparative analysis was executed to understand the pattern of codon usage bias between the high expression genes (HEG) and the whole genomes in two Archaeal phyla, Crenarchaea and Euryarchaea. The G+C% of the HEG was found to be less in comparison to the genome G+C% in Crenarchaea, whereas reverse was the case in Euryarchaea. The preponderance of U/A ending codons that code for HEG in Crenarchaea was in sharp contrast to the C/G ended ones in Euryarchaea. The analysis revealed prevalence of Uending codons even within theWWY(nucleotide ambiguity code) families in Crenarchaea vis-à-vis Euryarchaea, bacteria and Eukarya. No plausible interpretation of the observed disparity could be made either in the context of tRNA gene composition or genome G+C%. The results in this study attested that the preferential biasness for codons in HEG of Crenarchaea might be different from Euryarchaea. The main highlights are (i) varied CUB in the HEG and in the whole genomes in Euryarchaea and Crenarchaea. (ii) Crenarchaea was found to have some unusual optimal codons (OCs) compared to other organisms. (iii) G+C% (and GC3) of the HEG were different from the genome G+C% in the two phyla. (iv) Genome G+C% and tRNA gene number failed to explain CUB in Crenarchaea. (v) Translational selection is possibly responsible for A+T rich OCs in Crenarchaea. PMID:27659324

  9. Amino Acid Deletion at Codon 67 and Thr-to-Gly Change at Codon 69 of Human Immunodeficiency Virus Type 1 Reverse Transcriptase Confer Novel Drug Resistance Profiles

    PubMed Central

    Imamichi, Tomozumi; Murphy, Michael A.; Imamichi, Hiromi; Lane, H. Clifford

    2001-01-01

    The potential roles of an amino acid deletion at codon 67 (Δ67) and a Thr-to-Gly change at codon 69 (T69G) in the reverse transcriptase of human immunodeficiency virus (HIV) type 1 in drug sensitivity and relative replication fitness were studied. Our results suggest that the Δ67 and T69G changes can be categorized as mutations associated with multidrug resistance. The combination of both mutations with an L74I change (Δ67+T69G/L74I) leads to a novel 3′-azido-3′-deoxythymidine resistance motif and compensates for impaired HIV replication. PMID:11264389

  10. Multi-omics data driven analysis establishes reference codon biases for synthetic gene design in microbial and mammalian cells.

    PubMed

    Ang, Kok Siong; Kyriakopoulos, Sarantos; Li, Wei; Lee, Dong-Yup

    2016-06-01

    In this study, we analyzed multi-omics data and subsets thereof to establish reference codon usage biases for codon optimization in synthetic gene design. Specifically, publicly available genomic, transcriptomic, proteomic and translatomic data for microbial and mammalian expression hosts, Escherichia coli, Saccharomyces cerevisiae, Pichia pastoris and Chinese hamster ovary (CHO) cells, were compiled to derive their individual codon and codon pair frequencies. Then, host dependent and -omics specific codon biases were generated and compared by principal component analysis and hierarchical clustering. Interestingly, our results indicated the similar codon bias patterns of the highly expressed transcripts, highly abundant proteins, and efficiently translated mRNA in microbial cells, despite the general lack of correlation between mRNA and protein expression levels. However, for CHO cells, the codon bias patterns among various -omics subsets are not distinguishable, forming one cluster. Thus, we further investigated the effect of different input codon biases on codon optimized sequences using the codon context (CC) and individual codon usage (ICU) design parameters, via in silico case study on the expression of human IFNγ sequence in CHO cells. The results supported that CC is more robust design parameter than ICU for improved heterologous gene design. PMID:26850284

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

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

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

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

    2014-01-01

    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

  14. Effects of Deep Water Source-Sink Terms in 3rd generation Wave Model SWAN using different wind data in Black Sea

    NASA Astrophysics Data System (ADS)

    Kirezci, Cagil; Ozyurt Tarakcioglu, Gulizar

    2016-04-01

    Coastal development in Black Sea has increased in recent years. Therefore, careful monitoring of the storms and verification of numerical tools with reliable data has become important. Previous studies by Kirezci and Ozyurt (2015) investigated extreme events in Black Sea using different wind datasets (NCEP's CFSR and ECMWF's operational datasets) and different numerical tools (SWAN and Wavewatch III). These studies showed that significant effect to results is caused by the deep water source-sink terms (wave growth by wind, deep water dissipation of wave energy (whitecapping) and deep water non-linear wave-wave interactions). According to Timmermans(2015), uncertainty about wind forcing and the process of nonlinear wave-wave interactions are found to be dominant in numerical wave modelling. Therefore, in this study deep water source and sink term solution approaches of 3rd generation numerical tool (SWAN model) are tested, validated and compared using the selected extreme storms in Black Sea. 45 different storms and storm like events observed in Black Sea between years 1994-1999 are selected to use in the models. The storm selection depends on the instrumental wave data (significant wave heights, mean wave period and mean wave direction) obtained in NATO-TU Waves project by the deep water buoy measurements at Hopa, Sinop, Gelendzhik, and wind data (mean and peak wind speeds, storm durations) of the regarding events. 2 different wave growth by wind with the corresponding deep water dissipation terms and 3 different wave -wave interaction terms of SWAN model are used in this study. Wave growth by wind consist of two parts, linear growth which is explained by Cavaleri and Malanotte-Rizzoli(1981),and dominant exponential growth. There are two methods in SWAN model for exponential growth of wave, first one by Snyder et al. (1981), rescaled in terms of friction velocity by Komen et. al (1984) which is derived using driving wind speed at 10m elevation with related drag

  15. Effects of Deep Water Source-Sink Terms in 3rd generation Wave Model SWAN using different wind data in Black Sea

    NASA Astrophysics Data System (ADS)

    Kirezci, Cagil; Ozyurt Tarakcioglu, Gulizar

    2016-04-01

    Coastal development in Black Sea has increased in recent years. Therefore, careful monitoring of the storms and verification of numerical tools with reliable data has become important. Previous studies by Kirezci and Ozyurt (2015) investigated extreme events in Black Sea using different wind datasets (NCEP's CFSR and ECMWF's operational datasets) and different numerical tools (SWAN and Wavewatch III). These studies showed that significant effect to results is caused by the deep water source-sink terms (wave growth by wind, deep water dissipation of wave energy (whitecapping) and deep water non-linear wave-wave interactions). According to Timmermans(2015), uncertainty about wind forcing and the process of nonlinear wave-wave interactions are found to be dominant in numerical wave modelling. Therefore, in this study deep water source and sink term solution approaches of 3rd generation numerical tool (SWAN model) are tested, validated and compared using the selected extreme storms in Black Sea. 45 different storms and storm like events observed in Black Sea between years 1994-1999 are selected to use in the models. The storm selection depends on the instrumental wave data (significant wave heights, mean wave period and mean wave direction) obtained in NATO-TU Waves project by the deep water buoy measurements at Hopa, Sinop, Gelendzhik, and wind data (mean and peak wind speeds, storm durations) of the regarding events. 2 different wave growth by wind with the corresponding deep water dissipation terms and 3 different wave -wave interaction terms of SWAN model are used in this study. Wave growth by wind consist of two parts, linear growth which is explained by Cavaleri and Malanotte-Rizzoli(1981),and dominant exponential growth. There are two methods in SWAN model for exponential growth of wave, first one by Snyder et al. (1981), rescaled in terms of friction velocity by Komen et. al (1984) which is derived using driving wind speed at 10m elevation with related drag

  16. Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea.

    PubMed

    Whittle, Carrie A; Extavour, Cassandra G

    2015-11-01

    In protein-coding genes, synonymous codon usage and amino acid composition correlate to expression in some eukaryotes, and may result from translational selection. Here, we studied large-scale RNA-seq data from three divergent arthropod models, including cricket (Gryllus bimaculatus), milkweed bug (Oncopeltus fasciatus), and the amphipod crustacean Parhyale hawaiensis, and tested for optimization of codon and amino acid usage relative to expression level. We report strong signals of AT3 optimal codons (those favored in highly expressed genes) in G. bimaculatus and O. fasciatus, whereas weaker signs of GC3 optimal codons were found in P. hawaiensis, suggesting selection on codon usage in all three organisms. Further, in G. bimaculatus and O. fasciatus, high expression was associated with lowered frequency of amino acids with large size/complexity (S/C) scores in favor of those with intermediate S/C values; thus, selection may favor smaller amino acids while retaining those of moderate size for protein stability or conformation. In P. hawaiensis, highly transcribed genes had elevated frequency of amino acids with large and small S/C scores, suggesting a complex dynamic in this crustacean. In all species, the highly transcribed genes appeared to favor short proteins, high optimal codon usage, specific amino acids, and were preferentially involved in cell-cycling and protein synthesis. Together, based on examination of 1,680,067, 1,667,783, and 1,326,896 codon sites in G. bimaculatus, O. fasciatus, and P. hawaiensis, respectively, we conclude that translational selection shapes codon and amino acid usage in these three Pancrustacean arthropods. PMID:26384771

  17. A small segment of the MAT alpha 1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons.

    PubMed Central

    Caponigro, G; Muhlrad, D; Parker, R

    1993-01-01

    Differences in decay rates of eukaryotic transcripts can be determined by discrete sequence elements within mRNAs. Through the analysis of chimeric transcripts and internal deletions, we have identified a 65-nucleotide segment of the MAT alpha 1 mRNA coding region, termed the MAT alpha 1 instability element, that is sufficient to confer instability to a stable PGK1 reporter transcript and that accelerates turnover of the unstable MAT alpha 1 mRNA. This 65-nucleotide element is composed of two parts, one located within the 5' 33 nucleotides and the second located in the 3' 32 nucleotides. The first part, which can be functionally replaced by sequences containing rare codons, is unable to promote rapid decay by itself but can enhance the action of the 3' 32 nucleotides (positions 234 to 266 in the MAT alpha 1 mRNA) in accelerating turnover. A second portion of the MAT alpha 1 mRNA (nucleotides 265 to 290) is also sufficient to destabilize the PGK1 reporter transcript when positioned 3' of rare codons, suggesting that the 3' half of the MAT alpha 1 instability element is functionally reiterated within the MAT alpha 1 mRNA. The observation that rare codons are part of the 65-nucleotide MAT alpha 1 instability element suggests possible mechanisms through which translation and mRNA decay may be linked. Images PMID:8355674

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

    PubMed Central

    Björnsson, A; Isaksson, L A

    1996-01-01

    A RNA fragment which is protected from degradation by ribosome pausing at a stop codon has been identified in growing Escherichia coli. The fragment is 261 nt long and corresponds to the 3'-end of the mRNA expressed from a semi-synthetic model gene. The 5'-end of the RNA fragment, denoted rpRNA (ribosomal pause RNA), is located 13 bases upstream of the stop codon. In vivo decay of the complete mRNA and accumulation of rpRNA are dependent on the nature of the stop codon and its codon context. The data indicate that the rpRNA fragment arises from interrupted decay of the S3A'mRNA in the 5'-->m3'direction, in connection with a ribosomal pause at the stop codon. RF-2 decoding of UGA is less efficient than RF-1 decoding of UAG in identical codon contexts, as judged from rpRNA steady-state levels. The half-life of UGA-containing rpRNAs is at least 5 min, indicating that ribosomal pausing can be a major factor in stabilising downstream regions of messenger RNAs. PMID:8649996

  19. Codon usage bias analysis for the spermidine synthase gene from Camellia sinensis (L.) O. Kuntze.

    PubMed

    You, E; Wang, Y; Ding, Z T; Zhang, X F; Pan, L L; Zheng, C

    2015-07-03

    The spermidine synthase (SPDS) gene exists widely in all types of plants. In this paper, the codon usage of the SPDS gene from Camellia sinensis (CsSPDS) was analyzed. The results showed that the codon usage of the CsSPDS gene is biased towards the T-ended or A-ended codons, which is similar to that observed in 73 genes selected from the C. sinensis genome. An ENC-plot for 15 SPDS genes from various plant species suggested that mutational bias was the major factor in shaping codon usage in these genes. Codon usage frequency analysis indicated that there was little difference between the CsSPDS gene and dicot genomes, such as Arabidopsis thaliana and Nicotiana tabacum, but significant differences in codon usage were observed between the CsSPDS gene and monocot genomes, such as Triticum aestivum and Zea mays. Therefore, A. thaliana and N. tabacum expression systems may be more suitable for the expression of the CsSPDS gene.

  20. Decoding Mechanisms by which Silent Codon Changes Influence Protein Biogenesis and Function

    PubMed Central

    Bali, Vedrana; Bebok, Zsuzsanna

    2015-01-01

    Scope Synonymous codon usage has been a focus of investigation since the discovery of the genetic code and its redundancy. The occurrences of synonymous codons vary between species and within genes of the same genome, known as codon usage bias. Today, bioinformatics and experimental data allow us to compose a global view of the mechanisms by which the redundancy of the genetic code contributes to the complexity of biological systems from affecting survival in prokaryotes, to fine tuning the structure and function of proteins in higher eukaryotes. Studies analyzing the consequences of synonymous codon changes in different organisms have revealed that they impact nucleic acid stability, protein levels, structure and function without altering amino acid sequence. As such, synonymous mutations inevitably contribute to the pathogenesis of complex human diseases. Yet, fundamental questions remain unresolved regarding the impact of silent mutations in human disorders. In the present review we describe developments in this area concentrating on mechanisms by which synonymous mutations may affect protein function and human health. Purpose This synopsis illustrates the significance of synonymous mutations in disease pathogenesis. We review the different steps of gene expression affected by silent mutations, and assess the benefits and possible harmful effects of codon optimization applied in the development of therapeutic biologics. Physiological and medical relevance Understanding mechanisms by which synonymous mutations contribute to complex diseases such as cancer, neurodegeneration and genetic disorders, including the limitations of codon-optimized biologics, provides insight concerning interpretation of silent variants and future molecular therapies. PMID:25817479

  1. Evidence of codon usage in the nearest neighbor spacing distribution of bases in bacterial genomes

    NASA Astrophysics Data System (ADS)

    Higareda, M. F.; Geiger, O.; Mendoza, L.; Méndez-Sánchez, R. A.

    2012-02-01

    Statistical analysis of whole genomic sequences usually assumes a homogeneous nucleotide density throughout the genome, an assumption that has been proved incorrect for several organisms since the nucleotide density is only locally homogeneous. To avoid giving a single numerical value to this variable property, we propose the use of spectral statistics, which characterizes the density of nucleotides as a function of its position in the genome. We show that the cumulative density of bases in bacterial genomes can be separated into an average (or secular) plus a fluctuating part. Bacterial genomes can be divided into two groups according to the qualitative description of their secular part: linear and piecewise linear. These two groups of genomes show different properties when their nucleotide spacing distribution is studied. In order to analyze genomes having a variable nucleotide density, statistically, the use of unfolding is necessary, i.e., to get a separation between the secular part and the fluctuations. The unfolding allows an adequate comparison with the statistical properties of other genomes. With this methodology, four genomes were analyzed Burkholderia, Bacillus, Clostridium and Corynebacterium. Interestingly, the nearest neighbor spacing distributions or detrended distance distributions are very similar for species within the same genus but they are very different for species from different genera. This difference can be attributed to the difference in the codon usage.

  2. Multiparameter RNA and Codon Optimization: A Standardized Tool to Assess and Enhance Autologous Mammalian Gene Expression

    PubMed Central

    Fath, Stephan; Bauer, Asli Petra; Liss, Michael; Spriestersbach, Anne; Maertens, Barbara; Hahn, Peter; Ludwig, Christine; Schäfer, Frank; Graf, Marcus; Wagner, Ralf

    2011-01-01

    Autologous expression of recombinant human proteins in human cells for biomedical research and product development is often hampered by low expression yields limiting subsequent structural and functional analyses. Following RNA and codon optimization, 50 candidate genes representing five classes of human proteins – transcription factors, ribosomal and polymerase subunits, protein kinases, membrane proteins and immunomodulators – all showed reliable, and 86% even elevated expression. Analysis of three representative examples showed no detrimental effect on protein solubility while unaltered functionality was demonstrated for JNK1, JNK3 and CDC2 using optimized constructs. Molecular analysis of a sequence-optimized transgene revealed positive effects at transcriptional, translational, and mRNA stability levels. Since improved expression was consistent in HEK293T, CHO and insect cells, it was not restricted to distinct mammalian cell systems. Additionally, optimized genes represent powerful tools in functional genomics, as demonstrated by the successful rescue of an siRNA-mediated knockdown using a sequence-optimized counterpart. This is the first large-scale study addressing the influence of multiparameter optimization on autologous human protein expression. PMID:21408612

  3. Acoustic Evidence for Positional and Complexity Effects on Children's Production of Plural "-s"

    ERIC Educational Resources Information Center

    Theodore, Rachel M.; Demuth, Katherine; Shattuck-Hufnagel, Stefanie

    2011-01-01

    Purpose: Some variability in children's early productions of grammatical morphemes reflects phonological factors. For example, production of 3rd person singular "-s" is increased in utterance-final versus utterance-medial position and in simple versus cluster codas (e.g., "sees" vs. "hits"). Understanding the factors that govern such variability…

  4. Forced Ambiguity of the Leucine Codons for Multiple-Site-Specific Incorporation of a Noncanonical Amino Acid

    PubMed Central

    Kwon, Inchan; Choi, Eun Sil

    2016-01-01

    Multiple-site-specific incorporation of a noncanonical amino acid into a recombinant protein would be a very useful technique to generate multiple chemical handles for bioconjugation and multivalent binding sites for the enhanced interaction. Previously combination of a mutant yeast phenylalanyl-tRNA synthetase variant and the yeast phenylalanyl-tRNA containing the AAA anticodon was used to incorporate a noncanonical amino acid into multiple UUU phenylalanine (Phe) codons in a site-specific manner. However, due to the less selective codon recognition of the AAA anticodon, there was significant misincorporation of a noncanonical amino acid into unwanted UUC Phe codons. To enhance codon selectivity, we explored degenerate leucine (Leu) codons instead of Phe degenerate codons. Combined use of the mutant yeast phenylalanyl-tRNA containing the CAA anticodon and the yPheRS_naph variant allowed incorporation of a phenylalanine analog, 2-naphthylalanine, into murine dihydrofolate reductase in response to multiple UUG Leu codons, but not to other Leu codon sites. Despite the moderate UUG codon occupancy by 2-naphthylalaine, these results successfully demonstrated that the concept of forced ambiguity of the genetic code can be achieved for the Leu codons, available for multiple-site-specific incorporation. PMID:27028506

  5. Transfer RNA gene arrangement and codon usage in vertebrate mitochondrial genomes: a new insight into gene order conservation

    PubMed Central

    2010-01-01

    Background Mitochondrial (mt) gene arrangement has been highly conserved among vertebrates from jawless fishes to mammals for more than 500 million years. It remains unclear, however, whether such long-term persistence is a consequence of some constraints on the gene order. Results Based on the analysis of codon usage and tRNA gene positions, we suggest that tRNA gene order of the typical vertebrate mt-genomes may be important for their translational efficiency. The vertebrate mt-genome encodes 2 rRNA, 22 tRNA, and 13 transmembrane proteins consisting mainly of hydrophobic domains. We found that the tRNA genes specifying the hydrophobic residues were positioned close to the control region (CR), where the transcription efficiency is estimated to be relatively high. Using 47 vertebrate mt-genome sequences representing jawless fishes to mammals, we further found a correlation between codon usage and tRNA gene positions, implying that highly-used tRNA genes are located close to the CR. In addition, an analysis considering the asymmetric nature of mtDNA replication suggested that the tRNA loci that remain in single-strand for a longer time tend to have more guanine and thymine not suffering deamination mutations in their anticodon sites. Conclusions Our analyses imply the existence of translational constraint acting on the vertebrate mt-gene arrangement. Such translational constraint, together with the deamination-related constraint, may have contributed to long-term maintenance of gene order. PMID:20723209

  6. Synonymous codon usage affects the expression of wild type and F508del CFTR.

    PubMed

    Shah, Kalpit; Cheng, Yi; Hahn, Brian; Bridges, Robert; Bradbury, Neil A; Mueller, David M

    2015-03-27

    The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel composed of 1480 amino acids. The major mutation responsible for cystic fibrosis results in loss of amino acid residue, F508 (F508del). Loss of F508 in CFTR alters the folding pathway resulting in endoplasmic-reticulum-associated degradation. This study investigates the role of synonymous codon in the expression of CFTR and CFTR F508del in human HEK293 cells. DNA encoding the open reading frame (ORF) for CFTR containing synonymous codon replacements was expressed using a heterologous vector integrated into the genome. The results indicate that the codon usage greatly affects the expression of CFTR. While the promoter strength driving expression of the ORFs was largely unchanged and the mRNA half-lives were unchanged, the steady-state levels of the mRNA varied by as much as 30-fold. Experiments support that this apparent inconsistency is attributed to nonsense mediated decay independent of exon junction complex. The ratio of CFTR/mRNA indicates that mRNA containing native codons was more efficient in expressing mature CFTR as compared to mRNA containing synonymous high-expression codons. However, when F508del CFTR was expressed after codon optimization, a greater percentage of the protein escaped endoplasmic-reticulum-associated degradation resulting in considerable levels of mature F508del CFTR on the plasma membrane, which showed channel activity. These results indicate that codon usage has an effect on mRNA levels and protein expression, for CFTR, and likely on chaperone-assisted folding pathway, for F508del CFTR.

  7. Synonymous Codon Usage Affects the Expression of Wild Type and F508del CFTR

    PubMed Central

    Shah, Kalpit; Cheng, Yi; Hahn, Brian; Bridges, Robert; Bradbury, Neil; Mueller, David M.

    2015-01-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel composed of 1480 amino acids. The major mutation responsible for cystic fibrosis results in loss of amino acid residue, F508, (F508del). Loss of F508 in CFTR alters the folding pathway resulting in endoplasmic reticulum associated degradation (ERAD). This study investigates the role of synonymous codon in the expression of CFTR and CFTR F508del in human HEK293 cells. DNA encoding the open reading frame (ORF) for CFTR containing synonymous codon replacements, were expressed using a heterologous vector integrated into the genome. The results indicate that the codon usage greatly affects the expression of CFTR. While the promoter strength driving expression of the ORFs was largely unchanged and the mRNA half-lives were unchanged, the steady state levels of the mRNA varied by as much as 30 fold. Experiments support that this apparent inconsistency is attributed to exon junction complex independent nonsense mediated decay. The ratio of CFTR/mRNA indicates that mRNA containing native codons was more efficient in expressing mature CFTR as compared to mRNA containing synonymous high expression codons. However, when F508del CFTR was expressed after codon optimization, a greater percentage of the protein escaped ERAD resulting in considerable levels of mature F508del CFTR on the plasma membrane, which showed channel activity. These results indicate that for CFTR, codon usage has an effect on mRNA levels, protein expression and likely, for F508del CFTR, chaperone assisted folding pathway. PMID:25676312

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

    PubMed Central

    Carlini, David B; Stephan, Wolfgang

    2003-01-01

    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

  9. The preferential codon usages in variable and constant regions of immunoglobulin genes are quite distinct from each other.

    PubMed

    Miyata, T; Hayashida, H; Yasunaga, T; Hasegawa, M

    1979-12-20

    The pattern of codon utilization in the variable and constant regions of immunoglobulin genes are compared. It is shown that, in these regions, codon utilizations are quite distinct from one another: For most degenerate codons, there is a selective bias that prefers C and/or G ending codons to U and/or A ending codons in the constant region compared with the bias in the variable region. This would strongly suggest that, in immunoglobulin genes, the bias in code word usage is determined by other factors than those concerning with the translational mechanism such as tRNA availability and codon-anticodon interaction. A possibility is also suggested that this differance of code word usage between them is due to the existence of secondary structure in the constant region but not in the variable region.

  10. X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis.

    PubMed

    Singh, Nadia D; Davis, Jerel C; Petrov, Dmitri A

    2005-09-01

    Comparing patterns of molecular evolution between autosomes and sex chromosomes (such as X and W chromosomes) can provide insight into the forces underlying genome evolution. Here we investigate patterns of codon bias evolution on the X chromosome and autosomes in Drosophila and Caenorhabditis. We demonstrate that X-linked genes have significantly higher codon bias compared to autosomal genes in both Drosophila and Caenorhabditis. Furthermore, genes that become X-linked evolve higher codon bias gradually, over tens of millions of years. We provide several lines of evidence that this elevation in codon bias is due exclusively to their chromosomal location and not to any other property of X-linked genes. We present two possible explanations for these observations. One possibility is that natural selection is more efficient on the X chromosome due to effective haploidy of the X chromosomes in males and persistently low effective numbers of reproducing males compared to that of females. Alternatively, X-linked genes might experience stronger natural selection for higher codon bias as a result of maladaptive reduction of their dosage engendered by the loss of the Y-linked homologs.

  11. Codon influence on protein expression in E. coli correlates with mRNA levels

    PubMed Central

    Boël, Grégory; Wong, Kam-Ho; Su, Min; Luff, Jon; Valecha, Mayank; Everett, John K.; Acton, Thomas B.; Xiao, Rong; Montelione, Gaetano T.; Aalberts, Daniel P.; Hunt, John F.

    2016-01-01

    Degeneracy in the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, has an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyze the sequence features influencing protein expression levels in 6,348 experiments using bacteriophage T7 polymerase to synthesize messenger RNA in Escherichia coli. Logistic regression yields a new codon-influence metric that correlates only weakly with genomic codon-usage frequency, but strongly with global physiological protein concentrations and also mRNA concentrations and lifetimes in vivo. Overall, the codon content influences protein expression more strongly than mRNA-folding parameters, although the latter dominate in the initial ~16 codons. Genes redesigned based on our analyses are transcribed with unaltered efficiency but translated with higher efficiency in vitro. The less efficiently translated native sequences show greatly reduced mRNA levels in vivo. Our results suggest that codon content modulates a kinetic competition between protein elongation and mRNA degradation that is a central feature of the physiology and also possibly the regulation of translation in E. coli. PMID:26760206

  12. Analysis of synonymous codon usage patterns in sixty-four different bivalve species

    PubMed Central

    De Moro, Gianluca; Venier, Paola; Pallavicini, Alberto

    2015-01-01

    Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across different genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 different species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable differences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational efficiency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon in this large, commercially and environmentally important, class of marine invertebrates. PMID:26713259

  13. The effect of tRNA levels on decoding times of mRNA codons

    PubMed Central

    Dana, Alexandra; Tuller, Tamir

    2014-01-01

    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

  14. Codon usage, amino acid usage, transfer RNA and amino-acyl-tRNA synthetases in Mimiviruses.

    PubMed

    Colson, Philippe; Fournous, Ghislain; Diene, Seydina M; Raoult, Didier

    2013-01-01

    Mimiviruses are giant viruses that infect phagocytic protists, including Acanthamoebae spp., which were discovered during the past decade. They are the current record holder among viruses for their large particle and genome sizes. One group is composed of three lineages, referred to as A, B and C, which include the vast majority of the Mimiviridae members. Cafeteria roenbergensis virus represents a second group, though the Mimiviridae family is still expanding. We analyzed the codon and amino acid usages in mimiviruses, as well as both the transfer RNA (tRNA) and amino acyl-tRNA synthetases. We confirmed that the codon and amino acid usages of these giant viruses are highly dissimilar to those in their amoebal host Acanthamoeba castellanii and are instead correlated with the high adenine and thymine (AT) content of Mimivirus genomes. We further describe that the set of tRNAs and amino acyl-tRNA synthetases in mimiviruses is globally not adapted to the codon and amino acid usages of these viruses. Notwithstanding, Leu(TAA)tRNA, present in several Mimivirus genomes and in multiple copies in some viral genomes, may complement the amoebal tRNA pool and may contribute to accommodate the viral AT-rich codons. In addition, we found that the genes most highly expressed at the beginning of the Mimivirus replicative cycle have a nucleotide content more adapted to the codon usage in A.castellanii.

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

    PubMed Central

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

    2013-01-01

    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

  16. DNA repair gene XRCC4 codon 247 polymorphism modified diffusely infiltrating astrocytoma risk and prognosis.

    PubMed

    Lin, Zhong-Hui; Chen, Jin-Chun; Wang, Yun-Sun; Huang, Teng-Jiao; Wang, Jin; Long, Xi-Dai

    2013-12-27

    The DNA repair gene X-ray cross-complementary group 4 (XRCC4), an important caretaker of the overall genome stability, is thought to play a major role in human tumorigenesis. We investigated the association between an important polymorphic variant of this gene at codon 247 (rs373409) and diffusely infiltrating astrocytoma (DIA) risk and prognosis. This hospital-based case-control study investigated this association in the Guangxi population. In total, 242 cases with DIA and 358 age-, sex-, and race-matched healthy controls were genotyped using TaqMan-PCR technique. We found a significant difference in the frequency of XRCC4 genotypes between cases and controls. Compared with the homozygote of XRCC4 codon 247 Ala alleles (XRCC4-AA), the genotypes of XRCC4 codon 247 Ser alleles (namely XRCC4-AS or -SS) increased DIA risk (odds ratios [OR], 1.82 and 2.89, respectively). Furthermore, XRCC4 polymorphism was correlated with tumor dedifferentiation of DIA (r = 0.261, p < 0.01). Additionally, this polymorphism modified the overall survival of DIA patients (the median survival times were 26, 14, and 8 months for patients with XRCC4-AA, -AS, and -SS, respectively). Like tumor grade, XRCC4 codon 247 polymorphism was an independent prognostic factor influencing the survival of DIA. These results suggest that XRCC4 codon 247 polymorphism may be associated with DIA risk and prognosis among the Guangxi population.

  17. X-Linked juvenile retinoschisis associated with a 4-base pair insertion at codon 55 of the XLRS1 gene.

    PubMed

    Hiraoka, M; Trese, M T; Shastry, B S

    2000-02-16

    X-linked juvenile retinoschisis (RS) is a bilateral vitreoretinal disorder with no known cure. The gene responsible for the disease was recently isolated by positional cloning methods and a spectrum of mutations has been described in families with RS pathology. In this report, we screened six sporadic cases of RS for mutations in the RS gene to understand the etiology of isolated cases. Our extensive studies revealed a novel 4 bp insertion in one family and the remaining families did not show mutations in the RS gene. This mutation altered the reading frame including codon 55 resulting in nine aberrant amino acid residues. The unaffected mother did not contain this mutation. Additionally, it was not found in 60 normal control chromosomes, suggesting that the insertion mutation is disease related in the family analyzed. PMID:10679210

  18. Novel prion protein gene mutation at codon 196 (E196A) in a septuagenarian with Creutzfeldt-Jakob disease.

    PubMed

    Zhang, Hongliang; Wang, Meibo; Wu, Limin; Zhang, Haining; Jin, Tao; Wu, Jiang; Sun, Li

    2014-01-01

    Creutzfeldt-Jakob disease (CJD) is a rare and rapidly progressive neurodegenerative disease of the central nervous system, which may occur in inherited, acquired (variant and iatrogenic), or spontaneous (sporadic) forms. We report a 76-year-old Chinese man with CJD found to have a novel mutation in the prion protein gene (PRNP). The 14-3-3 protein was positive in the cerebrospinal fluid; diffusion-weighted MRI revealed ribbon-like high signal intensity in the bilateral cortices; and electroencephalography showed typical periodic synchronous discharge. CJD was diagnosed based on characteristic clinical manifestations. Interestingly, a point mutation of PRNP at codon 196 (E196A: GAG→GCG) was detected. In conclusion, we identified a patient with CJD with a novel PRNP mutation, which expands the spectrum of PRNP mutations in CJD.

  19. X-Linked juvenile retinoschisis associated with a 4-base pair insertion at codon 55 of the XLRS1 gene.

    PubMed

    Hiraoka, M; Trese, M T; Shastry, B S

    2000-02-16

    X-linked juvenile retinoschisis (RS) is a bilateral vitreoretinal disorder with no known cure. The gene responsible for the disease was recently isolated by positional cloning methods and a spectrum of mutations has been described in families with RS pathology. In this report, we screened six sporadic cases of RS for mutations in the RS gene to understand the etiology of isolated cases. Our extensive studies revealed a novel 4 bp insertion in one family and the remaining families did not show mutations in the RS gene. This mutation altered the reading frame including codon 55 resulting in nine aberrant amino acid residues. The unaffected mother did not contain this mutation. Additionally, it was not found in 60 normal control chromosomes, suggesting that the insertion mutation is disease related in the family analyzed.

  20. Analytical performance of a PCR assay for the detection of KRAS mutations (codons 12/13 and 61) in formalin-fixed paraffin-embedded tissue samples of colorectal carcinoma.

    PubMed

    Lee, Sung; Brophy, Victoria H; Cao, Jianli; Velez, Margot; Hoeppner, Corey; Soviero, Stephen; Lawrence, H Jeffrey

    2012-02-01

    KRAS mutation testing is mandatory before prescribing anti-epidermal growth factor monoclonal antibodies in the treatment of advanced colorectal cancer. We describe the performance of a TaqMelt polymerase chain reaction (PCR) assay-the cobas® KRAS Mutation Test-designed to detect 19 mutations in codons 12, 13, and 61. The limit of detection was determined using DNA blends from cell lines, plasmids, and formalin-fixed paraffin-embedded tissue specimens. Assay performance was compared to Sanger sequencing using a panel of 188 specimens. Discordant specimens were subjected to next generation pyrosequencing (454). Assay repeatability was assessed using a panel of six specimens. A >95% correct mutation call rate was obtained in all specimen types with ~5% mutant alleles at DNA inputs of 0.8-6.3 ng per PCR reaction; 100% detection rate was observed at the recommended DNA input of 50 ng. The positive percent agreement with Sanger was 97.5% (79/81) for codons 12/13 and 85.7% (6/7) for codon 61. Negative percent agreement was 94.4% (101/107) for codon 12/13 and 99.4% (180/181) for codon 61. Nine of 10 discordant specimens yielded 454 results consistent with the cobas® results. With repeated testing, the assay showed a correct call rate of 100% (192/192) for all operators, instruments, reagent lots, and days tested. The cobas® test detects KRAS mutations in codons 12, 13, and 61 at a limit of detection of <5%. The PCR assay was more sensitive and specific than Sanger sequencing, and performance was highly reproducible. Test performance was not influenced by various endogenous interfering substances or common gut microbes.

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

    PubMed Central

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

    2012-01-01

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

  2. Codon Usage in Signal Sequences Affects Protein Expression and Secretion Using Baculovirus/Insect Cell Expression System

    PubMed Central

    Tao, Shiheng; Chen, Hongying

    2015-01-01

    By introducing synonymous mutations into the coding sequences of GP64sp and FibHsp signal peptides, the influences of mRNA secondary structure and codon usage of signal sequences on protein expression and secretion were investigated using baculovirus/insect cell expression system. The results showed that mRNA structural stability of the signal sequences was not correlated with the protein production and secretion levels, and FibHsp was more tolerable to codon changes than GP64sp. Codon bias analyses revealed that codons for GP64sp were well de-optimized and contained more non-optimal codons than FibHsp. Synonymous mutations in GP64sp sufficiently increased its average codon usage frequency and resulted in dramatic reduction of the activity and secretion of luciferase. Protein degradation inhibition assay with MG-132 showed that higher codon usage frequency in the signal sequence increased the production as well as the degradation of luciferase protein, indicating that the synonymous codon substitutions in the signal sequence caused misfolding of luciferase instead of slowing down the protein production. Meanwhile, we found that introduction of more non-optimal codons into FibHsp could increase the production and secretion levels of luciferase, which suggested a new strategy to improve the production of secretory proteins in insect cells. PMID:26697848

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

    PubMed

    Doherty, Aoife; McInerney, James O

    2013-10-01

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

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

    PubMed

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

    2013-11-01

    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

  5. Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins

    NASA Astrophysics Data System (ADS)

    Tang, Nicholas C.; Chilkoti, Ashutosh

    2016-04-01

    Most genes are synthesized using seamless assembly methods that rely on the polymerase chain reaction (PCR). However, PCR of genes encoding repetitive proteins either fails or generates nonspecific products. Motivated by the need to efficiently generate new protein polymers through high-throughput gene synthesis, here we report a codon-scrambling algorithm that enables the PCR-based gene synthesis of repetitive proteins by exploiting the codon redundancy of amino acids and finding the least-repetitive synonymous gene sequence. We also show that the codon-scrambling problem is analogous to the well-known travelling salesman problem, and obtain an exact solution to it by using De Bruijn graphs and a modern mixed integer linear programme solver. As experimental proof of the utility of this approach, we use it to optimize the synthetic genes for 19 repetitive proteins, and show that the gene fragments are amenable to PCR-based gene assembly and recombinant expression.

  6. Combinatorial codon scrambling enables scalable gene synthesis and amplification of repetitive proteins.

    PubMed

    Tang, Nicholas C; Chilkoti, Ashutosh

    2016-04-01

    Most genes are synthesized using seamless assembly methods that rely on the polymerase chain reaction (PCR). However, PCR of genes encoding repetitive proteins either fails or generates nonspecific products. Motivated by the need to efficiently generate new protein polymers through high-throughput gene synthesis, here we report a codon-scrambling algorithm that enables the PCR-based gene synthesis of repetitive proteins by exploiting the codon redundancy of amino acids and finding the least-repetitive synonymous gene sequence. We also show that the codon-scrambling problem is analogous to the well-known travelling salesman problem, and obtain an exact solution to it by using De Bruijn graphs and a modern mixed integer linear programme solver. As experimental proof of the utility of this approach, we use it to optimize the synthetic genes for 19 repetitive proteins, and show that the gene fragments are amenable to PCR-based gene assembly and recombinant expression.

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

    PubMed Central

    Bohlke, Nina; Budisa, Nediljko

    2014-01-01

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

  8. Comprehensive risk reduction in patients with atrial fibrillation: emerging diagnostic and therapeutic options—a report from the 3rd Atrial Fibrillation Competence NETwork/European Heart Rhythm Association consensus conference

    PubMed Central

    Kirchhof, Paulus; Lip, Gregory Y.H.; Van Gelder, Isabelle C.; Bax, Jeroen; Hylek, Elaine; Kaab, Stefan; Schotten, Ulrich; Wegscheider, Karl; Boriani, Giuseppe; Brandes, Axel; Ezekowitz, Michael; Diener, Hans; Haegeli, Laurent; Heidbuchel, Hein; Lane, Deirdre; Mont, Luis; Willems, Stephan; Dorian, Paul; Aunes-Jansson, Maria; Blomstrom-Lundqvist, Carina; Borentain, Maria; Breitenstein, Stefanie; Brueckmann, Martina; Cater, Nilo; Clemens, Andreas; Dobrev, Dobromir; Dubner, Sergio; Edvardsson, Nils G.; Friberg, Leif; Goette, Andreas; Gulizia, Michele; Hatala, Robert; Horwood, Jenny; Szumowski, Lukas; Kappenberger, Lukas; Kautzner, Josef; Leute, Angelika; Lobban, Trudie; Meyer, Ralf; Millerhagen, Jay; Morgan, John; Muenzel, Felix; Nabauer, Michael; Baertels, Christoph; Oeff, Michael; Paar, Dieter; Polifka, Juergen; Ravens, Ursula; Rosin, Ludger; Stegink, W.; Steinbeck, Gerhard; Vardas, Panos; Vincent, Alphons; Walter, Maureen; Breithardt, Günter; Camm, A. John

    2012-01-01

    While management of atrial fibrillation (AF) patients is improved by guideline-conform application of anticoagulant therapy, rate control, rhythm control, and therapy of accompanying heart disease, the morbidity and mortality associated with AF remain unacceptably high. This paper describes the proceedings of the 3rd Atrial Fibrillation NETwork (AFNET)/European Heart Rhythm Association (EHRA) consensus conference that convened over 60 scientists and representatives from industry to jointly discuss emerging therapeutic and diagnostic improvements to achieve better management of AF patients. The paper covers four chapters: (i) risk factors and risk markers for AF; (ii) pathophysiological classification of AF; (iii) relevance of monitored AF duration for AF-related outcomes; and (iv) perspectives and needs for implementing better antithrombotic therapy. Relevant published literature for each section is covered, and suggestions for the improvement of management in each area are put forward. Combined, the propositions formulate a perspective to implement comprehensive management in AF. PMID:21791573

  9. Comprehensive risk reduction in patients with atrial fibrillation: emerging diagnostic and therapeutic options--a report from the 3rd Atrial Fibrillation Competence NETwork/European Heart Rhythm Association consensus conference.

    PubMed

    Kirchhof, Paulus; Lip, Gregory Y H; Van Gelder, Isabelle C; Bax, Jeroen; Hylek, Elaine; Kaab, Stefan; Schotten, Ulrich; Wegscheider, Karl; Boriani, Giuseppe; Brandes, Axel; Ezekowitz, Michael; Diener, Hans; Haegeli, Laurent; Heidbuchel, Hein; Lane, Deirdre; Mont, Luis; Willems, Stephan; Dorian, Paul; Aunes-Jansson, Maria; Blomstrom-Lundqvist, Carina; Borentain, Maria; Breitenstein, Stefanie; Brueckmann, Martina; Cater, Nilo; Clemens, Andreas; Dobrev, Dobromir; Dubner, Sergio; Edvardsson, Nils G; Friberg, Leif; Goette, Andreas; Gulizia, Michele; Hatala, Robert; Horwood, Jenny; Szumowski, Lukas; Kappenberger, Lukas; Kautzner, Josef; Leute, Angelika; Lobban, Trudie; Meyer, Ralf; Millerhagen, Jay; Morgan, John; Muenzel, Felix; Nabauer, Michael; Baertels, Christoph; Oeff, Michael; Paar, Dieter; Polifka, Juergen; Ravens, Ursula; Rosin, Ludger; Stegink, W; Steinbeck, Gerhard; Vardas, Panos; Vincent, Alphons; Walter, Maureen; Breithardt, Günter; Camm, A John

    2012-01-01

    While management of atrial fibrillation (AF) patients is improved by guideline-conform application of anticoagulant therapy, rate control, rhythm control, and therapy of accompanying heart disease, the morbidity and mortality associated with AF remain unacceptably high. This paper describes the proceedings of the 3rd Atrial Fibrillation NETwork (AFNET)/European Heart Rhythm Association (EHRA) consensus conference that convened over 60 scientists and representatives from industry to jointly discuss emerging therapeutic and diagnostic improvements to achieve better management of AF patients. The paper covers four chapters: (i) risk factors and risk markers for AF; (ii) pathophysiological classification of AF; (iii) relevance of monitored AF duration for AF-related outcomes; and (iv) perspectives and needs for implementing better antithrombotic therapy. Relevant published literature for each section is covered, and suggestions for the improvement of management in each area are put forward. Combined, the propositions formulate a perspective to implement comprehensive management in AF. PMID:21791573

  10. Lucky guess or knowledge: a cross-sectional study using the Bland and Altman analysis to compare confidence-based testing of pharmacological knowledge in 3rd and 5th year medical students.

    PubMed

    Kampmeyer, Daniela; Matthes, Jan; Herzig, Stefan

    2015-05-01

    Multiple-choice-questions are common in medical examinations, but guessing biases assessment results. Confidence-based-testing (CBT) integrates indicated confidence levels. It has been suggested that correctness of and confidence in an answer together indicate knowledge levels thus determining the quality of a resulting decision. We used a CBT approach to investigate whether decision quality improves during undergraduate medical education. 3rd- and 5th-year students attended formative multiple-choice exams on pharmacological issues. Students were asked to indicate their confidence in a given answer. Correctness of answers was scored binary (1-correct; 0-wrong) and confidence levels were transformed to an ordinal scale (guess: 0; rather unsure: 0.33; rather sure: 0.66; very sure: 1). 5th-year students gave more correct answers (73 ± 16 vs. 49 ± 13 %, p < 0.05) and were on average more confident regarding the correctness of their answers (0.61 ± 0.18 vs. 0.46 ± 0.13, p < 0.05). Correlation of these parameters was stronger for 5th-year students (r = 0.81 vs. r = 0.52), but agreement of confidence and correctness ('centration') was lower. By combining the Bland-and-Altman approach with categories of decision-quality we found that 5th-year students were more likely to be 'well-informed' (41 vs. 5 %), while more 3rd-students were 'uninformed' (24 vs. 76 %). Despite a good correlation of exam results and confidence in given answers increased knowledge might be accompanied by a more critical view at the own abilities. Combining the statistical Bland-and-Altman analysis with a theoretical approach to decision-quality, more advanced students are expected to apply correct beliefs, while their younger fellows are rather at risk to hesitate or to act amiss.

  11. Real-World Use of 3rd Line Therapy for Multiple Myeloma in Austria: An Austrian Myeloma Registry (AMR) Analysis of the Therapeutic Landscape and Clinical Outcomes prior to the Use of Next Generation Myeloma Therapeutics

    PubMed Central

    Willenbacher, Ella; Weger, Roman; Rochau, Ursula; Siebert, Uwe; Willenbacher, Wolfgang

    2016-01-01

    Objective Clinical trials demonstrate improving survival in patients with multiple myeloma (MM) after treatment. However, it is unclear whether increased survival translates to a similar benefit in a real world setting. Methods We analyzed the overall survival of 347 multiple myeloma patients in Austria by means of a national registry (AMR), focused on results from 3rd and later lines of therapy. This benchmark was chosen to define a baseline prior to the broad application of upcoming 2nd generation drugs (carfilzomib, pomalidomide). Results Projected 10 years survival for patients with MM in Austria is estimated to be 56% in patients diagnosed in between the years 2011–2014, 21% in patients with a diagnosis made between 2000–2005, and 39% in those with a diagnosis made between 2006–2010). For the same intervals a significant increase in the use of both bortezomib, lenalidomide and thalidomide—so called IMiDs (from 2005 onwards) and their simultaneous use in combination therapies (from 2010 onwards) could be shown. The use of autologous transplantation (ASCT) remained more or less constant at ~ 35% of patients in the 1st line setting over the whole period, comparing well to international practice patterns, while the use of 2nd line ASCT increased from 5.5% to 18.7% of patients. Patients in 3rd or later line treatment (n = 105), showed that even in relapsed and refractory disease median survival was 27 months with a considerable proportion of long-term survivors (~20%). Conclusion & Perspective With the expected emergence of additional active anti-myeloma compounds, we aim to assess survival in patients with relapsed and refractory MM. PMID:26937956

  12. Increased rate of depression and psychosomatic symptoms in Jewish migrants from the post-Soviet-Union to Germany in the 3rd generation after the Shoa.

    PubMed

    Ullmann, E; Barthel, A; Licinio, J; Petrowski, K; Bornstein, S R; Strauß, B

    2013-03-12

    The mental health status of persons with Jewish background living in Germany is discussed with special regard to social exclusion like anti-Semitism and overprotective parental rearing behavior, as a transmissional factor of the KZ-Syndrome. These stressors are considered in the context of a higher risk for depression/fear and psychosomatic disorders and also abnormal cortisol levels. The present sample (N=89) is derived from the Jewish population currently living in the German region of Saxony aged between 17-36 years that emigrated from the post-Soviet-Union areas. The mean age was 22.9 years. Two questionnaires to detect psychosomatic symptoms (Giessen complaint list (GBB)-24, hospital anxiety and depression scale) and one questionnaire addressing parental rearing behavior (FEE) were employed. Comparisons were drawn with normative data from the literature about the German residential population. In addition, questions were asked concerning the experience of anti-Semitism in Germany and in the post-Soviet-Union areas. A higher prevalence of depression/fear (10.3% versus 18.2%) and psychosomatic symptoms (M=14.03 versus 17.8; t=2.42; P<0.05) was observed in Jewish migrants to Germany as compared with non-Jewish German residents. Furthermore, anti-Semitic experiences in Germany correlated positively with depression (r=0.293; P<0.01) and fear (r=0.254; P<0.05). The anti-Semitic experiences in the post-Soviet-Union areas also correlated positively with limb pain (r=0.41, P<0.01), fatigue symptoms (r=0.296, P<0.01) and psychocardial symptoms (r=0.219, P<0.05). It was also confirmed that the male respondents recalled a controlling and overprotecting maternal rearing behavior more frequently than the German standard random sample (M=15.39 versus 18.6; t=2.68; P<0.01). The latter also correlated significantly positive with epigastric pain (r=0.349; P<0.01). The present results show that depression, fear and psychosomatic problems are common in Jewish residents with a

  13. Increased rate of depression and psychosomatic symptoms in Jewish migrants from the post-Soviet-Union to Germany in the 3rd generation after the Shoa

    PubMed Central

    Ullmann, E; Barthel, A; Licinio, J; Petrowski, K; Bornstein, S R; Strauß, B

    2013-01-01

    The mental health status of persons with Jewish background living in Germany is discussed with special regard to social exclusion like anti-Semitism and overprotective parental rearing behavior, as a transmissional factor of the KZ-Syndrome. These stressors are considered in the context of a higher risk for depression/fear and psychosomatic disorders and also abnormal cortisol levels. The present sample (N=89) is derived from the Jewish population currently living in the German region of Saxony aged between 17–36 years that emigrated from the post-Soviet-Union areas. The mean age was 22.9 years. Two questionnaires to detect psychosomatic symptoms (Giessen complaint list (GBB)-24, hospital anxiety and depression scale) and one questionnaire addressing parental rearing behavior (FEE) were employed. Comparisons were drawn with normative data from the literature about the German residential population. In addition, questions were asked concerning the experience of anti-Semitism in Germany and in the post-Soviet-Union areas. A higher prevalence of depression/fear (10.3% versus 18.2%) and psychosomatic symptoms (M=14.03 versus 17.8; t=2.42; P<0.05) was observed in Jewish migrants to Germany as compared with non-Jewish German residents. Furthermore, anti-Semitic experiences in Germany correlated positively with depression (r=0.293; P<0.01) and fear (r=0.254; P<0.05). The anti-Semitic experiences in the post-Soviet-Union areas also correlated positively with limb pain (r=0.41, P<0.01), fatigue symptoms (r=0.296, P<0.01) and psychocardial symptoms (r=0.219, P<0.05). It was also confirmed that the male respondents recalled a controlling and overprotecting maternal rearing behavior more frequently than the German standard random sample (M=15.39 versus 18.6; t=2.68; P<0.01). The latter also correlated significantly positive with epigastric pain (r=0.349; P<0.01). The present results show that depression, fear and psychosomatic problems are common in Jewish residents with a

  14. Increased rate of depression and psychosomatic symptoms in Jewish migrants from the post-Soviet-Union to Germany in the 3rd generation after the Shoa.

    PubMed

    Ullmann, E; Barthel, A; Licinio, J; Petrowski, K; Bornstein, S R; Strauß, B

    2013-01-01

    The mental health status of persons with Jewish background living in Germany is discussed with special regard to social exclusion like anti-Semitism and overprotective parental rearing behavior, as a transmissional factor of the KZ-Syndrome. These stressors are considered in the context of a higher risk for depression/fear and psychosomatic disorders and also abnormal cortisol levels. The present sample (N=89) is derived from the Jewish population currently living in the German region of Saxony aged between 17-36 years that emigrated from the post-Soviet-Union areas. The mean age was 22.9 years. Two questionnaires to detect psychosomatic symptoms (Giessen complaint list (GBB)-24, hospital anxiety and depression scale) and one questionnaire addressing parental rearing behavior (FEE) were employed. Comparisons were drawn with normative data from the literature about the German residential population. In addition, questions were asked concerning the experience of anti-Semitism in Germany and in the post-Soviet-Union areas. A higher prevalence of depression/fear (10.3% versus 18.2%) and psychosomatic symptoms (M=14.03 versus 17.8; t=2.42; P<0.05) was observed in Jewish migrants to Germany as compared with non-Jewish German residents. Furthermore, anti-Semitic experiences in Germany correlated positively with depression (r=0.293; P<0.01) and fear (r=0.254; P<0.05). The anti-Semitic experiences in the post-Soviet-Union areas also correlated positively with limb pain (r=0.41, P<0.01), fatigue symptoms (r=0.296, P<0.01) and psychocardial symptoms (r=0.219, P<0.05). It was also confirmed that the male respondents recalled a controlling and overprotecting maternal rearing behavior more frequently than the German standard random sample (M=15.39 versus 18.6; t=2.68; P<0.01). The latter also correlated significantly positive with epigastric pain (r=0.349; P<0.01). The present results show that depression, fear and psychosomatic problems are common in Jewish residents with a

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

    PubMed

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

    2012-02-28

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

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

    ERIC Educational Resources Information Center

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

    2009-01-01

    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…

  17. Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli.

    PubMed

    Sun, Shixiang; Xiao, Jingfa; Zhang, Huiyong; Zhang, Zhang

    2016-01-01

    Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias. PMID:27536275

  18. Pangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli

    PubMed Central

    Sun, Shixiang; Xiao, Jingfa; Zhang, Huiyong; Zhang, Zhang

    2016-01-01

    Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias. PMID:27536275

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

    PubMed Central

    Kessler, Michael D; Dean, Matthew D

    2014-01-01

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

  20. New LIC Vectors For Production of Proteins from Genes Containing Rare Codons

    PubMed Central

    Eschenfeldt, William H.; Makowska-Grzyska, Magdalena; Stols, Lucy; Donnelly, Mark; Jedrzejczak, Robert; Joachimiak, Andrzej

    2014-01-01

    In the effort to produce proteins coded by diverse genomes, structural genomics projects often must express genes containing codons that are rare in the production strain. To address this problem, genes expressing tRNAs corresponding to those codons are typically coexpressed from a second plasmid in the host strain, or from genes incorporated into production plasmids. Here we describe the modification of a series of LIC pMCSG vectors currently used in the high-throughput production of proteins to include crucial tRNA genes covering rare codons for Arg (AGG/AGA) and Ile (AUA). We also present variants of these new vectors that allow analysis of ligand binding or co-expression of multiple proteins introduced through two independent LIC steps. Additionally, to accommodate the cloning of multiple large proteins, the size of the plasmids was reduced by approximately one kilobase through the removal of non-essential DNA from the base vector. Production of proteins from core vectors of this series validated the desired enhanced capabilities: higher yields of proteins expressed from genes with rare codons occurred in most cases, biotinylated derivatives enabled detailed automated ligand binding analysis, and multiple proteins introduced by dual LIC cloning were expressed successfully and in near balanced stoichiometry, allowing tandem purification of interacting proteins. PMID:24057978

  1. Codon Usage and 3' UTR Length Determine Maternal mRNA Stability in Zebrafish.

    PubMed

    Mishima, Yuichiro; Tomari, Yukihide

    2016-03-17

    The control of mRNA stability plays a central role in regulating gene expression. In metazoans, the earliest stages of development are driven by maternally supplied mRNAs. The degradation of these maternal mRNAs is critical for promoting the maternal-to-zygotic transition of developmental programs, although the underlying mechanisms are poorly understood in vertebrates. Here, we characterized maternal mRNA degradation pathways in zebrafish using a transcriptome analysis and systematic reporter assays. Our data demonstrate that ORFs enriched with uncommon codons promote deadenylation by the CCR4-NOT complex in a translation-dependent manner. This codon-mediated mRNA decay is conditional on the context of the 3' UTR, with long 3' UTRs conferring resistance to deadenylation. These results indicate that the combined effect of codon usage and 3' UTR length determines the stability of maternal mRNAs in zebrafish embryos. Our study thus highlights the codon-mediated mRNA decay as a conserved regulatory mechanism in eukaryotes. PMID:26990990

  2. Suppression of galactocerebrosidase premature termination codon and rescue of galactocerebrosidase activity in twitcher cells.

    PubMed

    Luddi, Alice; Crifasi, Laura; Capaldo, Angela; Piomboni, Paola; Costantino-Ceccarini, Elvira

    2016-11-01

    Krabbe's disease (KD) is a degenerative lysosomal storage disease resulting from deficiency of β-galactocerebrosidase activity. Over 100 mutations are known to cause the disease, and these usually occur in compound heterozygote patterns. In affected patients, nonsense mutations leading to a nonfunctional enzyme are often found associated with other mutations. The twitcher mouse is a naturally occurring model of KD, containing in β-galactocerebrosidase a premature stop codon, W339X. Recent studies have shown that selected compounds may induce the ribosomal bypass of premature stop codons without affecting the normal termination codons. The rescue of β-galactocerebrosidase activity induced by treatment with premature termination codon (PTC) 124, a well-characterized compound known to induce ribosomal read-through, was investigated on oligodendrocytes prepared from twitcher mice and on human fibroblasts from patients bearing nonsense mutations. The effectiveness of the nonsense-mediated mRNA decay (NMD) inhibitor 1 (NMDI1), a newly identified inhibitor of NMD, was also tested. Incubation of these cell lines with PTC124 and NMDI1 increased the levels of mRNA and rescued galactocerebrosidase enzymatic activity in a dose-dependent manner. The low but sustained expression of β-galactocerebrosidase in oligodendrocytes was sufficient to improve the morphology of the differentiated cells. Our in vitro approach provides the basis for further investigation of ribosomal read-through as an alternative therapeutic strategy to ameliorate the quality of life in selected KD patients. © 2016 Wiley Periodicals, Inc. PMID:27638609

  3. Conservation of CFTR codon frequency through primates suggests synonymous mutations could have a functional effect.

    PubMed

    Pizzo, Lucilla; Iriarte, Andrés; Alvarez-Valin, Fernando; Marín, Mónica

    2015-05-01

    Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system, with a prevalence of about 1:3000 people. Cystic fibrosis is caused by mutations in CFTR gene, which lead to a defective function of the chloride channel, the cystic fibrosis transmembrane conductance regulator (CFTR). Up-to-date, more than 1900 mutations have been reported in CFTR. However for an important proportion of them, their functional effects and the relation to disease are still not understood. Many of these mutations are silent (or synonymous), namely they do not alter the encoded amino acid. These synonymous mutations have been considered as neutral to protein function. However, more recent evidence in bacterial and human proteins has put this concept under revision. With the aim of understanding possible functional effects of synonymous mutations in CFTR, we analyzed human and primates CFTR codon usage and divergence patterns. We report the presence of regions enriched in rare and frequent codons. This spatial pattern of codon preferences is conserved in primates, but this cannot be explained by sequence conservation alone. In sum, the results presented herein suggest a functional implication of these regions of the gene that may be maintained by purifying selection acting to preserve a particular codon usage pattern along the sequence. Overall these results support the idea that several synonymous mutations in CFTR may have functional importance, and could be involved in the disease.

  4. Screening for the APP codon 670/671 mutations in Alzheimer's disease.

    PubMed

    Houlden, H; Crawford, F; Rossor, M; Mullan, M

    1993-05-14

    A mutation at codons 670 and 671 of exon 16 of the amyloid precursor protein has recently been identified as a cause of early onset familial Alzheimer's disease. Using restriction enzyme digestion, screening failed to reveal the occurrence of this mutation in 43 families with early onset, 31 families with late onset, 30 cases of sporadic Alzheimer's disease or 30 clinically normal individuals.

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

    PubMed

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

    2014-01-01

    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

  6. System analysis of synonymous codon usage biases in archaeal virus genomes.

    PubMed

    Li, Sen; Yang, Jie

    2014-08-21

    Recent studies of geothermally heated aquatic ecosystems have found widely divergent viruses with unusual morphotypes. Archaeal viruses isolated from these hot habitats usually have double-stranded DNA genomes, linear or circular, and can infect members of the Archaea domain. In this study, the synonymous codon usage bias (SCUB) and dinucleotide composition in the available complete archaeal virus genome sequences have been investigated. It was found that there is a significant variation in SCUB among different Archaeal virus species, which is mainly determined by the base composition. The outcome of correspondence analysis (COA) and Spearman׳s rank correlation analysis shows that codon usage of selected archaeal virus genes depends mainly on GC richness of genome, and the gene׳s function, albeit with smaller effects, also contributes to codon usage in this virus. Furthermore, this investigation reveals that aromaticity of each protein is also critical in affecting SCUB of these viral genes although it was less important than that of the mutational bias. Especially, mutational pressure may influence SCUB in SIRV1, SIRV2, ARV1, AFV1, and PhiCh1 viruses, whereas translational selection could play a leading role in HRPV1׳s SCUB. These conclusions not only can offer an insight into the codon usage biases of archaeal virus and subsequently the possible relationship between archaeal viruses and their host, but also may help in understanding the evolution of archaeal viruses and their gene classification, and more helpful to explore the origin of life and the evolution of biology.

  7. Influenza A Virus Attenuation by Codon Deoptimization of the NS Gene for Vaccine Development

    PubMed Central

    Nogales, Aitor; Baker, Steven F.; Ortiz-Riaño, Emilio; Dewhurst, Stephen; Topham, David J.

    2014-01-01

    ABSTRACT Influenza viral infection represents a serious public health problem that causes contagious respiratory disease, which is most effectively prevented through vaccination to reduce transmission and future infection. The nonstructural (NS) gene of influenza A virus encodes an mRNA transcript that is alternatively spliced to express two viral proteins, the nonstructural protein 1 (NS1) and the nuclear export protein (NEP). The importance of the NS gene of influenza A virus for viral replication and virulence has been well described and represents an attractive target to generate live attenuated influenza viruses with vaccine potential. Considering that most amino acids can be synthesized from several synonymous codons, this study employed the use of misrepresented mammalian codons (codon deoptimization) for the de novo synthesis of a viral NS RNA segment based on influenza A/Puerto Rico/8/1934 (H1N1) (PR8) virus. We generated three different recombinant influenza PR8 viruses containing codon-deoptimized synonymous mutations in coding regions comprising the entire NS gene or the mRNA corresponding to the individual viral protein NS1 or NEP, without modifying the respective splicing and packaging signals of the viral segment. The fitness of these synthetic viruses was attenuated in vivo, while they retained immunogenicity, conferring both homologous and heterologous protection against influenza A virus challenges. These results indicate that influenza viruses can be effectively attenuated by synonymous codon deoptimization of the NS gene and open the possibility of their use as a safe vaccine to prevent infections with these important human pathogens. IMPORTANCE Vaccination serves as the best therapeutic option to protect humans against influenza viral infections. However, the efficacy of current influenza vaccines is suboptimal, and novel approaches are necessary for the prevention of disease cause by this important human respiratory pathogen. The nonstructural

  8. Structural characterization of eRF1 mutants indicate a complex mechanism of stop codon recognition

    PubMed Central

    Pillay, Shubhadra; Li, Yan; Wong, Leo E; Pervushin, Konstantin

    2016-01-01

    Eukarya translation termination requires the stop codon recognizing protein eRF1. In contrast to the multiple proteins required for translation termination in Bacteria, eRF1 retains the ability to recognize all three of the stop codons. The details of the mechanism that eRF1 uses to recognize stop codons has remained elusive. This study describes the structural effects of mutations in the eRF1 N-domain that have previously been shown to alter stop codon recognition specificity. Here, we propose a model of eRF1 binding to the pre-translation termination ribosomal complex that is based in part on our solution NMR structures of the wild-type and mutant eRF1 N-domains. Since structural perturbations induced by these mutations were spread throughout the protein structure, residual dipolar coupling (RDC) data were recorded to establish the long-range effects of the specific mutations, E55Q, Y125F, Q122FM(Y)F126. RDCs were recorded on 15N-labeled eRF1 N-domain weakly aligned in either 5% w/v n-octyl-penta (ethylene glycol)/octanol (C8E5) or the filamentous phage Pf1. These data indicate that the mutations alter the conformation and dynamics of the GTS loop that is distant from the mutation sites. We propose that the GTS loop forms a switch that is key for the multiple codon recognition capability of eRF1. PMID:26725946

  9. Association between p53 polymorphism at codon 72 and recurrent spontaneous abortion.

    PubMed

    Zhang, Ying; Wu, Yuan-Yuan; Qiao, Fu-Yuan; Zeng, Wan-Jiang

    2016-06-01

    p53 gene plays an important role in apoptosis, which is necessary for successful invasion of trophoblast cells. The change from an arginine (Arg) to a proline (Pro) at codon 72 can influence the biological activity of p53, which predisposes to an increased risk of recurrent spontaneous abortion (RSA). In order to investigate the association between p53 polymorphism at codon 72 and RSA, we conducted this meta-analysis. Pubmed, Embase and Web of science were used to identify the eligible studies. Odds ratio (OR) with 95% confidence interval (CI) was used to evaluate the strength of the association. Six studies containing 937 cases of RSA and 830 controls were included, and there was one study deviated from Hardy-Weinberg equilibrium (HWE). There was a significant association between p53 polymorphism at codon 72 and RSA in recessive model (Pro/Pro vs. Pro/Arg+Arg/Arg; OR=1.60, 95% CI: 1.14-2.24) and co-dominant model (Pro/Pro vs. Arg/Arg; OR=1.47, 95% CI: 1.02-2.12) whether the study that was deviated from HWE was eliminated or not. A significant association was observed in allelic model (Pro vs. Arg; OR=1.28, 95% CI: 1.04-1.57) after exclusion of the study that was deviated from HWE. No association was noted in recessive model (Pro/Pro+Pro/Arg vs. Arg/Arg; OR=1.05, 95% CI: 0.86-1.30) and co-dominant model (Pro/Arg vs. Arg/Arg; OR=0.96, 95% CI: 0.77-1.19). Subgroup analysis by ethnicity also indicated a significant association between p53 polymorphism at codon 72 and RSA in Caucasian group. No heterogeneity and publication bias were found. Our meta-analysis implied that p53 polymorphism at codon 72 carries high maternal risk of RSA. PMID:27376811

  10. Coevolution between Stop Codon Usage and Release Factors in Bacterial Species

    PubMed Central

    Wei, Yulong; Wang, Juan; Xia, Xuhua

    2016-01-01

    Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3. This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range. PMID:27297468

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

    PubMed

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

    2013-04-01

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

  12. Analysis of four families with the Stickler syndrome by linkage studies. Identification of a new premature stop codon in the COL2A1 gene in a family

    SciTech Connect

    Bonaventure, J.; Lasselin, C.; Toutain, A.

    1994-09-01

    The Stickler syndrome is an arthro-ophthalmopathy which associates progressive myopia with vitreal degeneration and retinal detachment. Cleft palate, cranio-facial abnormalities, deafness and osteoarthritis are often associated symptoms. Genetic heterogeneity of this autosomal dominant disease was consistent with its large clinical variability. Linkage studies have provided evidence for cosegregation of the disease with COL2A1, the gene coding for type II collagen, in about 50% of the families. Four additional families are reported here. Linkage analyses by using a VNTR located in the 3{prime} region of the gene were achieved. In three families, positive lod scores were obtained with a cumulative maximal value of 3.5 at a recombination fraction of 0. In one of these families, single strand conformation analysis of 25 exons disclosed a new mutation in exon 42. Codon for glutamic acid at position a1-803 was converted into a stop codon. The mutation was detected in DNA samples from all the affected members of the family but not in the unaffected. This result confirms that most of the Stickler syndromes linked to COL2A1 are due to premature stop codons. In a second family, an abnormal SSCP pattern of exon 34 was detected in all the affected individuals. The mutation is likely to correspond to a splicing defect in the acceptor site of intron 33. In one family the disease did not segregate with the COL2A1 locus. Further linkage studies with intragenic dimorphic sites in the COL10A1 gene and highly polymorphic markers close to the COL9A1 locus indicated that this disorder did not result from defects in these two genes.

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

    PubMed

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

    2014-11-01

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

  14. Collaborative study for the establishment of the WHO 3(rd) International Standard for Endotoxin, the Ph. Eur. endotoxin biological reference preparation batch 5 and the USP Reference Standard for Endotoxin Lot H0K354.

    PubMed

    Findlay, L; Desai, T; Heath, A; Poole, S; Crivellone, M; Hauck, W; Ambrose, M; Morris, T; Daas, A; Rautmann, G; Buchheit, K H; Spieser, J M; Terao, E

    2015-01-01

    An international collaborative study was organised jointly by the World Health Organization (WHO)/National Institute for Biological Standards and Control (NIBSC), the United States Pharmacopeia (USP) and the European Directorate for the Quality of Medicines & HealthCare (EDQM/Council of Europe) for the establishment of harmonised replacement endotoxin standards for these 3 organisations. Thirty-five laboratories worldwide, including Official Medicines Control Laboratories (OMCLs) and manufacturers enrolled in the study. Three candidate preparations (10/178, 10/190 and 10/196) were produced with the same material and same formulation as the current reference standards with the objective of generating a new (3(rd)) International Standard (IS) with the same potency (10 000 IU/vial) as the current (2(nd)) IS, as well as new European Pharmacopoeia (Ph. Eur.). and USP standards. The suitability of the candidate preparations to act as the reference standard in assays for endotoxin performed according to compendial methods was evaluated. Their potency was calibrated against the WHO 2(nd) IS for Endotoxin (94/580). Gelation and photometric methods produced similar results for each of the candidate preparations. The overall potency estimates for the 3 batches were comparable. Given the intrinsic assay precision, the observed differences between the batches may be considered unimportant for the intended use of these materials. Overall, these results were in line with those generated for the establishment of the current preparations of reference standards. Accelerated degradation testing of vials stored at elevated temperatures supported the long-term stability of the 3 candidate preparations. It was agreed between the 3 organisations that batch 10/178 be shared between WHO and EDQM and that batches 10/190 and 10/196 be allocated to USP, with a common assigned value of 10 000 IU/vial. This value maintains the continuity of the global harmonisation of reference materials and

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

    PubMed Central

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

    2013-01-01

    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

  16. Expression of varied GFPs in Saccharomyces cerevisiae: codon optimization yields stronger than expected expression and fluorescence intensity

    PubMed Central

    Kaishima, Misato; Ishii, Jun; Matsuno, Toshihide; Fukuda, Nobuo; Kondo, Akihiko

    2016-01-01

    Green fluorescent protein (GFP), which was originally isolated from jellyfish, is a widely used tool in biological research, and homologs from other organisms are available. However, researchers must determine which GFP is the most suitable for a specific host. Here, we expressed GFPs from several sources in codon-optimized and non-codon-optimized forms in the yeast Saccharomyces cerevisiae, which represents an ideal eukaryotic model. Surprisingly, codon-optimized mWasabi and mNeonGreen, which are typically the brightest GFPs, emitted less green fluorescence than did the other five codon-optimized GFPs tested in S. cerevisiae. Further, commercially available GFPs that have been optimized for mammalian codon usage (e.g., EGFP, AcGFP1 and TagGFP2) unexpectedly exhibited extremely low expression levels in S. cerevisiae. In contrast, codon-optimization of the GFPs for S. cerevisiae markedly increased their expression levels, and the fluorescence intensity of the cells increased by a maximum of 101-fold. Among the tested GFPs, the codon-optimized monomeric mUkG1 from soft coral showed the highest levels of both expression and fluorescence. Finally, the expression of this protein as a fusion-tagged protein successfully improved the reporting system’s ability to sense signal transduction and protein–protein interactions in S. cerevisiae and increased the detection rates of target cells using flow cytometry. PMID:27782154

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

    PubMed

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

    2005-12-01

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

  18. Human papillomavirus tumor-infiltrating T-regulatory lymphocytes and P53 codon 72 polymorphisms correlate with clinical staging and prognosis of oropharyngeal cancer.

    PubMed

    Rittà, Massimo; Landolfo, Vincenzo; Mazibrada, Jasenka; De Andrea, Marco; Dell'Oste, Valentina; Caneparo, Valeria; Peretti, Alberto; Giordano, Carlo; Pecorari, Giancarlo; Garzaro, Massimiliano; Landolfo, Santo

    2013-04-01

    The association between human papillomavirus (HPV) DNA positivity, p53 codon 72 polymorphisms, and the type of leukocyte infiltration in head and neck squamous cell carcinomas (HNSCC) and their combined impact upon patient survival is poorly investigated. For this reason, leukocyte infiltration profile and p53 codon 72 polymorphisms were assessed in freshly removed HNSCC specimens (N=71 patients). HPV detection was performed by nested-PCR followed by DNA sequencing. Viral loads were determined by quantitative RT-PCR. The choice to investigate fresh instead of archive paraffin-embedded specimens was privileged to avoid possible artifacts due to sample processing. HPV DNA was detected in 14% of cases. Oropharyngeal carcinomas were the most frequently associated with the presence of HPV16 DNA (41%) and were associated with p53 Pro/Pro or Pro/Arg polymorphisms. In HPV16-positive oropharyngeal carcinomas increased infiltrations of CD3+ and FoxP3+ T-cells correlated with higher HPV16 copy numbers. The presence of HPV may trigger a stronger immune response and may be considered a reliable marker for clinical staging and a more favorable prognosis of oropharyngeal carcinoma. PMID:23686119

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

    PubMed Central

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

    2006-01-01

    We replaced degenerate codons for nine amino acids within the capsid region of the Sabin type 2 oral poliovirus vaccine strain with corresponding nonpreferred synonymous codons. Codon replacements were introduced into four contiguous intervals spanning 97% of the capsid region. In the capsid region of the most highly modified virus construct, the effective number of codons used (NC) fell from 56.2 to 29.8, the number of CG dinucleotides rose from 97 to 302, and the G+C content increased from 48.4% to 56.4%. Replicative fitness in HeLa cells, measured by plaque areas and virus yields in single-step growth experiments, decreased in proportion to the number of replacement codons. Plaque areas decreased over an ∼10-fold range, and virus yields decreased over an ∼65-fold range. Perhaps unexpectedly, the synthesis and processing of viral proteins appeared to be largely unaltered by the restriction in codon usage. In contrast, total yields of viral RNA in infected cells were reduced ∼3-fold and specific infectivities of purified virions (measured by particle/PFU ratios) decreased ∼18-fold in the most highly modified virus. The replicative fitness of both codon replacement viruses and unmodified viruses increased with the passage number in HeLa cells. After 25 serial passages (∼50 replication cycles), most codon replacements were retained, and the relative fitness of the modified viruses remained well below that of the unmodified virus. The increased replicative fitness of high-passage modified virus was associated with the elimination of several CG dinucleotides. Potential applications for the systematic modulation of poliovirus replicative fitness by deoptimization of codon usage are discussed. PMID:16537593

  20. Radiation Therapy Physics, 3rd Edition

    NASA Astrophysics Data System (ADS)

    Hendee, William R.; Ibbott, Geoffrey S.; Hendee, Eric G.

    2004-08-01

    The Third Edition of Radiation Therapy Physics addresses in concise fashion the fundamental diagnostic radiologic physics principles as well as their clinical implications. Along with coverage of the concepts and applications for the radiation treatment of cancer patients, the authors have included reviews of the most up-to-date instrumentation and critical historical links. The text includes coverage of imaging in therapy planning and surveillance, calibration protocols, and precision radiation therapy, as well as discussion of relevant regulation and compliance activities. It contains an updated and expanded section on computer applications in radiation therapy and electron beam therapy, and features enhanced user-friendliness and visual appeal with a new, easy-to-follow format, including sidebars and a larger trim size. With its user-friendly presentation and broad, comprehensive coverage of radiotherapy physics, this Third Edition doubles as a medical text and handy professional reference.

  1. Coal mine ground control. 3rd ed.

    SciTech Connect

    Peng, S.S.

    2008-09-15

    The third edition not only completely revises and updates the original subject areas, but also is broadened to include a number of new topics such as high horizontal stresses, computer modeling, and highwall stability. The subject areas covered in this book define the current field of coal mine ground control, except for the recently emerging topic of mine seals and some conventional subjects such as coal/rock cutting and impoundment dams. It contains 1,134 references from all published sources, and archived since 1876.

  2. Cerebral computed tomography, 3rd Edition

    SciTech Connect

    Weisberg, L.; Nice, C.

    1988-01-01

    This book is an introduction to the utilization of computed tomography in evaluating patients with intracranial and orbital disorders. It features clinical correlations and provides an overview of general principles, performance, and normal anatomy of CT. It covers evaluation of specific neurologic signs and symptoms, including stroke, metastatic disease, increased intracranial pressure, head injury, pediatric conditions, and more.

  3. Peace Corps. 3rd Annual Report.

    ERIC Educational Resources Information Center

    Peace Corps, Washington, DC.

    Projects, operations, and future plans are covered in this annual report for the third year of the Peace Corps. An introduction comments on returning volunteers and presents regional maps with tables for Latin America, Africa, Near East and South Asia, and Far East. Section 1 contains letters and reports from volunteers in Peru, Ivory Coast,…

  4. Teaching Visually Impaired Children. 3rd Edition

    ERIC Educational Resources Information Center

    Bishop, Virginia E.

    2004-01-01

    In this exceptional new third edition, the author has retained much of the practical "how to" approach of the previous editions, but adds depth in two dimensions: learning theory and the educational process. This book is "so comprehensive in scope and complete in detail that it would be the most likely recommended" (from the foreword by Dr.…

  5. Fundamentals of nuclear pharmacy, 3rd Ed

    SciTech Connect

    Saha, G.B. )

    1992-01-01

    This book is a standard text/reference of nuclear pharmacy. New sections in the Third Edition include: instruments used for radiation detection and measurement; disposal of radioactive materials; clinical uses of all new and existing radiopharmaceuticals; 99m Tc and 123I-labeled radiopharmaceuticals, as well as radiolabeled leukocytes, platelets, and antibodies; and up-to-date descriptions of the latest FDA regulations.

  6. The 3rd International Microgravity Combustion Workshop

    NASA Technical Reports Server (NTRS)

    Ross, Howard D. (Compiler)

    1995-01-01

    This Conference Publication contains 71 papers presented at the Third International Microgravity Combustion Workshop held in Cleveland, Ohio, from April 11 to 13, 1995. The purpose of the workshop was twofold: to exchange information about the progress and promise of combustion science in microgravity and to provide a forum to discuss which areas in microgravity combustion science need to be expanded profitably and which should be included in upcoming NASA Research Announcements (NRA).

  7. The Physics of Glaciers, 3rd Edition

    NASA Astrophysics Data System (ADS)

    Bahr, David

    At one time or another, who among us has not marveled at the beauty of the snow and ice-covered Alps, or admired the tenacity of polar explorers and the adventurous spirits of climbers on the glacier-clad summits of the high Himalaya? The fascination of distant ice covered expanses has enlisted more than a few recruits into the ranks of glaciologists, but many, if not most, of today's students of glaciology are a slightly less romantic and more mathematical lot, attracted by the quantitative world of physics and the applied sciences of polar climatology, ice mechanics, and snow hydrology.Once a relatively quiet branch of geophysics filled with venturesome climbers capable of reaching the objects of their study, glaciology is now a field that is fueled by a rapid influx of talent, technology, and new ideas due to the increasingly acknowledged relationships between global climate, sea level, and ice sheets. While the understanding of glacier processes has seen significant progress, as a result there is also a sense of being overwhelmed by the voluminous and sometimes speculative theories and field observations associated with an expanding discipline.

  8. A Beginning. Revised 3rd Edition.

    ERIC Educational Resources Information Center

    Healy, Mary K.; Root, Phyllis

    This document contains a selection of materials focusing on man acting to know, preserve, and improve his environment. The booklet is divided into three parts. Part one presents a listing of objectives. They reflect a need for all to become aware of the problems that plague our environment. Furthermore, they indicate that the ecological…

  9. 3rd Brazilian Consensus on Helicobacter pylori.

    PubMed

    Coelho, Luiz Gonzaga; Maguinilk, Ismael; Zaterka, Schlioma; Parente, José Miguel; do Carmo Friche Passos, Maria; Moraes-Filho, Joaquim Prado P

    2013-04-01

    Signicant progress has been obtained since the Second Brazilian Consensus Conference on Helicobacter pylori Infection held in 2004, in São Paulo, SP, Brazil, and justify a third meeting to establish updated guidelines on the current management of H. pylori infection. The Third Brazilian Consensus Conference on H pylori Infection was organized by the Brazilian Nucleus for the Study of Helicobacter, a Department of the Brazilian Federation of Gastroenterology and took place on April 12-15, 2011, in Bento Gonçalves, RS, Brazil. Thirty-one delegates coming from the five Brazilian regions and one international guest, including gastroenterologists, pathologists, epidemiologists, and pediatricians undertook the meeting. The participants were allocated in one of the five main topics of the meeting: H pylori, functional dyspepsia and diagnosis; H pylori and gastric cancer; H pylori and other associated disorders; H pylori treatment and retreatment; and, epidemiology of H pylori infection in Brazil. The results of each subgroup were submitted to a final consensus voting to all participants. Relevant data were presented, and the quality of evidence, strength of recommendation, and level of consensus were graded. Seventy per cent and more votes were considered as acceptance for the final statement. This article presents the main recommendations and conclusions to guide Brazilian doctors involved in the management of H pylori infection.

  10. Elementary Science Guide -- 3rd Grade.

    ERIC Educational Resources Information Center

    Wieland, Anne; And Others

    Presented is a resource book to be used with instructional kits for elementary school science students, grade 3. The individual units at this grade level are based on curriculum which has been developed by the National Science Foundation in the 1960s and revised to meet student and teacher identified needs in Anchorage, Alaska. Six units are…

  11. Mutation at embB Codon 306, a Potential Marker for the Identification of Multidrug Resistance Associated with Ethambutol in Mycobacterium tuberculosis

    PubMed Central

    Cuevas-Córdoba, Betzaida; Juárez-Eusebio, Dulce María; Almaraz-Velasco, Raquel; Muñiz-Salazar, Raquel; Laniado-Laborin, Rafael

    2015-01-01

    Ethambutol inhibits arabinogalactan and lipoarabinomannan biosynthesis in mycobacteria. The occurrence of mutations in embB codon 306 in ethambutol-susceptible isolates and their absence in resistant isolates has raised questions regarding the utility of this codon as a potential marker for resistance against ethambutol. The characterization of mutations on embB 306 will contribute to a better understanding of the mechanisms of resistance to this drug; therefore, the purpose of this study was to investigate the association between embB 306 mutations and first-line drug resistance profiles in tuberculosis isolates. We sequenced the region surrounding the embB 306 codon in 175 tuberculosis clinical isolates, divided according to drug sensitivity, in three groups: 110 were resistant to at least one first-line drug, of which 61 were resistant to ethambutol (EMBr), 49 were sensitive to ethambutol (EMBs) but were resistant to another drug, and 65 were pansensitive isolates (Ps). The associations between embB 306 mutations and phenotypic resistance to all first-line drugs were determined, and their validity and safety as a diagnostic marker were assessed. One of the Ps isolates (1/65), one of the EMBs isolates (1/49), and 20 of the EMBr isolates (20/61) presented with an embB 306 mutation. Four different single-nucleotide polymorphisms (SNPs) at embB 306 were associated with simultaneous resistance to ethambutol, isoniazid, and rifampin (odds ratio [OR], 17.7; confidence interval [CI], 5.6 to 56.1) and showed a positive predictive value of 82%, with a specificity of 97% for diagnosing multidrug resistance associated with ethambutol, indicating its potential as a molecular marker for several drugs. PMID:26124153

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

    PubMed Central

    Williford, Anna; Demuth, Jeffery P.

    2012-01-01

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

  13. Itaconic acid production from glycerol using Escherichia coli harboring a random synonymous codon-substituted 5'-coding region variant of the cadA gene.

    PubMed

    Jeon, Ho-Geun; Cheong, Dae-Eun; Han, Yunjon; Song, Jae Jun; Choi, Jong Hyun

    2016-07-01

    Aspergillus terreus cadA, encoding cis-aconitate decarboxylase, is an essential gene for itaconic acid (IA) biosynthesis, but it is primarily expressed as insoluble aggregates in most industrial hosts. This has been a hurdle for the development of recombinant strategies for IA production. Here, we created a library of synonymous codon variants (scv) of the cadA gene containing synonymous codons in the first 10 codons (except ATG) and screened it in Escherichia coli. Among positive clones, E. coli scvCadA_No8 showed more than 95% of expressed CadA in the soluble fraction, and in production runs, produced threefold more IA than wild-type E. coli in Luria-Bertani broth supplemented with 0.5% glucose. In M9 minimal media containing 0.85 g/L citrate and 1% glycerol, E. coli scvCadA_No8 produced 985.6 ± 33.4 mg/L IA during a 72-h culture after induction with isopropyl β-D-1-thiogalactopyranoside. In a 2-L fed-batch fermentation consisting of two stages (growth and nitrogen limitation conditions), we obtained 7.2 g/L IA by using E. coli by introducing only the scv_cadA gene and optimizing culture conditions for IA production. These results could be combined with metabolic engineering and generate an E. coli strain as an industrial IA producer. Biotechnol. Bioeng. 2016;113: 1504-1510. © 2015 Wiley Periodicals, Inc. PMID:26704570

  14. Remote sensing investigation into the correlation between landslides caused by the 2002 November 3rd, 7.9M Denali Fault earthquake and a surge of the SE fork of McGinnis Peak Glacier.

    NASA Astrophysics Data System (ADS)

    Benowitz, J.

    2007-12-01

    The 2002 November 3rd, 7.9 M Denali Fault caused a large landslide that deposited 11.4 x 106m3 feet of rock and ice onto the SE fork of McGinnis Peak Glacier. The landslide left a large mass on the upper ice reservoir of the glacier and blocked the terminus outlet of the glacier with debris. Satellite images and historic photos were used to examine the terminus history of the glacier. Further landslides/mass wasting events during the spring of 2003, documented via Land Sat 7 images, covered the same upper ice reservoir as the 2002 landslides. Between 2004 and 2006 the SE fork Glacier of McGinnis Peak experienced a dramatic surge. There is no known history of such dramatic surge occurrences on the glacier of interest. Though causation is difficult to prove preliminary evidence points towards the implication that the landslides generated by the 2002 earthquake most likely either caused or contributed to the documented glacial surge. Examination of more satellite images is planned to further examine McGinnis Peak's glacier history and to refine the timing of the possible correlation between the earthquake generated landslides and the dramatic surge of the SE glacial fork of McGinnis Peak

  15. Costs, affordability, and feasibility of an essential package of cancer control interventions in low-income and middle-income countries: key messages from Disease Control Priorities, 3rd edition.

    PubMed

    Gelband, Hellen; Sankaranarayanan, Rengaswamy; Gauvreau, Cindy L; Horton, Susan; Anderson, Benjamin O; Bray, Freddie; Cleary, James; Dare, Anna J; Denny, Lynette; Gospodarowicz, Mary K; Gupta, Sumit; Howard, Scott C; Jaffray, David A; Knaul, Felicia; Levin, Carol; Rabeneck, Linda; Rajaraman, Preetha; Sullivan, Terrence; Trimble, Edward L; Jha, Prabhat

    2016-05-21

    Investments in cancer control--prevention, detection, diagnosis, surgery, other treatment, and palliative care--are increasingly needed in low-income and particularly in middle-income countries, where most of the world's cancer deaths occur without treatment or palliation. To help countries expand locally appropriate services, Cancer (the third volume of nine in Disease Control Priorities, 3rd edition) developed an essential package of potentially cost-effective measures for countries to consider and adapt. Interventions included in the package are: prevention of tobacco-related cancer and virus-related liver and cervical cancers; diagnosis and treatment of early breast cancer, cervical cancer, and selected childhood cancers; and widespread availability of palliative care, including opioids. These interventions would cost an additional US$20 billion per year worldwide, constituting 3% of total public spending on health in low-income and middle-income countries. With implementation of an appropriately tailored package, most countries could substantially reduce suffering and premature death from cancer before 2030, with even greater improvements in later decades.

  16. New approaches, new activities and new outcomes in international conferences on HIV/AIDS in Africa--report of the 3rd African Conference on the Social Aspects of HIV/AIDS, Dakar, 10-14 October 2005.

    PubMed

    Niang, C I; Shisana, O; Andrews, G; Kaseje, D; Simbayi, L; Peltzer, K; Toefy, Y

    2006-08-01

    Africa's HIV/AIDS situation remains cause for concern. The impact of HIV is considerable and threatens the survival and development of African societies. Although much has been attempted, the results still leave much to be desired. AIDS is an epidemic that needs to be addressed with much creativity and spirit of initiative. It is against this background that the 3rd African conference on the social aspects of HIV/AIDS brought innovations in the way international conferences are designed, activities implemented and results obtained. The innovations concerned the approach to international conferences and take into account reconceptualising HIV/AIDS so as to encourage holistic approaches and better visibility of vulnerable groups. The activities of the conference were organised in such a way as to get people living with HIV/AIDS (PLWHA), grassroots communities and marginalised groups to play a focal role. The conference offered an opportunity for developing cultural activities that would translate the African cultural concepts that had been identified as important in the HIV situation and response analysis. Interaction at the conference created an opportunity to analyse the various dimensions of the political, cultural and economic determinants. The conference offered food for thought around response construction while singling out the themes of urgency and acceleration of response, synergy construction, and coordination and conception of political responses.

  17. Report on the 3'rd scientific meeting of the "Verein zur Förderung des Wissenschaftlichen Nachwuchses in der Neurologie" (NEUROWIND e.V.) held in Motzen, Germany, Nov. 4'th - Nov. 6'th, 2011

    PubMed Central

    2012-01-01

    From November 4th- 6th 2011, the 3rd NEUROWIND e.V. meeting was held in Motzen, Brandenburg, Germany. Like in the previous years, the meeting provided an excellent platform for scientific exchange and the presentation of innovative projects for young colleagues in the fields of neurovascular research, neuroinflammation and neurodegeneration. As kick-off to the scientific sessions, Reinhard Hohlfeld, Head of the Institute for Clinical Neuroimmunology in Munich, gave an illustrious overview on the many fascinations of neuroimmunologic research. A particular highlight on the second day of the meeting was the award of the 1'st NEUROWIND e.V. prize for young academics in the field of experimental neurology. This award is posted for young colleagues under the age of 35 with a significant achievement in the field of neurovascular research, neuroinflammation or neurodegeneration and comprises an amount of 20.000 Euro, founded by Merck Serono GmbH, Darmstadt. Germany. The first prize was awarded to Ivana Nikic from Martin Kerschensteiner's group in Munich for her brilliant work on a reversible form of axon damage in experimental autoimmune encephalomyelitis and multiple sclerosis, published in Nature Medicine in 2011. This first prize award ceremony was a great incentive for the next call for proposals now upcoming in 2012. PMID:22360825

  18. Current practice of epidemiology in Africa: highlights of the 3rd conference of the African epidemiological association and 1st conference of the Cameroon society of epidemiology, Yaoundé, Cameroon, 2014

    PubMed Central

    Nkwescheu, Armand Seraphin; Fokam, Joseph; Tchendjou, Patrice; Nji, Akindeh; Ngouakam, Hermann; Andre, Bita Fouda; Joelle, Sobngwi; Uzochukwu, Benjamin; Akinroye, Kingsley; Mbacham, Wilfred; Colizzi, Vittorio; Leke, Rose; Victora, Cesar

    2015-01-01

    As the study of disease occurrence and health indicators in human populations, Epidemiology is a dynamic field that evolves with time and geographical context. In order to update African health workers on current epidemiological practices and to draw awareness of early career epidemiologists on concepts and opportunities in the field, the 3rd African Epidemiology Association and the 1st Cameroon Society of Epidemiology Conference was organized in June 2-6, 2014 at the Yaoundé Mont Febe Hotel, in Cameroon. Under the theme«Practice of Epidemiology in Africa: Stakes, Challenges and Perspectives», the conference attracted close to five hundred guest and participants from all continents. The two main programs were the pre-conference course for capacity building of African Early Career epidemiologists, and the conference itself, providing a forum for scientific exchanges on recent epidemiological concepts, encouraging the use of epidemiological methods in studying large disease burden and neglected tropical diseases; and highlighting existing opportunities. PMID:26523191

  19. Costs, affordability, and feasibility of an essential package of cancer control interventions in low-income and middle-income countries: key messages from Disease Control Priorities, 3rd edition.

    PubMed

    Gelband, Hellen; Sankaranarayanan, Rengaswamy; Gauvreau, Cindy L; Horton, Susan; Anderson, Benjamin O; Bray, Freddie; Cleary, James; Dare, Anna J; Denny, Lynette; Gospodarowicz, Mary K; Gupta, Sumit; Howard, Scott C; Jaffray, David A; Knaul, Felicia; Levin, Carol; Rabeneck, Linda; Rajaraman, Preetha; Sullivan, Terrence; Trimble, Edward L; Jha, Prabhat

    2016-05-21

    Investments in cancer control--prevention, detection, diagnosis, surgery, other treatment, and palliative care--are increasingly needed in low-income and particularly in middle-income countries, where most of the world's cancer deaths occur without treatment or palliation. To help countries expand locally appropriate services, Cancer (the third volume of nine in Disease Control Priorities, 3rd edition) developed an essential package of potentially cost-effective measures for countries to consider and adapt. Interventions included in the package are: prevention of tobacco-related cancer and virus-related liver and cervical cancers; diagnosis and treatment of early breast cancer, cervical cancer, and selected childhood cancers; and widespread availability of palliative care, including opioids. These interventions would cost an additional US$20 billion per year worldwide, constituting 3% of total public spending on health in low-income and middle-income countries. With implementation of an appropriately tailored package, most countries could substantially reduce suffering and premature death from cancer before 2030, with even greater improvements in later decades. PMID:26578033

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

    SciTech Connect

    Celi, F.S.; Silver, K.; Walston, J.

    1995-09-01

    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.

  1. Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles.

    PubMed

    Fabijanić, Maja; Vlahoviček, Kristian

    2016-01-01

    Metagenomics projects use next-generation sequencing to unravel genetic potential in microbial communities from a wealth of environmental niches, including those associated with human body and relevant to human health. In order to understand large datasets collected in metagenomics surveys and interpret them in context of how a community metabolism as a whole adapts and interacts with the environment, it is necessary to extend beyond the conventional approaches of decomposing metagenomes into microbial species' constituents and performing analysis on separate components. By applying concepts of translational optimization through codon usage adaptation on entire metagenomic datasets, we demonstrate that a bias in codon usage present throughout the entire microbial community can be used as a powerful analytical tool to predict for community lifestyle-specific metabolism. Here we demonstrate this approach combined with machine learning, to classify human gut microbiome samples according to the pathological condition diagnosed in the human host. PMID:27115650

  2. Maximum-Likelihood Tree Estimation Using Codon Substitution Models with Multiple Partitions

    PubMed Central

    Zoller, Stefan; Boskova, Veronika; Anisimova, Maria

    2015-01-01

    Many protein sequences have distinct domains that evolve with different rates, different selective pressures, or may differ in codon bias. Instead of modeling these differences by more and more complex models of molecular evolution, we present a multipartition approach that allows maximum-likelihood phylogeny inference using different codon models at predefined partitions in the data. Partition models can, but do not have to, share free parameters in the estimation process. We test this approach with simulated data as well as in a phylogenetic study of the origin of the leucin-rich repeat regions in the type III effector proteins of the pythopathogenic bacteria Ralstonia solanacearum. Our study does not only show that a simple two-partition model resolves the phylogeny better than a one-partition model but also gives more evidence supporting the hypothesis of lateral gene transfer events between the bacterial pathogens and its eukaryotic hosts. PMID:25911229

  3. When cells stop making sense: effects of nonsense codons on RNA metabolism in vertebrate cells.

    PubMed Central

    Maquat, L E

    1995-01-01

    It appears that no organism is immune to the effects of nonsense codons on mRNA abundance. The study of how nonsense codons alter RNA metabolism is still at an early stage, and our current understanding derives more from incidental vignettes than from experimental undertakings that address molecular mechanisms. Challenges for the future include identifying the gene products and RNA sequences that function in nonsense mediated RNA loss, resolving the cause and consequences of there apparently being more than one cellular site and mechanism for nonsense-mediated RNA loss, and understanding how these sites and mechanisms are related to both constitutive and specialized pathways of pre-mRNA processing and mRNA decay. PMID:7489507

  4. Codon Size Reduction as the Origin of the Triplet Genetic Code

    PubMed Central

    Baranov, Pavel V.; Venin, Maxime; Provan, Gregory

    2009-01-01

    The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon-anticodon interactions

  5. Nearly neutrality and the evolution of codon usage bias in eukaryotic genomes.

    PubMed

    Subramanian, Sankar

    2008-04-01

    Here I show that the mean codon usage bias of a genome, and of the lowly expressed genes in a genome, is largely similar across eukaryotes ranging from unicellular protists to vertebrates. Conversely, this bias in housekeeping genes and in highly expressed genes has a remarkable inverse relationship with species generation time that varies by more than four orders of magnitude. The relevance of these results to the nearly neutral theory of molecular evolution is discussed.

  6. HER2 codon 655 polymorphism and breast cancer risk: a meta-analysis.

    PubMed

    Tao, Weiyang; Wang, Chunyang; Han, Ruifa; Jiang, Hongchi

    2009-03-01

    To evaluate the association between HER2 codon 655 polymorphism and breast cancer risk in this meta-analysis. A comprehensive search was performed to identify all case-control studies investigating such association. Statistical analyses were conducted with software MIX 1.54. Twenty eligible reports, including 10,642 cases/11,259 controls, were identified. In overall analysis, the Val allele frequency in cases was significantly higher than that in controls (OR = 1.0921, 95% CI: 1.0013-1.191, P = 0.0466), while no associations were found in both recessive and dominant models. In subgroup analysis, HER2 codon 655 polymorphism was weakly associated with breast cancer risk in recessive (OR = 2.4624, 95% CI: 1.0619-5.7104, P = 0.0357), dominant (OR = 1.2781, 95% CI: 1.0353-1.5779, P = 0.0225), and co-dominant genetic models (OR = 1.2947, 95% CI: 1.0682-1.5693, P = 0.0085) in Asian population, respectively. Meanwhile, the susceptibility to breast cancer in people aged < or =45 was significantly increased in both recessive (OR = 2.2408; 95% CI: 1.2876-3.8998, P = 0.0043), and dominant models (OR = 1.2902, 95% CI: 1.1035-1.5085, P = 0.0014). No significant associations were observed in Caucasian, European, and Family history subgroups. So our analyses suggest HER2 codon 655 Val allele is weakly associated with an increased risk of breast cancer, and SNP at HER2 codon 655 could be considered as a susceptibility biomarker for breast cancer for Asian females or women age 45 years or younger. PMID:18438707

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

    PubMed

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

    2014-11-01

    Phylogenetic analyses using concatenation of genomic-scale data have been seen as the panacea for resolving the incongruences among inferences from few or single genes. However, phylogenomics may also suffer from systematic errors, due to the, perhaps cumulative, effects of saturation, among-taxa compositional (GC content) heterogeneity, or codon-usage bias plaguing the individual nucleotide loci that are concatenated. Here, we provide an example of how these factors affect the inferences of the phylogeny of early land plants based on mitochondrial genomic data. Mitochondrial sequences evolve slowly in plants and hence are thought to be suitable for resolving deep relationships. We newly assembled mitochondrial genomes from 20 bryophytes, complemented these with 40 other streptophytes (land plants plus algal outgroups), compiling a data matrix of 60 taxa and 41 mitochondrial genes. Homogeneous analyses of the concatenated nucleotide data resolve mosses as sister-group to the remaining land plants. However, the corresponding translated amino acid data support the liverwort lineage in this position. Both results receive weak to moderate support in maximum-likelihood analyses, but strong support in Bayesian inferences. Tests of alternative hypotheses using either nucleotide or amino acid data provide implicit support for their respective optimal topologies, and clearly reject the hypotheses that bryophytes are monophyletic, liverworts and mosses share a unique common ancestor, or hornworts are sister to the remaining land plants. We determined that land plant lineages differ in their nucleotide composition, and in their usage of synonymous codon variants. Composition heterogeneous Bayesian analyses employing a nonstationary model that accounts for variation in among-lineage composition, and inferences from degenerated nucleotide data that avoid the effects of synonymous substitutions that underlie codon-usage bias, again recovered liverworts being sister to the

  8. Codon usage bias and base composition of nuclear genes in Drosophila.

    PubMed

    Moriyama, E N; Hartl, D L

    1993-07-01

    The nuclear genes of Drosophila evolve at various rates. This variation seems to correlate with codon-usage bias. In order to elucidate the determining factors of the various evolutionary rates and codon-usage bias in the Drosophila nuclear genome, we compared patterns of codon-usage bias with base compositions of exons and introns. Our results clearly show the existence of selective constraints at the translational level for synonymous (silent) sites and, on the other hand, the neutrality or near neutrality of long stretches of nucleotide sequence within noncoding regions. These features were found for comparisons among nuclear genes in a particular species (Drosophila melanogaster, Drosophila pseudoobscura and Drosophila virilis) as well as in a particular gene (alcohol dehydrogenase) among different species in the genus Drosophila. The patterns of evolution of synonymous sites in Drosophila are more similar to those in the prokaryotes than they are to those in mammals. If a difference in the level of expression of each gene is a main reason for the difference in the degree of selective constraint, the evolution of synonymous sites of Drosophila genes would be sensitive to the level of expression among genes and would change as the level of expression becomes altered in different species. Our analysis verifies these predictions and also identifies additional selective constraints at the translational level in Drosophila.

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

    PubMed

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

    2014-10-01

    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.

  10. Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation

    PubMed Central

    Deng, Wenjun; Babu, I. Ramesh; Su, Dan; Yin, Shanye; Begley, Thomas J.; Dedon, Peter C.

    2015-01-01

    Post-transcriptional modifications of transfer RNAs (tRNAs) have long been recognized to play crucial roles in regulating the rate and fidelity of translation. However, the extent to which they determine global protein production remains poorly understood. Here we use quantitative proteomics to show a direct link between wobble uridine 5-methoxycarbonylmethyl (mcm5) and 5-methoxy-carbonyl-methyl-2-thio (mcm5s2) modifications catalyzed by tRNA methyltransferase 9 (Trm9) in tRNAArg(UCU) and tRNAGlu(UUC) and selective translation of proteins from genes enriched with their cognate codons. Controlling for bias in protein expression and alternations in mRNA expression, we find that loss of Trm9 selectively impairs expression of proteins from genes enriched with AGA and GAA codons under both normal and stress conditions. Moreover, we show that AGA and GAA codons occur with high frequency in clusters along the transcripts, which may play a role in modulating translation. Consistent with these results, proteins subject to enhanced ribosome pausing in yeast lacking mcm5U and mcm5s2U are more likely to be down-regulated and contain a larger number of AGA/GAA clusters. Together, these results suggest that Trm9-catalyzed tRNA modifications play a significant role in regulating protein expression within the cell. PMID:26670883

  11. Comparison of two codon optimization strategies enhancing recombinant Sus scrofa lysozyme production in Pichia pastoris.

    PubMed

    Zhu, D; Cai, G; Wu, D; Lu, J

    2015-01-01

    Lysozyme has played an important role in animal feed additive industry, food additive industry and biological engineering. For improving expression efficiency of recombinant lysozyme from Sus scrofa, two genes respectively designed by the most used codon optimization strategies, "one amino acid one codon" and "codon randomization", were synthesized and expressed in Pichia pastoris X—33. At shaking flask level, Sus scrofa lysozyme (SSL) under two conditions had a highest activity of 153.33±10.41 and 538.33±15.18 U/mL after a 5 days induction of 1% methanol, with secreted protein concentration 80.03±1.94 and 239.60±4.16 mg/L, respectively. Compared with the original SSL gene, the expression of optimized SSL gene by the second strategy showed a 2.6 fold higher level, while the first method had no obvious improvement in production. In total secreted protein, the proportions of recombinant SSL encoded by the original gene, first method optimized gene and the second—strategy optimized one were 75.06±0.25%, 74.56±0.14% and 79.00±0.14%, respectively, with the same molecular weight about 18 kDa, optimum acidity pH 6.0 and optimum temperature 35degC. PMID:26025401

  12. Enhanced expression of codon optimized Mycobacterium avium subsp. paratuberculosis antigens in Lactobacillus salivarius

    PubMed Central

    Johnston, Christopher D.; Bannantine, John P.; Govender, Rodney; Endersen, Lorraine; Pletzer, Daniel; Weingart, Helge; Coffey, Aidan; O'Mahony, Jim; Sleator, Roy D.

    2014-01-01

    It is well documented that open reading frames containing high GC content show poor expression in A+T rich hosts. Specifically, G+C-rich codon usage is a limiting factor in heterologous expression of Mycobacterium avium subsp. paratuberculosis (MAP) proteins using Lactobacillus salivarius. However, re-engineering opening reading frames through synonymous substitutions can offset codon bias and greatly enhance MAP protein production in this host. In this report, we demonstrate that codon-usage manipulation of MAP2121c can enhance the heterologous expression of the major membrane protein (MMP), analogous to the form in