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Sample records for fossil calibrations codon

  1. The Fossil Calibration Database-A New Resource for Divergence Dating.

    PubMed

    Ksepka, Daniel T; Parham, James F; Allman, James F; Benton, Michael J; Carrano, Matthew T; Cranston, Karen A; Donoghue, Philip C J; Head, Jason J; Hermsen, Elizabeth J; Irmis, Randall B; Joyce, Walter G; Kohli, Manpreet; Lamm, Kristin D; Leehr, Dan; Patané, Josés L; Polly, P David; Phillips, Matthew J; Smith, N Adam; Smith, Nathan D; Van Tuinen, Marcel; Ware, Jessica L; Warnock, Rachel C M

    2015-09-01

    Fossils provide the principal basis for temporal calibrations, which are critical to the accuracy of divergence dating analyses. Translating fossil data into minimum and maximum bounds for calibrations is the most important-often least appreciated-step of divergence dating. Properly justified calibrations require the synthesis of phylogenetic, paleontological, and geological evidence and can be difficult for nonspecialists to formulate. The dynamic nature of the fossil record (e.g., new discoveries, taxonomic revisions, updates of global or local stratigraphy) requires that calibration data be updated continually lest they become obsolete. Here, we announce the Fossil Calibration Database (http://fossilcalibrations.org), a new open-access resource providing vetted fossil calibrations to the scientific community. Calibrations accessioned into this database are based on individual fossil specimens and follow best practices for phylogenetic justification and geochronological constraint. The associated Fossil Calibration Series, a calibration-themed publication series at Palaeontologia Electronica, will serve as a key pipeline for peer-reviewed calibrations to enter the database. PMID:25922515

  2. Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents.

    PubMed

    Kimura, Yuri; Hawkins, Melissa T R; McDonough, Molly M; Jacobs, Louis L; Flynn, Lawrence J

    2015-01-01

    Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of the Karnimata clade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludes Rattus and its relatives. Combining the new interpretation with the widely accepted hypothesis that the Progonomys clade includes Mus, the lineage separation event in the Siwalik fossil record represents the Mus/Arvicanthis split. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating. PMID:26411391

  3. Corrected placement of Mus-Rattus fossil calibration forces precision in the molecular tree of rodents

    PubMed Central

    Kimura, Yuri; Hawkins, Melissa T. R.; McDonough, Molly M.; Jacobs, Louis L.; Flynn, Lawrence J.

    2015-01-01

    Time calibration derived from the fossil record is essential for molecular phylogenetic and evolutionary studies. Fossil mice and rats, discovered in the Siwalik Group of Pakistan, have served as one of the best-known fossil calibration points in molecular phylogenic studies. Although these fossils have been widely used as the 12 Ma date for the Mus/Rattus split or a more basal split, conclusive paleontological evidence for the nodal assignments has been absent. This study analyzes newly recognized characters that demonstrate lineage separation in the fossil record of Siwalik murines and examines the most reasonable nodal placement of the diverging lineages in a molecular phylogenetic tree by ancestral state reconstruction. Our specimen-based approach strongly indicates that Siwalik murines of the Karnimata clade are fossil members of the Arvicanthini-Otomyini-Millardini clade, which excludes Rattus and its relatives. Combining the new interpretation with the widely accepted hypothesis that the Progonomys clade includes Mus, the lineage separation event in the Siwalik fossil record represents the Mus/Arvicanthis split. Our test analysis on Bayesian age estimates shows that this new calibration point provides more accurate estimates of murine divergence than previous applications. Thus, we define this fossil calibration point and refine two other fossil-based points for molecular dating. PMID:26411391

  4. The fossilized birth–death process for coherent calibration of divergence-time estimates

    PubMed Central

    Heath, Tracy A.; Huelsenbeck, John P.; Stadler, Tanja

    2014-01-01

    Time-calibrated species phylogenies are critical for addressing a wide range of questions in evolutionary biology, such as those that elucidate historical biogeography or uncover patterns of coevolution and diversification. Because molecular sequence data are not informative on absolute time, external data—most commonly, fossil age estimates—are required to calibrate estimates of species divergence dates. For Bayesian divergence time methods, the common practice for calibration using fossil information involves placing arbitrarily chosen parametric distributions on internal nodes, often disregarding most of the information in the fossil record. We introduce the “fossilized birth–death” (FBD) process—a model for calibrating divergence time estimates in a Bayesian framework, explicitly acknowledging that extant species and fossils are part of the same macroevolutionary process. Under this model, absolute node age estimates are calibrated by a single diversification model and arbitrary calibration densities are not necessary. Moreover, the FBD model allows for inclusion of all available fossils. We performed analyses of simulated data and show that node age estimation under the FBD model results in robust and accurate estimates of species divergence times with realistic measures of statistical uncertainty, overcoming major limitations of standard divergence time estimation methods. We used this model to estimate the speciation times for a dataset composed of all living bears, indicating that the genus Ursus diversified in the Late Miocene to Middle Pliocene. PMID:25009181

  5. Genomic fossils calibrate the long-term evolution of hepadnaviruses.

    PubMed

    Gilbert, Clément; Feschotte, Cédric

    2010-01-01

    Because most extant viruses mutate rapidly and lack a true fossil record, their deep evolution and long-term substitution rates remain poorly understood. In addition to retroviruses, which rely on chromosomal integration for their replication, many other viruses replicate in the nucleus of their host's cells and are therefore prone to endogenization, a process that involves integration of viral DNA into the host's germline genome followed by long-term vertical inheritance. Such endogenous viruses are highly valuable as they provide a molecular fossil record of past viral invasions, which may be used to decipher the origins and long-term evolutionary characteristics of modern pathogenic viruses. Hepadnaviruses (Hepadnaviridae) are a family of small, partially double-stranded DNA viruses that include hepatitis B viruses. Here we report the discovery of endogenous hepadnaviruses in the genome of the zebra finch. We used a combination of cross-species analysis of orthologous insertions, molecular dating, and phylogenetic analyses to demonstrate that hepadnaviruses infiltrated repeatedly the germline genome of passerine birds. We provide evidence that some of the avian hepadnavirus integration events are at least 19 My old, which reveals a much deeper ancestry of Hepadnaviridae than could be inferred based on the coalescence times of modern hepadnaviruses. Furthermore, the remarkable sequence similarity between endogenous and extant avian hepadnaviruses (up to 75% identity) suggests that long-term substitution rates for these viruses are on the order of 10(-8) substitutions per site per year, which is a 1,000-fold slower than short-term rates estimated based on the sequences of circulating hepadnaviruses. Together, these results imply a drastic shift in our understanding of the time scale of hepadnavirus evolution, and suggest that the rapid evolutionary dynamics characterizing modern avian hepadnaviruses do not reflect their mode of evolution on a deep time scale. PMID

  6. Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology

    PubMed Central

    Hipsley, Christy A.; Müller, Johannes

    2014-01-01

    Molecular-based divergence dating methods, or molecular clocks, are the primary neontological tool for estimating the temporal origins of clades. While the appropriate use of vertebrate fossils as external clock calibrations has stimulated heated discussions in the paleontological community, less attention has been given to the quality and implementation of other calibration types. In lieu of appropriate fossils, many studies rely on alternative sources of age constraints based on geological events, substitution rates and heterochronous sampling, as well as dates secondarily derived from previous analyses. To illustrate the breadth and frequency of calibration types currently employed, we conducted a literature survey of over 600 articles published from 2007 to 2013. Over half of all analyses implemented one or more fossil dates as constraints, followed by geological events and secondary calibrations (15% each). Vertebrate taxa were subjects in nearly half of all studies, while invertebrates and plants together accounted for 43%, followed by viruses, protists and fungi (3% each). Current patterns in calibration practices were disproportionate to the number of discussions on their proper use, particularly regarding plants and secondarily derived dates, which are both relatively neglected in methodological evaluations. Based on our survey, we provide a comprehensive overview of the latest approaches in clock calibration, and outline strengths and weaknesses associated with each. This critique should serve as a call to action for researchers across multiple communities, particularly those working on clades for which fossil records are poor, to develop their own guidelines regarding selection and implementation of alternative calibration types. This issue is particularly relevant now, as time-calibrated phylogenies are used for more than dating evolutionary origins, but often serve as the backbone of investigations into biogeography, diversity dynamics and rates of

  7. Xenopus in Space and Time: Fossils, Node Calibrations, Tip-Dating, and Paleobiogeography.

    PubMed

    Cannatella, David

    2015-01-01

    Published data from DNA sequences, morphology of 11 extant and 15 extinct frog taxa, and stratigraphic ranges of fossils were integrated to open a window into the deep-time evolution of Xenopus. The ages and morphological characters of fossils were used as independent datasets to calibrate a chronogram. We found that DNA sequences, either alone or in combination with morphological data and fossils, tended to support a close relationship between Xenopus and Hymenochirus, although in some analyses this topology was not significantly better than the Pipa + Hymenochirus topology. Analyses that excluded DNA data found strong support for the Pipa + Hymenochirus tree. The criterion for selecting the maximum age of the calibration prior influenced the age estimates, and our age estimates of early divergences in the tree of frogs are substantially younger than those of published studies. Node-dating and tip-dating calibrations, either alone or in combination, yielded older dates for nodes than did a root calibration alone. Our estimates of divergence times indicate that overwater dispersal, rather than vicariance due to the splitting of Africa and South America, may explain the presence of Xenopus in Africa and its closest fossil relatives in South America. PMID:26279165

  8. A multi-calibrated mitochondrial phylogeny of extant Bovidae (Artiodactyla, Ruminantia) and the importance of the fossil record to systematics

    PubMed Central

    2013-01-01

    Background Molecular phylogenetics has provided unprecedented resolution in the ruminant evolutionary tree. However, molecular age estimates using only one or a few (often misapplied) fossil calibration points have produced a diversity of conflicting ages for important evolutionary events within this clade. I here identify 16 fossil calibration points of relevance to the phylogeny of Bovidae and Ruminantia and use these, individually and together, to construct a dated molecular phylogeny through a reanalysis of the full mitochondrial genome of over 100 ruminant species. Results The new multi-calibrated tree provides ages that are younger overall than found in previous studies. Among these are young ages for the origin of crown Ruminantia (39.3–28.8 Ma), and crown Bovidae (17.3–15.1 Ma). These are argued to be reasonable hypotheses given that many basal fossils assigned to these taxa may in fact lie on the stem groups leading to the crown clades, thus inflating previous age estimates. Areas of conflict between molecular and fossil dates do persist, however, especially with regard to the base of the rapid Pecoran radiation and the sister relationship of Moschidae to Bovidae. Results of the single-calibrated analyses also show that a very wide range of molecular age estimates are obtainable using different calibration points, and that the choice of calibration point can influence the topology of the resulting tree. Compared to the single-calibrated trees, the multi-calibrated tree exhibits smaller variance in estimated ages and better reflects the fossil record. Conclusions The use of a large number of vetted fossil calibration points with soft bounds is promoted as a better approach than using just one or a few calibrations, or relying on internal-congruency metrics to discard good fossil data. This study also highlights the importance of considering morphological and ecological characteristics of clades when delimiting higher taxa. I also illustrate how

  9. Multi-locus fossil-calibrated phylogeny of Atheriniformes (Teleostei, Ovalentaria).

    PubMed

    Campanella, Daniela; Hughes, Lily C; Unmack, Peter J; Bloom, Devin D; Piller, Kyle R; Ortí, Guillermo

    2015-05-01

    Phylogenetic relationships among families within the order Atheriniformes have been difficult to resolve on the basis of morphological evidence. Molecular studies so far have been fragmentary and based on a small number taxa and loci. In this study, we provide a new phylogenetic hypothesis based on sequence data collected for eight molecular markers for a representative sample of 103 atheriniform species, covering 2/3 of the genera in this order. The phylogeny is calibrated with six carefully chosen fossil taxa to provide an explicit timeframe for the diversification of this group. Our results support the subdivision of Atheriniformes into two suborders (Atherinopsoidei and Atherinoidei), the nesting of Notocheirinae within Atherinopsidae, and the monophyly of tribe Menidiini, among others. We propose taxonomic changes for Atherinopsoidei, but a few weakly supported nodes in our phylogeny suggests that further study is necessary to support a revised taxonomy of Atherinoidei. The time-calibrated phylogeny was used to infer ancestral habitat reconstructions to explain the current distribution of marine and freshwater taxa. Based on these results, the current distribution of Atheriniformes is likely due to widespread marine dispersal along the margins of continents, infrequent trans-oceanic dispersal, and repeated invasion of freshwater habitats. This conclusion is supported by post-Gondwanan divergence times among families within the order, and a high probability of a marine ancestral habitat. PMID:25769409

  10. An evaluation of fossil tip-dating versus node-age calibrations in tetraodontiform fishes (Teleostei: Percomorphaceae).

    PubMed

    Arcila, Dahiana; Alexander Pyron, R; Tyler, James C; Ortí, Guillermo; Betancur-R, Ricardo

    2015-01-01

    Time-calibrated phylogenies based on molecular data provide a framework for comparative studies. Calibration methods to combine fossil information with molecular phylogenies are, however, under active development, often generating disagreement about the best way to incorporate paleontological data into these analyses. This study provides an empirical comparison of the most widely used approach based on node-dating priors for relaxed clocks implemented in the programs BEAST and MrBayes, with two recently proposed improvements: one using a new fossilized birth-death process model for node dating (implemented in the program DPPDiv), and the other using a total-evidence or tip-dating method (implemented in MrBayes and BEAST). These methods are applied herein to tetraodontiform fishes, a diverse group of living and extinct taxa that features one of the most extensive fossil records among teleosts. Previous estimates of time-calibrated phylogenies of tetraodontiforms using node-dating methods reported disparate estimates for their age of origin, ranging from the late Jurassic to the early Paleocene (ca. 150-59Ma). We analyzed a comprehensive dataset with 16 loci and 210 morphological characters, including 131 taxa (95 extant and 36 fossil species) representing all families of fossil and extant tetraodontiforms, under different molecular clock calibration approaches. Results from node-dating methods produced consistently younger ages than the tip-dating approaches. The older ages inferred by tip dating imply an unlikely early-late Jurassic (ca. 185-119Ma) origin for this order and the existence of extended ghost lineages in their fossil record. Node-based methods, by contrast, produce time estimates that are more consistent with the stratigraphic record, suggesting a late Cretaceous (ca. 86-96Ma) origin. We show that the precision of clade age estimates using tip dating increases with the number of fossils analyzed and with the proximity of fossil taxa to the node under

  11. Notes on the birth-death prior with fossil calibrations for Bayesian estimation of species divergence times.

    PubMed

    Dos Reis, Mario

    2016-07-19

    Constructing a multi-dimensional prior on the times of divergence (the node ages) of species in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining different sources of information such as a speciation process with fossil calibration densities. Yang & Rannala (2006 Mol. Biol. Evol 23, 212-226. (doi:10.1093/molbev/msj024)) laid out the general approach to combine the birth-death process with arbitrary fossil-based densities to construct a prior on divergence times. They achieved this by calculating the density of node ages without calibrations conditioned on the ages of the calibrated nodes. Here, I show that the conditional density obtained by Yang & Rannala is misspecified. The misspecified density can sometimes be quite strange-looking and can lead to unintentionally informative priors on node ages without fossil calibrations. I derive the correct density and provide a few illustrative examples. Calculation of the density involves a sum over a large set of labelled histories, and so obtaining the density in a computer program seems hard at the moment. A general algorithm that may provide a way forward is given.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. PMID:27325826

  12. Phylogenetic Analysis of Pelecaniformes (Aves) Based on Osteological Data: Implications for Waterbird Phylogeny and Fossil Calibration Studies

    PubMed Central

    Smith, Nathan D.

    2010-01-01

    Background Debate regarding the monophyly and relationships of the avian order Pelecaniformes represents a classic example of discord between morphological and molecular estimates of phylogeny. This lack of consensus hampers interpretation of the group's fossil record, which has major implications for understanding patterns of character evolution (e.g., the evolution of wing-propelled diving) and temporal diversification (e.g., the origins of modern families). Relationships of the Pelecaniformes were inferred through parsimony analyses of an osteological dataset encompassing 59 taxa and 464 characters. The relationships of the Plotopteridae, an extinct family of wing-propelled divers, and several other fossil pelecaniforms (Limnofregata, Prophaethon, Lithoptila, ?Borvocarbo stoeffelensis) were also assessed. The antiquity of these taxa and their purported status as stem members of extant families makes them valuable for studies of higher-level avian diversification. Methodology/Principal Findings Pelecaniform monophyly is not recovered, with Phaethontidae recovered as distantly related to all other pelecaniforms, which are supported as a monophyletic Steganopodes. Some anatomical partitions of the dataset possess different phylogenetic signals, and partitioned analyses reveal that these discrepancies are localized outside of Steganopodes, and primarily due to a few labile taxa. The Plotopteridae are recovered as the sister taxon to Phalacrocoracoidea, and the relationships of other fossil pelecaniforms representing key calibration points are well supported, including Limnofregata (sister taxon to Fregatidae), Prophaethon and Lithoptila (successive sister taxa to Phaethontidae), and ?Borvocarbo stoeffelensis (sister taxon to Phalacrocoracidae). These relationships are invariant when ‘backbone’ constraints based on recent avian phylogenies are imposed. Conclusions/Significance Relationships of extant pelecaniforms inferred from morphology are more congruent with

  13. A reappraisal of the evolution of Asian snakehead fishes (Pisces, Channidae) using molecular data from multiple genes and fossil calibration.

    PubMed

    Adamson, Eleanor A S; Hurwood, David A; Mather, Peter B

    2010-08-01

    Freshwater snakehead fishes (Channidae) provide an interesting target for phylogenetic analysis for the following reasons, their unusual biology, potential for cryptic diversity and availability of a good fossil record. Here, a multi-locus molecular phylogeny was constructed and calibrated using two fossil dates to estimate divergence times within the family. Sampling aimed to explore interspecific divergence of Channa species across Southeast Asia and intra-specific variation where species possessed natural geographical ranges that were extensive. Results contradict divergence times estimated previously independently from single locus mitochondrial data or the fossil record and suggest that after divergence from African taxa 40-50 Ma, evolution of Asian snakeheads has been heavily influenced by multiple broad scale dispersal events across India and Southeast Asia. A similar pattern of divergence within multiple clades suggests that west-east dispersal was limited for many taxa during the Miocene. Deep intra-specific divergence was inferred for C. striata, indicating that long historical periods of isolation ( approximately 8Ma) have not resulted in the evolution of reproductive isolation within this species. Results support suggestions that C. marulia like fishes in northern Cambodia may constitute an undescribed species, and that Indian C. diplogramma warrants taxonomic recognition as being distinct from Southeast Asian C. micropeltes, with the two taxa last sharing a common ancestor in the mid- to late-Miocene. PMID:20359539

  14. Colonization and diversification in the African 'sky islands': insights from fossil-calibrated molecular dating of Lychnis (Caryophyllaceae).

    PubMed

    Gizaw, Abel; Brochmann, Christian; Nemomissa, Sileshi; Wondimu, Tigist; Masao, Catherine Aloyce; Tusiime, Felly Mugizi; Abdi, Ahmed Abdikadir; Oxelman, Bengt; Popp, Magnus; Dimitrov, Dimitar

    2016-07-01

    The flora on the isolated high African mountains or 'sky islands' is remarkable for its peculiar adaptations, local endemism and striking biogeographical connections to remote parts of the world. Ages of the plant lineages and the timing of their radiations have frequently been debated but remain contentious as there are few estimates based on explicit models and fossil-calibrated molecular clocks. We used the plastid region maturaseK (matK) and a Caryophylloflora paleogenica fossil to infer the age of the genus Lychnis, and constructed a data set of three plastid (matK; a ribosomal protein S16 (rps16); and an intergenic spacer (psbE-petL)) and two nuclear (internal transcribed spacer (ITS) and a region spanning exon 18-24 in the second largest subunit of RNA polymerase II (RPB2)) loci for joint estimation of the species tree and divergence time of the African representatives. The time of divergence of the African high-altitude Lychnis was placed in the late Miocene to early Pliocene. A single speciation event was inferred in the early Pliocene; subsequent speciation took place sporadically from the late Pliocene to the middle Pleistocene. We provide further support for a Eurasian origin of the African 'sky islands' floral elements, which seem to have been recruited via dispersals at different times: some old, as in Lychnis, and others very recent. We show that dispersal and diversification within Africa play an important role in shaping these isolated plant communities. PMID:27037925

  15. A rich fossil record yields calibrated phylogeny for Acanthaceae (Lamiales) and evidence for marked biases in timing and directionality of intercontinental disjunctions.

    PubMed

    Tripp, Erin A; McDade, Lucinda A

    2014-09-01

    More than a decade of phylogenetic research has yielded a well-sampled, strongly supported hypothesis of relationships within the large ( > 4000 species) plant family Acanthaceae. This hypothesis points to intriguing biogeographic patterns and asymmetries in sister clade diversity but, absent a time-calibrated estimate for this evolutionary history, these patterns have remained unexplored. Here, we reconstruct divergence times within Acanthaceae using fossils as calibration points and experimenting with both fossil selection and effects of invoking a maximum age prior related to the origin of Eudicots. Contrary to earlier reports of a paucity of fossils of Lamiales (an order of ∼ 23,000 species that includes Acanthaceae) and to the expectation that a largely herbaceous to soft-wooded and tropical lineage would have few fossils, we recovered 51 reports of fossil Acanthaceae. Rigorous evaluation of these for accurate identification, quality of age assessment and utility in dating yielded eight fossils judged to merit inclusion in analyses. With nearly 10 kb of DNA sequence data, we used two sets of fossils as constraints to reconstruct divergence times. We demonstrate differences in age estimates depending on fossil selection and that enforcement of maximum age priors substantially alters estimated clade ages, especially in analyses that utilize a smaller rather than larger set of fossils. Our results suggest that long-distance dispersal events explain present-day distributions better than do Gondwanan or northern land bridge hypotheses. This biogeographical conclusion is for the most part robust to alternative calibration schemes. Our data support a minimum of 13 Old World (OW) to New World (NW) dispersal events but, intriguingly, only one in the reverse direction. Eleven of these 13 were among Acanthaceae s.s., which comprises > 90% of species diversity in the family. Remarkably, if minimum age estimates approximate true history, these 11 events occurred within

  16. Multi-locus fossil-calibrated phylogeny, biogeography and a subgeneric revision of the Margaritiferidae (Mollusca: Bivalvia: Unionoida).

    PubMed

    Bolotov, Ivan N; Vikhrev, Ilya V; Bespalaya, Yulia V; Gofarov, Mikhail Y; Kondakov, Alexander V; Konopleva, Ekaterina S; Bolotov, Nikita N; Lyubas, Artyom A

    2016-10-01

    The taxonomy and biogeographic history of the bivalve family Margaritiferidae are controversial because previous molecular studies did not provide a well-resolved phylogenetic framework for these enigmatic freshwater mussels that have extensive but disjunct distribution in North America, Eurasia and North Africa. In this study, we present a new, fossil-calibrated phylogenetic hypothesis based on five molecular markers (∼4kb of total length) for ten species. Our results indicate that all recent margaritiferids are in the single genus, Margaritifera Schumacher, 1816. Additionally, we identified three relatively well-supported phylogenetic clades that are valid subgenera, i.e., Margaritifera s. str. (Holarctic), Margaritanopsis (=Cumberlandia) (southeast North America-southeast Asia disjunct) and Pseudunio (Mediterranean). We suggest that the crown lineage of the Margaritiferidae most likely originated in the Cretaceous (mean age 93Ma, 95% CI 66-126Ma). The combined results of ancestral area reconstructions based on the three different approaches (S-DIVA, DEC and S-DEC) showed that ancient vicariance events could have played an important role in speciation within the family. The rates of mitochondrial evolution of margaritiferids are notably slow, which may be associated with their longevity, long generation time and low metabolic rates. Our findings highlight the complex biogeographic history of the Margaritiferidae as an intermixing of ancient vicariance and dispersal events, which were most likely associated with some inland barriers, continental movements and a sea level dynamic. PMID:27444710

  17. Redundant 230Th/ 234U/ 238U, 231Pa/ 235U and 14C dating of fossil corals for accurate radiocarbon age calibration

    NASA Astrophysics Data System (ADS)

    Chiu, Tzu-Chien; Fairbanks, Richard G.; Mortlock, Richard A.; Cao, Li; Fairbanks, Todd W.; Bloom, Arthur L.

    2006-09-01

    230Th/ 234U/ 238U dating of fossil corals by mass spectrometry is remarkably precise, but some samples exposed to freshwater over thousands of years may gain and/or lose uranium and/or thorium and consequently yield inaccurate ages. Although a δ 234U initial value equivalent to modern seawater and modern corals has been an effective quality control criterion, for samples exposed to freshwater but having δ 234U initial values indistinguishable from modern seawater and modern corals, there remains a need for additional age validation in the most demanding applications such as the 14C calibration (Fairbanks et al., 2005. Radiocarbon calibration curve spanning 0 to 50,000 years BP based on paired 230Th/ 234U/ 238U and 14C dates on pristine corals. Quaternary Science Reviews 24(16-17), 1781-1796). In this paper we enhance screening criteria for fossil corals older than 30,000 years BP in the Fairbanks0805 radiocarbon calibration data set (Fairbanks et al., 2005) by measuring redundant 230Th/ 234U/ 238U and 231Pa/ 235U dates via multi-collector magnetic sector inductively coupled plasma mass spectrometry (MC-MS-ICPMS) using techniques described in Mortlock et al. (2005. 230Th/ 234U/ 238U and 231Pa/ 235U ages from a single fossil coral fragment by multi-collector magnetic-sector inductively coupled plasma mass spectrometry. Geochimica et Cosmochimica Acta 69(3), 649-657.). In our present study, we regard paired 231Pa/ 235U and 230Th/ 234U/ 238U ages concordant when the 231Pa/ 235U age (±2 σ) overlaps with the associated 230Th/ 234U/ 238U age (±2 σ). Out of a representative set of 11 Fairbanks0805 (Fairbanks et al., 2005) radiocarbon calibration coral samples re-measured in this study, nine passed this rigorous check on the accuracy of their 230Th/ 234U/ 238U ages. The concordancy observed between 230Th/ 234U/ 238U and 231Pa/ 235U dates provides convincing evidence to support closed system behavior of these fossil corals and validation of their 230Th/ 234U/ 238U

  18. New Eocene Coleoid (Cephalopoda) Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies

    PubMed Central

    Neige, Pascal; Lapierre, Hervé; Merle, Didier

    2016-01-01

    New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian) of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov.), Loliginidae (Loligo clarkei sp. nov.), and Ommastrephidae (genus indet.) families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data) indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya) but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a “knowledge bias” and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades. PMID:27192490

  19. New Eocene Coleoid (Cephalopoda) Diversity from Statolith Remains: Taxonomic Assignation, Fossil Record Analysis, and New Data for Calibrating Molecular Phylogenies.

    PubMed

    Neige, Pascal; Lapierre, Hervé; Merle, Didier

    2016-01-01

    New coleoid cephalopods are described from statolith remains from the Middle Eocene (Middle Lutetian) of the Paris Basin. Fifteen fossil statoliths are identified and assigned to the Sepiidae (Sepia boletzkyi sp. nov.,? Sepia pira sp. nov.), Loliginidae (Loligo clarkei sp. nov.), and Ommastrephidae (genus indet.) families. The sediments containing these fossils indicate permanent aquatic settings in the infralittoral domain. These sediments range in age from 46 Mya to 43 Mya. Analysis of the fossil record of statoliths (from findings described here, together with a review of previously published data) indicates marked biases in our knowledge. Fossil statoliths are known from as far back as the Early Jurassic (199.3 to 190.8 Mya) but surprisingly, to the best of our knowledge, no record occurs in the Cretaceous. This is a "knowledge bias" and clearly calls for further studies. Finally, we attempt to compare findings described here with fossils previously used to constrain divergence and/or diversification ages of some coleoid subclades in molecular phylogenies. This comparison clearly indicates that the new records detailed here will challenge some estimated divergence times of coleoid cephalopod subclades. PMID:27192490

  20. Calibration

    NASA Astrophysics Data System (ADS)

    Kunze, Hans-Joachim

    Commercial spectrographic systems are usually supplied with some wave-length calibration, but it is essential that the experimenter performs his own calibration for reliable measurements. A number of sources emitting well-known emission lines are available, and the best values of their wavelengths may be taken from data banks accessible on the internet. Data have been critically evaluated for many decades by the National Institute of Standards and Technology (NIST) of the USA [13], see also p. 3. Special data bases have been established by the astronomy and fusion communities (Appendix B).

  1. 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

  2. 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

  3. Age Estimates for the Buckwheat Family Polygonaceae Based on Sequence Data Calibrated by Fossils and with a Focus on the Amphi-Pacific Muehlenbeckia

    PubMed Central

    Kron, Kathleen A.

    2013-01-01

    The buckwheat family Polygonaceae is a diverse group of plants and is a good model for investigating biogeography, breeding systems, coevolution with symbionts such as ants and fungi, functional trait evolution, hybridization, invasiveness, morphological plasticity, pollen morphology and wood anatomy. The main goal of this study was to obtain age estimates for Polygonaceae by calibrating a Bayesian phylogenetic analysis, using a relaxed molecular clock with fossil data. Based on the age estimates, we also develop hypotheses about the historical biogeography of the Southern Hemisphere group Muehlenbeckia. We are interested in addressing whether vicariance or dispersal could account for the diversification of Muehlenbeckia, which has a “Gondwanan” distribution. Eighty-one species of Polygonaceae were analysed with MrBayes to infer species relationships. One nuclear (nrITS) and three chloroplast markers (the trnL-trnF spacer region, matK and ndhF genes) were used. The molecular data were also analysed with Beast to estimate divergence times. Seven calibration points including fossil pollen and a leaf fossil of Muehlenbeckia were used to infer node ages. Results of the Beast analyses indicate an age of 110.9 (exponential/lognormal priors)/118.7 (uniform priors) million years (Myr) with an uncertainty interval of (90.7–125.0) Myr for the stem age of Polygonaceae. This age is older than previously thought (Maastrichtian, approximately 65.5–70.6 Myr). The estimated divergence time for Muehlenbeckia is 41.0/41.6 (39.6–47.8) Myr and its crown clade is 20.5/22.3 (14.2–33.5) Myr old. Because the breakup of Gondwana occurred from 95–30 Myr ago, diversification of Muehlenbeckia is best explained by oceanic long-distance and maybe stepping-stone dispersal rather than vicariance. This study is the first to give age estimates for clades of Polygonaceae and functions as a jumping-off point for future studies on the historical biogeography of the family. PMID:23585884

  4. "Fossil" Forecasting.

    ERIC Educational Resources Information Center

    Brody, Michael J.; deOnis, Ann

    2001-01-01

    Presents a density study in which students calculate the density of limestone substrate to determine if the specimen contains any fossils. Explains how to make fossils and addresses national standards. (YDS)

  5. Marquee Fossils

    ERIC Educational Resources Information Center

    Clary, Renee; Wandersee, James

    2008-01-01

    Professors of an online graduate-level paleontology class developed the concept of marquee fossils--fossils that have one or more unique characteristics that capture the attention and direct observation of students. In the classroom, Marquee fossils integrate the geology, biology, and environmental science involved in the study of fossilized…

  6. Ediacara Fossils

    ERIC Educational Resources Information Center

    Science Teacher, 2005

    2005-01-01

    Now, a research team from Virginia Tech and Nanjing Institute of Geology and Paleontology has discovered uniquely well-preserved fossil forms from 550-million-year-old rocks of the Ediacaran Period. The research appears in the Proceedings of the National Academy of Sciences. The discovery of these unusually preserved fossils reveals unprecedented…

  7. Fossil Fuels.

    ERIC Educational Resources Information Center

    Crank, Ron

    This instructional unit is one of 10 developed by students on various energy-related areas that deals specifically with fossil fuels. Some topics covered are historic facts, development of fuels, history of oil production, current and future trends of the oil industry, refining fossil fuels, and environmental problems. Material in each unit may…

  8. Fossil spiders.

    PubMed

    Selden, Paul A; Penney, David

    2010-02-01

    Over the last three decades, the fossil record of spiders has increased from being previously biased towards Tertiary ambers and a few dubious earlier records, to one which reveals a much greater diversity in the Mesozoic, with many of the modern families present in that era, and with clearer evidence of the evolutionary history of the group. We here record the history of palaeoarachnology and the major breakthroughs which form the basis of studies on fossil spiders. Understanding the preservation and taphonomic history of spider fossils is crucial to interpretation of fossil spider morphology. We also review the more recent descriptions of fossil spiders and the effect these discoveries have had on the phylogenetic tree of spiders. We discuss some features of the evolutionary history of spiders and present ideas for future work. PMID:19961468

  9. Fossil Crinoids

    NASA Astrophysics Data System (ADS)

    Hess, Hans; Ausich, William I.; Brett, Carlton E.; Simms, Michael J.

    2003-01-01

    Crinoids have graced the oceans for more than 500 million years. Among the most attractive fossils, crinoids had a key role in the ecology of marine communities through much of the fossil record, and their remains are prominent rock forming constituents of many limestones. This is the first comprehensive volume to bring together their form and function, classification, evolutionary history, occurrence, preservation and ecology. The main part of the book is devoted to assemblages of intact fossil crinoids, which are described in their geological setting in twenty-three chapters ranging from the Ordovician to the Tertiary. The final chapter deals with living sea lilies and feather stars. The volume is exquisitely illustrated with abundant photographs and line drawings of crinoids from sites around the world. This authoritative account recreates a fascinating picture of fossil crinoids for paleontologists, geologists, evolutionary and marine biologists, ecologists and amateur fossil collectors.

  10. Fossil Crinoids

    NASA Astrophysics Data System (ADS)

    Hess, Hans; Ausich, William I.; Brett, Carlton E.; Simms, Michael J.

    1999-10-01

    Crinoids have graced the oceans for more than 500 million years. Among the most attractive fossils, crinoids had a key role in the ecology of marine communities through much of the fossil record, and their remains are prominent rock forming constituents of many limestones. This is the first comprehensive volume to bring together their form and function, classification, evolutionary history, occurrence, preservation and ecology. The main part of the book is devoted to assemblages of intact fossil crinoids, which are described in their geological setting in twenty-three chapters ranging from the Ordovician to the Tertiary. The final chapter deals with living sea lilies and feather stars. The volume is exquisitely illustrated with abundant photographs and line drawings of crinoids from sites around the world. This authoritative account recreates a fascinating picture of fossil crinoids for paleontologists, geologists, evolutionary and marine biologists, ecologists and amateur fossil collectors.

  11. Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

    PubMed Central

    Davis, James J.; Olsen, Gary J.

    2010-01-01

    Most genomes are heterogeneous in codon usage, so a codon usage study should start by defining the codon usage that is typical to the genome. Although this is commonly taken to be the genomewide average, we propose that the mode—the codon usage that matches the most genes—provides a more useful approximation of the typical codon usage of a genome. We provide a method for estimating the modal codon usage, which utilizes a continuous approximation to the number of matching genes and a simplex optimization. In a survey of bacterial and archaeal genomes, as many as 20% more of the genes in a given genome match the modal codon usage than the average codon usage. We use the mode to examine the evolution of the multireplicon genomes of Agrobacterium tumefaciens C58 and Borrelia burgdorferi B31. In A. tumefaciens, the circular and linear chromosomes are characterized by a common “chromosome-like” codon usage, whereas both plasmids share a distinct “plasmid-like” codon usage. In B. burgdorferi, in addition to different codon-usage biases on the leading and lagging strands of DNA replication found by McInerney (McInerney JO. 1998. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA. 95:10698–10703), we also detect a codon-usage similarity between linear plasmid lp38 and the leading strand of the chromosome and a high similarity among the cp32 family of plasmids. PMID:20018979

  12. Fossil Horses

    NASA Astrophysics Data System (ADS)

    MacFadden, Bruce J.

    1994-06-01

    The family Equidae have an extensive fossil record spanning the past 58 million years, and the evolution of the horse has frequently been used as a classic example of long-term evolution. In recent years, however, there have been many important discoveries of fossil horses, and these, in conjunction with such new methods as cladistics, and techniques such as precise geochronology, have allowed us to achieve a much greater understanding of the evolution and biology of this important group. This book synthesizes the large body of data and research relevant to an understanding of fossil horses from several disciplines including biology, geology and paleontology. Using horses as the central theme, the author weaves together in the text such topics as modern geochronology, paleobiogeography, climate change, evolution and extinction, functional morphology, and population biology during the Cenozoic period. This book will be exciting reading for researchers and graduate students in vertebrate paleontology, evolution, and zoology.

  13. Codon preferences in free-living microorganisms.

    PubMed Central

    Andersson, S G; Kurland, C G

    1990-01-01

    A popular interpretation of the major codon preference is that it reflects the operation of a regulatory device that controls the expression of individual proteins. In this popular model, rapidly translated codons are thought to promote the accumulation of the highly expressed proteins and slowly translated codons are thought to retard the expression of poorly expressed proteins. However, this widely accepted model is not supported by kinetic theory or by experimental results. A less fashionable model in which the major codon preference has nothing to do with the expression level of the individual proteins is forwarded. In this model, the major codon preference is viewed as a global strategy to support the efficient function of the translation system and thereby to maximize the growth rates of cells under favorable conditions. PMID:2194095

  14. 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.

  15. CodonPhyML: Fast Maximum Likelihood Phylogeny Estimation under Codon Substitution Models

    PubMed Central

    Gil, Manuel; Zoller, Stefan; Anisimova, Maria

    2013-01-01

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

  16. Di-codon Usage for Gene Classification

    NASA Astrophysics Data System (ADS)

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

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

  17. Codon usage trend in mitochondrial CYB gene.

    PubMed

    Uddin, Arif; Chakraborty, Supriyo

    2016-07-15

    Here we reported the pattern of codon usage and the factors which influenced the codon usage pattern in mitochondrial cytochrome B (MT-CYB) gene among pisces, aves and mammals. The F1 axis of correspondence analysis showed highly significant positive correlation with nucleobases A3, C and C3 and significant negative correlation with T and T3 while F2 of correspondence analysis showed significant positive correlation with C and C3 and significant negative correlation with A and A3. From the neutrality plot, it was evident that the GC12 was influenced by mutation pressure and natural selection with a ratio of 0.10/0.90=0.11 in pisces, 0.024/0.976=0.0245 in aves and in mammals 0.215/0.785=0.273, which indicated that the role of natural selection was more than mutation pressure on structuring the bases at the first and second codon positions. Natural selection played the major role; but compositional constraint and mutation pressure also played a significant role in codon usage pattern. Analysis of codon usage pattern has contributed to the better understanding of the mechanism of distribution of codons and the evolution of MT-CYB gene. PMID:27063508

  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. PMID:25303315

  19. The effect of context on synonymous codon usage in genes with low codon usage bias.

    PubMed Central

    Bulmer, M

    1990-01-01

    The effect of neighbouring bases on the usage of synonymous codons in genes with low codon usage bias in yeast and E. coli is examined. The codon adaptation index is employed to identify a group of genes in each organism with low codon usage bias, which are likely to be weakly expressed. A similar pattern is found in complementary sequences with respect to synonymous usage of A vs G or of U vs C. It is suggested that this may reflect an effect of context on mutation rates in weakly expressed genes. PMID:2190183

  20. 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

  1. 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

  2. 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.

  3. Are the oldest 'fossils', fossils

    NASA Technical Reports Server (NTRS)

    Schopf, J. W.

    1976-01-01

    A comparative statistical study has been carried out on populations of modern algae, Precambrian algal microfossils, the 'organized elements' of the Orgueil carbonaceous meteorite, and the oldest microfossil-like objects now known (spheroidal bodies from the Fig Tree and Onverwacht Groups of the Swaziland Supergroup, South Africa). The distribution patterns exhibited by the more than 3000 m.y.-old Swaziland microstructures bear considerable resemblance to those of the abiotic 'organized elements' but differ rather markedly from those exhibited by younger, assuredly biogenic, populations. Based on these comparisons, it is concluded that the Swaziland spheroids could be, at least in part, of nonbiologic origin; these oldest known fossil-like microstructures should not be regarded as constituting firm evidence of Archean life.

  4. Will My Fossil Float?

    ERIC Educational Resources Information Center

    Riesser, Sharon; Airey, Linda

    1993-01-01

    Explains how young students can be introduced to fossils. Suggests books to read and science activities including "Fossils to Eat" where students make fossils from peanut butter, honey, and powdered milk. (PR)

  5. Codon catalog usage and the genome hypothesis.

    PubMed Central

    Grantham, R; Gautier, C; Gouy, M; Mercier, R; Pavé, A

    1980-01-01

    Frequencies for each of the 61 amino acid codons have been determined in every published mRNA sequence of 50 or more codons. The frequencies are shown for each kind of genome and for each individual gene. A surprising consistency of choices exists among genes of the same or similar genomes. Thus each genome, or kind of genome, appears to possess a "system" for choosing between codons. Frameshift genes, however, have widely different choice strategies from normal genes. Our work indicates that the main factors distinguishing between mRNA sequences relate to choices among degenerate bases. These systematic third base choices can therefore be used to establish a new kind of genetic distance, which reflects differences in coding strategy. The choice patterns we find seem compatible with the idea that the genome and not the individual gene is the unit of selection. Each gene in a genome tends to conform to its species' usage of the codon catalog; this is our genome hypothesis. PMID:6986610

  6. 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

  7. Saccharomyces cerevisiae ribosomes recognize non-AUG initiation codons.

    PubMed Central

    Zitomer, R S; Walthall, D A; Rymond, B C; Hollenberg, C P

    1984-01-01

    A series of Saccharomyces cerevisiae plasmids and mutant derivatives containing fusions of the Escherichia coli galactokinase gene, galK, to the yeast iso-1-cytochrome c CYC1 transcription unit were used to study the sequences affecting the initiation of translation in S. cerevisiae. When the CYC1 AUG initiation codon preceded the galK AUG codon and coding sequence and either the two AUGs were out of frame with each other or a nonsense codon was located between them, the expression of the galK gene was extremely low. Deletion of the CYC1 AUG and its surrounding sequences resulted in a 100-fold increase in galK expression. This dependence of galK expression on the elimination of the CYC1 AUG codon was used to select mutations in that codon. Then the ability of these altered initiation codons to serve in translational initiation was determined by reconstruction of the CYC1 gene 3' to and in frame with them. Initiation was found to occur at the codons UUG and AUA, but not at the codons AAA and AUC. Furthermore the codon UUG, when preceded by an A three nucleotides upstream, served as a better initiation codon than when a U was substituted for the A. The efficiency of translation from these non-AUG codons was quantitated by using a CYC1/galK protein-coding fusion and measuring cellular galactokinase levels. Initiation at the UUG codon was 6.9% as efficient as initiation at the wild-type AUG codon when preceded by an A three nucleotides upstream, but was over 10-fold less efficient when a U was substituted for that A. Initiation at AUA was 0.5% as efficient as at AUG. The effects of the sequences preceding the initiation codon are discussed in light of these results. PMID:6390186

  8. The non-uniformity of fossil preservation.

    PubMed

    Holland, Steven M

    2016-07-19

    The fossil record provides the primary source of data for calibrating the origin of clades. Although minimum ages of clades are given by the oldest preserved fossil, these underestimate the true age, which must be bracketed by probabilistic methods based on multiple fossil occurrences. Although most of these methods assume uniform preservation rates, this assumption is unsupported over geological timescales. On geologically long timescales (more than 10 Myr), the origin and cessation of sedimentary basins, and long-term variations in tectonic subsidence, eustatic sea level and sedimentation rate control the availability of depositional facies that preserve the environments in which species lived. The loss of doomed sediments, those with a low probability of preservation, imparts a secular trend to fossil preservation. As a result, the fossil record is spatially and temporally non-uniform. Models of fossil preservation should reflect this non-uniformity by using empirical estimates of fossil preservation that are spatially and temporally partitioned, or by using indirect proxies of fossil preservation. Geologically, realistic models of preservation will provide substantially more reliable estimates of the origination of clades.This article is part of the themed issue 'Dating species divergences using rocks and clocks'. PMID:27325828

  9. Genome-wide analysis of codon usage bias in Ebolavirus.

    PubMed

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

    2015-01-22

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

  10. Evaluating Sense Codon Reassignment with a Simple Fluorescence Screen.

    PubMed

    Biddle, Wil; Schmitt, Margaret A; Fisk, John D

    2015-12-22

    Understanding the interactions that drive the fidelity of the genetic code and the limits to which modifications can be made without breaking the translational system has practical implications for understanding the molecular mechanisms of evolution as well as expanding the set of encodable amino acids, particularly those with chemistries not provided by Nature. Because 61 sense codons encode 20 amino acids, reassigning the meaning of sense codons provides an avenue for biosynthetic modification of proteins, furthering both fundamental and applied biochemical research. We developed a simple screen that exploits the absolute requirement for fluorescence of an active site tyrosine in green fluorescent protein (GFP) to probe the pliability of the degeneracy of the genetic code. Our screen monitors the restoration of the fluorophore of GFP by incorporation of a tyrosine in response to a sense codon typically assigned another meaning in the genetic code. We evaluated sense codon reassignment at four of the 21 sense codons read through wobble interactions in Escherichia coli using the Methanocaldococcus jannaschii orthogonal tRNA/aminoacyl tRNA synthetase pair originally developed and commonly used for amber stop codon suppression. By changing only the anticodon of the orthogonal tRNA, we achieved sense codon reassignment efficiencies between 1% (Phe UUU) and 6% (Lys AAG). Each of the orthogonal tRNAs preferentially decoded the codon traditionally read via a wobble interaction in E. coli with the exception of the orthogonal tRNA with an AUG anticodon, which incorporated tyrosine in response to both the His CAU and His CAC codons with approximately equal frequencies. We applied our screen in a high-throughput manner to evaluate a 10(9)-member combined tRNA/aminoacyl tRNA synthetase library to identify improved sense codon reassigning variants for the Lys AAG codon. A single rapid screen with the ability to broadly evaluate reassignable codons will facilitate

  11. 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

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

    PubMed Central

    2006-01-01

    Background Codon usage has direct utility in molecular characterization of species and is also a marker for molecular evolution. To understand codon usage within the diverse phylum Nematoda, we analyzed a total of 265,494 expressed sequence tags (ESTs) from 30 nematode species. The full genomes of Caenorhabditis elegans and C. briggsae were also examined. A total of 25,871,325 codons were analyzed and a comprehensive codon usage table for all species was generated. This is the first codon usage table available for 24 of these organisms. Results Codon usage similarity in Nematoda usually persists over the breadth of a genus but then rapidly diminishes even within each clade. Globodera, Meloidogyne, Pristionchus, and Strongyloides have the most highly derived patterns of codon usage. The major factor affecting differences in codon usage between species is the coding sequence GC content, which varies in nematodes from 32% to 51%. Coding GC content (measured as GC3) also explains much of the observed variation in the effective number of codons (R = 0.70), which is a measure of codon bias, and it even accounts for differences in amino acid frequency. Codon usage is also affected by neighboring nucleotides (N1 context). Coding GC content correlates strongly with estimated noncoding genomic GC content (R = 0.92). On examining abundant clusters in five species, candidate optimal codons were identified that may be preferred in highly expressed transcripts. Conclusion Evolutionary models indicate that total genomic GC content, probably the product of directional mutation pressure, drives codon usage rather than the converse, a conclusion that is supported by examination of nematode genomes. PMID:26271136

  13. Codon Usage Domains over Bacterial Chromosomes

    PubMed Central

    Bailly-Bechet, Marc; Danchin, Antoine; Iqbal, Mudassar; Marsili, Matteo; Vergassola, Massimo

    2006-01-01

    The geography of codon bias distributions over prokaryotic genomes and its impact upon chromosomal organization are analyzed. To this aim, we introduce a clustering method based on information theory, specifically designed to cluster genes according to their codon usage and apply it to the coding sequences of Escherichia coli and Bacillus subtilis. One of the clusters identified in each of the organisms is found to be related to expression levels, as expected, but other groups feature an over-representation of genes belonging to different functional groups, namely horizontally transferred genes, motility, and intermediary metabolism. Furthermore, we show that genes with a similar bias tend to be close to each other on the chromosome and organized in coherent domains, more extended than operons, demonstrating a role of translation in structuring bacterial chromosomes. It is argued that a sizeable contribution to this effect comes from the dynamical compartimentalization induced by the recycling of tRNAs, leading to gene expression rates dependent on their genomic and expression context. PMID:16683018

  14. Kinetics of Stop Codon Recognition by Release Factor 1

    PubMed Central

    Hetrick, Byron; Lee, Kristin; Joseph, Simpson

    2009-01-01

    Recognition of stop codons by class I release factors is a fundamental step in the termination phase of protein synthesis. Since premature termination is costly to the cell, release factors have to efficiently discriminate between stop and sense codons. In order to understand the mechanism of discrimination between stop and sense codons, we developed a new, pre-steady state kinetic assay to monitor the interaction of RF1 with the ribosome. Our results show that RF1 associates with similar association rate constants to ribosomes programmed with a stop or sense codons. However, dissociation of RF1 from sense codons is as much as three orders of magnitude faster than from stop codons. Interestingly, the affinity of RF1 for ribosomes programmed with different sense codons does not correlate with the defects in peptide release. Thus, discrimination against sense codons is achieved, both, by increasing the dissociation rates and by decreasing the rate of peptide release. These results suggest that sense codons inhibit conformational changes necessary for RF1 to stably bind to the ribosome and catalyze peptide release. PMID:19874047

  15. Comparative context analysis of codon pairs on an ORFeome scale

    PubMed Central

    Moura, Gabriela; Pinheiro, Miguel; Silva, Raquel; Miranda, Isabel; Afreixo, Vera; Dias, Gaspar; Freitas, Adelaide; Oliveira, José L; Santos, Manuel AS

    2005-01-01

    Codon context is an important feature of gene primary structure that modulates mRNA decoding accuracy. We have developed an analytical software package and a graphical interface for comparative codon context analysis of all the open reading frames in a genome (the ORFeome). Using the complete ORFeome sequences of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans and Escherichia coli, we show that this methodology permits large-scale codon context comparisons and provides new insight on the rules that govern the evolution of codon-pair context. PMID:15774029

  16. A computer program to display codon changes caused by mutagenesis.

    PubMed

    Sirotkin, K

    1988-04-01

    A FORTRAN program for displaying the correspondence between codon changes and different possible base changes is presented. Changes of both single bases and dimers are considered. The user can specify the mutagenesis spectrum. Additionally, the user can choose whether or not to consider single or double events in a codon and whether or not to consider the possibility that the change of two bases (a dimer) can overlap a codon boundary. Furthermore, a variety of ways may be chosen to display and summarize the codon changes that can result from the specified mutagenesis. A user-supplied sequence or the genetic code table can be analyzed. PMID:3167596

  17. Fossilized bioelectric wire - the trace fossil Trichichnus

    NASA Astrophysics Data System (ADS)

    Kędzierski, M.; Uchman, A.; Sawlowicz, Z.; Briguglio, A.

    2015-04-01

    The trace fossil Trichichnus is proposed as an indicator of fossil bioelectric bacterial activity at the oxic-anoxic interface zone of marine sediments. This fulfils the idea that such processes, commonly found in the modern realm, should be also present in the geological past. Trichichnus is an exceptional trace fossil due to its very thin diameter (mostly less than 1 mm) and common pyritic filling. It is ubiquitous in some fine-grained sediments, where it has been interpreted as a burrow formed deeper than any other trace fossils, below the redox boundary. Trichichnus, formerly referred to as deeply burrowed invertebrates, has been found as remnant of a fossilized intrasediment bacterial mat that is pyritized. As visualized in 3-D by means of X-ray computed microtomography scanner, Trichichnus forms dense filamentous fabric, which reflects that it is produced by modern large, mat-forming, sulfide-oxidizing bacteria, belonging mostly to Thioploca-related taxa, which are able to house a complex bacterial consortium. Several stages of Trichichnus formation, including filamentous, bacterial mat and its pyritization, are proposed to explain an electron exchange between oxic and suboxic/anoxic layers in the sediment. Therefore, Trichichnus can be considered a fossilized "electric wire".

  18. 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

  19. Nonsense codons trigger an RNA partitioning shift.

    PubMed

    Bhalla, Angela D; Gudikote, Jayanthi P; Wang, Jun; Chan, Wai-Kin; Chang, Yao-Fu; Olivas, O Renee; Wilkinson, Miles F

    2009-02-13

    T-cell receptor-beta (TCRbeta) genes naturally acquire premature termination codons (PTCs) as a result of programmed gene rearrangements. PTC-bearing TCRbeta transcripts are dramatically down-regulated to protect T-cells from the deleterious effects of the truncated proteins that would otherwise be produced. Here we provide evidence that two responses collaborate to elicit this dramatic down-regulation. One is rapid mRNA decay triggered by the nonsense-mediated decay (NMD) RNA surveillance pathway. We demonstrate that this occurs in highly purified nuclei lacking detectable levels of three different cytoplasmic markers, but containing an outer nuclear membrane marker, suggesting that decay occurs either in the nucleoplasm or at the outer nuclear membrane. The second response is a dramatic partitioning shift in the nuclear fraction-to-cytoplasmic fraction mRNA ratio that results in few TCRbeta transcripts escaping to the cytoplasmic fraction of cells. Analysis of TCRbeta mRNA kinetics after either transcriptional repression or induction suggested that this nonsense codon-induced partitioning shift (NIPS) response is not the result of cytoplasmic NMD but instead reflects retention of PTC(+) TCRbeta mRNA in the nuclear fraction of cells. We identified TCRbeta sequences crucial for NIPS but found that NIPS is not exclusively a property of TCRbeta transcripts, and we identified non-TCRbeta sequences that elicit NIPS. RNA interference experiments indicated that NIPS depends on the NMD factors UPF1 and eIF4AIII but not the NMD factor UPF3B. We propose that NIPS collaborates with NMD to retain and degrade a subset of PTC(+) transcripts at the outer nuclear membrane and/or within the nucleoplasm. PMID:19091751

  20. [Codon usage bias in the straw mushroom Volvariella volvacea].

    PubMed

    Jiang, Wei; Lü, Beibei; He, Jianhua; Wang, Jinbin; Wu, Xiao; Wu, Guogan; Bao, Dapeng; Chen, Mingjie; Zhang, Jinsong; Tan, Qi; Tang, Xueming

    2014-09-01

    We analyzed the whole genome coding sequence of Volvariella volvacea to study the pattern utilization of codons by Codon W 1.4.2. As results, 24 optimal codons were identified. Moreover, the frequency of codons usage was calculated by CUSP program. We compared the frequency of codons usage of V. volvacea with other organisms including 6 modal value species (Homo sapiens, Saccharomys cerevisiae, Arabidopsis thalian, Mus musculus, Danio rerio and Drosophila melanogaster) and 4 edible fungi (Coprinopsis cinerea, Agaricus bisporus, Lentinula edodes and Pleurotus ostreatus). We found that there were less differences in 3 edible fungi (excluding Pleurotus ostreatus) than 6 modal value species, comparing with the frequency of codons usage of V. volvacea. With software SPSS16.0, cluster analysis which showed differences in the size of codon bias, reflects the evolutionary relationships between species, which can be used as a reference of evolutionary relationships of species. This was the first time for analysis the codon preference among the whole coding sequences of edible fungi, serving as theoretical basis to apply genetic engineering of V. volvacea. PMID:25720157

  1. 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

  2. Modes of fossil preservation

    USGS Publications Warehouse

    Schopf, J.M.

    1975-01-01

    The processes of geologic preservation are important for understanding the organisms represented by fossils. Some fossil differences are due to basic differences in organization of animals and plants, but the interpretation of fossils has also tended to be influenced by modes of preservation. Four modes of preservation generally can be distinguished: (1) Cellular permineralization ("petrifaction") preserves anatomical detail, and, occasionally, even cytologic structures. (2) Coalified compression, best illustrated by structures from coal but characteristic of many plant fossils in shale, preserves anatomical details in distorted form and produces surface replicas (impressions) on enclosing matrix. (3) Authigenic preservation replicates surface form or outline (molds and casts) prior to distortion by compression and, depending on cementation and timing, may intergrade with fossils that have been subject to compression. (4) Duripartic (hard part) preservation is characteristic of fossil skeletal remains, predominantly animal. Molds, pseudomorphs, or casts may form as bulk replacements following dissolution of the original fossil material, usually by leaching. Classification of the kinds of preservation in fossils will aid in identifying the processes responsible for modifying the fossil remains of both animals and plants. ?? 1975.

  3. 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

  4. 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

  5. Restoring Fossil Creek

    ERIC Educational Resources Information Center

    Flaccus, Kathleen; Vlieg, Julie; Marks, Jane C.; LeRoy, Carri J.

    2004-01-01

    Fossil Creek had been dammed for the past 90 years, and plans were underway to restore the stream. The creek runs through Central Arizona and flows from the high plateaus to the desert, cutting through the same formations that form the Grand Canyon. This article discusses the Fossil Creek monitoring project. In this project, students and teachers…

  6. 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

  7. 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

  8. Premature termination codons in modern human genomes.

    PubMed

    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. Calibration age and quartet divergence date estimation.

    PubMed

    Brochu, Christopher A

    2004-06-01

    The date of a single divergence point--between living alligators and crocodiles--was estimated with quartet dating using calibrations of widely divergent ages. For five mitochondrial sequence datasets, there is a clear relationship between calibration age and quartet estimate--quartets based on two relatively recent calibrations support younger divergence estimates than do quartets based on two older calibrations. Some of the estimates supported by young quartets are impossibly young and exclude the first appearance of the group in the fossil record as too old. The older estimates--those based on two relatively old calibrations--may be overestimates, and those based on one old and one recent calibration support divergence estimates very close to fossil data. This suggests that quartet dating methods may be most effective when calibrations are applied from different parts of a clade's history. PMID:15266985

  11. Fossil fuels -- future fuels

    SciTech Connect

    1998-03-01

    Fossil fuels -- coal, oil, and natural gas -- built America`s historic economic strength. Today, coal supplies more than 55% of the electricity, oil more than 97% of the transportation needs, and natural gas 24% of the primary energy used in the US. Even taking into account increased use of renewable fuels and vastly improved powerplant efficiencies, 90% of national energy needs will still be met by fossil fuels in 2020. If advanced technologies that boost efficiency and environmental performance can be successfully developed and deployed, the US can continue to depend upon its rich resources of fossil fuels.

  12. 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

  13. Genetic Code Expansion by Degeneracy Reprogramming of Arginyl Codons.

    PubMed

    Lee, Ki Baek; Hou, Chen Yuan; Kim, Chae-Eun; Kim, Dong-Myung; Suga, Hiroaki; Kang, Taek Jin

    2016-07-01

    The genetic code in most organisms codes for 20 proteinogenic amino acids or translation stop. In order to encode more than 20 amino acids in the coding system, one of stop codons is usually reprogrammed to encode a non-proteinogenic amino acid. Although this approach works, usually only one amino acid is added to the amino acid repertoire. In this study, we incorporated non-proteinogenic amino acids into a protein by using a sense codon. As all the codons are allocated in the universal genetic code, we destroyed all the tRNA(Arg) in a cell-free protein synthesis system by using a tRNA(Arg) -specific tRNase, colicin D. Then by supplementing the system with tRNACCU , the translation system was partially restored. Through this creative destruction, reprogrammable codons were successfully created in the system to encode modified lysines along with the 20 proteinogenic amino acids. PMID:27151886

  14. Mononucleotide and dinucleotide frequencies, and codon usage in poliovirion RNA.

    PubMed Central

    Rothberg, P G; Wimmer, E

    1981-01-01

    The polio type 1 (Mahoney) RNA sequence (1) has been analyzed in terms of the distribution of its mononucleotides, dinucleotides and trinucleotides (codons). The distribution of adenosine in the sequence is nonuniform, being lower at the 5' end and higher at the 3' end. The dinucleotide CG is relatively rare and the dinucleotides UG and CA are relatively more common than expected. Codon usage is decidedly nonrandom. Codons containing CG are avoided and those ending in adenosine are favored. The asymmetric use of mononucleotides, dinucleotides and codons in polio RNA is unexplained at the present time although the lowered CG frequency may be the result of a DNA origin for polio RNA. PMID:6275352

  15. 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

  16. 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

  17. The Effect of Codon Mismatch on the Protein Translation System

    PubMed Central

    Cao, Liaoran; Li, Guohui; Cheng, Hong

    2016-01-01

    Incorrect protein translation, caused by codon mismatch, is an important problem of living cells. In this work, a computational model was introduced to quantify the effects of codon mismatch and the model was used to study the protein translation of Saccharomyces cerevisiae. According to simulation results, the probability of codon mismatch will increase when the supply of amino acids is unbalanced, and the longer is the codon sequence, the larger is the probability for incorrect translation to occur, making the synthesis of long peptide chain difficult. By comparing to simulation results without codon mismatch effects taken into account, the fraction of mRNAs with bound ribosome decrease faster along the mRNAs, making the 5’ ramp phenomenon more obvious. It was also found in our work that the premature mechanism resulted from codon mismatch can reduce the proportion of incorrect translation when the amino acid supply is extremely unbalanced, which is one possible source of high fidelity protein synthesis after peptidyl transfer. PMID:26840415

  18. Enhanced expression of codon optimized interferon gamma in CHO cells.

    PubMed

    Chung, Bevan Kai-Sheng; Yusufi, Faraaz N K; Mariati; Yang, Yuansheng; Lee, Dong-Yup

    2013-09-10

    The human interferon-gamma (IFN-γ) is a potential drug candidate for treating various diseases due to its immunomodulatory properties. The efficient production of this protein can be achieved through a popular industrial host, Chinese hamster ovary (CHO) cells. However, recombinant expression of foreign proteins is typically suboptimal possibly due to the usage of non-native codon patterns within the coding sequence. Therefore, we demonstrated the application of a recently developed codon optimization approach to design synthetic IFN-γ coding sequences for enhanced heterologous expression in CHO cells. For codon optimization, earlier studies suggested to establish the target usage distribution pattern in terms of selected design parameters such as individual codon usage (ICU) and codon context (CC), mainly based on the host's highly expressed genes. However, our RNA-Seq based transcriptome profiling indicated that the ICU and CC distribution patterns of different gene expression classes in CHO cell are relatively similar, unlike other microbial expression hosts, Escherichia coli and Saccharomyces cerevisiae. This finding was further corroborated through the in vivo expression of various ICU and CC optimized IFN-γ in CHO cells. Interestingly, the CC-optimized genes exhibited at least 13-fold increase in expression level compared to the wild-type IFN-γ while a maximum of 10-fold increase was observed for the ICU-optimized genes. Although design criteria based on individual codons, such as ICU, have been widely used for gene optimization, our experimental results suggested that codon context is relatively more effective parameter for improving recombinant IFN-γ expression in CHO cells. PMID:23876479

  19. Fossil Simulation in the Classroom

    ERIC Educational Resources Information Center

    Hoehn, Robert G.

    1977-01-01

    Describes classroom science demonstrations and experiments that simulate the process of fossil formation. Lists materials, procedures and suggestions for successful activities. Includes ten student activities (coral fossils, leaf fossils, leaf scars, carbonization, etc.). Describes a fossil game in which students work in pairs. (CS)

  20. Tooth Enamel Oxygen and Carbon Isotope Variations in Modern Central Asian Horses: Development of a Calibration Database for the Interpretation of Stable Isotope Signals Preserved in Fossil Horse Remains from Archaeological Sites

    NASA Astrophysics Data System (ADS)

    Sikora, M. T.; Rosenmeier, M. F.; Allard, F.; Olsen, S. L.

    2005-12-01

    Recent studies of early nomadic pastoralism within Central Asia have focused on the rich archaeological history of Mongolia and specifically the examination of so-called khirigsuur sites. These monumental Bronze Age (first and second millennium B.C.) structures consist of stone constructions that contain abundant horse remains (typically skulls) and occasionally human burials. Isotopic analysis of horse remains preserved within these sites may provide a wealth of paleoclimatic information. However, the accuracy of climate reconstructions from fossil teeth collected at archaeological sites in Mongolia is currently limited by insufficient knowledge of the relationship between local environmental conditions and tooth enamel isotope ratios as well as uncertainties attributed to intra-population variability. In this study we measured the oxygen and carbon isotope (δ18O and δ13C) values of enamel samples from modern horse teeth collected along a nearly 550 km latitudinal (northwest-southeast) transect within central Mongolia. Preliminary results suggest that modern tooth enamel records local environmental conditions, although δ18O and δ13C values are not always a direct proxy for climate and vegetation cover. The modern samples serve as a baseline for interpreting isotope signals preserved in fossil horses and thereby increase the accuracy of paleoclimatic reconstructions. Approximately one-hundred individuals were examined from highly varied geographic zones (forest steppe, grassland steppe, dry steppe, and semi-desert) and compared with the δ18O of meteoric waters and δ13C values of local vegetation. Oxygen isotope ratios of bulk enamel samples (spanning the entire vertical axis of tooth growth) parallel spatial trends observed in isotopic composition of meteoric waters and major north-south gradients in temperature and precipitation. Average δ13C values similarly increase with decreasing geographic latitude and likely correspond to documented increases in the

  1. 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

  2. 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

  3. 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

  4. Fossilization of feathers

    NASA Astrophysics Data System (ADS)

    Davis, Paul G.; Briggs, Derek E. G.

    1995-09-01

    Scanning electron microscopy of feathers has revealed evidence that a bacterial glycocalyx (a network of exocellular polysaccharide fibers) played a role in promoting their fossilization in some cases. This mode of preservation has not been reported in other soft tissues. The majority of fossil feathers are preserved as carbonized traces. More rarely, bacteria on the surface are replicated by authigenic minerals (bacterial autolithification). The feathers of Archaeopteryx are preserved mainly by imprintation following early lithification of the substrate and decay of the feather. Lacustrine settings provide the most important taphonomic window for feather preservation. Preservation in terrestrial and normal-marine settings involves very different processes (in amber and in authigenically mineralized coprolites, respectively). Therefore, there may be a significant bias in the avian fossil record in favor of inland water habitats.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. A backtranslation method based on codon usage strategy.

    PubMed Central

    Pesole, G; Attimonelli, M; Liuni, S

    1988-01-01

    This study describes a method for the backtranslation of an aminoacidic sequence, an extremely useful tool for various experimental approaches. It involves two computer programs CLUSTER and BACKTR written in Fortran 77 running on a VAX/VMS computer. CLUSTER generates a reliable codon usage table through a cluster analysis, based on a chi 2-like distance between the sequences. BACKTR produces backtranslated sequences according to different options when use is made of the codon usage table obtained in addition to selecting the least ambiguous potential oligonucleotide probes within an aminoacidic sequence. The method was tested by applying it to 158 yeast genes. PMID:3281142

  10. Trace Fossil Analysis

    NASA Astrophysics Data System (ADS)

    Hasiotis, Stephen T.

    2009-05-01

    Today, the study of trace fossils—ichnology—is an important subdiscipline of geology at the interface of paleontology and sedimentology, mostly because of the efforts of Adolf Seilacher. His ability to synthesize various aspects of ichnology and produce a hierarchy of marine ichna and sedimentary facies has made ichnology useful worldwide in interpreting paleodiversity, rates of sedimentation, oxygenation of bottom water and sediment pore water, and depositional energy. Seilacher's book Trace Fossil Analysis provides a glimpse into the mind, methodology, and insights of the father of modern ichnology, generated from his course notes as a professor and a guest lecturer. The title sounds misleading—readers looking for up-to-date principles and approaches to trace fossil analysis in marine and continental strata will be disappointed. In his preface, however, Seilacher clearly gives direction for the use of his text: “This is a course book—meaning that it is intended to confer not knowledge, but skill.” Thus, it is not meant as a total compilation of all trace fossils, ichnotaxonomy, ichnological interpretations, applications, or the most relevant and up-to-date references. Rather, it takes the reader on a personal journey, explaining how trace fossils are understood in the context of their three-dimensional (3-D) morphology and sedimentary facies.

  11. Fossil-Fired Boilers

    Energy Science and Technology Software Center (ESTSC)

    1993-09-23

    Boiler Performance Model (BPM 3.0S) is a set of computer programs developed to analyze the performance of fossil-fired utility boilers. The programs can model a wide variety of boiler designs, and can model coal, oil, or natural gas firing. The programs are intended for use by engineers performing analyses of alternative fuels, alternative operating modes, or boiler modifications.

  12. Fossil-energy

    NASA Astrophysics Data System (ADS)

    1981-08-01

    Progress in the following areas of fossil energy is reported: physiochemical cleaning and recovery of fine coal; a systematic investigation of the organosulfur components in coal; microstructures of coal; rapid analysis of mineral content in coal; coal blending experiments; performance characteristics of heavy media cyclones using fly ash derived heavy media; briquetting solvent treated coal; and coal preparation and testing.

  13. Advanced fossil energy utilization

    SciTech Connect

    Shekhawat, D.; Berry, D.; Spivey, J.; Pennline, H.; Granite, E.

    2010-01-01

    This special issue of Fuel is a selection of papers presented at the symposium ‘Advanced Fossil Energy Utilization’ co-sponsored by the Fuels and Petrochemicals Division and Research and New Technology Committee in the 2009 American Institute of Chemical Engineers (AIChE) Spring National Meeting Tampa, FL, on April 26–30, 2009.

  14. Sustainability of Fossil Fuels

    NASA Astrophysics Data System (ADS)

    Lackner, K. S.

    2002-05-01

    For a sustainable world economy, energy is a bottleneck. Energy is at the basis of a modern, technological society, but unlike materials it cannot be recycled. Energy or more precisely "negentropy" (the opposite of entropy) is always consumed. Thus, one either accepts the use of large but finite resources or must stay within the limits imposed by dilute but self-renewing resources like sunlight. The challenge of sustainable energy is exacerbated by likely growth in world energy demand due to increased population and increased wealth. Most of the world still has to undergo the transition to a wealthy, stable society with the near zero population growth that characterizes a modern industrial society. This represents a huge unmet demand. If ten billion people were to consume energy like North Americans do today, world energy demand would be ten times higher. In addition, technological advances while often improving energy efficiency tend to raise energy demand by offering more opportunity for consumption. Energy consumption still increases at close to the 2.3% per year that would lead to a tenfold increase over the course of the next century. Meeting future energy demands while phasing out fossil fuels appears extremely difficult. Instead, the world needs sustainable or nearly sustainable fossil fuels. I propose the following definition of sustainable under which fossil fuels would well qualify: The use of a technology or resource is sustainable if the intended and unintended consequences will not force its abandonment within a reasonable planning horizon. Of course sustainable technologies must not be limited by resource depletion but this is only one of many concerns. Environmental impacts, excessive land use, and other constraints can equally limit the use of a technology and thus render it unsustainable. In the foreseeable future, fossil fuels are not limited by resource depletion. However, environmental concerns based on climate change and other environmental

  15. 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

  16. 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

  17. 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

  18. 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

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

    PubMed Central

    Tong, Yigang

    2014-01-01

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

  20. Evolution of Synonymous Codon Usage in Neurospora tetrasperma and Neurospora discreta

    PubMed Central

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

    2011-01-01

    Neurospora comprises a primary model system for the study of fungal genetics and biology. In spite of this, little is known about genome evolution in Neurospora. For example, the evolution of synonymous codon usage is largely unknown in this genus. In the present investigation, we conducted a comprehensive analysis of synonymous codon usage and its relationship to gene expression and gene length (GL) in Neurospora tetrasperma and Neurospora discreta. For our analysis, we examined codon usage among 2,079 genes per organism and assessed gene expression using large-scale expressed sequenced tag (EST) data sets (279,323 and 453,559 ESTs for N. tetrasperma and N. discreta, respectively). Data on relative synonymous codon usage revealed 24 codons (and two putative codons) that are more frequently used in genes with high than with low expression and thus were defined as optimal codons. Although codon-usage bias was highly correlated with gene expression, it was independent of selectively neutral base composition (introns); thus demonstrating that translational selection drives synonymous codon usage in these genomes. We also report that GL (coding sequences [CDS]) was inversely associated with optimal codon usage at each gene expression level, with highly expressed short genes having the greatest frequency of optimal codons. Optimal codon frequency was moderately higher in N. tetrasperma than in N. discreta, which might be due to variation in selective pressures and/or mating systems. PMID:21402862

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

    PubMed Central

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

    2013-01-01

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

  2. 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…

  3. Molecular decay of the tooth gene Enamelin (ENAM) mirrors the loss of enamel in the fossil record of placental mammals.

    PubMed

    Meredith, Robert W; Gatesy, John; Murphy, William J; Ryder, Oliver A; Springer, Mark S

    2009-09-01

    Vestigial structures occur at both the anatomical and molecular levels, but studies documenting the co-occurrence of morphological degeneration in the fossil record and molecular decay in the genome are rare. Here, we use morphology, the fossil record, and phylogenetics to predict the occurrence of "molecular fossils" of the enamelin (ENAM) gene in four different orders of placental mammals (Tubulidentata, Pholidota, Cetacea, Xenarthra) with toothless and/or enamelless taxa. Our results support the "molecular fossil" hypothesis and demonstrate the occurrence of frameshift mutations and/or stop codons in all toothless and enamelless taxa. We then use a novel method based on selection intensity estimates for codons (omega) to calculate the timing of iterated enamel loss in the fossil record of aardvarks and pangolins, and further show that the molecular evolutionary history of ENAM predicts the occurrence of enamel in basal representatives of Xenarthra (sloths, anteaters, armadillos) even though frameshift mutations are ubiquitous in ENAM sequences of living xenarthrans. The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin's theory. PMID:19730686

  4. Cycles in fossil diversity

    SciTech Connect

    Rohde, Robert A.; Muller, Richard A.

    2004-10-20

    It is well-known that the diversity of life appears to fluctuate during the course the Phanerozoic, the eon during which hard shells and skeletons left abundant fossils (0-542 Ma). Using Sepkoski's compendium of the first and last stratigraphic appearances of 36380 marine genera, we report a strong 62 {+-} 3 Myr cycle, which is particularly strong in the shorter-lived genera. The five great extinctions enumerated by Raup and Sepkoski may be an aspect of this cycle. Because of the high statistical significance, we also consider contributing environmental factors and possible causes.

  5. Visualization of codon-dependent conformational rearrangements during translation termination

    PubMed Central

    He, Shan L.; Green, Rachel

    2010-01-01

    While the recognition of stop codons by class 1 release factors (RFs) on the ribosome takes place with extremely high fidelity, the molecular mechanisms behind this remarkable process are poorly understood. Here we performed structural probing experiments with Fe(II)-derivatized RFs to compare the conformation of cognate and near-cognate ribosome termination complexes. The structural differences that we document provide an unprecedented view of signal transduction on the ribosome that depends on authentic stop codon recognition. These events initiate with very close interactions between RF and the small subunit decoding center (DC), lead to increased interactions between the switch loop of the RF and specific regions of the subunit interface and end in the precise orientation of the RF for maximal catalytic activity in the large subunit peptidyl transferase center (PTC). PMID:20208546

  6. 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

  7. 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

  8. The Fungus Candida albicans Tolerates Ambiguity at Multiple Codons.

    PubMed

    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

  9. Decoding RAS isoform and codon-specific signalling

    PubMed Central

    Newlaczyl, Anna U.; Hood, Fiona E.; Coulson, Judy M.; Prior, Ian A.

    2014-01-01

    RAS proteins are key signalling hubs that are oncogenically mutated in 30% of all cancer cases. Three genes encode almost identical isoforms that are ubiquitously expressed, but are not functionally redundant. The network responses associated with each isoform and individual oncogenic mutations remain to be fully characterized. In the present article, we review recent data defining the differences between the RAS isoforms and their most commonly mutated codons and discuss the underlying mechanisms. PMID:25109951

  10. 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

  11. Computational codon optimization of synthetic gene for protein expression

    PubMed Central

    2012-01-01

    Background The construction of customized nucleic acid sequences allows us to have greater flexibility in gene design for recombinant protein expression. Among the various parameters considered for such DNA sequence design, individual codon usage (ICU) has been implicated as one of the most crucial factors affecting mRNA translational efficiency. However, previous works have also reported the significant influence of codon pair usage, also known as codon context (CC), on the level of protein expression. Results In this study, we have developed novel computational procedures for evaluating the relative importance of optimizing ICU and CC for enhancing protein expression. By formulating appropriate mathematical expressions to quantify the ICU and CC fitness of a coding sequence, optimization procedures based on genetic algorithm were employed to maximize its ICU and/or CC fitness. Surprisingly, the in silico validation of the resultant optimized DNA sequences for Escherichia coli, Lactococcus lactis, Pichia pastoris and Saccharomyces cerevisiae suggests that CC is a more relevant design criterion than the commonly considered ICU. Conclusions The proposed CC optimization framework can complement and enhance the capabilities of current gene design tools, with potential applications to heterologous protein production and even vaccine development in synthetic biotechnology. PMID:23083100

  12. Novel small molecules potentiate premature termination codon readthrough by aminoglycosides.

    PubMed

    Baradaran-Heravi, Alireza; Balgi, Aruna D; Zimmerman, Carla; Choi, Kunho; Shidmoossavee, Fahimeh S; Tan, Jason S; Bergeaud, Célia; Krause, Alexandra; Flibotte, Stéphane; Shimizu, Yoko; Anderson, Hilary J; Mouly, Vincent; Jan, Eric; Pfeifer, Tom; Jaquith, James B; Roberge, Michel

    2016-08-19

    Nonsense mutations introduce premature termination codons and underlie 11% of genetic disease cases. High concentrations of aminoglycosides can restore gene function by eliciting premature termination codon readthrough but with low efficiency. Using a high-throughput screen, we identified compounds that potentiate readthrough by aminoglycosides at multiple nonsense alleles in yeast. Chemical optimization generated phthalimide derivative CDX5-1 with activity in human cells. Alone, CDX5-1 did not induce readthrough or increase TP53 mRNA levels in HDQ-P1 cancer cells with a homozygous TP53 nonsense mutation. However, in combination with aminoglycoside G418, it enhanced readthrough up to 180-fold over G418 alone. The combination also increased readthrough at all three nonsense codons in cancer cells with other TP53 nonsense mutations, as well as in cells from rare genetic disease patients with nonsense mutations in the CLN2, SMARCAL1 and DMD genes. These findings open up the possibility of treating patients across a spectrum of genetic diseases caused by nonsense mutations. PMID:27407112

  13. Fossil Microorganisms in Archaean

    NASA Technical Reports Server (NTRS)

    Astafleva, Marina; Hoover, Richard; Rozanov, Alexei; Vrevskiy, A.

    2006-01-01

    Ancient Archean and Proterozoic rocks are the model objects for investigation of rocks comprising astromaterials. The first of Archean fossil microorganisms from Baltic shield have been reported at the last SPIE Conference in 2005. Since this confeence biomorphic structures have been revealed in Archean rocks of Karelia. It was determined that there are 3 types of such bion structures: 1. structures found in situ, in other words microorganisms even-aged with rock matrix, that is real Archean fossils biomorphic structures, that is to say forms inhabited early formed rocks, and 3. younger than Archean-Protherozoic minerali microorganisms, that is later contamination. We made attempt to differentiate these 3 types of findings and tried to understand of burial of microorganisms. The structures belongs (from our point of view) to the first type, or real Archean, forms were under examination. Practical investigation of ancient microorganisms from Green-Stone-Belt of Northern Karelia turns to be very perspective. It shows that even in such ancient time as Archean ancient diverse world existed. Moreover probably such relatively highly organized cyanobacteria and perhaps eukaryotic formes existed in Archean world.

  14. Evolutionary timescale of monocots determined by the fossilized birth-death model using a large number of fossil records.

    PubMed

    Eguchi, Satoshi; Tamura, Minoru N

    2016-05-01

    Although the phylogenetic relationships between monocot orders are sufficiently understood, a timescale of their evolution is needed. Several studies on molecular clock dating are available, but their results have been biased by their calibration schemes. Recently, the fossilized birth-death model, a type of Bayesian dating method, was proposed, and it does not require prior calibration and allows the use all available fossils. Using this model, we conducted divergence-time estimations of monocots to explore their evolutionary timeline without calibration bias. This is the first application of this model to seed plants. The dataset contained the matK and rbcL chloroplast genes of 118 monocot genera covering all extant orders. We employed information from 247 monocot fossils, which exceeded previous dating analyses that used a maximum of 12 monocot fossils. The crown group of monocots was dated to approximately the Late Jurassic-Early Cretaceous periods, and most extant monocot orders were estimated to diverge throughout the Early Cretaceous. Our results overlapped with the divergence time of insect lineages, such as beetles and flies, suggesting an association with pollinators in early monocot evolution. In addition, we proposed three new orders based on divergence time: Orchidales separated from Asparagales and Tofieldiales and Arales separated from Aslimatales. PMID:27061096

  15. 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

  16. Analysis of synonymous codon usage in porcine reproductive and respiratory syndrome virus.

    PubMed

    Liu, Yong-sheng; Zhou, Jian-hua; Chen, Hao-tai; Ma, Li-na; Ding, Yao-zhong; Wang, Meng; Zhang, Jie

    2010-08-01

    In this study, we calculated the relative synonymous codon usage (RSCU) values and codon usage bias (CUB) values to implement a comparative analysis of codon usage pattern of open reading frames (ORFs) which belong to the two main genotypes of porcine reproductive and respiratory syndrome virus (PRRSV). By analysis of synonymous codon usage values in each ORF of PRRSV, the optimal codons for most amino acids were all C or G-ended codons except GAU for Asp, CAU for His, UUU for Phe and CCU for Pro. The synonymous codon usage patterns in different ORFs of PRRSV were different and genetically conserved. Among them, ORF1a, ORF4, ORF5 and ORF7 could cluster these strains into the two main serotypes (EU and US). Due to mutational pressure, compositional constraint played an important role in shaping the synonymous codon usage pattern in different ORFs, and the synonymous codon usage diversity in ORFs was correlated with gene function. The degree of CUB for some particular amino acids under strong selection pressure probably served as a potential genetic marker for each ORF in PRRSV. However, gene length and translational selection in nature had no effect on the synonymous codon usage pattern in PRRSV. These conclusions could not only offer an insight into the synonymous codon usage pattern and differentiation of gene function, but also assist in understanding the discrepancy of evolution among ORFs in PRRSV. PMID:20438864

  17. Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach.

    PubMed

    Foroughmand-Araabi, Mohammad-Hadi; Goliaei, Bahram; Alishahi, Kasra; Sadeghi, Mehdi; Goliaei, Sama

    2015-04-01

    Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of synonymous codons. Also, we built a multinomial logistic regression statistical model for codon usage, which considers the effect of patterns on codon usage. This model justifies the observed codon usage preference better than the classic organism dependent codon usage. Our results showed that the codon usage plays a role in controlling protein levels, for genes that participate in a specific biological function. This is the first time that this phenomenon is reported. PMID:25409941

  18. 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

  19. 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

  20. 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

  1. Bioinformatics analysis of codon usage patterns and influencing factors in Penaeus monodon nudivirus.

    PubMed

    Tyagi, Anuj; Singh, Niraj K; Gurtler, Volker; Karunasagar, Indrani

    2016-02-01

    Penaeus monodon nudivirus (PmNV) is one of the most important and most commonly reported shrimp viruses. In the present study, codon usage of PmNV was studied in detail. Based on effective number of codons (ENC) values, strong to low codon usage bias was observed in PmNV genes. Nucleotide composition-ENC correlation analysis and the GC3 versus ENC relationship indicated that compositional constraint has a major effect on codon usage of PmNV. At the whole-genome level, relative synonymous codon usage (RSCU) analysis showed almost complete antagonism between the codon usage pattern of PmNV and its host P. monodon. However, codon adaptive index (CAI) values indicated that forces of selective/translational constraints have been able to overcome this antagonism in some genes. PMID:26586333

  2. 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

  3. 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

  4. Radioactivity in fossils at the Hagerman Fossil Beds National Monument.

    PubMed

    Farmer, C Neal; Kathren, Ronald L; Christensen, Craig

    2008-08-01

    Since 1996, higher than background levels of naturally occurring radioactivity have been documented in both fossil and mineral deposits at Hagerman Fossil Beds National Monument in south-central Idaho. Radioactive fossil sites occur primarily within an elevation zone of 900-1000 m above sea level and are most commonly found associated with ancient river channels filled with sand. Fossils found in clay rich deposits do not exhibit discernable levels of radioactivity. Out of 300 randomly selected fossils, approximately three-fourths exhibit detectable levels of natural radioactivity ranging from 1 to 2 orders of magnitude above ambient background levels when surveyed with a portable hand held Geiger-Muller survey instrument. Mineral deposits in geologic strata also show above ambient background levels of radioactivity. Radiochemical lab analysis has documented the presence of numerous natural radioactive isotopes. It is postulated that ancient groundwater transported radioactive elements through sand bodies containing fossils which precipitated out of solution during the fossilization process. The elevated levels of natural radioactivity in fossils may require special precautions to ensure that exposures to personnel from stored or displayed items are kept as low as reasonably achievable (ALARA). PMID:18442873

  5. Anemometer calibrator

    NASA Technical Reports Server (NTRS)

    Bate, T.; Calkins, D. E.; Price, P.; Veikins, O.

    1971-01-01

    Calibrator generates accurate flow velocities over wide range of gas pressure, temperature, and composition. Both pressure and flow velocity can be maintained within 0.25 percent. Instrument is essentially closed loop hydraulic system containing positive displacement drive.

  6. Biogeographic calibrations for the molecular clock

    PubMed Central

    Ho, Simon Y. W.; Tong, K. Jun; Foster, Charles S. P.; Ritchie, Andrew M.; Lo, Nathan; Crisp, Michael D.

    2015-01-01

    Molecular estimates of evolutionary timescales have an important role in a range of biological studies. Such estimates can be made using methods based on molecular clocks, including models that are able to account for rate variation across lineages. All clock models share a dependence on calibrations, which enable estimates to be given in absolute time units. There are many available methods for incorporating fossil calibrations, but geological and climatic data can also provide useful calibrations for molecular clocks. However, a number of strong assumptions need to be made when using these biogeographic calibrations, leading to wide variation in their reliability and precision. In this review, we describe the nature of biogeographic calibrations and the assumptions that they involve. We present an overview of the different geological and climatic events that can provide informative calibrations, and explain how such temporal information can be incorporated into dating analyses. PMID:26333662

  7. Re-exploration of the Codon Context Effect on Amber Codon-Guided Incorporation of Noncanonical Amino Acids in Escherichia coli by the Blue-White Screening Assay.

    PubMed

    Xu, Huan; Wang, Yan; Lu, Jiaqi; Zhang, Bo; Zhang, Ziwei; Si, Longlong; Wu, Ling; Yao, Tianzhuo; Zhang, Chuanling; Xiao, Sulong; Zhang, Lihe; Xia, Qing; Zhou, Demin

    2016-07-01

    The effect of codon context on amber codon-guided incorporation of noncanonical amino acids (NAAs) has been previously examined by antibiotic selection. Here, we re-explored this effect by screening a library in which three nucleotides upstream and downstream of the amber codon were randomised, and inserted within the lacZ-α gene. Thousands of clones were obtained and distinguished by the depth of blue colour upon exposure to X-gal. Large-scale sequencing revealed remarkable preferences in nucleotides downstream of the amber codon, and moderate preferences for upstream nucleotides. Nucleotide preference was quantified by a dual-luciferase assay, which verified that the optimum context for NAA incorporation, AATTAGACT, was applicable to different proteins. Our work provides a general guide for engineering amber codons into genes of interest in bacteria. PMID:27028123

  8. Giving the early fossil record of sponges a squeeze.

    PubMed

    Antcliffe, Jonathan B; Callow, Richard H T; Brasier, Martin D

    2014-11-01

    Twenty candidate fossils with claim to be the oldest representative of the Phylum Porifera have been re-analysed. Three criteria are used to assess each candidate: (i) the diagnostic criteria needed to categorize sponges in the fossil record; (ii) the presence, or absence, of such diagnostic features in the putative poriferan fossils; and (iii) the age constraints for the candidate fossils. All three criteria are critical to the correct interpretation of any fossil and its placement within an evolutionary context. Our analysis shows that no Precambrian fossil candidate yet satisfies all three of these criteria to be a reliable sponge fossil. The oldest widely accepted candidate, Mongolian silica hexacts from c. 545 million years ago (Ma), are here shown to be cruciform arsenopyrite crystals. The oldest reliable sponge remains are siliceous spicules from the basal Cambrian (Protohertzina anabarica Zone) Soltanieh Formation, Iran, which are described and analysed here in detail for the first time. Extensive archaeocyathan sponge reefs emerge and radiate as late as the middle of the Fortunian Stage of the Cambrian and demonstrate a gradual assembly of their skeletal structure through this time coincident with the evolution of other metazoan groups. Since the Porifera are basal in the Metazoa, their presence within the late Proterozoic has been widely anticipated. Molecular clock calibration for the earliest Porifera and Metazoa should now be based on the Iranian hexactinellid material dated to c. 535 Ma. The earliest convincing fossil sponge remains appeared at around the time of the Precambrian-Cambrian boundary, associated with the great radiation events of that interval. PMID:24779547

  9. 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

  10. 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.

  11. Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance*

    PubMed Central

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

    2014-01-01

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

  12. 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

  13. Fossil energy materials needs assessment

    NASA Astrophysics Data System (ADS)

    King, R. T.; Judkins, R. R.

    1980-07-01

    An assessment of needs for materials of construction for fossil energy systems was prepared by Oak Ridge National Laboratories staff members who conducted a literature search and interviewed various individuals and organizations that are active in the area of fossil energy technology. Critical materials problems associated with fossil energy systems are identified. Background information relative to the various technologies is given and materials research needed to enhance the viability and improve the economics of fossil energy processes is discussed. The assessment is presented on the basis of materials-related disciplines that impact fossil energy material development. These disciplines include the design-materials interface, materials fabrication technology, corrosion and materials compatibility, wear phenomena, ceramic materials, and nondestructive testing.

  14. Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes

    PubMed Central

    Xiang, Heng; Zhang, Ruizhi; Butler, Robert R.; Liu, Tie; Zhang, Li; Pombert, Jean-François; Zhou, Zeyang

    2015-01-01

    The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species. PMID:26057384

  15. Comparative Analysis of Codon Usage Bias Patterns in Microsporidian Genomes.

    PubMed

    Xiang, Heng; Zhang, Ruizhi; Butler, Robert R; Liu, Tie; Zhang, Li; Pombert, Jean-François; Zhou, Zeyang

    2015-01-01

    The sub-3 Mbp genomes from microsporidian species of the Encephalitozoon genus are the smallest known among eukaryotes and paragons of genomic reduction and compaction in parasites. However, their diminutive stature is not characteristic of all Microsporidia, whose genome sizes vary by an order of magnitude. This large variability suggests that different evolutionary forces are applied on the group as a whole. In this study, we have compared the codon usage bias (CUB) between eight taxonomically distinct microsporidian genomes: Encephalitozoon intestinalis, Encephalitozoon cuniculi, Spraguea lophii, Trachipleistophora hominis, Enterocytozoon bieneusi, Nematocida parisii, Nosema bombycis and Nosema ceranae. While the CUB was found to be weak in all eight Microsporidia, nearly all (98%) of the optimal codons in S. lophii, T. hominis, E. bieneusi, N. parisii, N. bombycis and N. ceranae are fond of A/U in third position whereas most (64.6%) optimal codons in the Encephalitozoon species E. intestinalis and E. cuniculi are biased towards G/C. Although nucleotide composition biases are likely the main factor driving the CUB in Microsporidia according to correlation analyses, directed mutational pressure also likely affects the CUB as suggested by ENc-plots, correspondence and neutrality analyses. Overall, the Encephalitozoon genomes were found to be markedly different from the other microsporidians and, despite being the first sequenced representatives of this lineage, are uncharacteristic of the group as a whole. The disparities observed cannot be attributed solely to differences in host specificity and we hypothesize that other forces are at play in the lineage leading to Encephalitozoon species. PMID:26057384

  16. Association of HER2 codon 655 polymorphism with ovarian cancer.

    PubMed

    Watrowski, Rafał; Castillo-Tong, Dan Cacsire; Schuster, Eva; Fischer, Michael B; Speiser, Paul; Zeillinger, Robert

    2016-06-01

    The role of the human epidermal growth factor receptor 2 (HER2) codon 655 (Ile655Val) polymorphism in ovarian cancer is not fully understood. Two studies indicated a possible association between the Val allele and elevated risk or reduced prognosis of ovarian cancer. We investigated the HER2 codon 655 (rs1136201) polymorphism in 242 Austrian women-142 ovarian cancer patients and 100 healthy controls-by polymerase chain reaction and pyrosequencing. Associations between Ile655Val polymorphism and clinicopathological variables (e.g., age, FIGO stage, grading, serous vs. non-serous histology) were evaluated. The genotype distributions in ovarian cancer patients and controls were: AA; 66.2 %, AG; 25.35 %, GG; 8.45 %, and AA; 63 %, AG; 34 %, GG; 3.7 %, respectively (OR 1.15, CI 95 % 0.67-1.96). We observed a non-significant trend toward elevated cancer risk in Val/Val genotype (OR 2.98, CI 95 % 0.82-10.87, p = 0.10). Of note, 11 out of 12 Val/Val homozygotes were postmenopausal. The link between the Val/Val homozygosity and age over 50 years at diagnosis (OR 0.15, CI 95 % 0.02-1.2) was barely significant (p = 0.056). Summarizing, our data indicated a non-significant trend toward increased ovarian cancer risk in the Val/Val homozygosity, especially in women aged above 50 years. Further large-cohort studies focusing on the role of the HER2 codon 655 Val allele are needed. PMID:26666819

  17. 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

  18. 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

  19. Diversification of Neoaves: integration of molecular sequence data and fossils

    PubMed Central

    Ericson, Per G.P; Anderson, Cajsa L; Britton, Tom; Elzanowski, Andrzej; Johansson, Ulf S; Källersjö, Mari; Ohlson, Jan I; Parsons, Thomas J; Zuccon, Dario; Mayr, Gerald

    2006-01-01

    Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves. PMID:17148284

  20. Organic molecules as chemical fossils - The molecular fossil record

    NASA Technical Reports Server (NTRS)

    Eglinton, G.

    1983-01-01

    The study of biochemical clues to the early earth and the origin of life is discussed. The methods used in such investigation are described, including the extraction, fractionation, and analysis of geolipids and the analysis of kerogen. The occurrence of molecular fossils in the geological record is examined, discussing proposed precursor-product relationships and the molecular assessment of deep sea sediments, ancient sediments, and crude petroleums. Alterations in the molecular record due to diagenesis and catagenesis are considered, and the use of microbial lipids as molecular fossils is discussed. The results of searches for molecular fossils in Precambrian sediments are assessed.

  1. Fossil fuel furnace reactor

    DOEpatents

    Parkinson, William J.

    1987-01-01

    A fossil fuel furnace reactor is provided for simulating a continuous processing plant with a batch reactor. An internal reaction vessel contains a batch of shale oil, with the vessel having a relatively thin wall thickness for a heat transfer rate effective to simulate a process temperature history in the selected continuous processing plant. A heater jacket is disposed about the reactor vessel and defines a number of independent controllable temperature zones axially spaced along the reaction vessel. Each temperature zone can be energized to simulate a time-temperature history of process material through the continuous plant. A pressure vessel contains both the heater jacket and the reaction vessel at an operating pressure functionally selected to simulate the continuous processing plant. The process yield from the oil shale may be used as feedback information to software simulating operation of the continuous plant to provide operating parameters, i.e., temperature profiles, ambient atmosphere, operating pressure, material feed rates, etc., for simulation in the batch reactor.

  2. 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

  3. 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

  4. Image Calibration

    NASA Technical Reports Server (NTRS)

    Peay, Christopher S.; Palacios, David M.

    2011-01-01

    Calibrate_Image calibrates images obtained from focal plane arrays so that the output image more accurately represents the observed scene. The function takes as input a degraded image along with a flat field image and a dark frame image produced by the focal plane array and outputs a corrected image. The three most prominent sources of image degradation are corrected for: dark current accumulation, gain non-uniformity across the focal plane array, and hot and/or dead pixels in the array. In the corrected output image the dark current is subtracted, the gain variation is equalized, and values for hot and dead pixels are estimated, using bicubic interpolation techniques.

  5. Eukaryotic Evolutionary Transitions Are Associated with Extreme Codon Bias in Functionally-Related Proteins

    PubMed Central

    Hudson, Nicholas J.; Gu, Quan; Nagaraj, Shivashankar H.; Ding, Yong-Sheng; Dalrymple, Brian P.; Reverter, Antonio

    2011-01-01

    Codon bias in the genome of an organism influences its phenome by changing the speed and efficiency of mRNA translation and hence protein abundance. We hypothesized that differences in codon bias, either between-species differences in orthologous genes, or within-species differences between genes, may play an evolutionary role. To explore this hypothesis, we compared the genome-wide codon bias in six species that occupy vital positions in the Eukaryotic Tree of Life. We acquired the entire protein coding sequences for these organisms, computed the codon bias for all genes in each organism and explored the output for relationships between codon bias and protein function, both within- and between-lineages. We discovered five notable coordinated patterns, with extreme codon bias most pronounced in traits considered highly characteristic of a given lineage. Firstly, the Homo sapiens genome had stronger codon bias for DNA-binding transcription factors than the Saccharomyces cerevisiae genome, whereas the opposite was true for ribosomal proteins – perhaps underscoring transcriptional regulation in the origin of complexity. Secondly, both mammalian species examined possessed extreme codon bias in genes relating to hair – a tissue unique to mammals. Thirdly, Arabidopsis thaliana showed extreme codon bias in genes implicated in cell wall formation and chloroplast function – which are unique to plants. Fourthly, Gallus gallus possessed strong codon bias in a subset of genes encoding mitochondrial proteins – perhaps reflecting the enhanced bioenergetic efficiency in birds that co-evolved with flight. And lastly, the G. gallus genome had extreme codon bias for the Ciliary Neurotrophic Factor – which may help to explain their spontaneous recovery from deafness. We propose that extreme codon bias in groups of genes that encode functionally related proteins has a pathway-level energetic explanation. PMID:21966531

  6. FOSSIL2 energy policy model documentation: FOSSIL2 documentation

    SciTech Connect

    1980-10-01

    This report discusses the structure, derivations, assumptions, and mathematical formulation of the FOSSIL2 model. Each major facet of the model - supply/demand interactions, industry financing, and production - has been designed to parallel closely the actual cause/effect relationships determining the behavior of the United States energy system. The data base for the FOSSIL2 program is large, as is appropriate for a system dynamics simulation model. When possible, all data were obtained from sources well known to experts in the energy field. Cost and resource estimates are based on DOE data whenever possible. This report presents the FOSSIL2 model at several levels. Volumes II and III of this report list the equations that comprise the FOSSIL2 model, along with variable definitions and a cross-reference list of the model variables. Volume III lists the model equations and a one line definition for equations, in a short, readable format.

  7. 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.

  8. A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.

    PubMed

    Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

    2016-07-01

    The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. PMID:27197221

  9. Translationally optimal codons associate with aggregation-prone sites in proteins.

    PubMed

    Lee, Yaelim; Zhou, Tong; Tartaglia, Gian Gaetano; Vendruscolo, Michele; Wilke, Claus O

    2010-12-01

    We analyze the relationship between codon usage bias and residue aggregation propensity in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse, as well as the archaeon Halobacterium species NRC-1. Using the Mantel-Haenszel procedure, we find that translationally optimal codons associate with aggregation-prone residues. Our results are qualitatively and quantitatively similar to those of an earlier study where we found an association between translationally optimal codons and buried residues. We also combine the aggregation-propensity data with solvent-accessibility data. Although the resulting data set is small, and hence statistical power low, results indicate that the association between optimal codons and aggregation-prone residues exists both at buried and at exposed sites. By comparing codon usage at different combinations of sites (exposed, aggregation-prone sites versus buried, non-aggregation-prone sites; buried, aggregation-prone sites versus exposed, non-aggregation-prone sites), we find that aggregation propensity and solvent accessibility seem to have independent effects of (on average) comparable magnitude on codon usage. Finally, in fly, we assess whether optimal codons associate with sites at which amino acid substitutions lead to an increase in aggregation propensity, and find only a very weak effect. These results suggest that optimal codons may be required to reduce the frequency of translation errors at aggregation-prone sites that coincide with certain functional sites, such as protein-protein interfaces. Alternatively, optimal codons may be required for rapid translation of aggregation-prone regions. PMID:21046618

  10. 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

  11. 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.

  12. 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

  13. 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

  14. 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

  15. Fossilized bioelectric wire – the trace fossil Trichichnus

    PubMed Central

    Kędzierski, M.; Uchman, A.; Sawlowicz, Z.; Briguglio, A.

    2015-01-01

    The trace fossil Trichichnus is proposed as an indicator of fossil bioelectric bacterial activity at the oxic–anoxic interface zone of marine sediments. This fulfils the idea that such processes, commonly found in the modern realm, should be also present in the geological past. Trichichnus is an exceptional trace fossil due to its very thin diameter (mostly less than 1 mm) and common pyritic filling. It is ubiquitous in some fine-grained sediments, where it has been interpreted as a burrow formed deeper than any other trace fossils, below the redox boundary. Trichichnus, formerly referred to as deeply burrowed invertebrates, has been found as remnant of a fossilized intrasediment bacterial mat that is pyritized. As visualized in 3-D by means of X-ray computed microtomography scanner, Trichichnus forms dense filamentous fabric, which reflects that it is produced by modern large, mat-forming, sulfide-oxidizing bacteria, belonging mostly to Thioploca-related taxa, which are able to house a complex bacterial consortium. Several stages of Trichichnus formation, including filamentous, bacterial mat and its pyritization, are proposed to explain an electron exchange between oxic and suboxic/anoxic layers in the sediment. Therefore, Trichichnus can be considered a fossilized “electric wire”. PMID:26290671

  16. 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.

  17. 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

  18. Dating Fossil Pollen: A Simulation.

    ERIC Educational Resources Information Center

    Sheridan, Philip

    1992-01-01

    Describes a hands-on simulation in which students determine the age of "fossil" pollen samples based on the pollen types present when examined microscopically. Provides instructions for the preparation of pollen slides. (MDH)

  19. An Introduction to Fossil Plants

    ERIC Educational Resources Information Center

    Thomas, B. A.

    1976-01-01

    Introduces methods of studying fossil plants and of teaching palaeobotany. Brief accounts are given of different types of preservation and where to find specimens. An annotated bibliography is provided. (Author/SL)

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

    PubMed

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

    2013-04-01

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

  1. An empirical test of the concomitantly variable codon hypothesis

    PubMed Central

    Merlo, Lauren M. F.; Lunzer, Mark; Dean, Antony M.

    2007-01-01

    A central assumption of models of molecular evolution, that each site in a sequence evolves independently of all other sites, lacks empirical support. We investigated the extent to which sites evolve codependently in triosephosphate isomerase (TIM), a ubiquitous glycolytic enzyme conserved in both structure and function. Codependencies among sites, or concomitantly variable codons (covarions), are evident from the reduced function and misfolding of hybrid TIM proteins. Although they exist, we find covarions are relatively rare, and closely related proteins are unlikely to have developed them. However, the potential for covarions increases with genetic distance so that highly divergent proteins may have evolved codependencies between many sites. The evolution of covarions undermines a key assumption in phylogenetics and calls into question our ability to disentangle ancient relationships among major taxonomic groups. PMID:17578921

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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 ...

  8. 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

  9. Characterization of codon usage pattern and influencing factors in Japanese encephalitis virus.

    PubMed

    Singh, Niraj K; Tyagi, Anuj; Kaur, Rajinder; Verma, Ramneek; Gupta, Praveen K

    2016-08-01

    Recently, several outbreaks of Japanese encephalitis (JE), caused by Japanese encephalitis virus (JEV), have been reported and it has become cause of concern across the world. In this study, detailed analysis of JEV codon usage pattern was performed. The relative synonymous codon usage (RSCU) values along with mean effective number of codons (ENC) value of 55.30 indicated the presence of low codon usages bias in JEV. The effect of mutational pressure on codon usage bias was confirmed by significant correlations of A3s, U3s, G3s, C3s, GC3s, ENC values, with overall nucleotide contents (A%, U%, G%, C%, and GC%). The correlation analysis of A3s, U3s, G3s, C3s, GC3s, with axis values of correspondence analysis (CoA) further confirmed the role of mutational pressure. However, the correlation analysis of Gravy values and Aroma values with A3s, U3s, G3s, C3s, and GC3s, indicated the presence of natural selection on codon usage bias in addition to mutational pressure. The natural selection was further confirmed by codon adaptation index (CAI) analysis. Additionally, relative dinucleotide frequencies, geographical distribution, and evolutionary processes also influenced the codon usage pattern to some extent. PMID:27189042

  10. 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

  11. Polypeptide release factors and stop codon recognition in the apicoplast and mitochondrion of Plasmodium falciparum.

    PubMed

    Vaishya, Suniti; Kumar, Vikash; Gupta, Ankit; Siddiqi, Mohammad Imran; Habib, Saman

    2016-06-01

    Correct termination of protein synthesis would be a critical step in translation of organellar open reading frames (ORFs) of the apicoplast and mitochondrion of the malaria parasite. We identify release factors (RFs) responsible for recognition of the UAA and UGA stop-codons of apicoplast ORFs and the sole UAA stop-codon that terminates translation from the three mitochondrial ORFs. A single nuclear-encoded canonical RF2, PfRF2Api , localizes to the apicoplast. It has a conserved tripeptide motif (SPF) for stop-codon recognition and is sufficient for peptidyl-tRNA hydrolysis (PTH) from both UAA and UGA. Two RF family proteins are targeted to the parasite mitochondrion; a canonical RF1, PfRF1Mit , with a variant codon-recognition motif (PxN instead of the conserved RF1 PxT) is the major peptidyl-hydrolase with specific recognition of the UAA codon relevant to mitochondrial ORFs. Mutation of the N residue of the PfRF1Mit PxN motif and two other conserved residues of the codon recognition domain lowers PTH activity from pre-termination ribosomes indicating their role in codon-recognition. The second RF imported by the mitochondrion is the non-canonical PfICT1 that functions as a dimer and mediates codon nonspecific peptide release. Our results help delineate a critical step in organellar translation in Plasmodium, which is an important target for anti-malarials. PMID:26946524

  12. 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

  13. 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

  14. 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

  15. Testing for size and allometric differences in fossil hominin body mass estimation.

    PubMed

    Uhl, Natalie M; Rainwater, Christopher W; Konigsberg, Lyle W

    2013-06-01

    Body size reconstructions of fossil hominins allow us to infer many things about their evolution and lifestyle, including diet, metabolic requirements, locomotion, and brain/body size relationships. The importance of these implications compels anthropologists to attempt body mass estimation from fragmentary fossil hominin specimens. Most calculations require a known "calibration" sample usually composed of modern humans or other extant apes. Caution must be taken in these analyses, as estimates are sensitive to overall size and allometric differences between the fossil hominin and the reference sample. PMID:23588924

  16. 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

  17. Cytochrome P450 genes in coronary artery diseases: Codon usage analysis reveals genomic GC adaptation.

    PubMed

    Malakar, Arup Kumar; Halder, Binata; Paul, Prosenjit; Chakraborty, Supriyo

    2016-09-15

    Establishing codon usage biases are imperative for understanding the etiology of coronary artery diseases (CAD) as well as the genetic factors associated with these diseases. The aim of this study was to evaluate the contribution of 18 responsible cytochrome P450 (CYP) genes for the risk of CAD. Effective number of codon (Nc) showed a negative correlation with both GC3 and synonymous codon usage order (SCUO) suggesting an antagonistic relationship between codon usage and Nc of genes. The dinucleotide analysis revealed that CG and TA dinucleotides have the lowest odds ratio in these genes. Principal component analysis showed that GC composition has a profound effect in separating the genes along the first major axis. Our findings revealed that mutational pressure and natural selection could possibly be the major factors responsible for codon bias in these genes. The study not only offers an insight into the mechanisms of genomic GC adaptation, but also illustrates the complexity of CYP genes in CAD. PMID:27275533

  18. A revised checklist of Nepticulidae fossils (Lepidoptera) indicates an Early Cretaceous origin.

    PubMed

    Doorenweerd, Camiel; Nieukerken, Erik J Van; Sohn, Jae-Cheon; Labandeira, Conrad C

    2015-01-01

    With phylogenetic knowledge of Lepidoptera rapidly increasing, catalysed by increasingly powerful molecular techniques, the demand for fossil calibration points to estimate an evolutionary timeframe for the order is becoming an increasingly pressing issue. The family Nepticulidae is a species rich, basal branch within the phylogeny of the Lepidoptera, characterized by larval leaf-mining habits, and thereby represents a potentially important lineage whose evolutionary history can be established more thoroughly with the potential use of fossil calibration points. Using our experience with extant global Nepticulidae, we discuss a list of characters that may be used to assign fossil leaf mines to Nepticulidae, and suggest useful methods for classifying relevant fossil material. We present a checklist of 79 records of Nepticulidae representing adult and leaf-mine fossils mentioned in literature, often with multiple exemplars constituting a single record. We provide our interpretation of these fossils. Two species now are included in the collective generic name Stigmellites: Stigmellites resupinata (Krassilov, 2008) comb. nov. (from Ophiheliconoma) and Stigmellites almeidae (Martins-Neto, 1989) comb. nov. (from Nepticula). Eleven records are for the first time attributed to Nepticulidae. After discarding several dubious records, including one possibly placing the family at a latest Jurassic position, we conclude that the oldest fossils likely attributable to Nepticulidae are several exemplars representing a variety of species from the Dakota Formation (USA). The relevant strata containing these earliest fossils are now dated at 102 Ma (million years ago) in age, corresponding to the latest Albian Stage of the Early Cretaceous. Integration of all records in the checklist shows that a continuous presence of nepticulid-like leaf mines preserved as compression-impression fossils and by amber entombment of adults have a fossil record extending to the latest Early Cretaceous

  19. Travels with the Fossil Hunters

    NASA Astrophysics Data System (ADS)

    Whybrow, Peter J.

    2000-04-01

    Whether dodging bullets in West Africa, or rabid dogs in Pakistan, surviving yak-butter tea in Tibet, or eating raw fish in China, the life of a globe-trotting fossil hunter is often hazardous and always filled with surprises. Travels with the Fossil Hunters lets readers share the wonder, joys of discovery, and excitement of these intrepid scientists. Packed with more than 100 beautiful, full-color photographs, the volume takes readers on twelve expeditions to remote parts of the world in search of diverse fossil remains, from those of dinosaurs to human ancestors. Each expedition by paleontologists from London's Natural History Museum reveals the problems and challenges of working in extreme conditions, from the deserts of the Sahara and Yemen to the frozen wastes of Antarctica, from the mountains of India to the forests of Latvia. Along the way they also describe the paleontology and geology of the countries they visit and the scientific reasons for their expeditions. With a foreword from Sir David Attenborough and an introduction from Richard Fortey, this fascinating book will appeal to amateur and professional fossil hunters alike and to readers interested in accounts of exotic locales. Peter Whybrow is a research scientist at the Natural History Museum, London. His research interests include Arabian Miocene vertebrates, paleoclimates, paleogeography, and biotic diversity. He is senior editor with A. Hill of Fossil Vertebrates of Arabia (Yale University Press, New Haven, 1999).

  20. 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

  1. 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

  2. A Galactic Fossil

    NASA Astrophysics Data System (ADS)

    2007-05-01

    How old are the oldest stars? Using ESO's VLT, astronomers recently measured the age of a star located in our Galaxy. The star, a real fossil, is found to be 13.2 billion years old, not very far from the 13.7 billion years age of the Universe. The star, HE 1523-0901, was clearly born at the dawn of time. "Surprisingly, it is very hard to pin down the age of a star", the lead author of the paper reporting the results, Anna Frebel, explains. "This requires measuring very precisely the abundance of the radioactive elements thorium or uranium, a feat only the largest telescopes such as ESO's VLT can achieve." ESO PR Photo 23a/07 ESO PR Photo 23a/07 The 'Cosmic Clock' This technique is analogous to the carbon-14 dating method that has been so successful in archaeology over time spans of up to a few tens of thousands of years. In astronomy, however, this technique must obviously be applied to vastly longer timescales. For the method to work well, the right choice of radioactive isotope is critical. Unlike other, stable elements that formed at the same time, the abundance of a radioactive (unstable) isotope decreases all the time. The faster the decay, the less there will be left of the radioactive isotope after a certain time, so the greater will be the abundance difference when compared to a stable isotope, and the more accurate is the resulting age. Yet, for the clock to remain useful, the radioactive element must not decay too fast - there must still be enough left of it to allow an accurate measurement, even after several billion years. "Actual age measurements are restricted to the very rare objects that display huge amounts of the radioactive elements thorium or uranium," says Norbert Christlieb, co-author of the report. ESO PR Photo 23b/07 ESO PR Photo 23b/07 Uranium Line in the Spectrum of an Old Star Large amounts of these elements have been found in the star HE 1523-0901, an old, relatively bright star that was discovered within the Hamburg/ESO survey [1]. The

  3. Tips and nodes are complementary not competing approaches to the calibration of molecular clocks

    PubMed Central

    2016-01-01

    Molecular clock methodology provides the best means of establishing evolutionary timescales, the accuracy and precision of which remain reliant on calibration, traditionally based on fossil constraints on clade (node) ages. Tip calibration has been developed to obviate undesirable aspects of node calibration, including the need for maximum age constraints that are invariably very difficult to justify. Instead, tip calibration incorporates fossil species as dated tips alongside living relatives, potentially improving the accuracy and precision of divergence time estimates. We demonstrate that tip calibration yields node calibrations that violate fossil evidence, contributing to unjustifiably young and ancient age estimates, less precise and (presumably) accurate than conventional node calibration. However, we go on to show that node and tip calibrations are complementary, producing meaningful age estimates, with node minima enforcing realistic ages and fossil tips interacting with node calibrations to objectively define maximum age constraints on clade ages. Together, tip and node calibrations may yield evolutionary timescales that are better justified, more precise and accurate than either calibration strategy can achieve alone. PMID:27095263

  4. ALTEA calibration

    NASA Astrophysics Data System (ADS)

    Zaconte, V.; Altea Team

    The ALTEA project is aimed at studying the possible functional damages to the Central Nervous System (CNS) due to particle radiation in space environment. The project is an international and multi-disciplinary collaboration. The ALTEA facility is an helmet-shaped device that will study concurrently the passage of cosmic radiation through the brain, the functional status of the visual system and the electrophysiological dynamics of the cortical activity. The basic instrumentation is composed by six active particle telescopes, one ElectroEncephaloGraph (EEG), a visual stimulator and a pushbutton. The telescopes are able to detect the passage of each particle measuring its energy, trajectory and released energy into the brain and identifying nuclear species. The EEG and the Visual Stimulator are able to measure the functional status of the visual system, the cortical electrophysiological activity, and to look for a correlation between incident particles, brain activity and Light Flash perceptions. These basic instruments can be used separately or in any combination, permitting several different experiments. ALTEA is scheduled to fly in the International Space Station (ISS) in November, 15th 2004. In this paper the calibration of the Flight Model of the silicon telescopes (Silicon Detector Units - SDUs) will be shown. These measures have been taken at the GSI heavy ion accelerator in Darmstadt. First calibration has been taken out in November 2003 on the SDU-FM1 using C nuclei at different energies: 100, 150, 400 and 600 Mev/n. We performed a complete beam scan of the SDU-FM1 to check functionality and homogeneity of all strips of silicon detector planes, for each beam energy we collected data to achieve good statistics and finally we put two different thickness of Aluminium and Plexiglas in front of the detector in order to study fragmentations. This test has been carried out with a Test Equipment to simulate the Digital Acquisition Unit (DAU). We are scheduled to

  5. FOSSIL2 energy policy model documentation: FOSSIL2 documentation

    SciTech Connect

    1980-10-01

    This report discusses the structure, derivations, assumptions, and mathematical formulation of the FOSSIL2 model. Each major facet of the model - supply/demand interactions, industry financing, and production - has been designed to parallel closely the actual cause/effect relationships determining the behavior of the United States energy system. The data base for the FOSSIL2 program is large, as is appropriate for a system dynamics simulation model. When possible, all data were obtained from sources well known to experts in the energy field. Cost and resource estimates are based on DOE data whenever possible. This report presents the FOSSIL2 model at several levels. Volumes II and III of this report list the equations that comprise the FOSSIL2 model, along with variable definitions and a cross-reference list of the model variables. Volume II provides the model equations with each of their variables defined, while Volume III lists the equations, and a one line definition for equations, in a shorter, more readable format.

  6. A total-evidence approach to dating with fossils, applied to the early radiation of the hymenoptera.

    PubMed

    Ronquist, Fredrik; Klopfstein, Seraina; Vilhelmsen, Lars; Schulmeister, Susanne; Murray, Debra L; Rasnitsyn, Alexandr P

    2012-12-01

    Phylogenies are usually dated by calibrating interior nodes against the fossil record. This relies on indirect methods that, in the worst case, misrepresent the fossil information. Here, we contrast such node dating with an approach that includes fossils along with the extant taxa in a Bayesian total-evidence analysis. As a test case, we focus on the early radiation of the Hymenoptera, mostly documented by poorly preserved impression fossils that are difficult to place phylogenetically. Specifically, we compare node dating using nine calibration points derived from the fossil record with total-evidence dating based on 343 morphological characters scored for 45 fossil (4--20 complete) and 68 extant taxa. In both cases we use molecular data from seven markers (∼5 kb) for the extant taxa. Because it is difficult to model speciation, extinction, sampling, and fossil preservation realistically, we develop a simple uniform prior for clock trees with fossils, and we use relaxed clock models to accommodate rate variation across the tree. Despite considerable uncertainty in the placement of most fossils, we find that they contribute significantly to the estimation of divergence times in the total-evidence analysis. In particular, the posterior distributions on divergence times are less sensitive to prior assumptions and tend to be more precise than in node dating. The total-evidence analysis also shows that four of the seven Hymenoptera calibration points used in node dating are likely to be based on erroneous or doubtful assumptions about the fossil placement. With respect to the early radiation of Hymenoptera, our results suggest that the crown group dates back to the Carboniferous, ∼309 Ma (95% interval: 291--347 Ma), and diversified into major extant lineages much earlier than previously thought, well before the Triassic. [Bayesian inference; fossil dating; morphological evolution; relaxed clock; statistical phylogenetics.]. PMID:22723471

  7. Fossil Groups in the Local Universe

    NASA Technical Reports Server (NTRS)

    OSullivan, Ewan

    2005-01-01

    The two galaxies observed as part of this project were originally selected as fossil group candidates because of their isolation from other galaxies and their apparent high X-ray luminosity and extended X-ray emission. However, the X-ray data available was minimal, being drawn from the ROSAT All-Sky Survey. We have performed an initial analysis of the XMM data from both galaxies and found that their gaseous halos are smaller, cooler, and less luminous than expected. In the case of NGC 57, the RASS estimate of extent and luminosity was biased because of a previously unidentified background group which is visible in the XMM data to one side of the galaxy. In the case of IC 153 1, the contribution from background point sources near the galaxy appears to be to blame. This suggests that both galaxies should be reclassified as isolated ellipticals. Such systems are very rare, and currently poorly understood; for comparison, there are now 6-10 known fossil groups, but only one isolated elliptical with useful X-ray data. We are currently re-analyzing the data for the two galaxies to take advantage of the calibration improvements of SAS 6.1, and to include calculations of the mass profiles of the two systems. A paper is currently in preparation dealing with the X-ray properties and environment of the galaxies, and we expect to submit this to the Astrophysical Journal within the next two months. Multi-band optical imaging of the field surrounding NGC 57 has been acquired to confirm its isolated status and provide more information on the background group. IC 1531 was accepted as a target in Chandra cycle 6 as part of a related proposal, and we intend to add this new observation to our XMM data when it becomes available. A second paper is planned to include the results of this combined analysis.

  8. Gaining Insights into the Codon Usage Patterns of TP53 Gene across Eight Mammalian Species

    PubMed Central

    Mazumder, Tarikul Huda; Chakraborty, Supriyo

    2015-01-01

    TP53 gene is known as the “guardian of the genome” as it plays a vital role in regulating cell cycle, cell proliferation, DNA damage repair, initiation of programmed cell death and suppressing tumor growth. Non uniform usage of synonymous codons for a specific amino acid during translation of protein known as codon usage bias (CUB) is a unique property of the genome and shows species specific deviation. Analysis of codon usage bias with compositional dynamics of coding sequences has contributed to the better understanding of the molecular mechanism and the evolution of a particular gene. In this study, the complete nucleotide coding sequences of TP53 gene from eight different mammalian species were used for CUB analysis. Our results showed that the codon usage patterns in TP53 gene across different mammalian species has been influenced by GC bias particularly GC3 and a moderate bias exists in the codon usage of TP53 gene. Moreover, we observed that nature has highly favored the most over represented codon CTG for leucine amino acid but selected against the ATA codon for isoleucine in TP53 gene across all mammalian species during the course of evolution. PMID:25807269

  9. 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

  10. 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

  11. 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

  12. 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

  13. Expanding the amino acid repertoire of ribosomal polypeptide synthesis via the artificial division of codon boxes.

    PubMed

    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. PMID:27001726

  14. 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

  15. 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. PMID:24454907

  16. 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.

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

    PubMed Central

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

    1986-01-01

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

  18. 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

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

    PubMed

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

    2007-01-01

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

  20. 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. PMID:24867343

  1. Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast.

    PubMed

    Gamble, Caitlin E; Brule, Christina E; Dean, Kimberly M; Fields, Stanley; Grayhack, Elizabeth J

    2016-07-28

    Translation elongation efficiency is largely thought of as the sum of decoding efficiencies for individual codons. Here, we find that adjacent codon pairs modulate translation efficiency. Deploying an approach in Saccharomyces cerevisiae that scored the expression of over 35,000 GFP variants in which three adjacent codons were randomized, we have identified 17 pairs of adjacent codons associated with reduced expression. For many pairs, codon order is obligatory for inhibition, implying a more complex interaction than a simple additive effect. Inhibition mediated by adjacent codons occurs during translation itself as GFP expression is restored by increased tRNA levels or by non-native tRNAs with exact-matching anticodons. Inhibition operates in endogenous genes, based on analysis of ribosome profiling data. Our findings suggest translation efficiency is modulated by an interplay between tRNAs at adjacent sites in the ribosome and that this concerted effect needs to be considered in predicting the functional consequences of codon choice. PMID:27374328

  2. 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. PMID:26544153

  3. 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

  4. 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

  5. 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

  6. Fossil power plant systems description

    SciTech Connect

    Not Available

    1984-01-01

    This single-volume, looseleaf text presents the functions and relationships between each major component and its auxiliaries within a system. The text also describes the relationships between systems. All major components are addressed, and system boundaries are defined for a generic fossil power plant.

  7. Progress of fossil fuel science

    SciTech Connect

    Demirbas, M.F.

    2007-07-01

    Coal is the most abundant and widely distributed fossil fuel. More than 45% of the world's electricity is generated from coal, and it is the major fuel for generating electricity worldwide. The known coal reserves in the world are enough for more than 215 years of consumption, while the known oil reserves are only about 39 times of the world's consumption and the known natural gas reserves are about 63 times of the world's consumption level in 1998. In recent years, there have been effective scientific investigations on Turkish fossil fuels, which are considerable focused on coal resources. Coal is a major fossil fuel source for Turkey. Turkish coal consumption has been stable over the past decade and currently accounts for about 24% of the country's total energy consumption. Lignite coal has had the biggest share in total fossil fuel production, at 43%, in Turkey. Turkish researchers may investigate ten broad pathways of coal species upgrading, such as desulfurization and oxydesulfurization, pyrolysis and hydropyrolysis, liquefaction and hydroliquefaction, extraction and supercritical fluid extraction, gasification, oxidation, briquetting, flotation, and structure identification.

  8. Fossils of big bang turbulence

    NASA Astrophysics Data System (ADS)

    Gibson, C. H.

    2004-12-01

    A model is proposed connecting turbulence, fossil turbulence, and the big bang origin of the universe. While details are incomplete, the model is consistent with our knowledge of these processes and is supported by observations. Turbulence arises in a hot-big-bang quantum-gravitational-dynamics scenario at Planck scales. Chaotic, eddy-like-motions produce an exothermic Planck particle cascade from 10-35 m at 1032 K to 108 larger, 104 cooler, quark-gluon scales. A Planck-Kerr instability gives high-Reynolds-number (Re 106) turbulent combustion, space-time-energy-entropy and turbulent mixing. Batchelor-Obukhov-Corrsin turbulent-temperature fluctuations are preserved as the first fossil-turbulence by inflation stretching the patterns beyond the horizon ct of causal connection faster than light speed c in time t 10-33 seconds. Fossil-big-bang-temperature-turbulence re-enters the horizon and imprints nucleosynthesis of H-He densities that seed fragmentation by gravity at 1012 s in the low Reynolds number plasma before its transition to gas at t 1013 s and T 3000 K. Multi-scaling coefficients of the cosmic-microwave-background (CMB) temperature anisotropies closely match those for high Reynolds number turbulence, Bershadskii and Sreenivasan 2002, 2003. CMB spectra support the interpretation that big-bang-turbulence-fossils triggered fragmentation of the viscous plasma at supercluster to galaxy mass scales from 1046 to 1042 kg, Gibson 1996, 2000, 2004ab.

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

    PubMed

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

    2014-01-01

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

  10. Fossil Energy: Drivers and Challenges.

    NASA Astrophysics Data System (ADS)

    Friedmann, Julio

    2007-04-01

    Concerns about rapid economic growth, energy security, and global climate change have created a new landscape for fossil energy exploration, production, and utilization. Since 85% of primary energy supply comes from fossil fuels, and 85% of greenhouse gas emissions come from fossil fuel consumption, new and difficult technical and political challenges confront commercial, governmental, and public stakeholders. As such, concerns over climate change are explicitly weighed against security of international and domestic energy supplies, with economic premiums paid for either or both. Efficiency improvements, fuel conservation, and deployment of nuclear and renewable supplies will help both concerns, but are unlikely to offset growth in the coming decades. As such, new technologies and undertakings must both provide high quality fossil energy with minimal environmental impacts. The largest and most difficult of these undertakings is carbon management, wherein CO2 emissions are sequestered indefinitely at substantial incremental cost. Geological formations provide both high confidence and high capacity for CO2 storage, but present scientific and technical challenges. Oil and gas supply can be partially sustained and replaced through exploitation of unconventional fossil fuels such as tar-sands, methane hydrates, coal-to-liquids, and oil shales. These fuels provide enormous reserves that can be exploited at current costs, but generally require substantial energy to process. In most cases, the energy return on investment (EROI) is dropping, and unconventional fuels are generally more carbon intensive than conventional, presenting additional carbon management challenges. Ultimately, a large and sustained science and technology program akin to the Apollo project will be needed to address these concerns. Unfortunately, real funding in energy research has dropped dramatically (75%) in the past three decades, and novel designs in fission and fusion are not likely to provide any

  11. Fossil group origins. VII. Galaxy substructures in fossil systems

    NASA Astrophysics Data System (ADS)

    Zarattini, S.; Girardi, M.; Aguerri, J. A. L.; Boschin, W.; Barrena, R.; del Burgo, C.; Castro-Rodriguez, N.; Corsini, E. M.; D'Onghia, E.; Kundert, A.; Méndez-Abreu, J.; Sánchez-Janssen, R.

    2016-02-01

    Context. Fossil groups (FG) are expected to be the final product of galaxy merging within galaxy groups. In simulations, they are predicted to assemble their mass at high redshift. This early formation allows for the innermost M∗ galaxies to merge into a massive central galaxy. Then, they are expected to maintain their fossil status because of the few interactions with the large-scale structure. In this context, the magnitude gap between the two brightest galaxies of the system is considered a good indicator of its dynamical status. As a consequence, the systems with the largest gaps should be dynamically relaxed. Aims: In order to examine the dynamical status of these systems, we systematically analyze, for the first time, the presence of galaxy substructures in a sample of 12 spectroscopically-confirmed fossil systems with redshift z ≤ 0.25. Methods: We apply a number of tests to investigate the substructure in fossil systems in the two-dimensional space of projected positions out to R200. Moreover, for a subsample of five systems with at least 30 spectroscopically-confirmed members we also analyze the substructure in the velocity and in the three-dimensional velocity-position spaces. Additionally, we look for signs of recent mergers in the regions around the central galaxies. Results: We find that an important fraction of fossil systems show substructure. The fraction depends critically on the adopted test, since each test is more sensitive to a particular type of substructure. Conclusions: Our interpretation of the results is that fossil systems are not, in general, as relaxed as expected from simulations. Our sample of 12 spectroscopically-confirmed fossil systems need to be extended to compute an accurate fraction, but our conclusion is that this fraction is similar to the fraction of substructure detected in nonfossil clusters. This result points out that the magnitude gap alone is not a good indicator of the dynamical status of a system. However, the

  12. 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

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

    PubMed Central

    Harms, E; Umbarger, H E

    1987-01-01

    Leucine participates in multivalent repression of the Serratia marcescens ilvGMEDA operon by attenuation (J.-H. Hsu, E. Harms, and H.E. Umbarger, J. Bacteriol. 164:217-222, 1985), although there is only one single leucine codon that could be involved in this type of control. This leucine codon is the rarely used CUA. The contribution of this leucine codon to the control of transcription by attenuation was examined by replacing it with the commonly used leucine codon CUG and with a nonregulatory proline codon, CCG. These changes left intact the proposed secondary structure of the leader. The effects of the codon changes were assessed by placing the mutant leader regions upstream of the ilvGME structural genes or the cat gene and measuring acetohydroxy acid synthase II, transaminase B, or chloramphenicol acetyltransferase activities in cells grown under limiting and repressing conditions. The presence of the common leucine codon in place of the rare leucine codon reduced derepression by about 70%. Eliminating the leucine codon by converting it to proline abolished leucine control. Furthermore, a possible context effect of the adjacent upstream serine codon on leucine control was examined by changing it into a glycine codon. PMID:2824442

  14. Advanced thermometrics for fossil power plant process improvement

    SciTech Connect

    Shepard, R.L.; Weiss, J.M.; Holcomb, D.E.

    1996-04-30

    Improved temperature measurements in fossil power plants can reduce heat rate and uncertainties in power production efficiencies, extend the life of plant components, reduce maintenance costs, and lessen emissions. Conventional instruments for measurement of combustion temperatures, steam temperatures, and structural component temperatures can be improved by better specification, in situ calibration, signal processing, and performance monitoring. Innovative instruments can enhance, augment, or replace conventional instruments. Several critical temperatures can be accessed using new methods that were impossible with conventional instruments. Such instruments include high temperature resistance temperature detectors (RTDs), thermometric phosphors, inductive thermometry, and ultrasonic thermometry.

  15. The most deviated codon position in AT-rich bacterial genomes: a function related analysis.

    PubMed

    Ma, Bin-Guang; Chen, Ling-Ling

    2005-10-01

    We have performed systematic study on more than 120 archaeal and bacterial genomes. Based on the index proposed in the current paper, clear patterns are observed showing the relation between the base compositional deviation at three codon positions and the genomic GC content. For AT-rich genomes, the Most Deviated Codon Position (MDCP) is the 1st codon position, while for GC-rich genomes, MDCP appears at the 2nd or 3rd codon position alternatively. According to MDCP, the CDSs of a genome can be classified into two types: typical and atypical. In AT-rich genomes the typical represent the majority and account for about 3/4 of all the CDSs. Based on the functional classification of COG database, the two types of CDSs are examined. An apparent bias of distribution is observed that the CDSs with the function of 'information processing' are more likely to present in typical type. PMID:16060688

  16. CodHonEditor: Spreadsheets for Codon Optimization and Editing of Protein Coding Sequences.

    PubMed

    Takai, Kazuyuki

    2016-05-01

    Gene synthesis is getting more important with the growing availability of low-cost commercial services. The coding sequences are often "optimized" as for the relative synonymous codon usage (RSCU) before synthesis, which is generally included in the commercial services. However, the codon optimization processes are different among different providers and are often hidden from the users. Here, the d'Hondt method, which is widely adopted as a method for determining the number of seats for each party in proportional-representation public elections, is applied to RSCU fitting. This allowed me to make a set of electronic spreadsheets for manual design of protein coding sequences for expression in Escherichia coli, with which users can see the process of codon optimization and can manually edit the codons after the automatic optimization. The spreadsheets may also be useful for molecular biology education. PMID:27002987

  17. Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons.

    PubMed Central

    Berry, M J; Banu, L; Harney, J W; Larsen, P R

    1993-01-01

    We investigated the requirements for selenocysteine insertion at single or multiple UGA codons in eukaryotic selenoproteins. Two functional SECIS elements were identified in the 3' untranslated region of the rat selenoprotein P mRNA, with predicted stem-loops and critical nucleotides similar to those in the SECIS elements in the type I iodothyronine 5' deiodinase (5'DI) and glutathione peroxidase selenoprotein mRNAs. Site-directed mutational analyses of three SECIS elements confirmed that conserved nucleotides in the loop and in unpaired regions of the stem are critical for activity. This indicates that multiple contact sites are required for SECIS function. Stop codon function at any of five out-of-context UGA codons in the 5'DI mRNA was suppressed by SECIS elements from the 5'DI or selenoprotein P genes linked downstream. Thus, the presence of SECIS elements in eukaryotic selenoprotein mRNAs permits complete flexibility in UGA codon position. Images PMID:8344267

  18. 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

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

    PubMed Central

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

    1981-01-01

    Oocytes from Xenopus laevis were injected with purified amber (UAG), ochre (UAA), and opal (UGA) suppressor tRNAs from yeasts. The radioactively labeled proteins translated from the endogenous mRNAs were then separated on two-dimensional gels. All three termination codons are used in a single cell, the Xenopus laevis oocyte. But a surprisingly low number of readthrough polypeptides were observed from the 600 mRNAs studied in comparison to uninjected oocytes. The experimental data are compared with the conclusions obtained from the compilation of all available termination sequences on eukaryotic and prokaryotic mRNAs. This comparison indicates that the apparent resistance of natural termination codons against readthrough, as observed by the microinjection experiments, cannot be explained by tandem or very close second stop codons. Instead it suggests that specific context sequences around the termination codons may play a role in the efficiency of translation termination. Images PMID:7024919

  20. Understanding discrimination by the ribosome: stability testing and groove measurement of codon-anticodon pairs.

    PubMed

    Sanbonmatsu, K Y; Joseph, S

    2003-04-18

    The ribosome must discriminate between correct and incorrect tRNAs with sufficient speed and accuracy to sustain an adequate rate of cell growth. Here, we report the results of explicit solvent molecular dynamics simulations, which address the mechanism of discrimination by the ribosome. The universally conserved 16S rRNA base A1493 and the kink in mRNA between A and P sites amplify differences in stability between cognate and near-cognate codon-anticodon pairs. Destabilization by the mRNA kink also provides a geometric explanation for the higher error rates observed for mismatches in the first codon position relative to mismatches in the second codon position. For more stable near-cognates, the repositioning of the universally conserved bases A1492 and G530 results in increased solvent exposure and an uncompensated loss of hydrogen bonds, preventing correct codon-anticodon-ribosome interactions from forming. PMID:12683995

  1. Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes

    PubMed Central

    Hinnebusch, Alan G.

    2011-01-01

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

  2. Fossil groups of galaxies: Are they groups? Are they fossils?

    NASA Astrophysics Data System (ADS)

    Dupke, Renato de Alencar; Miller, Eric; de Oliveira, Claudia Mendes; Sodre, Laerte; Rykoff, Eli; de Oliveira, Raimundo Lopes; Proctor, Rob

    2010-11-01

    Fossil groups present a puzzle to current theories of structure formation. Despite the low number of bright galaxies, their high velocity dispersions and high TX indicate cluster-like potential wells. Measured concentration parameters seem very high indicating early formation epochs in contradiction with the observed lack of large and well defined cooling cores. There are very few fossil groups with good quality X-ray data and their idiosyncrasies may enhance these apparent contradictions. The standard explanation for their formation suggests that bright galaxies within half the virial radii of these systems were wiped out by cannibalism forming the central galaxy. Since dry mergers, typically invoked to explain the formation of the central galaxies, are not expected to change the IGM energetics significantly, thus not preventing the formation of cooling cores, we investigate the scenario where recent gaseous (wet) mergers formed the central galaxy injecting energy and changing the chemistry of the IGM in fossil groups. We show a test for this scenario using fossil groups with enough X-ray flux in the Chandra X-ray Observatory archive by looking at individual metal abundance ratio distributions near the core. Secondary SN II powered winds would tend to erase the dominance of SN IA ejecta in the core of these systems and would help to erase previously existing cold cores. Strong SN II-powered galactic winds resulting from galaxy merging would be trapped by their deep potential wells reducing the central enhancement of SN Ia/SN II iron mass fraction ratio. The results indicate that there is a decrement in the ratio of SN Ia to SN II iron mass fraction in the central regions of the systems analyzed, varying from 99±1% in the outer regions to 85±2% within the cooling radius (Figure 1) and would inject enough energy into the IGM preventing central gas cooling. The results are consistent with a scenario of later formation epoch for fossil groups, as they are defined

  3. 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

  4. Codon and Amino Acid Usage Are Shaped by Selection Across Divergent Model Organisms of the Pancrustacea

    PubMed Central

    Whittle, Carrie A.; Extavour, Cassandra G.

    2015-01-01

    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

  5. FOSSIL SPRINGS ROADLESS AREA, ARIZONA.

    USGS Publications Warehouse

    Beard, L.S.; Ellis, C.E.

    1984-01-01

    Based on field studies, the Fossil Springs Roadless Area in central Arizona is concluded to have little promise for the occurrence of mineral or energy resources. Rocks in the Supai Formation (Pennsylvanian-Permian) near the central part of the roadless area contain widespread but spotty copper mineralization and trace amounts of uranium. Analyses obtained during the study define geochemical anomalies in two portions of the area that remain unexplained. The suites of anomalous metals suggest the possibility of hydrothermal veins and the presence of ultramafic rocks; neither were found in the field. Although there is little promise for the occurrence of mineral resources in the Fossil Springs Roadless Area, studies to identify the source of the geochemical anomalies could have valuable implications for regional studies and mineral exploration in the surrounding area.

  6. Looking at Fossils in New Ways

    ERIC Educational Resources Information Center

    Flannery, Maura C.

    2005-01-01

    Existing fossils could be studied from a different prospective with the use of new methods of analysis for gathering more information. The new techniques of studying fossils binds the new and the old techniques and information and provides another way to look at fossils.

  7. Cycads: Fossil evidence of late paleozoic origin

    USGS Publications Warehouse

    Mamay, S.H.

    1969-01-01

    Plant fossils from Lower Permian strata of the southwestern United States have been interpreted as cycadalean megasporophylls. They are evidently descended from spermopterid elements of the Pennsylvanian Taeniopteris complex; thus the known fossil history of the cycads is extended from the Late Triassic into the late Paleozoic. Possible implications of the Permian fossils toward evolution of the angiosperm carpel are considered.

  8. Liquid fossil-fuel technology

    NASA Astrophysics Data System (ADS)

    1982-07-01

    Highlights of research activities at Bartlesville Energy Technology Center for the quarter ending March 1982 are summarized. Major research areas are: liquid fossil fuel cycle; extraction (resource assessment and enhanced production); processing (characterization, thermodynamics, processing technology); utilization; and product integration and technology transfer. Special reports include: EOR data base, major new industry tool; properties of crude oils available via telephone hookup; alternative fuels data bank stresses transportation.

  9. Extinction and the fossil record

    NASA Technical Reports Server (NTRS)

    Sepkoski, J. J. Jr; Sepkoski JJ, ,. J. r. (Principal Investigator)

    1994-01-01

    The author examines evidence of mass extinctions in the fossil record and searches for reasons for such large extinctions. Five major mass extinctions eliminated at least 40 percent of animal genera in the oceans and from 65 to 95 percent of ocean species. Questions include the occurrence of gradual or catastrophic extinctions, causes, environment, the capacity of a perturbation to cause extinctions each time it happens, and the possibility and identification of complex events leading to a mass extinction.

  10. Fossilization causes organisms to appear erroneously primitive by distorting evolutionary trees

    PubMed Central

    Sansom, Robert S.; Wills, Matthew A.

    2013-01-01

    Fossils are vital for calibrating rates of molecular and morphological change through geological time, and are the only direct source of data documenting macroevolutionary transitions. Many evolutionary studies therefore require the robust phylogenetic placement of extinct organisms. Here, we demonstrate that the inevitable bias of the fossil record to preserve just hard, skeletal morphology systemically distorts phylogeny. Removal of soft part characters from 78 modern vertebrate and invertebrate morphological datasets resulted in significant changes to phylogenetic signal; it caused individual taxa to drift from their original position, predominately downward toward the root of their respective trees. This last bias could systematically inflate evolutionary rates inferred from molecular data because first fossil occurrences will not be recognised as such. Stem-ward slippage, whereby fundamental taphonomic biases cause fossils to be interpreted as erroneously primitive, is therefore a ubiquitous problem for all biologists attempting to infer macroevolutionary rates or sequences. PMID:23985991

  11. 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

  12. 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

  13. Reassignment of a rare sense codon to a non-canonical amino acid in Escherichia coli

    PubMed Central

    Mukai, Takahito; Yamaguchi, Atsushi; Ohtake, Kazumasa; Takahashi, Mihoko; Hayashi, Akiko; Iraha, Fumie; Kira, Satoshi; Yanagisawa, Tatsuo; Yokoyama, Shigeyuki; Hoshi, Hiroko; Kobayashi, Takatsugu; Sakamoto, Kensaku

    2015-01-01

    The immutability of the genetic code has been challenged with the successful reassignment of the UAG stop codon to non-natural amino acids in Escherichia coli. In the present study, we demonstrated the in vivo reassignment of the AGG sense codon from arginine to l-homoarginine. As the first step, we engineered a novel variant of the archaeal pyrrolysyl-tRNA synthetase (PylRS) able to recognize l-homoarginine and l-N6-(1-iminoethyl)lysine (l-NIL). When this PylRS variant or HarRS was expressed in E. coli, together with the AGG-reading tRNAPylCCU molecule, these arginine analogs were efficiently incorporated into proteins in response to AGG. Next, some or all of the AGG codons in the essential genes were eliminated by their synonymous replacements with other arginine codons, whereas the majority of the AGG codons remained in the genome. The bacterial host's ability to translate AGG into arginine was then restricted in a temperature-dependent manner. The temperature sensitivity caused by this restriction was rescued by the translation of AGG to l-homoarginine or l-NIL. The assignment of AGG to l-homoarginine in the cells was confirmed by mass spectrometric analyses. The results showed the feasibility of breaking the degeneracy of sense codons to enhance the amino-acid diversity in the genetic code. PMID:26240376

  14. 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

  15. 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.

  16. 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

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

    PubMed

    Pisareva, Vera P; Pisarev, Andrey V

    2016-05-19

    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

  18. Calibration of sound calibrators: an overview

    NASA Astrophysics Data System (ADS)

    Milhomem, T. A. B.; Soares, Z. M. D.

    2016-07-01

    This paper presents an overview of calibration of sound calibrators. Initially, traditional calibration methods are presented. Following, the international standard IEC 60942 is discussed emphasizing parameters, target measurement uncertainty and criteria for conformance to the requirements of the standard. Last, Regional Metrology Organizations comparisons are summarized.

  19. THE NATURE OF FOSSIL GALAXY GROUPS: ARE THEY REALLY FOSSILS?

    SciTech Connect

    La Barbera, F.; Sorrentino, G.; De Carvalho, R. R.; De la Rosa, I. G.; Gal, R. R.; Kohl-Moreira, J. L.

    2009-04-15

    We use SDSS-DR4 photometric and spectroscopic data out to redshift z {approx} 0.1 combined with ROSAT All Sky Survey X-ray data to produce a sample of 25 fossil groups (FGs), defined as bound systems dominated by a single, luminous elliptical galaxy with extended X-ray emission. We examine possible biases introduced by varying the parameters used to define the sample, and the main pitfalls are also discussed. The spatial density of FGs, estimated via the V/V {sub MAX} test, is 2.83 x 10{sup -6} h {sup 3} {sub 75} Mpc{sup -3} for L{sub X} > 0.89 x 10{sup 42} h {sup -2} {sub 75} erg s{sup -1} consistent with Vikhlinin et al., who examined an X-ray overluminous elliptical galaxy sample (OLEG). We compare the general properties of FGs identified here with a sample of bright field ellipticals generated from the same data set. These two samples show no differences in the distribution of neighboring faint galaxy density excess, distance from the red sequence in the color-magnitude diagram, and structural parameters such as a {sub 4} and internal color gradients. Furthermore, examination of stellar populations shows that our 25 FGs have similar ages, metallicities, and {alpha}-enhancement as the bright field ellipticals, undermining the idea that these systems represent fossils of a physical mechanism that occurred at high redshift. Our study reveals no difference between FGs and field ellipticals, suggesting that FGs might not be a distinct family of true fossils, but rather the final stage of mass assembly in the universe.

  20. 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

  1. Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles

    PubMed Central

    Prabhakaran, Ramanandan; Chithambaram, Shivapriya

    2015-01-01

    Rapid biosynthesis is key to the success of bacteria and viruses. Highly expressed genes in bacteria exhibit a strong codon bias corresponding to the differential availability of tRNAs. However, a large clade of lambdoid coliphages exhibits relatively poor codon adaptation to the host translation machinery, in contrast to other coliphages that exhibit strong codon adaptation to the host. Three possible explanations were previously proposed but dismissed: (1) the phage-borne tRNA genes that reduce the dependence of phage translation on host tRNAs, (2) lack of time needed for evolving codon adaptation due to recent host switching, and (3) strong strand asymmetry with biased mutation disrupting codon adaptation. Here, we examined the possibility that phages with relatively poor codon adaptation have poor translation initiation which would weaken the selection on codon adaptation. We measured translation initiation by: (1) the strength and position of the Shine–Dalgarno (SD) sequence, and (2) the stability of the secondary structure of sequences flanking the SD and start codon known to affect accessibility of the SD sequence and start codon. Phage genes with strong codon adaptation had significantly stronger SD sequences than those with poor codon adaptation. The former also had significantly weaker secondary structure in sequences flanking the SD sequence and start codon than the latter. Thus, lambdoid phages do not exhibit strong codon adaptation because they have relatively inefficient translation initiation and would benefit little from increased elongation efficiency. We also provided evidence suggesting that phage lifestyle (virulent versus temperate) affected selection intensity on the efficiency of translation initiation and elongation. PMID:25614589

  2. 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

  3. Dinosaur Fossils Predict Body Temperatures

    PubMed Central

    Allen, Andrew P; Charnov, Eric L

    2006-01-01

    Perhaps the greatest mystery surrounding dinosaurs concerns whether they were endotherms, ectotherms, or some unique intermediate form. Here we present a model that yields estimates of dinosaur body temperature based on ontogenetic growth trajectories obtained from fossil bones. The model predicts that dinosaur body temperatures increased with body mass from approximately 25 °C at 12 kg to approximately 41 °C at 13,000 kg. The model also successfully predicts observed increases in body temperature with body mass for extant crocodiles. These results provide direct evidence that dinosaurs were reptiles that exhibited inertial homeothermy. PMID:16817695

  4. Fossil energy program. Summary document

    SciTech Connect

    1980-05-01

    This program summary document presents a comprehensive overview of the research, development, and demonstration (RD and D) activities that will be performed in FY 1981 by the Assistant Secretary for Fossil Energy (ASFE), US Department of Energy (DOE). The ASFE technology programs for the fossil resources of coal, petroleum (including oil shale) and gas have been established with the goal of making substantive contributions to the nation's future supply and efficienty use of energy. On April 29, 1977, the Administration submitted to Congress the National Energy Plan (NEP) and accompanying legislative proposals designed to establish a coherent energy policy structure for the United States. Congress passed the National Energy Act (NEA) on October 15, 1978, which allows implementation of the vital parts of the NEP. The NEP was supplemented by additional energy policy statements culminating in the President's address on July 15, 1979, presenting a program to further reduce dependence on imported petroleum. The passage of the NEA-related energy programs represent specific steps by the Administration and Congress to reorganize, redirect, and clarify the role of the Federal Government in the formulation and execution of national energy policy and programs. The energy technology RD and D prog4rams carried out by ASFE are an important part of the Federal Government's effort to provide the combination and amounts of energy resources needed to ensure national security and continued economic growth.

  5. Cycling operation of fossil plants

    SciTech Connect

    Devendorf, D.; Kulczycky, T.G. )

    1991-05-01

    A necessity for many utilities today is the cycling of their fossil units. Fossil plants with their higher fuel costs are being converted to cycling operation to accommodate daily load swings and to decrease the overall system fuel costs. For a large oil-fired unit, such as Oswego Steam Station Unit 5, millions of dollars can be saved annually in fuel costs if the unit operates in a two-shift mode. However, there are also penalties attributable to cycling operation which are associated with availability and thermal performance. The objectives of Niagara Mohawk Power Corporation were to minimize the losses in availability and performance, and the degradation in the life of the equipment by incorporating certain cycling modifications into the unit. The objective of this project was to evaluate the effectiveness of three of these cycling modifications: (1) the superheater and turbine bypass (Hot Restart System), (2) the use of variable pressure operation, and (3) the full-flow condensate polishing system. To meet this objective, Unit 5 was tested using the cycling modifications, and a dynamic mathematical model of this unit was developed using the Modular Modeling System (MMS) Code from EPRI. This model was used to evaluate various operating modes and to assist in the assessment of operating procedures. 15 refs., 41 figs., 22 tabs.

  6. Cloning and expression of codon-optimized recombinant darbepoetin alfa in Leishmania tarentolae T7-TR.

    PubMed

    Kianmehr, Anvarsadat; Golavar, Raziyeh; Rouintan, Mandana; Mahrooz, Abdolkarim; Fard-Esfahani, Pezhman; Oladnabi, Morteza; Khajeniazi, Safoura; Mostafavi, Seyede Samaneh; Omidinia, Eskandar

    2016-02-01

    Darbepoetin alfa is an engineered and hyperglycosylated analog of recombinant human erythropoietin (EPO) which is used as a drug in treating anemia in patients with chronic kidney failure and cancer. This study desribes the secretory expression of a codon-optimized recombinant form of darbepoetin alfa in Leishmania tarentolae T7-TR. Synthetic codon-optimized gene was amplified by PCR and cloned into the pLEXSY-I-blecherry3 vector. The resultant expression vector, pLEXSYDarbo, was purified, digested, and electroporated into the L. tarentolae. Expression of recombinant darbepoetin alfa was evaluated by ELISA, reverse-transcription PCR (RT-PCR), Western blotting, and biological activity. After codon optimization, codon adaptation index (CAI) of the gene raised from 0.50 to 0.99 and its GC% content changed from 56% to 58%. Expression analysis confirmed the presence of a protein band at 40 kDa. Furthermore, reticulocyte experiment results revealed that the activity of expressed darbepoetin alfa was similar to that of its equivalent expressed in Chinese hamster ovary (CHO) cells. These data suggested that the codon optimization and expression in L. tarentolae host provided an efficient approach for high level expression of darbepoetin alfa. PMID:26546410

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

    PubMed

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

    2013-10-01

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

  8. 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

  9. Codon influence on protein expression in E. coli correlates with mRNA levels.

    PubMed

    Boël, Grégory; Letso, Reka; Neely, Helen; Price, W Nicholson; Wong, Kam-Ho; Su, Min; Luff, Jon D; Valecha, Mayank; Everett, John K; Acton, Thomas B; Xiao, Rong; Montelione, Gaetano T; Aalberts, Daniel P; Hunt, John F

    2016-01-21

    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 analyse 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

  10. Enhancement of premature stop codon readthrough in the CFTR gene by Ataluren (PTC124) derivatives.

    PubMed

    Pibiri, Ivana; Lentini, Laura; Melfi, Raffaella; Gallucci, Giulia; Pace, Andrea; Spinello, Angelo; Barone, Giampaolo; Di Leonardo, Aldo

    2015-08-28

    Premature stop codons are the result of nonsense mutations occurring within the coding sequence of a gene. These mutations lead to the synthesis of a truncated protein and are responsible for several genetic diseases. A potential pharmacological approach to treat these diseases is to promote the translational readthrough of premature stop codons by small molecules aiming to restore the full-length protein. The compound PTC124 (Ataluren) was reported to promote the readthrough of the premature UGA stop codon, although its activity was questioned. The potential interaction of PTC124 with mutated mRNA was recently suggested by molecular dynamics (MD) studies highlighting the importance of H-bonding and stacking π-π interactions. To improve the readthrough activity we changed the fluorine number and position in the PTC124 fluoroaryl moiety. The readthrough ability of these PTC124 derivatives was tested in human cells harboring reporter plasmids with premature stop codons in H2BGFP and FLuc genes as well as in cystic fibrosis (CF) IB3.1 cells with a nonsense mutation. Maintaining low toxicity, three of these molecules showed higher efficacy than PTC124 in the readthrough of the UGA premature stop codon and in recovering the expression of the CFTR protein in IB3.1 cells from cystic fibrosis patient. Molecular dynamics simulations performed with mutated CFTR mRNA fragments and active or inactive derivatives are in agreement with the suggested interaction of PTC124 with mRNA. PMID:26142488

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

    PubMed Central

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

    1993-01-01

    It has been reported that CUG, a universal leucine codon, is read as serine in an asporogenic yeast, Candida cylindracea. The distribution of this non-universal genetic code in various yeast species was studied using an in vitro translation assay system with a synthetic messenger RNA containing CUG codons in-frame. It was found that CUG is used as a serine codon in six out of the fourteen species examined, while it is used for leucine in the remaining eight. The tRNA species responsible for the translation of codon CUG as serine was detected in all the six species in which CUG is translated as serine. The grouping according to the CUG codon assignments in these yeast species shows a good correlation with physiological classification by the chain lengths of the isoprenoid moiety of ubiquinone and the cell-wall sugar contained in the yeasts. The six Candida species examined in which CUG is used as serine belong to one distinct group in Hemiascomycetes. PMID:8371978

  12. Hydroxylation and translational adaptation to stress: some answers lie beyond the STOP codon.

    PubMed

    Katz, M J; Gándara, L; De Lella Ezcurra, A L; Wappner, P

    2016-05-01

    Regulation of protein synthesis contributes to maintenance of homeostasis and adaptation to environmental changes. mRNA translation is controlled at various levels including initiation, elongation and termination, through post-transcriptional/translational modifications of components of the protein synthesis machinery. Recently, protein and RNA hydroxylation have emerged as important enzymatic modifications of tRNAs, elongation and termination factors, as well as ribosomal proteins. These modifications enable a correct STOP codon recognition, ensuring translational fidelity. Recent studies are starting to show that STOP codon read-through is related to the ability of the cell to cope with different types of stress, such as oxidative and chemical insults, while correlations between defects in hydroxylation of protein synthesis components and STOP codon read-through are beginning to emerge. In this review we will discuss our current knowledge of protein synthesis regulation through hydroxylation of components of the translation machinery, with special focus on STOP codon recognition. We speculate on the possibility that programmed STOP codon read-through, modulated by hydroxylation of components of the protein synthesis machinery, is part of a concerted cellular response to stress. PMID:26874685

  13. The Effect of an Alternate Start Codon on Heterologous Expression of a PhoA Fusion Protein in Mycoplasma gallisepticum.

    PubMed

    Panicker, Indu S; Browning, Glenn F; Markham, Philip F

    2015-01-01

    While the genomes of many Mycoplasma species have been sequenced, there are no collated data on translational start codon usage, and the effects of alternate start codons on gene expression have not been studied. Analysis of the annotated genomes found that ATG was the most prevalent translational start codon among Mycoplasma spp. However in Mycoplasma gallisepticum a GTG start codon is commonly used in the vlhA multigene family, which encodes a highly abundant, phase variable lipoprotein adhesin. Therefore, the effect of this alternate start codon on expression of a reporter PhoA lipoprotein was examined in M. gallisepticum. Mutation of the start codon from ATG to GTG resulted in a 2.5 fold reduction in the level of transcription of the phoA reporter, but the level of PhoA activity in the transformants containing phoA with a GTG start codon was only 63% of that of the transformants with a phoA with an ATG start codon, suggesting that GTG was a more efficient translational initiation codon. The effect of swapping the translational start codon in phoA reporter gene expression was less in M. gallisepticum than has been seen previously in Escherichia coli or Bacillus subtilis, suggesting the process of translational initiation in mycoplasmas may have some significant differences from those used in other bacteria. This is the first study of translational start codon usage in mycoplasmas and the impact of the use of an alternate start codon on expression in these bacteria. PMID:26010086

  14. The Effect of an Alternate Start Codon on Heterologous Expression of a PhoA Fusion Protein in Mycoplasma gallisepticum

    PubMed Central

    Panicker, Indu S.; Browning, Glenn F.; Markham, Philip F.

    2015-01-01

    While the genomes of many Mycoplasma species have been sequenced, there are no collated data on translational start codon usage, and the effects of alternate start codons on gene expression have not been studied. Analysis of the annotated genomes found that ATG was the most prevalent translational start codon among Mycoplasma spp. However in Mycoplasma gallisepticum a GTG start codon is commonly used in the vlhA multigene family, which encodes a highly abundant, phase variable lipoprotein adhesin. Therefore, the effect of this alternate start codon on expression of a reporter PhoA lipoprotein was examined in M. gallisepticum. Mutation of the start codon from ATG to GTG resulted in a 2.5 fold reduction in the level of transcription of the phoA reporter, but the level of PhoA activity in the transformants containing phoA with a GTG start codon was only 63% of that of the transformants with a phoA with an ATG start codon, suggesting that GTG was a more efficient translational initiation codon. The effect of swapping the translational start codon in phoA reporter gene expression was less in M. gallisepticum than has been seen previously in Escherichia coli or Bacillus subtilis, suggesting the process of translational initiation in mycoplasmas may have some significant differences from those used in other bacteria. This is the first study of translational start codon usage in mycoplasmas and the impact of the use of an alternate start codon on expression in these bacteria. PMID:26010086

  15. Fossil energy biotechnology: A research needs assessment

    NASA Astrophysics Data System (ADS)

    1993-11-01

    The Office of Program Analysis of the U.S. Department of Energy commissioned this study to evaluate and prioritize research needs in fossil energy biotechnology. The objectives were to identify research initiatives in biotechnology that offer timely and strategic options for the more efficient and effective uses of the Nation's fossil resource base, particularly the early identification of new and novel applications of biotechnology for the use or conversion of domestic fossil fuels. Fossil energy biotechnology consists of a number of diverse and distinct technologies, all related by the common denominator -- biocatalysis. The expert panel organized 14 technical subjects into three interrelated biotechnology programs: (1) upgrading the fuel value of fossil fuels; (2) bioconversion of fossil feedstocks and refined products to added value chemicals; and (3) the development of environmental management strategies to minimize and mitigate the release of toxic and hazardous petrochemical wastes.

  16. 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.

  17. 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. PMID:25901796

  18. 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

  19. Fossilization Processes in Thermal Springs

    NASA Technical Reports Server (NTRS)

    Farmer, Jack D.; Cady, Sherry; Desmarais, David J.; Chang, Sherwood (Technical Monitor)

    1995-01-01

    To create a comparative framework for the study of ancient examples, we have been carrying out parallel studies of the microbial biosedimentology, taphonomy and geochemistry of modem and sub-Recent thermal spring deposits. One goal of the research is the development of integrated litho- and taphofacies models for siliceous and travertline sinters. Thermal springs are regarded as important environments for the origin and early evolution of life on Earth, and we seek to utilize information from the fossil record to reconstruct the evolution of high temperature ecosystems. Microbial contributions to the fabric of thermal spring sinters occur when population growth rates keep pace with, or exceed rates of inorganic precipitation, allowing for the development of continuous biofilms or mats. In siliceous thermal springs, microorganisms are typically entombed while viable. Modes of preservation reflect the balance between rates of organic matter degradation, silica precipitation and secondary infilling. Subaerial sinters are initially quite porous and permeable and at temperatures higher than about 20 C, organic materials are usually degraded prior to secondary infilling of sinter frameworks. Thus, organically-preserved microfossils are rare and fossil information consists of characteristic biofabrics formed by the encrustation and underplating of microbial mat surfaces. This probably accounts for the typically low total organic carbon values observed in thermal spring deposits. In mid-temperature, (approx. 35 - 59 C) ponds and outflows, the surface morphology of tufted Phormidium mats is preserved through mat underplating by thin siliceous: crusts. Microbial taxes lead to clumping of ceils and/or preferred filament orientations that together define higher order composite fabrics in thermal spring stromatolites (e.g. network, coniform, and palisade). At lower temperatures (less than 35 C), Calothrix mats cover shallow terracette pools forming flat carpets or pustular

  20. Experimental taphonomy and the anatomy and diversity of the earliest fossil vertebrates (Chengjiang Biota, Cambrian, China)

    NASA Astrophysics Data System (ADS)

    Purnell, Mark; Gabbott, Sarah; Murdock, Duncan; Cong, Peiyun

    2016-04-01

    The oldest fossil vertebrates are from the Lower Cambrian Chengjiang biota of China, which contains four genera of fish-like, primitive vertebrates: Haikouichthys, Myllokunmingia, Zhongjianichthys and Zhongxiniscus. These fossils play key roles in calibrating molecular clocks and informing our view of the anatomy of animals close to the origin of vertebrates, potentially including transitional forms between vertebrates and their nearest relatives. Despite the evident importance of these fossils, the degree to which taphonomic processes have affected their anatomical completeness has not been investigated. For example, some or all might have been affected by stemward slippage - the pattern observed in experimental decay of non-biomineralised chordates in which preferential decay of synapomorphies and retention of plesiomorphic characters would cause fossil taxa to erroneously occupy more basal positions than they should. This hypothesis is based on experimental data derived from decay of non-biomineralised chordates under laboratory conditions. We have expanded this analysis to include a broader range of potentially significant environmental variables; we have also compared and combined the results of experiments from several taxa to identify general patterns of chordate decay. Examination of the Chengjiang vertebrates in the light of these results demonstrates that, contrary to some assertions, experimentally derived models of phylogenetic bias are applicable to fossils. Anatomical and phylogenetic interpretations of early vertebrates that do not take taphonomic biases into account risk overestimating diversity and the evolutionary significance of differences between fossil specimens.

  1. Deoxygenation in cycling fossil plants

    SciTech Connect

    Pearl, W.L.; Hobart, R.L.; Hook, T.A.; McNea, D.A. )

    1992-04-01

    In a previous EPRI study (Phase 1 of RP1184-9) at the Port Everglades plant of Florida Power and Light, it was demonstrated that minimizing shutdown oxygen levels at a cycling plant could reduce corrosion product transport to the boilers. A continuation of the program was performed to demonstrate the use of two forms of activated carbon to catalyze the hydrazine/oxygen reaction as a method to minimize the oxygen levels of cycling fossil plants. An activated carbon impregnated fiber overlay on a powdered resin precoat was tested at TU Electric's Tradinghouse Creek Unit 1 and a carbon bed followed by a deep bed demineralizer was tested at Duquesne's Elrama Unit 4. The improvement in attainable oxygen control was demonstrated and the effect on corrosion product transport during cyclic operation was evaluated. The study also demonstrated the application of a data acquisition system for prompt data assessment, control of chemical additions, identification of problems, and development of responsive corrective actions.

  2. Fossil diatoms and neogene paleolimnology

    USGS Publications Warehouse

    Platt, Bradbury J.

    1988-01-01

    Diatoms have played an important role in the development of Neogene continental biostratigraphy and paleolimnology since the mid-19th Century. The history of progress in Quaternary diatom biostratigraphy has developed as a result of improved coring techniques that enable sampling sediments beneath existing lakes coupled with improved chronological control (including radiometric dating and varve enumeration), improved statistical treatment of fossil diatom assemblages (from qualitative description to influx calculations of diatom numbers or volumes), and improved ecological information about analogous living diatom associations. The last factor, diatom ecology, is the most critical in many ways, but progresses slowly. Fortunately, statistical comparison of modern diatom assemblages and insightful studies of the nutrient requirements of some common freshwater species are enabling diatom paleolimnologists to make more detailed interpretations of the Quaternary record than had been possible earlier, and progress in the field of diatom biology and ecology will continue to refine paleolimnological studies. The greater age and geologic setting of Tertiary diatomaceous deposits has prompted their study in the contexts of geologic history, biochronology and evolution. The distribution of diatoms of marine affinities in continental deposits has given geologists insights about tectonism and sea-level change, and the distribution of distinctive (extinct?) diatoms has found utilization both in making stratigraphic correlations between outcrops of diatomaceous deposits and in various types of biochronological studies that involve dating deposits in different areas. A continental diatom biochronologic scheme will rely upon evolution, such as the appearance of new genera within a family, in combination with regional environmental changes that are responsible for the wide distribution of distinctive diatom species. The increased use of the scanning electron microscope for the

  3. Improving self-calibration

    NASA Astrophysics Data System (ADS)

    Enßlin, Torsten A.; Junklewitz, Henrik; Winderling, Lars; Greiner, Maksim; Selig, Marco

    2014-10-01

    Response calibration is the process of inferring how much the measured data depend on the signal one is interested in. It is essential for any quantitative signal estimation on the basis of the data. Here, we investigate self-calibration methods for linear signal measurements and linear dependence of the response on the calibration parameters. The common practice is to augment an external calibration solution using a known reference signal with an internal calibration on the unknown measurement signal itself. Contemporary self-calibration schemes try to find a self-consistent solution for signal and calibration by exploiting redundancies in the measurements. This can be understood in terms of maximizing the joint probability of signal and calibration. However, the full uncertainty structure of this joint probability around its maximum is thereby not taken into account by these schemes. Therefore, better schemes, in sense of minimal square error, can be designed by accounting for asymmetries in the uncertainty of signal and calibration. We argue that at least a systematic correction of the common self-calibration scheme should be applied in many measurement situations in order to properly treat uncertainties of the signal on which one calibrates. Otherwise, the calibration solutions suffer from a systematic bias, which consequently distorts the signal reconstruction. Furthermore, we argue that nonparametric, signal-to-noise filtered calibration should provide more accurate reconstructions than the common bin averages and provide a new, improved self-calibration scheme. We illustrate our findings with a simplistic numerical example.

  4. 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

  5. Implicit Spacecraft Gyro Calibration

    NASA Technical Reports Server (NTRS)

    Harman, Richard; Bar-Itzhack, Itzhack Y.

    2003-01-01

    This paper presents an implicit algorithm for spacecraft onboard instrument calibration, particularly to onboard gyro calibration. This work is an extension of previous work that was done where an explicit gyro calibration algorithm was applied to the AQUA spacecraft gyros. The algorithm presented in this paper was tested using simulated data and real data that were downloaded from the Microwave Anisotropy Probe (MAP) spacecraft. The calibration tests gave very good results. A comparison between the use of the implicit calibration algorithm used here with the explicit algorithm used for AQUA spacecraft indicates that both provide an excellent estimation of the gyro calibration parameters with similar accuracies.

  6. Forty Years Later: Updating the Fossilization Hypothesis

    ERIC Educational Resources Information Center

    Han, ZhaoHong

    2013-01-01

    A founding concept in second language acquisition (SLA) research, fossilization has been fundamental to understanding second language (L2) development. The Fossilization Hypothesis, introduced in Selinker's seminal text (1972), has thus been one of the most influential theories, guiding a significant bulk of SLA research for four decades; 2012…

  7. The original colours of fossil beetles

    PubMed Central

    McNamara, Maria E.; Briggs, Derek E. G.; Orr, Patrick J.; Noh, Heeso; Cao, Hui

    2012-01-01

    Structural colours, the most intense, reflective and pure colours in nature, are generated when light is scattered by complex nanostructures. Metallic structural colours are widespread among modern insects and can be preserved in their fossil counterparts, but it is unclear whether the colours have been altered during fossilization, and whether the absence of colours is always real. To resolve these issues, we investigated fossil beetles from five Cenozoic biotas. Metallic colours in these specimens are generated by an epicuticular multi-layer reflector; the fidelity of its preservation correlates with that of other key cuticular ultrastructures. Where these other ultrastructures are well preserved in non-metallic fossil specimens, we can infer that the original cuticle lacked a multi-layer reflector; its absence in the fossil is not a preservational artefact. Reconstructions of the original colours of the fossils based on the structure of the multi-layer reflector show that the preserved colours are offset systematically to longer wavelengths; this probably reflects alteration of the refractive index of the epicuticle during fossilization. These findings will allow the former presence, and original hue, of metallic structural colours to be identified in diverse fossil insects, thus providing critical evidence of the evolution of structural colour in this group. PMID:21957131

  8. Automated Camera Calibration

    NASA Technical Reports Server (NTRS)

    Chen, Siqi; Cheng, Yang; Willson, Reg

    2006-01-01

    Automated Camera Calibration (ACAL) is a computer program that automates the generation of calibration data for camera models used in machine vision systems. Machine vision camera models describe the mapping between points in three-dimensional (3D) space in front of the camera and the corresponding points in two-dimensional (2D) space in the camera s image. Calibrating a camera model requires a set of calibration data containing known 3D-to-2D point correspondences for the given camera system. Generating calibration data typically involves taking images of a calibration target where the 3D locations of the target s fiducial marks are known, and then measuring the 2D locations of the fiducial marks in the images. ACAL automates the analysis of calibration target images and greatly speeds the overall calibration process.

  9. 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

  10. 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

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

    PubMed Central

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

    2012-01-01

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

  12. 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…

  13. Analytical multicollimator camera calibration

    USGS Publications Warehouse

    Tayman, W.P.

    1978-01-01

    Calibration with the U.S. Geological survey multicollimator determines the calibrated focal length, the point of symmetry, the radial distortion referred to the point of symmetry, and the asymmetric characteristiecs of the camera lens. For this project, two cameras were calibrated, a Zeiss RMK A 15/23 and a Wild RC 8. Four test exposures were made with each camera. Results are tabulated for each exposure and averaged for each set. Copies of the standard USGS calibration reports are included. ?? 1978.

  14. 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

  15. 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

  16. 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. PMID:25839760

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

    PubMed

    Kessler, Michael D; Dean, Matthew D

    2014-10-01

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic dive...

  19. Partitioning between recoding and termination at a stop codon-selenocysteine insertion sequence.

    PubMed

    Kotini, Suresh Babu; Peske, Frank; Rodnina, Marina V

    2015-07-27

    Selenocysteine (Sec) is inserted into proteins by recoding a UGA stop codon followed by a selenocysteine insertion sequence (SECIS). UGA recoding by the Sec machinery is believed to be very inefficient owing to RF2-mediated termination at UGA. Here we show that recoding efficiency in vivo is 30-40% independently of the cell growth rate. Efficient recoding requires sufficient selenium concentrations in the medium. RF2 is an unexpectedly poor competitor of Sec. We recapitulate the major characteristics of SECIS-dependent UGA recoding in vitro using a fragment of fdhF-mRNA encoding a natural bacterial selenoprotein. Only 40% of actively translating ribosomes that reach the UGA codon insert Sec, even in the absence of RF2, suggesting that the capacity to insert Sec into proteins is inherently limited. RF2 does not compete with the Sec incorporation machinery; rather, it terminates translation on those ribosomes that failed to incorporate Sec. The data suggest a model in which early recruitment of Sec-tRNA(Sec)-SelB-GTP to the SECIS blocks the access of RF2 to the stop codon, thereby prioritizing recoding over termination at Sec-dedicated stop codons. PMID:26040702

  20. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. Effects of codon modification on human BMP2 gene expression in tobacco plants.

    PubMed

    Suo, Guangli; Chen, Bing; Zhang, Jingyu; Duan, Ziyuan; He, Zhengquan; Yao, Wei; Yue, Chaoyin; Dai, Jianwu

    2006-07-01

    Bone morphogenetic protein 2 (BMP2) has great potential in therapeutic applications. We are working on generating transgenic plants as a bioreactor to produce BMP2. We have studied the effects of codon optimization on the expression of human BMP2 (hBMP2) in tobacco plants. Three modified hBMP2 genes were transformed into tobacco under the control of either cauliflower mosaic virus 35S (CaMV35S) promoter or double-CaMV35S promoter plus alfalfa mosaic virus (AMV) enhancer. The fused beta-glucuronidase (GUS) reporter gene was used to facilitate the assay of protein expression. The results indicated that codon optimization could increase the protein expression level obviously under CaMV35S promoter. However, under relatively stronger initiation condition (double-CaMV35S promoter plus AMV enhancer), only the gene with the lowest degree of codon optimization could increase the protein expression level. Our findings suggest that the action of codon optimization may be influenced by the factors of promoter strength and A+T content in tobacco plants. PMID:16491379

  3. Solving the riddle of codon usage preferences: a test for translational selection

    PubMed Central

    Reis, Mario dos; Savva, Renos; Wernisch, Lorenz

    2004-01-01

    Translational selection is responsible for the unequal usage of synonymous codons in protein coding genes in a wide variety of organisms. It is one of the most subtle and pervasive forces of molecular evolution, yet, establishing the underlying causes for its idiosyncratic behaviour across living kingdoms has proven elusive to researchers over the past 20 years. In this study, a statistical model for measuring translational selection in any given genome is developed, and the test is applied to 126 fully sequenced genomes, ranging from archaea to eukaryotes. It is shown that tRNA gene redundancy and genome size are interacting forces that ultimately determine the action of translational selection, and that an optimal genome size exists for which this kind of selection is maximal. Accordingly, genome size also presents upper and lower boundaries beyond which selection on codon usage is not possible. We propose a model where the coevolution of genome size and tRNA genes explains the observed patterns in translational selection in all living organisms. This model finally unifies our understanding of codon usage across prokaryotes and eukaryotes. Helicobacter pylori, Saccharomyces cerevisiae and Homo sapiens are codon usage paradigms that can be better understood under the proposed model. PMID:15448185

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

    PubMed Central

    Roymondal, Uttam; Das, Shibsankar; Sahoo, Satyabrata

    2009-01-01

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

  5. 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

  6. The future of fossil fuels

    NASA Astrophysics Data System (ADS)

    Lackner, Klaus

    2007-03-01

    With today's energy technology, the world faces a stark choice between economic growth and a healthy environment. The accumulation of CO2 in the atmosphere must stop, while energy services to a growing world population striving for a high standard of living must improve. New technologies must eliminate CO2 emissions. Only carbon capture and storage can maintain access to fossil carbon reserves that by themselves could satisfy energy demand for centuries. Technologies for CO2 capture at power plants and other large sources already exist. A new generation of efficient, clean power plants could capture its CO2 and deliver it for underground injection or mineral sequestration. However, the remaining CO2 emissions from distributed sources are too large to be ignored. Either hydrogen or electricity need to substitute for carbonaceous energy carriers, or CO2 emissions must be balanced out by capturing an equivalent amount of carbon from the environment. Biomass growth offers one such option; direct capture of CO2 from the air provides another. Carbon capture and storage technologies can close the anthropogenic carbon cycle and, thus, provide one possible avenue to a world that is not limited by energy constraints.

  7. Cycling operation of fossil plants

    SciTech Connect

    Bhatnagar, U.S.; Weiss, M.D.; White, W.H. ); Buchanan, T.L.; Harvey, L.E.; Shewchuk, P.K.; Weinstein, R.E. )

    1991-05-01

    This report presents a methodology for examining the economic feasibility of converting fossil power plants from baseload to cycling service. It employs this approach to examine a proposed change of Pepco's Potomac River units 3, 4, and 5 from baseload operation of two-shift cycling. The project team first reviewed all components and listed potential cycling effects involved in the conversion of Potomac River units 3, 4, and 5. They developed general cycling plant screening criteria including the number of hot, warm, or cold restart per year and desired load ramp rates. In addition, they evaluated specific limitations on the boiler, turbine, and the balance of plant. They estimated the remaining life of the facility through component evaluation and boiler testing and also identified and prioritized potential component deficiencies by their impact on key operational factors: safety, heat rate, turn down, startup/shutdown time, and plant availability. They developed solutions to these problems; and, since many solutions mitigate more than one problem, they combined and reprioritized these synergistic solutions. Economic assessments were performed on all solutions. 13 figs., 20 tabs.

  8. Estimating the Phanerozoic history of the Ascomycota lineages: combining fossil and molecular data.

    PubMed

    Beimforde, Christina; Feldberg, Kathrin; Nylinder, Stephan; Rikkinen, Jouko; Tuovila, Hanna; Dörfelt, Heinrich; Gube, Matthias; Jackson, Daniel J; Reitner, Joachim; Seyfullah, Leyla J; Schmidt, Alexander R

    2014-09-01

    The phylum Ascomycota is by far the largest group in the fungal kingdom. Ecologically important mutualistic associations such as mycorrhizae and lichens have evolved in this group, which are regarded as key innovations that supported the evolution of land plants. Only a few attempts have been made to date the origin of Ascomycota lineages by using molecular clock methods, which is primarily due to the lack of satisfactory fossil calibration data. For this reason we have evaluated all of the oldest available ascomycete fossils from amber (Albian to Miocene) and chert (Devonian and Maastrichtian). The fossils represent five major ascomycete classes (Coniocybomycetes, Dothideomycetes, Eurotiomycetes, Laboulbeniomycetes, and Lecanoromycetes). We have assembled a multi-gene data set (18SrDNA, 28SrDNA, RPB1 and RPB2) from a total of 145 taxa representing most groups of the Ascomycota and utilized fossil calibration points solely from within the ascomycetes to estimate divergence times of Ascomycota lineages with a Bayesian approach. Our results suggest an initial diversification of the Pezizomycotina in the Ordovician, followed by repeated splits of lineages throughout the Phanerozoic, and indicate that this continuous diversification was unaffected by mass extinctions. We suggest that the ecological diversity within each lineage ensured that at least some taxa of each group were able to survive global crises and rapidly recovered. PMID:24792086

  9. Molecules and fossils reveal punctuated diversification in Caribbean “faviid” corals

    PubMed Central

    2012-01-01

    Background Even with well-known sampling biases, the fossil record is key to understanding macro-evolutionary patterns. During the Miocene to Pleistocene in the Caribbean Sea, the fossil record of scleractinian corals shows a remarkable period of rapid diversification followed by massive extinction. Here we combine a time-calibrated molecular phylogeny based on three nuclear introns with an updated fossil stratigraphy to examine patterns of radiation and extinction in Caribbean corals within the traditional family Faviidae. Results Concatenated phylogenetic analysis showed most species of Caribbean faviids were monophyletic, with the exception of two Manicina species. The time-calibrated tree revealed the stem group originated around the closure of the Tethys Sea (17.0 Ma), while the genus Manicina diversified during the Late Miocene (8.20 Ma), when increased sedimentation and productivity may have favored free-living, heterotrophic species. Reef and shallow water specialists, represented by Diploria and Favia, originate at the beginning of the Pliocene (5 – 6 Ma) as the Isthmus of Panama shoaled and regional productivity declined. Conclusions Later origination of the stem group than predicted from the fossil record corroborates the hypothesis of morphological convergence in Diploria and Favia genera. Our data support the rapid evolution of morphological and life-history traits among faviid corals that can be linked to Mio-Pliocene environmental changes. PMID:22831179

  10. Codon reassignment to facilitate genetic engineering and biocontainment in the chloroplast of Chlamydomonas reinhardtii.

    PubMed

    Young, Rosanna E B; Purton, Saul

    2016-05-01

    There is a growing interest in the use of microalgae as low-cost hosts for the synthesis of recombinant products such as therapeutic proteins and bioactive metabolites. In particular, the chloroplast, with its small, genetically tractable genome (plastome) and elaborate metabolism, represents an attractive platform for genetic engineering. In Chlamydomonas reinhardtii, none of the 69 protein-coding genes in the plastome uses the stop codon UGA, therefore this spare codon can be exploited as a useful synthetic biology tool. Here, we report the assignment of the codon to one for tryptophan and show that this can be used as an effective strategy for addressing a key problem in chloroplast engineering: namely, the assembly of expression cassettes in Escherichia coli when the gene product is toxic to the bacterium. This problem arises because the prokaryotic nature of chloroplast promoters and ribosome-binding sites used in such cassettes often results in transgene expression in E. coli, and is a potential issue when cloning genes for metabolic enzymes, antibacterial proteins and integral membrane proteins. We show that replacement of tryptophan codons with the spare codon (UGG→UGA) within a transgene prevents functional expression in E. coli and in the chloroplast, and that co-introduction of a plastidial trnW gene carrying a modified anticodon restores function only in the latter by allowing UGA readthrough. We demonstrate the utility of this system by expressing two genes known to be highly toxic to E. coli and discuss its value in providing an enhanced level of biocontainment for transplastomic microalgae. PMID:26471875

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

    PubMed

    Martín-Galiano, Antonio J; Wells, Jerry M; de la Campa, Adela G

    2004-07-01

    A codon-profile strategy was used to predict gene expression levels in Streptococcus pneumoniae. Predicted highly expressed (PHE) genes included those encoding glycolytic and fermentative enzymes, sugar-conversion systems and carbohydrate-transporters. Additionally, some genes required for infection that are involved in oxidative metabolism and hydrogen peroxide production were PHE. Low expression values were predicted for genes encoding specific regulatory proteins like two-component systems and competence genes. Correspondence analysis localized 484 ORFs which shared a distinctive codon profile in the right horn. These genes had a mean G+C content (33.4 %) that was lower than the bulk of the genome coding sequences (39.7 %), suggesting that many of them were acquired by horizontal transfer. Half of these genes (242) were pseudogenes, ORFs shorter than 80 codons or without assigned function. The remaining genes included several virulence factors, such as capsular genes, iga, lytB, nanB, pspA, choline-binding proteins, and functions related to DNA acquisition, such as restriction-modification systems and comDE. In order to compare predicted translation rate with the relative amounts of mRNA for each gene, the codon adaptation index (CAI) values were compared with microarray fluorescence intensity values following hybridization of labelled RNA from laboratory-grown cultures. High mRNA amounts were observed in 32.5 % of PHE genes and in 64 % of the 25 genes with the highest CAI values. However, high relative amounts of RNA were also detected in 10.4 % of non-PHE genes, such as those encoding fatty acid metabolism enzymes and proteases, suggesting that their expression might also be regulated at the level of transcription or mRNA stability under the conditions tested. The effects of codon bias and mRNA amount on different gene groups in S. pneumoniae are discussed. PMID:15256573

  12. 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

  13. Coevolution between Stop Codon Usage and Release Factors in Bacterial Species.

    PubMed

    Wei, Yulong; Wang, Juan; Xia, Xuhua

    2016-09-01

    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

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

    PubMed Central

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

    2009-01-01

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

  15. Selective Constraints on Amino Acids Estimated by a Mechanistic Codon Substitution Model with Multiple Nucleotide Changes

    PubMed Central

    Miyazawa, Sanzo

    2011-01-01

    Background Empirical substitution matrices represent the average tendencies of substitutions over various protein families by sacrificing gene-level resolution. We develop a codon-based model, in which mutational tendencies of codon, a genetic code, and the strength of selective constraints against amino acid replacements can be tailored to a given gene. First, selective constraints averaged over proteins are estimated by maximizing the likelihood of each 1-PAM matrix of empirical amino acid (JTT, WAG, and LG) and codon (KHG) substitution matrices. Then, selective constraints specific to given proteins are approximated as a linear function of those estimated from the empirical substitution matrices. Results Akaike information criterion (AIC) values indicate that a model allowing multiple nucleotide changes fits the empirical substitution matrices significantly better. Also, the ML estimates of transition-transversion bias obtained from these empirical matrices are not so large as previously estimated. The selective constraints are characteristic of proteins rather than species. However, their relative strengths among amino acid pairs can be approximated not to depend very much on protein families but amino acid pairs, because the present model, in which selective constraints are approximated to be a linear function of those estimated from the JTT/WAG/LG/KHG matrices, can provide a good fit to other empirical substitution matrices including cpREV for chloroplast proteins and mtREV for vertebrate mitochondrial proteins. Conclusions/Significance The present codon-based model with the ML estimates of selective constraints and with adjustable mutation rates of nucleotide would be useful as a simple substitution model in ML and Bayesian inferences of molecular phylogenetic trees, and enables us to obtain biologically meaningful information at both nucleotide and amino acid levels from codon and protein sequences. PMID:21445250

  16. Structural characterization of eRF1 mutants indicate a complex mechanism of stop codon recognition.

    PubMed

    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, Q(122)FM(Y)F(126). RDCs were recorded on (15)N-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

  17. 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

  18. 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

  19. Methods for the quantitative comparison of molecular estimates of clade age and the fossil record.

    PubMed

    Clarke, Julia A; Boyd, Clint A

    2015-01-01

    together to describe the relationship between time trees and a set of fossil data, which we recommend be phylogenetically vetted and referred on the basis of apomorphy. Differences from previously proposed metrics and the utility of MDI and DIG range are illustrated in three empirical case studies from angiosperms, ostracods, and birds. These case studies also illustrate the ways in which MDI and DIG range may be used to assess time trees resultant from analyses varying in calibration regime, divergence dating approach or molecular sequence data analyzed. PMID:25281846

  20. SUMS calibration test report

    NASA Technical Reports Server (NTRS)

    Robertson, G.

    1982-01-01

    Calibration was performed on the shuttle upper atmosphere mass spectrometer (SUMS). The results of the calibration and the as run test procedures are presented. The output data is described, and engineering data conversion factors, tables and curves, and calibration on instrument gauges are included. Static calibration results which include: instrument sensitive versus external pressure for N2 and O2, data from each scan of calibration, data plots from N2 and O2, and sensitivity of SUMS at inlet for N2 and O2, and ratios of 14/28 for nitrogen and 16/32 for oxygen are given.

  1. Selective Preservation of Fossil Ghost Fish

    NASA Astrophysics Data System (ADS)

    Meacham, Amanda

    2016-04-01

    A unique type of fossil fish preservation has been discovered in the Angelo Member (Fossil Lake) of the Green River Formation. The Angelo Member is a predominately evaporative deposit dominated by dolomite, but contains facies of fossiliferous laminated calcimicrite. Fossil fish occurring in two beds conspicuously lack bones. Fish in the lower bed are only preserved as organic material, including skin, pigments, and eyes. Fish in the upper bed have three-dimensional etching where bones once existed but also contain skin, pigments, and eyes. The top third of the upper bed often contains calcite crystals that are pseudomorphs after trona and possibly halite. Preliminary mineralogical analysis and mapping of evaporate facies suggests that this unique preservation may be related to lake geochemical conditions, such as high pH and alkalinity. To our knowledge, this is the first time this type of preservation has been observed and studied. Fossils and sediments within these beds are being studied both vertically and laterally through the one-meter thick sequence containing the fossil fish using XRD, isotopic, SEM, thin section, and total organic carbon analysis. Nine quarries, 0.5-1 meter square, were excavated for both fossils and rock samples along with 17 additional rock sample locations across an approximately 25-kilometer square region. This investigation has the capability of reconstructing the paleoenvironment and lake chemistry of Fossil Lake during the deposition of the "ghost-fish" beds and solving the mystery of the "missing bones" and the unusual process of preservation.

  2. Fossil oak galls preserve ancient multitrophic interactions

    PubMed Central

    Stone, Graham N; van der Ham, Raymond W.J.M; Brewer, Jan G

    2008-01-01

    Trace fossils of insect feeding have contributed substantially to our understanding of the evolution of insect–plant interactions. The most complex phenotypes of herbivory are galls, whose diagnostic morphologies often allow the identification of the gall inducer. Although fossil insect-induced galls over 300 Myr old are known, most are two-dimensional impressions lacking adequate morphological detail either for the precise identification of the causer or for detection of the communities of specialist parasitoids and inquilines inhabiting modern plant galls. Here, we describe the first evidence for such multitrophic associations in Pleistocene fossil galls from the Eemian interglacial (130 000–115 000 years ago) of The Netherlands. The exceptionally well-preserved fossils can be attributed to extant species of Andricus gallwasps (Hymenoptera: Cynipidae) galling oaks (Quercus), and provide the first fossil evidence of gall attack by herbivorous inquiline gallwasps. Furthermore, phylogenetic placement of one fossil in a lineage showing obligate host plant alternation implies the presence of a second oak species, Quercus cerris, currently unknown from Eemian fossils in northwestern Europe. This contrasts with the southern European native range of Q. cerris in the current interglacial and suggests that gallwasp invasions following human planting of Q. cerris in northern Europe may represent a return to preglacial distribution limits. PMID:18559323

  3. The fossil record of evolution: Data on diversification and extinction

    NASA Technical Reports Server (NTRS)

    Sepkoski, J. J., Jr.

    1991-01-01

    Understanding of the evolution of complex life, and of the roles that changing terrestrial and extraterrestrial environments played in life's history, is dependent upon synthetic knowledge of the fossil record. Paleontologists have been describing fossils for more that two centuries. However, much of this information is dispersed in monographs and journal articles published throughout the world. Over the past several years, this literature was surveyed, and a data base on times of origination and extinction of fossil genera was compiled. The data base, which now holds approximately 32,000 genera, covers all taxonomic groups of marine animals, incorporates the most recent taxonomic assignments, and uses a detailed global time framework that can resolve originations and extinctions to intervals averaging three million years in duration. These data can be used to compile patterns of global biodiversity, measure rates of taxic evolution, and test hypotheses concerning adaptive radiations, mass extinctions, etc. Thus far, considerable effort was devoted to using the data to test the hypothesis of periodicity of mass extinction. Rates of extinction measured from the data base have also been used to calibrate models of evolutionary radiations in marine environments. It was observed that new groups, or clades of animals (i.e., orders and classes) tend to reach appreciable diversity first in nearshore environments and then to radiate in more offshore environments; during decline, these clades may disappear from the nearshore while persisting in offshore, deep water habitats. These observations have led to suggestions that there is something special about stressful or perturbed environments that promotes the evolution of novel kinds of animals that can rapidly replace their predecessors. The numerical model that is being investigated to study this phenomenon treats environments along onshore-offshore gradients as if they were discrete habitats. Other aspects of this

  4. Bayesian phylogenetic estimation of fossil ages.

    PubMed

    Drummond, Alexei J; Stadler, Tanja

    2016-07-19

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth-death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the 'morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue 'Dating species divergences using

  5. Bayesian phylogenetic estimation of fossil ages

    PubMed Central

    Drummond, Alexei J.; Stadler, Tanja

    2016-01-01

    Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses. This article is part of the themed issue ‘Dating species divergences

  6. Residual gas analyzer calibration

    NASA Technical Reports Server (NTRS)

    Lilienkamp, R. H.

    1972-01-01

    A technique which employs known gas mixtures to calibrate the residual gas analyzer (RGA) is described. The mass spectra from the RGA are recorded for each gas mixture. This mass spectra data and the mixture composition data each form a matrix. From the two matrices the calibration matrix may be computed. The matrix mathematics requires the number of calibration gas mixtures be equal to or greater than the number of gases included in the calibration. This technique was evaluated using a mathematical model of an RGA to generate the mass spectra. This model included shot noise errors in the mass spectra. Errors in the gas concentrations were also included in the valuation. The effects of these errors was studied by varying their magnitudes and comparing the resulting calibrations. Several methods of evaluating an actual calibration are presented. The effects of the number of gases in then, the composition of the calibration mixture, and the number of mixtures used are discussed.

  7. Spitzer Digs Up Galactic Fossil

    NASA Technical Reports Server (NTRS)

    2004-01-01

    [figure removed for brevity, see original site] Figure 1

    [figure removed for brevity, see original site] Figure 2

    This false-color image taken by NASA's Spitzer Space Telescope shows a globular cluster previously hidden in the dusty plane of our Milky Way galaxy. Globular clusters are compact bundles of old stars that date back to the birth of our galaxy, 13 or so billion years ago. Astronomers use these galactic 'fossils' as tools for studying the age and formation of the Milky Way.

    Most clusters orbit around the center of the galaxy well above its dust-enshrouded disc, or plane, while making brief, repeated passes through the plane that each last about a million years. Spitzer, with infrared eyes that can see into the dusty galactic plane, first spotted the newfound cluster during its current pass. A visible-light image (inset of Figure 1) shows only a dark patch of sky.

    The red streak behind the core of the cluster is a dust cloud, which may indicate the cluster's interaction with the Milky Way. Alternatively, this cloud may lie coincidentally along Spitzer's line of sight.

    Follow-up observations with the University of Wyoming Infrared Observatory helped set the distance of the new cluster at about 9,000 light-years from Earth - closer than most clusters - and set the mass at the equivalent of 300,000 Suns. The cluster's apparent size, as viewed from Earth, is comparable to a grain of rice held at arm's length. It is located in the constellation Aquila.

    Astronomers believe that this cluster may be one of the last in our galaxy to be uncovered.

    This image composite was taken on April 21, 2004, by Spitzer's infrared array camera. It is composed of images obtained at four wavelengths: 3.6 microns (blue), 4.5 microns (green), 5.8 microns (orange) and 8 microns (red).

    Galactic Fossil Found Behind Curtain of Dust In Figure 2, the image mosaic shows the same patch of sky in various wavelengths of light. While the

  8. A Fossil Group in Formation

    NASA Astrophysics Data System (ADS)

    Miller, Eric D.; Rappaport, Saul A.; McDonald, Michael; Bautz, Mark W.; Grant, Catherine E.; Veilleux, Sylvain

    2016-04-01

    In the current picture of hierarchical structure formation, galaxy groups play a vital role as the seeds from which large assemblies of matter form. Compact groups are also important environments in which to watch the fueling of star formation and AGN activity, as the conditions are ideal for galaxy-galaxy interactions. We have identified a galaxy system that may represent an intermediate or transition stage in group evolution. Shakhbazyan 1 (or SHK 1) is a remarkably compact collection of about ten massive, red-sequence galaxies within a region 100 kpc across. Several of these galaxies show signs of AGN activity, and new, deep optical observations with the Discovery Channel Telescope reveal an extended stellar envelope surrounding the galaxies. This envelope is much more extended than what would be expected from a superposition of normal galaxy envelopes, and it indicates a large amount of intra-group starlight, evidence that the galaxies in SHK 1 are dynamically interacting.We here present new Chandra spectral imaging observations of this unusual system that confirm the presence of an X-ray-emitting diffuse intra-group medium (IGM), with a temperature of 1.5 keV and X-ray luminosity of 1043 erg/s. Assuming hydrostatic equilibrium, the system is about 1/3 as massive as expected from the optical richness. In addition, three of the ten central galaxies exhibit signatures of X-ray AGN. The under-luminous IGM, high density of bright galaxies, and evidence for galaxy-galaxy interaction indicate that this system may be in a transition stage of galaxy merging, similar to that expected in the formation of a fossil group. Alternatively, SHK 1 may consist of multiple poor groups in the final stages of merging along our line of sight. We explore these scenarios and outline paths of future study for this enigmatic system.

  9. Assessing the fidelity of the fossil record by using marine bivalves

    PubMed Central

    Valentine, James W.; Jablonski, David; Kidwell, Susan; Roy, Kaustuv

    2006-01-01

    Taxa that fail to become incorporated into the fossil record can reveal much about the biases of this record and provide the information needed to correct such biases in empirical analyses of the history of life. Yet little is known about the characteristics of taxa missing from the fossil record. For the marine Bivalvia, which have become a model system for macroevolutionary and macroecological analysis in the fossil record, 308 of the 1,292 living genera and subgenera (herein termed “taxa”) are not recorded as fossils. These missing taxa are not a random sample of the clade, but instead tend to have small body size, reactive shell structures, commensal or parasitic habit, deep-sea distribution, narrow geographic range, restriction to regions exposing few Neogene marine sediments, or recent date of formal taxonomic description in the neontological literature. Most missing taxa show two or more of these features and tend to be concentrated in particular families. When we exclude the smallest taxa (<1 cm) and deep-sea endemics, date of published description and geographic range become the strongest predictors of the missing taxa; other factors are statistically insignificant or have relatively small effects. These biases might influence a variety of analyses including the use of fossil data in support of phylogenetic analyses, molecular clock calibrations, and analyses of spatial and temporal dynamics of clades and biotas. Clade inventories such as these can be used to develop protocols that minimize the biases imposed by sampling and preservation. PMID:16617108

  10. 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

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

    PubMed Central

    2013-01-01

    Background The human APOBEC3G (A3G) protein activity is associated with innate immunity against HIV-1 by inducing high rates of guanosines to adenosines (G-to-A) mutations (viz., hypermutation) in the viral DNA. If hypermutation is not enough to disrupt the reading frames of viral genes, it may likely increase the HIV-1 diversity. To counteract host innate immunity HIV-1 encodes the Vif protein that binds A3G protein and form complexes to be degraded by cellular proteolysis. Methods Here we studied the pattern of substitutions in the vif gene and its association with clinical status of HIV-1 infected individuals. To perform the study, unique vif gene sequences were generated from 400 antiretroviral-naïve individuals. Results The codon pairs: 78–154, 85–154, 101–157, 105–157, and 105–176 of vif gene were associated with CD4+ T cell count lower than 500 cells per mm3. Some of these codons were located in the 81LGQGVSIEW89 region and within the BC-Box. We also identified codons under positive selection clustered in the N-terminal region of Vif protein, between 21WKSLVK26 and 40YRHHY44 regions (i.e., 31, 33, 37, 39), within the BC-Box (i.e., 155, 159) and the Cullin5-Box (i.e., 168) of vif gene. All these regions are involved in the Vif-induced degradation of A3G/F complexes and the N-terminal of Vif protein binds to viral and cellular RNA. Conclusions Adaptive evolution of vif gene was mostly to optimize viral RNA binding and A3G/F recognition. Additionally, since there is not a fully resolved structure of the Vif protein, codon pairs associated with CD4+ T cell count may elucidate key regions that interact with host cell factors. Here we identified and discriminated codons under positive selection and codons under functional constraint in the vif gene of HIV-1. PMID:23578255

  12. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.

    PubMed

    Grote, Andreas; Hiller, Karsten; Scheer, Maurice; Münch, Richard; Nörtemann, Bernd; Hempel, Dietmar C; Jahn, Dieter

    2005-07-01

    A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values. In one example, all genes of the genome of Caenorhabditis elegans were adapted to Escherichia coli codon usage and further optimized to avoid commonly used restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene codon usage was adapted to E.coli codon usage with parallel avoidance of the same restriction sites. For both, the degree of introduced changes was documented and evaluated. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. JCat is freely accessible at http://www.prodoric.de/JCat. PMID:15980527

  13. Development incentives for fossil fuel subsidy reform

    NASA Astrophysics Data System (ADS)

    Jakob, Michael; Chen, Claudine; Fuss, Sabine; Marxen, Annika; Edenhofer, Ottmar

    2015-08-01

    Reforming fossil fuel subsidies could free up enough funds to finance universal access to water, sanitation, and electricity in many countries, as well as helping to cut global greenhouse-gas emissions.

  14. Proceedings: 1990 fossil plant cycling conference

    SciTech Connect

    Not Available

    1991-12-01

    Fossil plant cycling continues to be a key issue for many electric utilities. EPRI's previous cycling workshops, held in 1983, 1985, and 1987, allowed utilities to benefit from collective industry experience in the conversion of baseload fossil units to cyclic operation. Continued improvements in equipment, retrofits, diagnostics, and controls were highlighted at the 1990 conference. The objective is to provide a forum for utility discussions of the cycling operation of fossil fuel power plants. Potomac Electric Power Company (PEPCO) hosted the 1990 EPRI Fossil Fuel Cycling Conference in Washington, DC, on December 4--6, 1990. More than 130 representatives from utilities, vendors, government agencies, universities, and industry associations attended the conference. Following the general session, technical sessions covered such topics as plant modifications, utility retrofit experience, cycling economics, life assessment, controls, environmental controls, and energy storage. Attendees also toured PEPCO's Potomac River generating station, the site of an earlier EPRI cycling conversion study.

  15. Expected anomalies in the fossil record.

    PubMed

    Fischer, Mareike; Steel, Mike

    2008-01-01

    The problem of intermediates in the fossil record has been frequently discussed ever since Darwin. The extent of 'gaps' (missing transitional stages) has been used to argue against gradual evolution from a common ancestor. Traditionally, gaps have often been explained by the improbability of fossilization and the discontinuous selection of found fossils. Here we take an analytical approach and demonstrate why, under certain sampling conditions, we may not expect intermediates to be found. Using a simple null model, we show mathematically that the question of whether a taxon sampled from some time in the past is likely to be morphologically intermediate to other samples (dated earlier and later) depends on the shape and dimensions of the underlying phylogenetic tree that connects the taxa, and the times from which the fossils are sampled. PMID:19204808

  16. Fossil Finds Expand Early Hominid Anatomy.

    ERIC Educational Resources Information Center

    Bower, B.

    1991-01-01

    Hominid fossils found in late 1990 in Ethiopia are reported. A controversy surrounding these remains and those of earlier expeditions, including Lucy, over whether more than one species of hominid are represented is discussed. (CW)

  17. Microbial Fossils Detected in Desert Varnish

    NASA Astrophysics Data System (ADS)

    Flood, B. E.; Allen, C.; Longazo, T.

    2003-03-01

    Desert varnish, a mixture of clays, Mn-oxides, and Fe-oxides, is a potential terrestrial analogue to Martian hematite. A scanning electron microscopic examination of samples from Pilbara, Australia revealed evidence of microbial fossilization.

  18. The fossil record of the sixth extinction.

    PubMed

    Plotnick, Roy E; Smith, Felisa A; Lyons, S Kathleen

    2016-05-01

    Comparing the magnitude of the current biodiversity crisis with those in the fossil record is difficult without an understanding of differential preservation. Integrating data from palaeontological databases with information on IUCN status, ecology and life history characteristics of contemporary mammals, we demonstrate that only a small and biased fraction of threatened species (< 9%) have a fossil record, compared with 20% of non-threatened species. We find strong taphonomic biases related to body size and geographic range. Modern species with a fossil record tend to be large and widespread and were described in the 19(th) century. The expected magnitude of the current extinction based only on species with a fossil record is about half of that of one based on all modern species; values for genera are similar. The record of ancient extinctions may be similarly biased, with many species having originated and gone extinct without leaving a tangible record. PMID:26932459

  19. Fossil energy program. Progress report, July 1980

    SciTech Connect

    McNeese, L. E.

    1980-10-01

    This report - the seventy-second of a series - is a compendium of monthly progress reports for the ORNL research and development programs that are in support of the increased utilization of coal and other fossil fuel alternatives to oil and gas as sources of clean energy. The projects reported this month include those for coal conversion development, chemical research and development, materials technology, component development and process evaluation, technical support to major liquefaction projects, process and program analysis, fossil energy environmental analysis, coal preparation and waste utilization, coal preparation plant automation, atmospheric fluidized bed coal combustor for cogeneration, technical support to the TVA fluidized bed combustion demonstration plant program, fossil energy applications assessments, performance assurance system support for fossil energy projects, international assessment of atmospheric fluidized bed combustion technology, and PFBC systems analysis.

  20. Fossil facies of the Greater Caspian region

    NASA Astrophysics Data System (ADS)

    Svitoch, A. A.

    2015-05-01

    The Pliocene-Pleistocene marine sediments of the Great Caspian region host various lithological fossil facies, which reflect specific sedimentation conditions caused by different structural-geomorphologic settings, tectonic regimes, climates, and hydrologies. The facies of shelf, epicontinental basins, ingression gulfs and estuaries, intermontane and mountainous basins, and deep-sea depressions form a hierarchy of geological bodies from types to subtypes. Paragenetic associations of fossil facies, which form various series in space and along the section, are typical of marine sediments.

  1. 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

  2. Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses

    PubMed Central

    Endres, Lauren; Dedon, Peter C; Begley, Thomas J

    2015-01-01

    tRNA (tRNA) is a key molecule used for protein synthesis, with multiple points of stress-induced regulation that can include transcription, transcript processing, localization and ribonucleoside base modification. Enzyme-catalyzed modification of tRNA occurs at a number of base and sugar positions and has the potential to influence specific anticodon-codon interactions and regulate translation. Notably, altered tRNA modification has been linked to mitochondrial diseases and cancer progression. In this review, specific to Eukaryotic systems, we discuss how recent systems-level analyses using a bioanalytical platform have revealed that there is extensive reprogramming of tRNA modifications in response to cellular stress and during cell cycle progression. Combined with genome-wide codon bias analytics and gene expression studies, a model emerges in which stress-induced reprogramming of tRNA drives the translational regulation of critical response proteins whose transcripts display a distinct codon bias. Termed Modification Tunable Transcripts (MoTTs),1 we define them as (1) transcripts that use specific degenerate codons and codon biases to encode critical stress response proteins, and (2) transcripts whose translation is influenced by changes in wobble base tRNA modification. In this review we note that the MoTTs translational model is also applicable to the process of stop-codon recoding for selenocysteine incorporation, as stop-codon recoding involves a selective codon bias and modified tRNA to decode selenocysteine during the translation of a key subset of oxidative stress response proteins. Further, we discuss how in addition to RNA modification analytics, the comprehensive characterization of translational regulation of specific transcripts requires a variety of tools, including high coverage codon-reporters, ribosome profiling and linked genomic and proteomic approaches. Together these tools will yield important new insights into the role of translational

  3. Improving the efficiency of the genetic code by varying the codon length--the perfect genetic code.

    PubMed

    Doig, A J

    1997-10-01

    The function of DNA is to specify protein sequences. The four-base "alphabet" used in nucleic acids is translated to the 20 base alphabet of proteins (plus a stop signal) via the genetic code. The code is neither overlapping nor punctuated, but has mRNA sequences read in successive triplet codons until reaching a stop codon. The true genetic code uses three bases for every amino acid. The efficiency of the genetic code can be significantly increased if the requirement for a fixed codon length is dropped so that the more common amino acids have shorter codon lengths and rare amino acids have longer codon lengths. More efficient codes can be derived using the Shannon-Fano and Huffman coding algorithms. The compression achieved using a Huffman code cannot be improved upon. I have used these algorithms to derive efficient codes for representing protein sequences using both two and four bases. The length of DNA required to specify the complete set of protein sequences could be significantly shorter if transcription used a variable codon length. The restriction to a fixed codon length of three bases means that it takes 42% more DNA than the minimum necessary, and the genetic code is 70% efficient. One can think of many reasons why this maximally efficient code has not evolved: there is very little redundancy so almost any mutation causes an amino acid change. Many mutations will be potentially lethal frame-shift mutations, if the mutation leads to a change in codon length. It would be more difficult for the machinery of transcription to cope with a variable codon length. Nevertheless, in the strict and narrow sense of coding for protein sequences using the minimum length of DNA possible, the Huffman code derived here is perfect. PMID:9344740

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

    PubMed

    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

  5. 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

  6. Reconciling molecular phylogenies with the fossil record.

    PubMed

    Morlon, Hélène; Parsons, Todd L; Plotkin, Joshua B

    2011-09-27

    Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ~10 Myr. PMID:21930899

  7. Reconciling molecular phylogenies with the fossil record

    PubMed Central

    Morlon, Hélène; Parsons, Todd L.; Plotkin, Joshua B.

    2011-01-01

    Historical patterns of species diversity inferred from phylogenies typically contradict the direct evidence found in the fossil record. According to the fossil record, species frequently go extinct, and many clades experience periods of dramatic diversity loss. However, most analyses of molecular phylogenies fail to identify any periods of declining diversity, and they typically infer low levels of extinction. This striking inconsistency between phylogenies and fossils limits our understanding of macroevolution, and it undermines our confidence in phylogenetic inference. Here, we show that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies. To make this inference, we derive an analytic expression for the likelihood of a phylogeny that accommodates scenarios of declining diversity, time-variable rates, and incomplete sampling; we show that this likelihood expression reliably detects periods of diversity loss using simulation. We then study the cetaceans (whales, dolphins, and porpoises), a group for which standard phylogenetic inferences are strikingly inconsistent with fossil data. When the cetacean phylogeny is considered as a whole, recently radiating clades, such as the Balaneopteridae, Delphinidae, Phocoenidae, and Ziphiidae, mask the signal of extinctions. However, when isolating these groups, we infer diversity dynamics that are consistent with the fossil record. These results reconcile molecular phylogenies with fossil data, and they suggest that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr. PMID:21930899

  8. SAR calibration technology review

    NASA Technical Reports Server (NTRS)

    Walker, J. L.; Larson, R. W.

    1981-01-01

    Synthetic Aperture Radar (SAR) calibration technology including a general description of the primary calibration techniques and some of the factors which affect the performance of calibrated SAR systems are reviewed. The use of reference reflectors for measurement of the total system transfer function along with an on-board calibration signal generator for monitoring the temporal variations of the receiver to processor output is a practical approach for SAR calibration. However, preliminary error analysis and previous experimental measurements indicate that reflectivity measurement accuracies of better than 3 dB will be difficult to achieve. This is not adequate for many applications and, therefore, improved end-to-end SAR calibration techniques are required.

  9. 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.

  10. Fossil group origins. IV. Characterization of the sample and observational properties of fossil systems

    NASA Astrophysics Data System (ADS)

    Zarattini, S.; Barrena, R.; Girardi, M.; Castro-Rodriguez, N.; Boschin, W.; Aguerri, J. A. L.; Méndez-Abreu, J.; Sánchez-Janssen, R.; Catalán-Torrecilla, C.; Corsini, E. M.; del Burgo, C.; D'Onghia, E.; Herrera-Ruiz, N.; Iglesias-Páramo, J.; Jimenez Bailon, E.; Lozada Muoz, M.; Napolitano, N.; Vilchez, J. M.

    2014-05-01

    Context. Virialized halos grow by the accretion of smaller ones in the cold dark matter scenario. The rate of accretion depends on the different properties of the host halo. Those halos for which this accretion rate was very fast and efficient resulted in systems dominated by a central galaxy surrounded by smaller galaxies that were at least two magnitudes fainter. These galaxy systems are called fossil systems, and they can be the fossil relics of ancient galaxy structures. Aims: We started an extensive observational program to characterize a sample of 34 fossil group candidates spanning a broad range of physical properties. Methods: Deep r-band images were obtained with the 2.5-m Isaac Newton Telescope and Nordic Optic Telescope. Optical spectroscopic observations were performed at the 3.5-m Telescopio Nazionale Galileo for ~1200 galaxies. This new dataset was completed with Sloan Digital Sky Survey Data Release 7 archival data to obtain robust cluster membership and global properties of each fossil group candidate. For each system, we recomputed the magnitude gaps between the two brightest galaxies (Δm12) and the first and fourth ranked galaxies (Δm14) within 0.5 R200. We consider fossil systems to be those with Δm12 ≥ 2 mag or Δm14 ≥ 2.5 mag within the errors. Results: We find that 15 candidates turned out to be fossil systems. Their observational properties agree with those of non-fossil systems. Both follow the same correlations, but the fossil systems are always extreme cases. In particular, they host the brightest central galaxies, and the fraction of total galaxy light enclosed in the brightest group galaxy is larger in fossil than in non-fossil systems. Finally, we confirm the existence of genuine fossil clusters. Conclusions: Combining our results with others in the literature, we favor the merging scenario in which fossil systems formed from mergers of L∗ galaxies. The large magnitude gap is a consequence of the extreme merger ratio within

  11. Fossil group origins - VI. Global X-ray scaling relations of fossil galaxy clusters

    NASA Astrophysics Data System (ADS)

    Kundert, A.; Gastaldello, F.; D'Onghia, E.; Girardi, M.; Aguerri, J. A. L.; Barrena, R.; Corsini, E. M.; De Grandi, S.; Jiménez-Bailón, E.; Lozada-Muñoz, M.; Méndez-Abreu, J.; Sánchez-Janssen, R.; Wilcots, E.; Zarattini, S.

    2015-11-01

    We present the first pointed X-ray observations of 10 candidate fossil galaxy groups and clusters. With these Suzaku observations, we determine global temperatures and bolometric X-ray luminosities of the intracluster medium (ICM) out to r500 for six systems in our sample. The remaining four systems show signs of significant contamination from non-ICM sources. For the six objects with successfully determined r500 properties, we measure global temperatures in the range 2.8 ≤ TX ≤ 5.3 keV, bolometric X-ray luminosities of 0.8 × 1044 ≤ LX, bol ≤ 7.7 × 1044 erg s-1, and estimate masses, as derived from TX, of M500 ≳ 1014 M⊙. Fossil cluster scaling relations are constructed for a sample that combines our Suzaku observed fossils with fossils in the literature. Using measurements of global X-ray luminosity, temperature, optical luminosity, and velocity dispersion, scaling relations for the fossil sample are then compared with a control sample of non-fossil systems. We find the fits of our fossil cluster scaling relations are consistent with the relations for normal groups and clusters, indicating fossil clusters have global ICM X-ray properties similar to those of comparable mass non-fossil systems.

  12. Radiometer Calibration and Characterization

    Energy Science and Technology Software Center (ESTSC)

    1994-12-31

    The Radiometer Calibration and Characterization (RCC) software is a data acquisition and data archival system for performing Broadband Outdoor Radiometer Calibrations (BORCAL). RCC provides a unique method of calibrating solar radiometers using techniques that reduce measurement uncertainty and better characterize a radiometer’s response profile. The RCC software automatically monitors and controls many of the components that contribute to uncertainty in an instrument’s responsivity.

  13. 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

  14. 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

  15. 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.

  16. A POPULATION-SPECIFIC HTR2B STOP CODON PREDISPOSES TO SEVERE IMPULSIVITY

    PubMed Central

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

    2011-01-01

    SUMMARY Impulsivity, describing action without foresight, is an important feature of several psychiatric diseases, suicidality and violent behavior. The complex origins of impulsivity hinder identification of the genes influencing both it and diseases with which it is associated. We performed exon-centric sequencing of impulsive individuals in a founder population, targeting fourteen genes belonging to the serotonin and dopamine domain. A stop codon in HTR2B that is common (MAF >1%) but exclusive to Finns was identified. Expression of the gene in the human brain was assessed, as well as the molecular functionality of the stop codon that was associated with psychiatric diseases marked by impulsivity in both population and family-based analyses. Knockout of Htr2b increased impulsive behaviors in mice, indicative of predictive validity. Our study shows the potential for identifying and tracing effects of rare alleles in complex behavioral phenotypes using founder populations, and suggests a role for HTR2B in impulsivity. PMID:21179162

  17. Key for protein coding sequences identification: computer analysis of codon strategy.

    PubMed Central

    Rodier, F; Gabarro-Arpa, J; Ehrlich, R; Reiss, C

    1982-01-01

    The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be detected at N-termini of the proteins, the A/U enrichment results from a biased usage of the code degeneracy. A computer analysis is presented which allows easy detection of the codon strategy. N-terminal codons carry rather systematically A or U in third position, which suggests a mechanism for translation initiation and helps to detect protein coding sequences in sequenced DNA. PMID:7038623

  18. LWIR polarimeter calibration

    NASA Astrophysics Data System (ADS)

    Blumer, Robert V.; Miller, Miranda A.; Howe, James D.; Stevens, Mark A.

    2002-01-01

    Performance reported efforts to calibrate a MWIR imaging polarimeter met with moderate success. Recent efforts to calibrate a LWIR sensor using a different technique have been much more fruitful. For our sensor, which is based on a rotating retarder, we have improved system calibration substantially be including nonuniformity correction at all measurement positions of the retarder in our polarization data analysis. This technique can account for effects such as spurious optical reflections within a camera system that had been masquerading as false polarization in our previous data analysis methodology. Our techniques will be described and our calibration results will be quantified. Data from field-testing will be presented.

  19. The Science of Calibration

    NASA Astrophysics Data System (ADS)

    Kent, S. M.

    2016-05-01

    This paper presents a broad overview of the many issues involved in calibrating astronomical data, covering the full electromagnetic spectrum from radio waves to gamma rays, and considering both ground-based and space-based missions. These issues include the science drivers for absolute and relative calibration, the physics behind calibration and the mechanisms used to transfer it from the laboratory to an astronomical source, the need for networks of calibrated astronomical standards, and some of the challenges faced by large surveys and missions.

  20. Energy calibration via correlation

    NASA Astrophysics Data System (ADS)

    Maier, Daniel; Limousin, Olivier

    2016-03-01

    The main task of an energy calibration is to find a relation between pulse-height values and the corresponding energies. Doing this for each pulse-height channel individually requires an elaborated input spectrum with an excellent counting statistics and a sophisticated data analysis. This work presents an easy to handle energy calibration process which can operate reliably on calibration measurements with low counting statistics. The method uses a parameter based model for the energy calibration and concludes on the optimal parameters of the model by finding the best correlation between the measured pulse-height spectrum and multiple synthetic pulse-height spectra which are constructed with different sets of calibration parameters. A CdTe-based semiconductor detector and the line emissions of an 241Am source were used to test the performance of the correlation method in terms of systematic calibration errors for different counting statistics. Up to energies of 60 keV systematic errors were measured to be less than ~ 0.1 keV. Energy calibration via correlation can be applied to any kind of calibration spectra and shows a robust behavior at low counting statistics. It enables a fast and accurate calibration that can be used to monitor the spectroscopic properties of a detector system in near realtime.

  1. The COS Calibration Pipeline

    NASA Astrophysics Data System (ADS)

    Hodge, Philip E.; Keyes, C.; Kaiser, M.

    2007-12-01

    The COS calibration pipeline (CALCOS) includes three main components: basic calibration, wavelength calibration, and spectral extraction. Calibration of modes using the far ultraviolet (FUV) and near ultraviolet (NUV) detectors share a common structure, although the individual reference files differ and there are some additional steps for the FUV channel. The pipeline is designed to calibrate data acquired in either ACCUM or time-tag mode. The basic calibration includes pulse-height filtering and geometric correction for FUV, and flat-field, deadtime, and Doppler correction for both detectors. Wavelength calibration can be done either by using separate lamp exposures or by taking several short lamp exposures concurrently with a science exposure. For time-tag data, the latter mode ("tagflash") will allow better correction of potential drift of the spectrum on the detector. One-dimensional spectra will be extracted and saved in a FITS binary table. Separate columns will be used for the flux-calibrated spectrum, error estimate, and the associated wavelengths. CALCOS is written in Python, with some functions in C. It is similar in style to other HST pipeline code in that it uses an association table to specify which files to be included, and the calibration steps to be performed and the reference files to use are specified by header keywords. Currently, in conjunction with the Instrument Definition Team (led by J. Green), the ground-based reference files are being refined, delivered, and tested with the pipeline.

  2. Laser interferometer calibration station

    NASA Astrophysics Data System (ADS)

    Campolmi, R. W.; Krupski, S. J.

    1981-10-01

    The laser interferometer is a versatile tool, used for calibration over both long and short distances. It is considered traceable to the National Bureau of Standards. The system developed under this project was to be capable of providing for the calibration of many types of small linear measurement devices. The logistics of the original concept of one location for calibration of all mics, calipers, etc. at a large manufacturing facility proved unworkable. The equipment was instead used for the calibration of the large machines used to manufacture cannon tubes.

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

    PubMed

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

    2013-02-01

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

  4. Mutational analysis of IDH1 codon 132 in glioblastomas and other common cancers.

    PubMed

    Kang, Mi Ran; Kim, Min Sung; Oh, Ji Eun; Kim, Yoo Ri; Song, Sang Yong; Seo, Seong Il; Lee, Ji Youl; Yoo, Nam Jin; Lee, Sug Hyung

    2009-07-15

    Missense somatic mutations in IDH1 gene affecting codon 132 have recently been reported in glioblastoma multiforme (GBM) and other gliomas. The recurrent nature of the IDH1 mutations in the same amino acid strongly suggests that the mutations may play important roles in the pathogenesis of glial tumors. The aim of this study was to see whether the IDH1 codon 132 mutations occur in other human cancers besides glial tumors. We also attempted to confirm the occurrence of the IDH1 mutations in GBM of Korean patients. We have analyzed 1,186 cancer tissues from various origins, including carcinomas from breast, colon, lung, stomach, esophagus, liver, prostate, urinary bladder, ovary, uterine cervix, skin and kidney, and malignant mesotheliomas, primary GBM, malignant meningiomas, multiple myelomas and acute leukemias by single-strand conformation polymorphism analysis. We found four IDH1 codon 132 mutations in the GBM (4/25; 16.0%), two in the prostate carcinomas (2/75; 2.7%) and one in the B-acute lymphoblastic leukemias (B-ALL) (1/60; 1.7%), but none in other cancers. The IDH1 mutations consisted of five p.R132H and two p.R132C mutations. The data indicate that IDH1 codon 132 mutations occur not only in GBM, but also in prostate cancers and B-ALL. This study suggests that despite the infrequent incidence of the IDH1 mutations in prostate cancers and B-ALL, mutated IDH1 could be therapeutically targeted in these cancers and in glial tumors with the IDH1 mutations. PMID:19378339

  5. Two-codon T-box riboswitch binding two tRNAs

    PubMed Central

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

    2013-01-01

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

  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. 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

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

    PubMed Central

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

    1985-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Sneppen, Kim; Semsey, Szabolcs

    2014-12-01

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

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

    PubMed

    Sneppen, Kim; Semsey, Szabolcs

    2014-01-01

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

  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. Highly reproductive Escherichia coli cells with no specific assignment to the UAG codon

    PubMed Central

    Mukai, Takahito; Hoshi, Hiroko; Ohtake, Kazumasa; Takahashi, Mihoko; Yamaguchi, Atsushi; Hayashi, Akiko; Yokoyama, Shigeyuki; Sakamoto, Kensaku

    2015-01-01

    Escherichia coli is a widely used host organism for recombinant technology, and the bacterial incorporation of non-natural amino acids promises the efficient synthesis of proteins with novel structures and properties. In the present study, we developed E. coli strains in which the UAG codon was reserved for non-natural amino acids, without compromising the reproductive strength of the host cells. Ninety-five of the 273 UAG stop codons were replaced synonymously in the genome of E. coli BL21(DE3), by exploiting the oligonucleotide-mediated base-mismatch-repair mechanism. This genomic modification allowed the safe elimination of the UAG-recognizing cellular component (RF-1), thus leaving the remaining 178 UAG codons with no specific molecule recognizing them. The resulting strain B-95.ΔA grew as vigorously as BL21(DE3) in rich medium at 25–42°C, and its derivative B-95.ΔAΔfabR was better adapted to low temperatures and minimal media than B-95.ΔA. UAG was reassigned to synthetic amino acids by expressing the specific pairs of UAG-reading tRNA and aminoacyl-tRNA synthetase. Due to the preserved growth vigor, the B-95.ΔA strains showed superior productivities for hirudin molecules sulfonated on a particular tyrosine residue, and the Fab fragments of Herceptin containing multiple azido groups. PMID:25982672

  13. Optimization of Codon Translation Rates via tRNA Modifications Maintains Proteome Integrity

    PubMed Central

    Nedialkova, Danny D.; Leidel, Sebastian A.

    2015-01-01

    Summary Proteins begin to fold as they emerge from translating ribosomes. The kinetics of ribosome transit along a given mRNA can influence nascent chain folding, but the extent to which individual codon translation rates impact proteome integrity remains unknown. Here, we show that slower decoding of discrete codons elicits widespread protein aggregation in vivo. Using ribosome profiling, we find that loss of anticodon wobble uridine (U34) modifications in a subset of tRNAs leads to ribosome pausing at their cognate codons in S. cerevisiae and C. elegans. Cells lacking U34 modifications exhibit gene expression hallmarks of proteotoxic stress, accumulate aggregates of endogenous proteins, and are severely compromised in clearing stress-induced protein aggregates. Overexpression of hypomodified tRNAs alleviates ribosome pausing, concomitantly restoring protein homeostasis. Our findings demonstrate that modified U34 is an evolutionarily conserved accelerator of decoding and reveal an unanticipated role for tRNA modifications in maintaining proteome integrity. PMID:26052047

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

    PubMed Central

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

    2014-01-01

    Summary During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit. Here, we present a cryoEM reconstruction of a yeast preinitiation complex at 4.0 Å resolution with initiator tRNA in the PIN state, prior to eIF1 release. The structure reveals stabilization of the codon-anticodon duplex by the N-terminal tail of eIF1A, changes in the structure of eIF1 likely instrumental in its subsequent release, and changes in the conformation of eIF2. The mRNA traverses the entire mRNA cleft and makes connections to the regulatory domain of eIF2α, eIF1A, and ribosomal elements that allow recognition of context nucleotides surrounding the AUG codon. PMID:25417110

  15. 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.

  16. 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

  17. 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 which it is produced natively by MAP bacilli. When heterologously over-expressed, antigenic determinants were preserved in synthetic MMP proteins as shown by monoclonal antibody mediated ELISA. Moreover, MMP is a membrane protein in MAP, which is also targeted to the cellular surface of recombinant L. salivarius at levels comparable to MAP. Additionally, we previously engineered MAP3733c (encoding MptD) and show herein that MptD displays the tendency to associate with the cytoplasmic membrane boundary under confocal microscopy and the intracellularly accumulated protein selectively adheres to the MptD-specific bacteriophage fMptD. This work demonstrates there is potential for L. salivarius as a viable antigen delivery vehicle for MAP, which may provide an effective mucosal vaccine against Johne's disease. PMID:25237653

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

    PubMed

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

    2014-01-01

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

  19. On the Age of Eukaryotes: Evaluating Evidence from Fossils and Molecular Clocks

    PubMed Central

    Eme, Laura; Sharpe, Susan C.; Brown, Matthew W.; Roger, Andrew J.

    2014-01-01

    Our understanding of the phylogenetic relationships among eukaryotic lineages has improved dramatically over the few past decades thanks to the development of sophisticated phylogenetic methods and models of evolution, in combination with the increasing availability of sequence data for a variety of eukaryotic lineages. Concurrently, efforts have been made to infer the age of major evolutionary events along the tree of eukaryotes using fossil-calibrated molecular clock-based methods. Here, we review the progress and pitfalls in estimating the age of the last eukaryotic common ancestor (LECA) and major lineages. After reviewing previous attempts to date deep eukaryote divergences, we present the results of a Bayesian relaxed-molecular clock analysis of a large dataset (159 proteins, 85 taxa) using 19 fossil calibrations. We show that for major eukaryote groups estimated dates of divergence, as well as their credible intervals, are heavily influenced by the relaxed molecular clock models and methods used, and by the nature and treatment of fossil calibrations. Whereas the estimated age of LECA varied widely, ranging from 1007 (943–1102) Ma to 1898 (1655–2094) Ma, all analyses suggested that the eukaryotic supergroups subsequently diverged rapidly (i.e., within 300 Ma of LECA). The extreme variability of these and previously published analyses preclude definitive conclusions regarding the age of major eukaryote clades at this time. As more reliable fossil data on eukaryotes from the Proterozoic become available and improvements are made in relaxed molecular clock modeling, we may be able to date the age of extant eukaryotes more precisely. PMID:25085908

  20. The properties of fossil groups of galaxies

    NASA Astrophysics Data System (ADS)

    Eigenthaler, P.; Zeilinger, W. W.

    2009-12-01

    Numerical simulations as well as optical and X-ray observations over the last few years have shown that poor groups of galaxies can evolve to what is called a fossil group. Dynamical friction as the driving process leads to the coalescence of individual galaxies in ordinary poor groups leaving behind nothing more than a central, massive elliptical galaxy supposed to contain the merger history of the whole group. Due to merging timescales for less-massive galaxies and gas cooling timescales of the X-ray intragroup medium exceeding a Hubble time, a surrounding faint-galaxy population having survived this galactic cannibalism as well as an extended X-ray halo similar to that found in ordinary groups, is expected. Recent studies suggest that fossil groups are very abundant and could be the progenitors of brightest cluster galaxies (BCGs) in the centers of rich galaxy clusters. However, only a few objects are known to the literature. This article aims to summarize the results of observational fossil group research over the last few years and presents ongoing work by the authors. Complementary to previous research, the SDSS and RASS surveys have been cross-correlated to identify new fossil structures yielding 34 newly detected fossil group candidates. Observations with ISIS at the 4.2 m William Herschel Telescope on La Palma have been carried out to study the stellar populations of the central ellipticals of 6 fossil groups. In addition multi-object spectroscopy with VLTs VIMOS has been performed to study the shape of the OLF of one fossil system.

  1. Dental development in living and fossil orangutans.

    PubMed

    Smith, Tanya M

    2016-05-01

    Numerous studies have investigated molar development in extant and fossil hominoids, yet relatively little is known about orangutans, the only great ape with an extensive fossil record. This study characterizes aspects of dental development, including cuspal enamel daily secretion rate, long-period line periodicities, cusp-specific molar crown formation times and extension rates, and initiation and completion ages in living and fossil orangutan postcanine teeth. Daily secretion rate and periodicities in living orangutans are similar to previous reports, while crown formation times often exceed published values, although direct comparisons are limited. One wild Bornean individual died at 4.5 years of age with fully erupted first molars (M1s), while a captive individual and a wild Sumatran individual likely erupted their M1s around five or six years of age. These data underscore the need for additional samples of orangutans of known sex, species, and developmental environment to explore potential sources of variation in molar emergence and their relationship to life history variables. Fossil orangutans possess larger crowns than living orangutans, show similarities in periodicities, and have faster daily secretion rate, longer crown formation times, and slower extension rates. Molar crown formation times exceed reported values for other fossil apes, including Gigantopithecus blacki. When compared to African apes, both living and fossil orangutans show greater cuspal enamel thickness values and periodicities, resulting in longer crown formation times and slower extension rates. Several of these variables are similar to modern humans, representing examples of convergent evolution. Molar crown formation does not appear to be equivalent among extant great apes or consistent within living and fossil members of Pongo or Homo. PMID:27178461

  2. African fossil tali: further multivariate morphometric studies.

    PubMed

    Lisowski, F P; Albrecht, G H

    1976-07-01

    Analysis of measurements from the tali of 21 individual fossil primates from Africa shows that the specimens fall into five clearly defined groups. Accordingly, these specimens have been included as groups along with extant species in a subsequent canonical analysis thus allowing the fossils to play their part in the determination of the canonical separations. The results of this procedure show that the five fossil groups lie in a part of the canonical space not occupied by any extant African primate. Their positions are between the envelope of Asiatic apes (Hylobates and Pongo) and the envelope of African forms near the edge which contains Pan and Papio. One fossil group is so similar to Hylobates that its talus may have functioned in locomotion in a parallel manner. Others lie near to Pongo in directions proceeding towards Pan and Papio and it is possible that this similarity may indicate remnants of morphological adaptation for climbing in these fossils. At the same time, however, individual specimens are closer to one or another of the extant groups and this considerable spread suggests that the locomotor adaptations as evidenced by talar morphology, of the primate fauna in Africa, may have been very different from those of the present day. This would not the inconsistent with the different habitats, floras and non-primate faunas that may have characterized the East African scene at these earlier times. Particular fossils from Olduvai and Kromdraai that are supposed to be australopithecine and therefore bipeds, are confirmed (Oxnard, '72; Lisowski et al., '74) as being totally different from man in their talar morphology and essentially rather similar to the majority of the other fossil tali examined. PMID:961834

  3. Downregulating viral gene expression: codon usage bias manipulation for the generation of novel influenza A virus vaccines

    PubMed Central

    Baker, Steven F; Nogales, Aitor; Martínez-Sobrido, Luis

    2015-01-01

    Vaccination represents the best option to protect humans against influenza virus. However, improving the effectiveness of current vaccines could better stifle the health burden caused by viral infection. Protein synthesis from individual genes can be downregulated by synthetically deoptimizing a gene’s codon usage. With more rapid and affordable nucleotide synthesis, generating viruses that contain genes with deoptimized codons is now feasible. Attenuated, vaccine-candidate viruses can thus be engineered with hitherto uncharacterized properties. With eight gene segments, influenza A viruses with variably recoded genomes can produce a spectrum of attenuation that is contingent on the gene segment targeted and the number of codon changes. This review summarizes different targets and approaches to deoptimize influenza A virus codons for novel vaccine generation. PMID:26213563

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

    PubMed Central

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

    2011-01-01

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

  5. Self-catalytic DNA depurination underlies human β-globin gene mutations at codon 6 that cause anemias and thalassemias.

    PubMed

    Alvarez-Dominguez, Juan R; Amosova, Olga; Fresco, Jacques R

    2013-04-19

    The human β-globin gene contains an 18-nucleotide coding strand sequence centered at codon 6 and capable of forming a stem-loop structure that can self-catalyze depurination of the 5'G residue of that codon. The resultant apurinic lesion is subject to error-prone repair, consistent with the occurrence about this codon of mutations responsible for 6 anemias and β-thalassemias and additional substitutions without clinical consequences. The 4-residue loop of this stem-loop-forming sequence shows the highest incidence of mutation across the gene. The loop and first stem base pair-forming residues appeared early in the mammalian clade. The other stem-forming segments evolved more recently among primates, thereby conferring self-depurination capacity at codon 6. These observations indicate a conserved molecular mechanism leading to β-globin variants underlying phenotypic diversity and disease. PMID:23457306

  6. Photogrammetric camera calibration

    USGS Publications Warehouse

    Tayman, W.P.; Ziemann, H.

    1984-01-01

    Section 2 (Calibration) of the document "Recommended Procedures for Calibrating Photogrammetric Cameras and Related Optical Tests" from the International Archives of Photogrammetry, Vol. XIII, Part 4, is reviewed in the light of recent practical work, and suggestions for changes are made. These suggestions are intended as a basis for a further discussion. ?? 1984.

  7. Calibration facility safety plan

    NASA Technical Reports Server (NTRS)

    Fastie, W. G.

    1971-01-01

    A set of requirements is presented to insure the highest practical standard of safety for the Apollo 17 Calibration Facility in terms of identifying all critical or catastrophic type hazard areas. Plans for either counteracting or eliminating these areas are presented. All functional operations in calibrating the ultraviolet spectrometer and the testing of its components are described.

  8. OLI Radiometric Calibration

    NASA Technical Reports Server (NTRS)

    Markham, Brian; Morfitt, Ron; Kvaran, Geir; Biggar, Stuart; Leisso, Nathan; Czapla-Myers, Jeff

    2011-01-01

    Goals: (1) Present an overview of the pre-launch radiance, reflectance & uniformity calibration of the Operational Land Imager (OLI) (1a) Transfer to orbit/heliostat (1b) Linearity (2) Discuss on-orbit plans for radiance, reflectance and uniformity calibration of the OLI

  9. Differentiating between Near- and Non-Cognate Codons in Saccharomyces cerevisiae

    PubMed Central

    Plant, Ewan P.; Nguyen, Phuc; Russ, Jonathan R.; Pittman, Yvette R.; Nguyen, Thai; Quesinberry, Jack T.; Kinzy, Terri Goss; Dinman, Jonathan D.

    2007-01-01

    Background Decoding of mRNAs is performed by aminoacyl tRNAs (aa-tRNAs). This process is highly accurate, however, at low frequencies (10−3 – 10−4) the wrong aa-tRNA can be selected, leading to incorporation of aberrant amino acids. Although our understanding of what constitutes the correct or cognate aa-tRNA:mRNA interaction is well defined, a functional distinction between near-cognate or single mismatched, and unpaired or non-cognate interactions is lacking. Methodology/Principal Findings Misreading of several synonymous codon substitutions at the catalytic site of firefly luciferase was assayed in Saccharomyces cerevisiae. Analysis of the results in the context of current kinetic and biophysical models of aa-tRNA selection suggests that the defining feature of near-cognate aa-tRNAs is their potential to form mini-helical structures with A-site codons, enabling stimulation of GTPase activity of eukaryotic Elongation Factor 1A (eEF1A). Paromomycin specifically stimulated misreading of near-cognate but not of non-cognate aa-tRNAs, providing a functional probe to distinguish between these two classes. Deletion of the accessory elongation factor eEF1Bγ promoted increased misreading of near-cognate, but hyperaccurate reading of non-cognate codons, suggesting that this factor also has a role in tRNA discrimination. A mutant of eEF1Bα, the nucleotide exchange factor for eEF1A, promoted a general increase in fidelity, suggesting that the decreased rates of elongation may provide more time for discrimination between aa-tRNAs. A mutant form of ribosomal protein L5 promoted hyperaccurate decoding of both types of codons, even though it is topologically distant from the decoding center. Conclusions/Signficance It is important to distinguish between near-cognate and non-cognate mRNA:tRNA interactions, because such a definition may be important for informing therapeutic strategies for suppressing these two different categories of mutations underlying many human

  10. Sandia WIPP calibration traceability

    SciTech Connect

    Schuhen, M.D.; Dean, T.A.

    1996-05-01

    This report summarizes the work performed to establish calibration traceability for the instrumentation used by Sandia National Laboratories at the Waste Isolation Pilot Plant (WIPP) during testing from 1980-1985. Identifying the calibration traceability is an important part of establishing a pedigree for the data and is part of the qualification of existing data. In general, the requirement states that the calibration of Measuring and Test equipment must have a valid relationship to nationally recognized standards or the basis for the calibration must be documented. Sandia recognized that just establishing calibration traceability would not necessarily mean that all QA requirements were met during the certification of test instrumentation. To address this concern, the assessment was expanded to include various activities.

  11. Fossil fuels in a trillion tonne world

    NASA Astrophysics Data System (ADS)

    Scott, Vivian; Haszeldine, R. Stuart; Tett, Simon F. B.; Oschlies, Andreas

    2015-05-01

    The useful energy services and energy density value of fossil carbon fuels could be retained for longer timescales into the future if their combustion is balanced by CO2 recapture and storage. We assess the global balance between fossil carbon supply and the sufficiency (size) and capability (technology, security) of candidate carbon stores. A hierarchy of value for extraction-to-storage pairings is proposed, which is augmented by classification of CO2 containment as temporary (<1,000 yr) or permanent (>100,000 yr). Using temporary stores is inefficient and defers an intergenerational problem. Permanent storage capacity is adequate to technically match current fossil fuel reserves. However, rates of storage creation cannot balance current and expected rates of fossil fuel extraction and CO2 consequences. Extraction of conventional natural gas is uniquely holistic because it creates the capacity to re-inject an equivalent tonnage of carbon for storage into the same reservoir and can re-use gas-extraction infrastructure for storage. By contrast, balancing the extraction of coal, oil, biomass and unconventional fossil fuels requires the engineering and validation of additional carbon storage. Such storage is, so far, unproven in sufficiency.

  12. Macroevolutionary developmental biology: Embryos, fossils, and phylogenies.

    PubMed

    Organ, Chris L; Cooper, Lisa Noelle; Hieronymus, Tobin L

    2015-10-01

    The field of evolutionary developmental biology is broadly focused on identifying the genetic and developmental mechanisms underlying morphological diversity. Connecting the genotype with the phenotype means that evo-devo research often considers a wide range of evidence, from genetics and morphology to fossils. In this commentary, we provide an overview and framework for integrating fossil ontogenetic data with developmental data using phylogenetic comparative methods to test macroevolutionary hypotheses. We survey the vertebrate fossil record of preserved embryos and discuss how phylogenetic comparative methods can integrate data from developmental genetics and paleontology. Fossil embryos provide limited, yet critical, developmental data from deep time. They help constrain when developmental innovations first appeared during the history of life and also reveal the order in which related morphologies evolved. Phylogenetic comparative methods provide a powerful statistical approach that allows evo-devo researchers to infer the presence of nonpreserved developmental traits in fossil species and to detect discordant evolutionary patterns and processes across levels of biological organization. PMID:26250386

  13. 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

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

    PubMed Central

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

    2013-01-01

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

  15. 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

  16. 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

  17. Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

    PubMed Central

    Yahara, Koji; Furuta, Yoshikazu; Morimoto, Shinpei; Kikutake, Chie; Komukai, Sho; Matelska, Dorota; Dunin-Horkawicz, Stanisław; Bujnicki, Janusz M.; Uchiyama, Ikuo; Kobayashi, Ichizo

    2016-01-01

    Selection has been a central issue in biology in eukaryotes as well as prokaryotes. Inference of selection in recombining bacterial species, compared with clonal ones, has been a challenge. It is not known how codons under diversifying selection are distributed along the chromosome or among functional categories or how frequently such codons are subject to mutual homologous recombination. Here, we explored these questions by analysing genes present in >90% among 29 genomes of Helicobacter pylori, one of the bacterial species with the highest mutation and recombination rates. By a method for recombining sequences, we identified codons under diversifying selection (dN/dS > 1), which were widely distributed and accounted for ∼0.2% of all the codons of the genome. The codons were enriched in genes of host interaction/cell surface and genome maintenance (DNA replication, recombination, repair, and restriction modification system). The encoded amino acid residues were sometimes found adjacent to critical catalytic/binding residues in protein structures. Furthermore, by estimating the intensity of homologous recombination at a single nucleotide level, we found that these codons appear to be more frequently subject to recombination. We expect that the present study provides a new approach to population genomics of selection in recombining prokaryotes. PMID:26961370

  18. Deviation from major codons in the Toll-like receptor genes is associated with low Toll-like receptor expression

    PubMed Central

    Zhong, Fei; Cao, Weiping; Chan, Edmund; Tay, Puei Nam; Cahya, Florence Feby; Zhang, Haifeng; Lu, Jinhua

    2005-01-01

    Microbial structures activate Toll-like receptors (TLRs) and TLR-mediated cell signalling elicits and regulates host immunity. Most TLRs are poorly expressed but the underlying expression mechanism is not clear. Examination TLR sequences revealed that most human TLR genes deviated from using major human codons. CD14 resembles TLRs in sequence but its gene preferentially uses major codons. Indeed, CD14 expression on monocytes was higher than expression of TLR1 and TLR2. The TLR9 gene is abundant in major codons and it also showed higher expression than TLR1, TLR2 and TLR7 in transfected 293T cells. Change of the 5′-end 302 base pairs of the TLR2 sequence into major human codons markedly increased TLR2 expression, which led to increased TLR2-mediated constitutive nuclear factor-κB activation. Change of the 5′-end 381 base pairs of the CD14 sequence into prevalent TLR codons markedly reduced CD14 expression. These results collectively show that the deviation of TLR sequences from using major codons dictates the low TLR expression and this may protect the host against excessive inflammation and tissue damages. PMID:15606798

  19. 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

  20. The Association Between p53 Codon 72 Polymorphism and Endometrial Cancer Risk: A System Review and Meta-analysis.

    PubMed

    Yi, Ke; Yang, LingYun; Lan, Zhu; Xi, MingRong

    2016-07-01

    Polymorphism of p53 codon 72 plays an important role in pathogenesis and development of cancer. Published data on the association between the p53 codon 72 polymorphism and endometrial cancer risk are controversial. A meta-analysis was performed to assess whether the polymorphism of p53 codon 72 is associated with endometrial cancer risk. Medline, Embase, China National Knowledge Infrastructure, and Chinese Biomedicine Databases were searched to identify eligible studies. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) for p53 codon 72 polymorphism and endometrial cancer were appropriately derived from fixed-effects or random effects models. A total of 12 studies were enrolled in this meta-analysis. The pooled analyses revealed that p53 codon 72 polymorphism was not associated with endometrial cancer risk. Stratified analysis by Hardy-Weinberg equilibrium exhibited a significantly increased risk of endometrial cancer among studies deviated from Hardy-Weinberg equilibrium in heterozygote comparison (Pro/Arg vs Arg/Arg; OR, 0.61; 95% CI, 0.42-0.87) and dominant model (Pro/Pro + Pro/Arg vs Arg/Arg; OR, 0.66; 95% CI, 0.47-0.92). This study indicated that the p53 codon 72 polymorphism may not be associated with endometrial cancer risk. PMID:27327151

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

    PubMed Central

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

    2014-01-01

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

  2. Calibration method for spectroscopic systems

    DOEpatents

    Sandison, David R.

    1998-01-01

    Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets.

  3. Calibration method for spectroscopic systems

    DOEpatents

    Sandison, D.R.

    1998-11-17

    Calibration spots of optically-characterized material placed in the field of view of a spectroscopic system allow calibration of the spectroscopic system. Response from the calibration spots is measured and used to calibrate for varying spectroscopic system operating parameters. The accurate calibration achieved allows quantitative spectroscopic analysis of responses taken at different times, different excitation conditions, and of different targets. 3 figs.

  4. Major Radiations in the Evolution of Caviid Rodents: Reconciling Fossils, Ghost Lineages, and Relaxed Molecular Clocks

    PubMed Central

    Pérez, María Encarnación; Pol, Diego

    2012-01-01

    Background Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”). Results A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. Conclusions The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone. PMID

  5. Fossil evidence of the zygomycetous fungi.

    PubMed

    Krings, M; Taylor, T N; Dotzler, N

    2013-06-01

    Molecular clock data indicate that the first zygomycetous fungi occurred on Earth during the Precambrian, however, fossil evidence of these organisms has been slow to accumulate. In this paper, the fossil record of the zygomycetous fungi is compiled, with a focus on structurally preserved Carboniferous and Triassic fossils interpreted as zygosporangium-gametangia complexes and resembling those of modern Endogonales. Enigmatic microfossils from the Precambrian to Cenozoic that have variously been interpreted as, or compared to, zygomycetous fungi are also discussed. Among these, the spherical structures collectively termed 'sporocarps' are especially interesting because of their complex investments and abundance in certain Carboniferous and Triassic rocks. Circumstantial evidence suggests that at least some 'sporocarp' types represent mantled zygosporangia. Zygomycetous fungi probably were an important element in terrestrial paleoecosystems at least by the Carboniferous. PMID:24027344

  6. Application of biochemical interactions in fossil fuels

    SciTech Connect

    Lin, M.S.; Premuzic, E.T.

    1994-12-31

    Certain extreme environments tolerant microorganisms interact with heavy crude oils by means of multiple biochemical reactions, asphaltenes, and bituminous materials. These reactions proceed via pathways which involve characteristic components of oils and coals such as asphaltenes, and in the chemically related constituents found in bituminous coals. These chemical components serve as markers of the interactions between microorganisms and fossil fuels. Studies in which temperature, pressure, and salinity tolerant microorganisms have been allowed to interact with different crude oils and bituminous coals, have shown that biochemically induced changes occur in the distribution of hydrocarbons and in the chemical nature of organometallic and heterocyclic compounds. Such structural chemical rearrangements have direct applications in monitoring the efficiency, the extent, and the chemical nature of the fossil fuels bioconversion. Recent developments of chemical marker applications in the monitoring of fossil fuels bioconversion will be discussed.

  7. Cerium anomaly at microscale in fossils.

    PubMed

    Gueriau, Pierre; Mocuta, Cristian; Bertrand, Loïc

    2015-09-01

    Patterns in rare earth element (REE) concentrations are essential instruments to assess geochemical processes in Earth and environmental sciences. Excursions in the "cerium anomaly" are widely used to inform on past redox conditions in sediments. This proxy resources to the specificity of cerium to adopt both the +III and +IV oxidation states, while most rare earths are purely trivalent and share very similar reactivity and transport properties. In practical terms, the level of cerium anomaly is established through elemental point quantification and profiling. All these models rely on a supposed homogeneity of the cerium oxidation state within the samples. However, this has never been demonstrated, whereas the cerium concentration can significantly vary within a sample, as shown for fossils, which would vastly complicate interpretation of REE patterns. Here, we report direct micrometric mapping of Ce speciation through synchrotron X-ray absorption spectroscopy and production of local rare earth patterns in paleontological fossil tissues through X-ray fluorescence mapping. The sensitivity of the approach is demonstrated on well-preserved fishes and crustaceans from the Late Cretaceous (ca. 95 million years (Myr) old). The presence of Ce under the +IV form within the fossil tissues is attributed to slightly oxidative local conditions of burial and agrees well with the limited negative cerium anomaly observed in REE patterns. The [Ce(IV)]/[Ce(tot)] ratio appears remarkably stable at the microscale within each fossil and is similar between fossils from the locality. Speciation maps were obtained from an original combination of synchrotron microbeam X-ray fluorescence, absorption spectroscopy, and diffraction, together with light and electron microscopy. This work also highlights the need for more systematic studies of cerium geochemistry at the microscale in paleontological contexts, in particular across fossil histologies. PMID:26239283

  8. Gemini facility calibration unit

    NASA Astrophysics Data System (ADS)

    Ramsay-Howat, Suzanne K.; Harris, John W.; Gostick, David C.; Laidlaw, Ken; Kidd, Norrie; Strachan, Mel; Wilson, Ken

    2000-08-01

    High-quality, efficient calibration instruments is a pre- requisite for the modern observatory. Each of the Gemini telescopes will be equipped with identical facility calibration units (GCALs) designed to provide wavelength and flat-field calibrations for the suite of instruments. The broad range of instrumentation planned for the telescopes heavily constrains the design of GCAL. Short calibration exposures are required over wavelengths from 0.3micrometers to 5micrometers , field sizes up to 7 arcminutes and spectral resolution from R-5 to 50,000. The output from GCAL must mimic the f-16 beam of the telescope and provide a uniform illumination of the focal plane. The calibration units are mounted on the Gemini Instrument Support Structure, two meters from the focal pane, necessitating the use of large optical components. We will discuss the opto-mechanical design of the Gemini calibration unit, with reference to those feature which allow these stringent requirements to be met. A novel reflector/diffuser unit replaces the integration sphere more normally found in calibration systems. The efficiency of this system is an order of magnitude greater than for an integration sphere. A system of two off-axis mirrors reproduces the telescope pupil and provides the 7 foot focal plane. The results of laboratory test of the uniformity and throughput of the GCAL will be presented.

  9. The COS Calibration Pipeline

    NASA Astrophysics Data System (ADS)

    Hodge, Philip E.; Kaiser, M. E.; Keyes, C. D.; Ake, T. B.; Aloisi, A.; Friedman, S. D.; Oliveira, C. M.; Shaw, B.; Sahnow, D. J.; Penton, S. V.; Froning, C. S.; Beland, S.; Osterman, S.; Green, J.; COS/STIS STScI Team; IDT, COS

    2008-05-01

    The Cosmic Origins Spectrograph, COS, (Green, J, et al., 2000, Proc SPIE, 4013) will be installed in the Hubble Space Telescope (HST) during the next servicing mission. This will be the most sensitive ultraviolet spectrograph ever flown aboard HST. The program (CALCOS) for pipeline calibration of HST/COS data has been developed by the Space Telescope Science Institute. As with other HST pipelines, CALCOS uses an association table to list the data files to be included, and it employs header keywords to specify the calibration steps to be performed and the reference files to be used. COS includes both a cross delay line detector for the far ultraviolet (FUV) and a MAMA detector for the near ultraviolet (NUV). CALCOS uses a common structure for both channels, but the specific calibration steps differ. The calibration steps include pulse-height filtering and geometric correction for FUV, and flat-field, deadtime, and Doppler correction for both detectors. A 1-D spectrum will be extracted and flux calibrated. Data will normally be taken in TIME-TAG mode, recording the time and location of each detected photon, although ACCUM mode will also be supported. The wavelength calibration uses an on-board spectral line lamp. To enable precise wavelength calibration, default operations will simultaneously record the science target and lamp spectrum by executing brief (tag-flash) lamp exposures at least once per external target exposure.

  10. Insect diversity in the fossil record

    NASA Technical Reports Server (NTRS)

    Labandeira, C. C.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)

    1993-01-01

    Insects possess a surprisingly extensive fossil record. Compilation of the geochronologic ranges of insect families demonstrates that their diversity exceeds that of preserved vertebrate tetrapods through 91 percent of their evolutionary history. The great diversity of insects was achieved not by high origination rates but rather by low extinction rates comparable to the low rates of slowly evolving marine invertebrate groups. The great radiation of modern insects began 245 million years ago and was not accelerated by the expansion of angiosperms during the Cretaceous period. The basic trophic machinery of insects was in place nearly 100 million years before angiosperms appeared in the fossil record.

  11. Microbial Fossils Detected in Desert Varnish

    NASA Technical Reports Server (NTRS)

    Flood, B. E.; Allen, C.; Longazo, T.

    2003-01-01

    Mars Global Surveyor Thermal Emission Spectrometer data indicate regions with significant levels of hematite (_Fe2O3). Fe-oxides, like hematite, can form as aqueous mineral precipitates and as such may preserve microscopic fossils or other biosignatures. Several potential terrestrial analogues to martian hematite like hydrothermal vents have preserved microfossils. Microbial fossilization in Fe-oxides is often a function of biomineralization. For example, goethite (FeO2H) encrustation of fungal mycelia from the mid-Tertiary preserved fungal morphologies such that their genera could be determined.

  12. Fossil generation restructuring in the Ukraine

    SciTech Connect

    Galambas, J.W.

    1996-12-31

    This paper describes the Ukrainian electrical system as it was in 1991, defines the need for restructuring, outlines the restructuring process, identifies a number of major obstacles that are hindering the implementation of the fossil generation, restructuring process, and points out major problems in the coal procurement system. It describes the visits to several Ukrainian power plants, defines restructuring success to date, makes suggestions for improved restructuring progress, highlights lessons learned, and enlightens the audience on the opportunities of investing in the Ukrainian power generation industry. The primary focus is on the Fossil Generator Advisor task, which was carried out under the direction of Hagler Bailly Consulting, Inc. (Hagler Bailly).

  13. Fossils, Genes and The Origin of Organs

    SciTech Connect

    Shubin, Neil

    2011-04-20

    A toolkit of experimental and comparative biology can be applied to understand the great transformations in the history of life. Expeditionary paleontology can be used to target key nodes of the tree of life for which new fossils can provide insights into major morphological transformations. These fossils often have intermediate conditions that allow extant creatures to be compared in new ways. The tools of developmental genetics can then be used to explore these new comparisons to understand the genetic basis for macroevolutionary change. These different approaches can be used to predict new discoveries and this is only possible because of the empirical content of the tree of life.

  14. Fossils as candidate material for orthopedic applications.

    PubMed

    Pesenti, Hector; Leoni, Matteo; Motta, Antonella; Scardi, Paolo

    2011-01-01

    Ceramic powders from fossil deposits were thoroughly characterized from the material point of view and sintered to produce massive components. The raw material, a mixture of apatite minerals, feldspars, and quartz, seems ideally suitable to obtain a biologically compatible glass ceramic. Preliminary in vitro tests of proliferation and adhesion of MG63 human osteoblast-like cell line on a selected sample are encouraging. Results are correlated with sintering conditions and phase composition: the fossil can be sintered to almost full density at temperatures as low as 900 °C and seems to quickly promote cell activation with respect to hydroxylapatite. PMID:20089607

  15. Aquatic ape theory and fossil hominids.

    PubMed

    Verhaegen, M J

    1991-06-01

    While most older palaeo-anthropological studies emphasise the similarities of the fossil hominids with modern man, recent studies often stress the unique and the apelike features of the australopithecine dentitions, skulls and postcranial bones. It is worth reconsidering the features of Australopithecus, Homo erectus and Homo neanderthalensis in the light of the so-called Aquatic Ape Theory (AAT) of Hardy and Morgan, and to compare the skeletal parts of our fossil relatives with those of (semi)aquatic animals. Possible convergences are observed with proboscis monkeys, beavers, sea-otters, hippopotamuses, seals, sea-lions, walruses, sea-cows, whales, dolphins, porpoises, penguins and crocodiles. PMID:1909768

  16. DIRBE External Calibrator (DEC)

    NASA Technical Reports Server (NTRS)

    Wyatt, Clair L.; Thurgood, V. Alan; Allred, Glenn D.

    1987-01-01

    Under NASA Contract No. NAS5-28185, the Center for Space Engineering at Utah State University has produced a calibration instrument for the Diffuse Infrared Background Experiment (DIRBE). DIRBE is one of the instruments aboard the Cosmic Background Experiment Observatory (COBE). The calibration instrument is referred to as the DEC (Dirbe External Calibrator). DEC produces a steerable, infrared beam of controlled spectral content and intensity and with selectable point source or diffuse source characteristics, that can be directed into the DIRBE to map fields and determine response characteristics. This report discusses the design of the DEC instrument, its operation and characteristics, and provides an analysis of the systems capabilities and performance.

  17. Airdata Measurement and Calibration

    NASA Technical Reports Server (NTRS)

    Haering, Edward A., Jr.

    1995-01-01

    This memorandum provides a brief introduction to airdata measurement and calibration. Readers will learn about typical test objectives, quantities to measure, and flight maneuvers and operations for calibration. The memorandum informs readers about tower-flyby, trailing cone, pacer, radar-tracking, and dynamic airdata calibration maneuvers. Readers will also begin to understand how some data analysis considerations and special airdata cases, including high-angle-of-attack flight, high-speed flight, and nonobtrusive sensors are handled. This memorandum is not intended to be all inclusive; this paper contains extensive reference and bibliography sections.

  18. Lidar Calibration Centre

    NASA Astrophysics Data System (ADS)

    Pappalardo, Gelsomina; Freudenthaler, Volker; Nicolae, Doina; Mona, Lucia; Belegante, Livio; D'Amico, Giuseppe

    2016-06-01

    This paper presents the newly established Lidar Calibration Centre, a distributed infrastructure in Europe, whose goal is to offer services for complete characterization and calibration of lidars and ceilometers. Mobile reference lidars, laboratories for testing and characterization of optics and electronics, facilities for inspection and debugging of instruments, as well as for training in good practices are open to users from the scientific community, operational services and private sector. The Lidar Calibration Centre offers support for trans-national access through the EC HORIZON2020 project ACTRIS-2.

  19. Compact radiometric microwave calibrator

    SciTech Connect

    Fixsen, D. J.; Wollack, E. J.; Kogut, A.; Limon, M.; Mirel, P.; Singal, J.; Fixsen, S. M.

    2006-06-15

    The calibration methods for the ARCADE II instrument are described and the accuracy estimated. The Steelcast coated aluminum cones which comprise the calibrator have a low reflection while maintaining 94% of the absorber volume within 5 mK of the base temperature (modeled). The calibrator demonstrates an absorber with the active part less than one wavelength thick and only marginally larger than the mouth of the largest horn and yet black (less than -40 dB or 0.01% reflection) over five octaves in frequency.

  20. Fossil and molecular evidence constrain scenarios for the early evolutionary and biogeographic history of hystricognathous rodents.

    PubMed

    Sallam, Hesham M; Seiffert, Erik R; Steiper, Michael E; Simons, Elwyn L

    2009-09-29

    The early evolutionary and paleobiogeographic history of the diverse rodent clade Hystricognathi, which contains Hystricidae (Old World porcupines), Caviomorpha (the endemic South American rodents), and African Phiomorpha (cane rats, dassie rats, and blesmols) is of great interest to students of mammalian evolution, but remains poorly understood because of a poor early fossil record. Here we describe the oldest well-dated hystricognathous rodents from an earliest late Eocene (approximately 37 Ma) fossil locality in the Fayum Depression of northern Egypt. These taxa exhibit a combination of primitive and derived features, the former shared with Asian "baluchimyine" rodents, and the latter shared with Oligocene phiomorphs and caviomorphs. Phylogenetic analysis incorporating morphological, temporal, geographic, and molecular information places the new taxa as successive sister groups of crown Hystricognathi, and supports an Asian origin for stem Hystricognathi and an Afro-Arabian origin for crown Hystricognathi, stem Hystricidae, and stem Caviomorpha. Molecular dating of early divergences within Hystricognathi, using a Bayesian "relaxed clock" approach and multiple fossil calibrations, suggests that the split between Hystricidae and the phiomorph-caviomorph clade occurred approximately 39 Ma, and that phiomorphs and caviomorphs diverged approximately 36 Ma. These results are remarkably congruent with our phylogenetic results and the fossil record of hystricognathous rodent evolution in Afro-Arabia and South America. PMID:19805363

  1. Phylogeny and Divergence Times of Lemurs Inferred with Recent and Ancient Fossils in the Tree.

    PubMed

    Herrera, James P; Dávalos, Liliana M

    2016-09-01

    Paleontological and neontological systematics seek to answer evolutionary questions with different data sets. Phylogenies inferred for combined extant and extinct taxa provide novel insights into the evolutionary history of life. Primates have an extensive, diverse fossil record and molecular data for living and extinct taxa are rapidly becoming available. We used two models to infer the phylogeny and divergence times for living and fossil primates, the tip-dating (TD) and fossilized birth-death process (FBD). We collected new morphological data, especially on the living and extinct endemic lemurs of Madagascar. We combined the morphological data with published DNA sequences to infer near-complete (88% of lemurs) time-calibrated phylogenies. The results suggest that primates originated around the Cretaceous-Tertiary boundary, slightly earlier than indicated by the fossil record and later than previously inferred from molecular data alone. We infer novel relationships among extinct lemurs, and strong support for relationships that were previously unresolved. Dates inferred with TD were significantly older than those inferred with FBD, most likely related to an assumption of a uniform branching process in the TD compared with a birth-death process assumed in the FBD. This is the first study to combine morphological and DNA sequence data from extinct and extant primates to infer evolutionary relationships and divergence times, and our results shed new light on the tempo of lemur evolution and the efficacy of combined phylogenetic analyses. PMID:27113475

  2. U-series dating of diagenetically altered fossil reef corals

    NASA Astrophysics Data System (ADS)

    Scholz, Denis; Mangini, Augusto; Felis, Thomas

    2004-01-01

    Initial ( 234U/ 238U) activity ratios higher than those expected from closed system evolution of seawater are an outstanding problem in U-series dating of fossil reef corals. The increased activity ratios are ascribed to post-depositional diagenesis. We analysed six Last Interglacial and one Holocene coral of the genus Porites collected near the northern end of the Gulf of Aqaba (northern Red Sea) together with three recent corals from this location as a modern reference. While the values measured on the recent samples show no deviation from expected values, the Holocene and Last Interglacial corals display highly elevated ( 234U/ 238U) activity ratios as well as increased 238U and 232Th concentrations. ( 234U/ 238U) activity ratios are strongly correlated with ( 230Th/ 238U) and total uranium content. A model assuming different degrees of uranium addition and subsequent loss in different sub-samples of one coral produces straight lines (isochrons) on a ( 234U/ 238U)-( 230Th/ 238U) plot and predicts that the true age of the coral can be calculated by intersecting this isochron with the seawater evolution curve. We used the strong correlation detected in the Aqaba corals to calculate isochron ages. The isochron age of the Holocene coral (3116 +167 -156 yr) is concordant with its calibrated 14C age (2963 +92 -103 yr). The ages of the Last Interglacial corals are between 121 (+6.7 -5.3) and 121.9 (+7.0 -6.3) kyr for a higher terrace (7-10 m asl) and 106.4 (+8.9 -8.1) and 117.1 (+19.7 -15.3) kyr for a lower terrace (4-5 m asl). One Last Interglacial coral with an aragonite content of ˜85% could not be dated. The elevation and ages of the fossil terraces are consistent with existing sea level reconstructions from the Red Sea.

  3. Fossil struthionid eggshells from Laetoli, Tanzania: Taxonomic and biostratigraphic significance

    NASA Astrophysics Data System (ADS)

    Harrison, Terry; Msuya, Charles P.

    2005-04-01

    Recent paleontological investigations at Laetoli and neighboring localities in northern Tanzania have produced a large collection of fossil ostrich eggshells from the Pliocene-aged Laetolil Beds (˜3.5-4.5 Ma) and Ndolanya Beds (˜2.6-2.7 Ma). A detailed analysis of the morphology of the eggshells and their taxonomic affinities indicates that two different species of Struthio are represented. In the Lower Laetolil Beds and in the Upper Laetolil Beds below Tuff 3 a new species is recognized— Struthio kakesiensis. This is replaced in the Upper Laetolil Beds by Struthio camelus, the modern species of ostrich. Since radiometric age determinations are available for the stratigraphic sequence at Laetoli, it is possible to precisely date the first appearance of S. camelus at ˜3.6-3.8 Ma. Comparisons of the Laetoli material with specimens from the well-dated sequences at Lothagam and Kanapoi in northern Kenya, allow the taxonomic and biochronological analysis to be extended back in time to the late Miocene. At about 6.5 Ma, Diamantornis and elephant birds were replaced in East Africa by ostriches belonging to the genus Struthio. Three time-successive species of ostriches are identified in the fossil record of East Africa, beginning with Struthio. cf. karingarabensis (˜6.5-4.2 Ma), followed by S. kakesiensis (˜4.5-3.6 Ma) and then S. camelus (˜3.8 Ma onwards). A similar sequence of taxa has previously been recorded from localities in Namibia, but at these sites there is no possibility to precisely calibrate the ages of the different species using radiometric dating. Nevertheless, the broadly similar evolutionary sequence and the close correspondence in inferred ages for the succession of species in East Africa and Namibia suggest that ostrich eggshells are a very useful tool for biochronological correlation of paleontological sites in sub-Saharan Africa.

  4. Role of GC-biased mutation pressure on synonymous codon choice in Micrococcus luteus, a bacterium with a high genomic GC-content.

    PubMed Central

    Ohama, T; Muto, A; Osawa, S

    1990-01-01

    The GC (G + C, or G or C)-contents of codon silent positions in all two-codon sets and three codons AUY/A (IIe), and in most of the family boxes of Micrococcus luteus (genomic GC-content: 74%) are 95% to 100% in both the highly and weakly expressed genes. In some family boxes, there is a decrease in NNC codons and an increase in NNG codons from the highly expressed to weakly expressed genes without apparent involvement of NNU and NNA codons. From these observations, we conclude that the selective use of synonymous codons in M. luteus may be largely determined by GC-biased mutation pressure and that in the highly expressed genes tRNAs would act as a weak selection pressure in some family boxes. Available data suggest that the effect of selection pressure by tRNAs on the synonymous codon choice becomes more apparent in the highly expressed genes in eubacteria with intermediate GC-contents such as Escherichia coli and Bacillus subtilis, and that the U/C ratio of the codon third positions in NNU/C-type two-codon sets in the weakly expressed genes would represent the approximate magnitude of directional mutation pressure throughout eubacteria. PMID:2326195

  5. Calibrated Properties Model

    SciTech Connect

    C.F. Ahlers, H.H. Liu

    2001-12-18

    The purpose of this Analysis/Model Report (AMR) is to document the Calibrated Properties Model that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process models for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the AMR Development Plan for U0035 Calibrated Properties Model REV00 (CRWMS M&O 1999c). These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport Model (UZ Model), drift seepage models, drift-scale and mountain-scale coupled-processes models, and Total System Performance Assessment (TSPA) models as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process models provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.

  6. WFPC2 Pipeline Calibration

    NASA Astrophysics Data System (ADS)

    Burrows, Chris

    2004-03-01

    This document contains a listing of all WFPC2 reference files, grouped by type, that are presently available in the Calibration Data Base (CDB) System, and a summary of how they are used in the calibration of WFPC2 data. A summary memo is kept on STEIS and kept up to date as the reference files change. That memo is intended to inform observers as to the quality of the calibration applied to their data by the PODPS pipeline processing and to provide an aid in selecting appropriate reference files for the re-calibration of WFPC2 observations. The datafiles may be requested by name from the STScI in the same fashion as any other nonproprietary data products.

  7. SRAM Detector Calibration

    NASA Technical Reports Server (NTRS)

    Soli, G. A.; Blaes, B. R.; Beuhler, M. G.

    1994-01-01

    Custom proton sensitive SRAM chips are being flown on the BMDO Clementine missions and Space Technology Research Vehicle experiments. This paper describes the calibration procedure for the SRAM proton detectors and their response to the space environment.

  8. Roundness calibration standard

    DOEpatents

    Burrus, Brice M.

    1984-01-01

    A roundness calibration standard is provided with a first arc constituting the major portion of a circle and a second arc lying between the remainder of the circle and the chord extending between the ends of said first arc.

  9. Calibrated Properties Model

    SciTech Connect

    C. Ahlers; H. Liu

    2000-03-12

    The purpose of this Analysis/Model Report (AMR) is to document the Calibrated Properties Model that provides calibrated parameter sets for unsaturated zone (UZ) flow and transport process models for the Yucca Mountain Site Characterization Project (YMP). This work was performed in accordance with the ''AMR Development Plan for U0035 Calibrated Properties Model REV00. These calibrated property sets include matrix and fracture parameters for the UZ Flow and Transport Model (UZ Model), drift seepage models, drift-scale and mountain-scale coupled-processes models, and Total System Performance Assessment (TSPA) models as well as Performance Assessment (PA) and other participating national laboratories and government agencies. These process models provide the necessary framework to test conceptual hypotheses of flow and transport at different scales and predict flow and transport behavior under a variety of climatic and thermal-loading conditions.

  10. Functional polypeptides can be synthesized from human mitochondrial transcripts lacking termination codons.

    PubMed Central

    Chrzanowska-Lightowlers, Zofia M A; Temperley, Richard J; Smith, Paul M; Seneca, Sara H; Lightowlers, Robert N

    2004-01-01

    The human mitochondrial genome (mtDNA) is a small, circular DNA duplex found in multi-copy in the mitochondrial matrix. It is almost fully transcribed from both strands to produce large polycistronic RNA units that are processed and matured. The 13 mtDNA-encoded polypeptides are translated from mt-mRNAs that have been matured by polyadenylation of their free 3'-termini. A patient with clinical features consistent with an mtDNA disorder was recently shown to carry a microdeletion, resulting in the loss of the termination codon for MTATP6 and in its juxtaposition with MTCO3. Cell lines from this patient exhibited low steady-state levels of RNA14, the bi-cistronic transcript encoding subunits 6 and 8 of the F(o)F(1)-ATP synthase, complex V, consistent with a decreased stability. Recent reports of 'non-stop' mRNA decay systems in the cytosol have failed to determine the fate of gene products derived from transcripts lacking termination codons, although enhanced decay clearly required the 'non-stop' transcripts to be translated. We wished to determine whether functional translation products could still be expressed from non-stop transcripts in the human mitochondrion. Although a minor defect in complex V assembly was noted in the patient-derived cell lines, the steady-state level of ATPase 6 was similar to controls, consistent with the pattern of de novo mitochondrial protein synthesis. Moreover, no significant difference in ATP synthase activity could be detected. We conclude that, in the absence of a functional termination codon, although mitochondrial transcripts are more rapidly degraded, they are also translated to generate stable polypeptides that are successfully integrated into functional enzyme complexes. PMID:14585098

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

    PubMed Central

    Wang, Pei; Song, Fan; Cai, Wanzhi

    2014-01-01

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

  12. The TGA codons are present in the open reading frame of selenoprotein P cDNA

    SciTech Connect

    Hill, K.E.; Lloyd, R.S.; Read, R.; Burk, R.F. )

    1991-03-11

    The TGA codon in DNA has been shown to direct incorporation of selenocysteine into protein. Several proteins from bacteria and animals contain selenocysteine in their primary structures. Each of the cDNA clones of these selenoproteins contains one TGA codon in the open reading frame which corresponds to the selenocysteine in the protein. A cDNA clone for selenoprotein P (SeP), obtained from a {gamma}ZAP rat liver library, was sequenced by the dideoxy termination method. The correct reading frame was determined by comparison of the deduced amino acid sequence with the amino acid sequence of several peptides from SeP. Using SeP labelled with {sup 75}Se in vivo, the selenocysteine content of the peptides was verified by the collection of carboxymethylated {sup 77}Se-selenocysteine as it eluted from the amino acid analyzer and determination of the radioactivity contained in the collected samples. Ten TGA codons are present in the open reading frame of the cDNA. Peptide fragmentation studies and the deduced sequence indicate that selenium-rich regions are located close to the carboxy terminus. Nine of the 10 selenocysteines are located in the terminal 26% of the sequence with four in the terminal 15 amino acids. The deduced sequence codes for a protein of 385 amino acids. Cleavage of the signal peptide gives the mature protein with 366 amino acids and a calculated mol wt of 41,052 Da. Searches of PIR and SWISSPROT protein databases revealed no similarity with glutathione peroxidase or other selenoproteins.

  13. Solid modeling of fossil small mammal teeth

    NASA Astrophysics Data System (ADS)

    Marschallinger, Robert; Hofmann, Peter; Daxner-Höck, Gudrun; Ketcham, Richard A.

    2011-09-01

    This paper presents an approach to create solid models of fossil small mammal teeth using a combination of microcomputed tomography, object based image analysis and voxel modeling. Small mammal teeth, because of their durability, are widely found in Cenozioc sediments the world over and play a key role in stratigraphy as well as in researching the rapid evolution and the paleogeographic spreading of small mammals. Recent advances in microcomputed tomography make this non-destructive analysis method an ideal data source for high-resolution 3D models of fossil small animal teeth. To derive internally consistent solid models of such fossils from micro-CT imagery, we propose a combination of 3D object based image analysis and solid modeling. Incorporating paleontological expert knowledge in the image processing cycle, object based image analysis yields topologically consistent image stacks classified by the main tooth components—enamel, dentine and pulp. Forwarding these data to a voxel modeling system, they can be quantitatively analyzed in an unprecedented manner: going beyond the possibilities of the state-of-art surface models, solid models are capable of unambiguously portraying the entire object volume—teeth can be peeled by material properties, subvolumes can be extracted and automatically analyzed by Boolean operations. The proposed method, which can be flexibly extended to handle a range of paleontological and geological micro-objects, is demonstrated with two typical fossil small mammal teeth.

  14. Fundamentals of fossil simulator instructor training

    SciTech Connect

    Not Available

    1984-01-01

    This single-volume, looseleaf text introduces the beginning instructor to fundamental instructor training principles, and then shows how to apply those principles to fossil simulator training. Topics include the fundamentals of classroom instruction, the learning process, course development, and the specifics of simulator training program development.

  15. Fossil Cores In The Kepler Data

    NASA Astrophysics Data System (ADS)

    Jackson, Brian

    Most gas giant exoplanets with orbital periods < few days are unstable against tidal decay and may be tidally disrupted before their host stars leave the main sequence. These gas giants probably contain rocky/icy cores, and so their cores will be stranded near their progenitor's Roche limit (few hours orbital period). These fossil cores will evade the Kepler mission's transit search because it is focused on periods > 0.5 days, but finding these fossil cores would provide unprecedented insights into planetary interiors and formation ? e.g., they would be a smoking gun favoring formation of gas giants via core accretion. We propose to search for and characterize fossil cores in the Kepler dataset. We will vet candidates using the Kepler photometry and auxiliary data, collect ground-based spectra of the host stars and radial-velocity (RV) and adaptive optics (AO) data to corroborate candidates. We will also constrain stellar tidal dissipation efficiencies (parameterized by Q) by determining our survey's completeness, elucidating dynamical origins and evolution of exoplanets even if we find no fossil cores. Our preliminary search has already found several dozen candidates, so the proposed survey has a high likelihood of success.

  16. Learning about Fossil Formation by Classroom Simulation.

    ERIC Educational Resources Information Center

    Schlenker, Richard M.; Yoshida, Sarah J.

    1991-01-01

    Activities in which students build their own simulations of fossils, using seashells, chicken bones, toy dinosaurs, or leaves as models and plaster of paris, sand, mud, clay, or a mixture of gravel and clay as a matrix are presented. Curriculum extensions are included. (KR)

  17. Evolution: Fossil Ears and Underwater Sonar.

    PubMed

    Lambert, Olivier

    2016-08-22

    A key innovation in the history of whales was the evolution of a sonar system together with high-frequency hearing. Fossils of an archaic toothed whale's inner ear bones provide clues for a stepwise emergence of underwater echolocation ability. PMID:27554653

  18. Fossil fuels supplies modeling and research

    SciTech Connect

    Leiby, P.N.

    1996-06-01

    The fossil fuel supplies modeling and research effort focuses on models for US Strategic Petroleum Reserve (SPR) planning and management. Topics covered included new SPR oil valuation models, updating models for SPR risk analysis, and fill-draw planning. Another task in this program area is the development of advanced computational tools for three-dimensional seismic analysis.

  19. Fossil Energy Materials Program conference proceedings

    SciTech Connect

    Judkins, R.R.

    1987-08-01

    The US Department of Energy Office of Fossil Energy has recognized the need for materials research and development to assure the adequacy of materials of construction for advanced fossil energy systems. The principal responsibility for identifying needed materials research and for establishing a program to address these needs resides within the Office of Technical Coordination. That office has established the Advanced Research and Technology Development (AR and TD) Fossil Energy Materials Program to fulfill that responsibility. In addition to the AR and TD Materials Program, which is designed to address in a generic way the materials needs of fossil energy systems, specific materials support activities are also sponsored by the various line organizations such as the Office of Coal Gasification. A conference was held at Oak Ridge, Tennessee on May 19-21, 1987, to present and discuss the results of program activities during the past year. The conference program was organized in accordance with the research thrust areas we have established. These research thrust areas include structural ceramics (particularly fiber-reinforced ceramic composites), corrosion and erosion, and alloy development and mechanical properties. Eighty-six people attended the conference. Papers have been entered individually into EDB and ERA. (LTN)

  20. Fossils of reionization in the local group

    SciTech Connect

    Gnedin, Nickolay Y.; Kravtsov, Andrey V.; /KICP, Chicago /Chicago U., EFI /Chicago U., Astron. Astrophys. Ctr.

    2006-01-01

    We use a combination of high-resolution gas dynamics simulations of high-redshift dwarf galaxies and dissipationless simulations of a Milky Way sized halo to estimate the expected abundance and spatial distribution of the dwarf satellite galaxies that formed most of their stars around z {approx} 8 and evolved only little since then. Such galaxies can be considered as fossils of the reionization era, and studying their properties could provide a direct window into the early, pre-reionization stages of galaxy formation. We show that 5-15% of the objects existing at z {approx} 8 do indeed survive until the present in the MW like environment without significant evolution. This implies that it is plausible that the fossil dwarf galaxies do exist in the Local Group. Because such galaxies form their stellar systems early during the period of active merging and accretion, they should have spheroidal morphology regardless of their current distance from the host galaxy. We show that both the expected luminosity function and spatial distribution of dark matter halos which are likely to host fossil galaxies agree reasonably well with the observed distributions of the luminous (L{sub V} > 10{sup 6} Lsun) Local Group fossil candidates near the host galaxy (d<200 kpc). However, the predicted abundance is substantially larger (by a factor of 2-3) for fainter galaxies (L{sub V} < 10{sup 6} Lsun) at larger distances (d>300 kpc). We discuss several possible explanations for this discrepancy.

  1. The Fascinating Story of Fossil Fuels

    ERIC Educational Resources Information Center

    Asimov, Isaac

    1973-01-01

    How this energy source was created, its meaning to mankind, our drastically reduced supply, and why we cannot wait for nature to make more are considered. Today fossil fuels supply 96 percent of the energy used but we must find alternate energy options if we are to combat the energy crisis. (BL)

  2. Thermal dissolution of solid fossil fuels

    SciTech Connect

    E.G. Gorlov

    2007-10-15

    The use of oil shales and coals in the processes of thermal dissolution is considered. It is shown that thermal dissolution is a mode of liquefaction of solid fossil fuels and can be used both independently and in combination with liquefaction of coals and processing of heavy petroleum residues.

  3. 5,10-Methylenetetrahydrofolate reductase codon 677 and 1298 polymorphisms and colon cancer in African Americans and whites.

    PubMed

    Keku, Temitope; Millikan, Robert; Worley, Kendra; Winkel, Scott; Eaton, Allison; Biscocho, Lorna; Martin, Christopher; Sandler, Robert

    2002-12-01

    We evaluated polymorphisms in methylenetetrahydrofolate reductase (MTHFR), folate intake and alcohol consumption in relation to risk of colon cancer in a population-based case-control study in North Carolina. The study included 555 cases (244 African Americans and 311 whites) and 875 controls (331 African Americans and 544 whites). Total folate intake of <400 versus > or =400 microg/day showed a weak positive association with colon cancer among both African Americans [adjusted odds ratio (OR) = 1.4, 95% confidence interval (CI) = 1.0-2.0] and whites (OR = 1.6, 95% CI = 1.2-2.2). No association was observed with use of alcohol. Compared with wild-type genotypes, there was no association between the low activity MTHFR codon 677 TT genotype and colon cancer, but the low activity codon 1298 CC genotype was inversely associated with colon cancer in whites (OR = 0.5, 95% CI = 0.3-0.9). Unlike previous studies, we did not observe a strong protective effect of the codon 677 TT low-activity genotype when folate intake was high. Instead, we observed an increased risk of colon cancer when folate intake was low for participants with wild- type genotypes. Adjusted ORs for the combined effects of codon 677 CC and codon 1298 AA genotypes and folate intake <400 microg/day were 1.9 (95% CI = 1.1-3.4) in African Americans and 2.5 (95% CI = 1.2-5.2) in whites. Our results suggest that variation at MTHFR codon 1298 (within the COOH-terminal region) may be more important for colon cancer than variation at codon 677 (NH(2)-terminal region), and in populations where folate intake is low, wild-type MTHFR activity may increase risk for colon cancer. PMID:12496052

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

    PubMed Central

    Puigbò, Pere; Bravo, Ignacio G; Garcia-Vallvé, Santiago

    2008-01-01

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

  5. Dating placentalia: Morphological clocks fail to close the molecular fossil gap.

    PubMed

    Puttick, Mark N; Thomas, Gavin H; Benton, Michael J

    2016-04-01

    Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Although it is likely that crown-group placentals originated in the Late Cretaceous, nearly all molecular clock estimates point to a deeper Cretaceous origin. An approach with the potential to reconcile this discrepancy could be the application of a morphological clock. This would permit the direct incorporation of fossil data in node dating, and would break long internal branches of the tree, so leading to improved estimates of node ages. Here, we use a large morphological dataset and the tip-calibration approach of MrBayes. We find that the estimated date for the origin of crown mammals is much older, ∼130-145 million years ago (Ma), than fossil and molecular clock data (∼80-90 Ma). Our results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data. This can be partially overcome by constraining the ages of internal nodes on the tree; however, when this was applied to our dataset, the estimated dates were still substantially more ancient than expected. We recommend that results obtained using tip calibration, and possibly morphological dating more generally, should be treated with caution. PMID:26990798

  6. Unique graphical representation of protein sequences based on nucleotide triplet codons

    NASA Astrophysics Data System (ADS)

    Randić, Milan; Zupan, Jure; Balaban, Alexandru T.

    2004-10-01

    We consider a graphical representation of proteins as an alternative to the usual representation of proteins as a sequence listing the natural amino acids. The approach is based on a graphical representation of triplets of DNA in which the interior of a square or the interior of a tetrahedron is used to accommodate 64 sites for the 64 codons. By associating a zigzag curve and various matrices with a protein, just as was the case with graphical representation of DNA, one can construct selected invariants to serve as protein descriptors. The approach is illustrated on the A-chain of human insulin.

  7. Constraining the Deep Origin of Parasitic Flatworms and Host-Interactions with Fossil Evidence.

    PubMed

    De Baets, Kenneth; Dentzien-Dias, Paula; Upeniece, Ieva; Verneau, Olivier; Donoghue, Philip C J

    2015-01-01

    Novel fossil discoveries have contributed to our understanding of the evolutionary appearance of parasitism in flatworms. Furthermore, genetic analyses with greater coverage have shifted our views on the coevolution of parasitic flatworms and their hosts. The putative record of parasitic flatworms is consistent with extant host associations and so can be used to put constraints on the evolutionary origin of the parasites themselves. The future lies in new molecular clock analyses combined with additional discoveries of exceptionally preserved flatworms associated with hosts and coprolites. Besides direct evidence, the host fossil record and biogeography have the potential to constrain their evolutionary history, albeit with caution needed to avoid circularity, and a need for calibrations to be implemented in the most conservative way. This might result in imprecise, but accurate divergence estimates for the evolution of parasitic flatworms. PMID:26597066

  8. HAWC Timing Calibration

    NASA Astrophysics Data System (ADS)

    Kelley-Hoskins, Nathan; Huentemeyer, Petra; Matthews, John; Dingus, Brenda; HAWC Collaboration

    2011-04-01

    The High-Altitude Water Cherenkov (HAWC) Experiment is a second-generation high sensitivity gamma-ray and cosmic-ray detector that builds on the experience and technology of the Milagro observatory. HAWC utilizes the water Cherenkov technique to measure extensive air showers. Instead of a pond filled with water (as in Milagro), an array of closely packed water tanks with 3 PMTs each is used. The cosmic ray's direction will be reconstructed using the times when the PMTs in each tank are triggered. Therefore, the timing calibration will be crucial for reaching an angular resolution as low as 0.1 degrees. We propose to use a laser calibration system, patterned after the calibration system in Milagro. The HAWC optical calibration system uses less than 1 ns laser light pulses, directed into two optical fiber networks. Each network will use optical fan-outs and switches to direct light to specific tanks. The first network is used to measure the light transit time out to each pair of tanks, and the second network sends light to each tank, calibrating each tank's 3 PMTs. Time slewing corrections will be made using neutral density filters to control the light intensity over 4 orders of magnitude. This system is envisioned to run both continuously at a low rate, or at a high rate with many intensity levels. In this presentation, we present the design of the calibration system and first measurements of its performance.

  9. Selection of aminoacyl-tRNAs at sense codons: the size of the tRNA variable loop determines whether the immediate 3' nucleotide to the codon has a context effect.

    PubMed Central

    Curran, J F; Poole, E S; Tate, W P; Gross, B L

    1995-01-01

    Codon context can affect translational efficiency by several molecular mechanisms. The base stacking interactions between a codon-anticodon complex and the neighboring nucleotide immediately 3' can facilitate translation by amber suppressors and the tRNA structure is also known to modulate the sensitivity to context. In this study the relative rates of aminoacyl-tRNA selection were measured at four sense codons (UGG, CUC, UUC and UCA), in all four 3' nucleotide contexts, through direct competition with a programmed frameshift at a site derived from the release factor 2 gene. Two codons (UGG and UUC) are read by tRNAs with small variable regions and their rates of aminoacyl-tRNA selection correlated with the potential base stacking strength of the 3' neighboring nucleotide. The other two codons (CUC and UCA) are read by tRNAs with large variable regions and the rate of selection of the aminoacyl-tRNAs in these cases varied little among the four contexts. Re-examination of published data on amber suppression also revealed an inverse correlation between context sensitivity and the size of the variable region. Collectively the data suggest that a large variable loop in a tRNA decreases the influence of the 3' context on tRNA selection, probably by strengthening tRNA-ribosomal interactions. PMID:7479072

  10. Integrated calibration sphere and calibration step fixture for improved coordinate measurement machine calibration

    DOEpatents

    Clifford, Harry J.

    2011-03-22

    A method and apparatus for mounting a calibration sphere to a calibration fixture for Coordinate Measurement Machine (CMM) calibration and qualification is described, decreasing the time required for such qualification, thus allowing the CMM to be used more productively. A number of embodiments are disclosed that allow for new and retrofit manufacture to perform as integrated calibration sphere and calibration fixture devices. This invention renders unnecessary the removal of a calibration sphere prior to CMM measurement of calibration features on calibration fixtures, thereby greatly reducing the time spent qualifying a CMM.

  11. Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone‡

    PubMed Central

    Gilchrist, Michael A.; Chen, Wei-Chen; Shah, Premal; Landerer, Cedric L.; Zaretzki, Russell

    2015-01-01

    Extracting biologically meaningful information from the continuing flood of genomic data is a major challenge in the life sciences. Codon usage bias (CUB) is a general feature of most genomes and is thought to reflect the effects of both natural selection for efficient translation and mutation bias. Here we present a mechanistically interpretable, Bayesian model (ribosome overhead costs Stochastic Evolutionary Model of Protein Production Rate [ROC SEMPPR]) to extract meaningful information from patterns of CUB within a genome. ROC SEMPPR is grounded in population genetics and allows us to separate the contributions of mutational biases and natural selection against translational inefficiency on a gene-by-gene and codon-by-codon basis. Until now, the primary disadvantage of similar approaches was the need for genome scale measurements of gene expression. Here, we demonstrate that it is possible to both extract accurate estimates of codon-specific mutation biases and translational efficiencies while simultaneously generating accurate estimates of gene expression, rather than requiring such information. We demonstrate the utility of ROC SEMPPR using the Saccharomyces cerevisiae S288c genome. When we compare our model fits with previous approaches we observe an exceptionally high agreement between estimates of both codon-specific parameters and gene expression levels (ρ>0.99 in all cases). We also observe strong agreement between our parameter estimates and those derived from alternative data sets. For example, our estimates of mutation bias and those from mutational accumulation experiments are highly correlated (ρ=0.95). Our estimates of codon-specific translational inefficiencies and tRNA copy number-based estimates of ribosome pausing time (ρ=0.64), and mRNA and ribosome profiling footprint-based estimates of gene expression (ρ=0.53−0.74) are also highly correlated, thus supporting the hypothesis that selection against translational inefficiency is an

  12. Segmentation of DNA into Coding and Noncoding Regions Based on Recursive Entropic Segmentation and Stop-Codon Statistics

    NASA Astrophysics Data System (ADS)

    Nicorici, Daniel; Astola, Jaakko

    2004-12-01

    Heterogeneous DNA sequences can be partitioned into homogeneous domains that are comprised of the four nucleotides A, C, G, and T and the stop-codons. Recursively, we apply a new entropic segmentation method on DNA sequences using Jensen-Shannon and Jensen-Rényi divergences in order to find the borders between coding and noncoding DNA regions. We have chosen 12- and 18-symbol alphabets that capture (i) the differential nucleotide composition in codons, and (ii) the differential stop-codon composition along all the three phases in both strands of the DNA. The new segmentation method is based on the Jensen-Rényi divergence measure, nucleotide statistics, and stop-codon statistics in both DNA strands. The recursive segmentation process requires no prior training on known datasets. Consequently, for three entire genomes of bacteria, we find that the use of nucleotide composition, stop-codon composition, and Jensen-Rényi divergence improve the accuracy of finding the borders between coding and noncoding regions in DNA sequences.

  13. Effects of nucleotide usage on the synonymous codon usage patterns of biofilm-associated genes in Haemophilus parasuis.

    PubMed

    Wang, L Y; Ma, L N; Liu, Y S

    2016-01-01

    To provide a new perspective on the evolutionary characteristics shaping the genetic diversity of Haemophilus parasuis biofilms, the relative synonymous codon usage values, codon usage bias values, effective number of codons (ENC) values, codon adaptation index (CAI) values, and the base components were calculated. Our objective was to implement a comparative analysis to evaluate the dynamic evolution of biofilm-associated genes in H. parasuis. The analysis of genetic diversity provides evidence that some biofilm-associated genes have similar genetic features. However, other genes show some variations in genetic direction. Furthermore, preferential selection of the synonymous codons and amino acids is apparent in biofilm-associated genes. Additionally, the ENC and CAI data from this study all strongly suggested that biofilm-associated genes may depend on deoptimization to adapt to environmental changes, and the mutation effect of biofilm-associated genes in H. parasuis plays an important role in shaping the genetic features. Our results reveal that the mutations of biofilm-associated genes form a set of sophisticated strategies for combating the environmental changes arising from the host cell in the evolution of H. parasuis. PMID:27323145

  14. Enhanced production of recombinant Mycobacterium tuberculosis antigens in Escherichia coli by replacement of low-usage codons.

    PubMed

    Lakey, D L; Voladri, R K; Edwards, K M; Hager, C; Samten, B; Wallis, R S; Barnes, P F; Kernodle, D S

    2000-01-01

    A major obstacle to development of subunit vaccines and diagnostic reagents for tuberculosis is the inability to produce large quantities of these proteins. To test the hypothesis that poor expression of some mycobacterial genes in Escherichia coli is due, in part, to the presence of low-usage E. coli codons, we used site-directed mutagenesis to convert low-usage codons to high-usage codons for the same amino acid in the Mycobacterium tuberculosis genes for antigens 85A and 85B and superoxide dismutase. Replacement of five codons in the wild-type gene for antigen 85B increased recombinant protein production in E. coli 54-fold. The recombinant antigen elicited proliferation and gamma interferon production by lymphocytes from healthy tuberculin reactors and was recognized by monoclonal antibodies to native antigen 85, indicating that the recombinant antigen contained T-cell and B-cell epitopes. Northern blotting demonstrated only a 1.7- to 2.5-fold increase in antigen 85B mRNA, suggesting that the enhanced protein production was due primarily to enhanced efficiency of translation. Codon replacement in the genes encoding antigen 85A and superoxide dismutase yielded four- to sixfold increases in recombinant protein production, suggesting that this strategy may be generally applicable to overexpression of mycobacterial genes in E. coli. PMID:10603393

  15. A premature termination codon within an alternative exon affecting only the metabolism of transcripts that retain this exon.

    PubMed

    Maillet, P; Dalla Venezia, N; Lorenzo, F; Morinière, M; Bozon, M; Noël, B; Delaunay, J; Baklouti, F

    1999-01-01

    Protein 4.1 pre-mRNA splicing is regulated in tissue- and development-specific manners. Exon 16, which encodes the N-terminal region of the spectrin/actin-binding domain, is one of the alternatively spliced sequence motifs. It is present in late differentiated erythroid cells but absent from early erythroblasts and from lymphoid cells. We describe a single nucleotide deletion of the erythroid protein 4.1 gene associated with hereditary elliptocytosis. The deletion located in exon 16 leads to a frameshift and a premature termination codon within the same exon. In an effort to examine the premature stop codon effect in relationship with exon 16 alternative splicing, we analyzed erythroid and lymphoid protein 4.1 mRNAs using the mutation and a linked downstream polymorphism as markers. We found that the premature stop codon does not affect the tissue-specific alternative splicing among the two cell types analyzed and that the resulting alteration of mRNA metabolism correlates with the retention of exon 16 in reticulocytes. Conversely, skipping of exon 16 in lymphoid cells converts the mutant mRNA to a normal lymphoid-specific mRNA isoform, hence bypassing the nonsense codon. Consistent with data obtained on constitutive nonsense exons, our observations argue in favor of a stop codon recognition mechanism that occurs after the regulated splicing status of the nonsense exon has been achieved. PMID:10425037

  16. Changing the Codon Usage of hfq Gene has Profound Effect on Phenotype and Pathogenicity of Salmonella Typhimurium.

    PubMed

    Behera, Parthasarathi; Kutty, V H Muhammed; Kumar, Ajeet; Sharma, Bhaskar

    2016-03-01

    Genome recoding with bias codons (synonymous rare codons) or codon pair bias is being used as a method to attenuate virulence mostly in viruses. The target gene chosen for attenuation in general in bacteria is mostly toxin or virulence gene. We have used RNA chaperone hfq, a global post-transcriptional regulator of bacterial gene expression that regulates about 20 % genes in Salmonella, as the target of recoding. The hfq gene was recoded by replacing the codons of hfq gene with synonymous rare codons. Recoding decreased the expression of Hfq protein about two-fold in the mutant as compared to the parent strain. Recoding did not affect growth kinetics, but in growth competition the mutant strain was outcompeted by the parent strain. There was significant decrease in survivability of mutant strain in macrophage as compared to the parent strain. The biofilm formation was significantly impaired in case of recoded mutant. The mutants were also less motile as compared to the parent strain. Intraperitoneal infection of mice with the mutant strain had shown better survival as compared to parent strain. The results show that recoding is an effective method of reducing virulence. PMID:26620536

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

    PubMed

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

    2014-07-01

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

  18. Ribosomes can slide over and beyond “hungry” codons, resuming protein chain elongation many nucleotides downstream

    PubMed Central

    Gallant, Jonathan A.; Lindsley, Dale

    1998-01-01

    In cells subjected to moderate aminoacyl-tRNA limitation, the peptidyl-tRNA–ribosome complex stalled at the “hungry” codon can slide well beyond it on the messenger RNA and resume translation further downstream. This behavior is proved by unequivocal amino acid sequence data, showing a protein that lacks the bypassed sequence encoded between the hungry codon and specific landing sites. The landing sites are codons cognate to the anticodon of the peptidyl-tRNA. The efficiency of this behavior can be as high as 10–20% but declines with the length of the slide. Interposition of “trap” sites (nonproductive landing sites) in the bypassed region reduces the frequency of successful slides, confirming that the ribosome–peptidyl-tRNA complex passes through the untranslated region of the message. This behavior appears to be quite general: it can occur at the two kinds of hungry codons tested, AUA and AAG; the sliding peptidyl-tRNA can be any of three species tested, phenylalanine, tyrosine, or leucine tRNA; the peptidyl component can be either of two very different peptide sequences; and translation can resume at any of the three codons tested. PMID:9811876

  19. Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9.

    PubMed

    Newman, Zachary R; Young, Janet M; Ingolia, Nicholas T; Barton, Gregory M

    2016-03-01

    The innate immune system detects diverse microbial species with a limited repertoire of immune receptors that recognize nucleic acids. The cost of this immune surveillance strategy is the potential for inappropriate recognition of self-derived nucleic acids and subsequent autoimmune disease. The relative expression of two closely related receptors, Toll-like receptor (TLR) 7 and TLR9, is balanced to allow recognition of microbial nucleic acids while limiting recognition of self-derived nucleic acids. Situations that tilt this balance toward TLR7 promote inappropriate responses, including autoimmunity; therefore, tight control of expression is critical for proper homeostasis. Here we report that differences in codon bias limit TLR7 expression relative to TLR9. Codon optimization of Tlr7 increases protein levels as well as responses to ligands, but, unexpectedly, these changes only modestly affect translation. Instead, we find that much of the benefit attributed to codon optimization is actually the result of enhanced transcription. Our findings, together with other recent examples, challenge the dogma that codon optimization primarily increases translation. We propose that suboptimal codon bias, which correlates with low guanine-cytosine (GC) content, limits transcription of certain genes. This mechanism may establish low levels of proteins whose overexpression leads to particularly deleterious effects, such as TLR7. PMID:26903634

  20. An early Oligocene fossil demonstrates treeshrews are slowly evolving "living fossils".

    PubMed

    Li, Qiang; Ni, Xijun

    2016-01-01

    Treeshrews are widely considered a "living model" of an ancestral primate, and have long been called "living fossils". Actual fossils of treeshrews, however, are extremely rare. We report a new fossil species of Ptilocercus treeshrew recovered from the early Oligocene (~34 Ma) of China that represents the oldest definitive fossil record of the crown group of treeshrews and nearly doubles the temporal length of their fossil record. The fossil species is strikingly similar to the living Ptilocercus lowii, a species generally recognized as the most plesiomorphic extant treeshrew. It demonstrates that Ptilocercus treeshrews have undergone little evolutionary change in their morphology since the early Oligocene. Morphological comparisons and phylogenetic analysis support the long-standing idea that Ptilocercus treeshrews are morphologically conservative and have probably retained many characters present in the common stock that gave rise to archontans, which include primates, flying lemurs, plesiadapiforms and treeshrews. This discovery provides an exceptional example of slow morphological evolution in a mammalian group over a period of 34 million years. The persistent and stable tropical environment in Southeast Asia through the Cenozoic likely played a critical role in the survival of such a morphologically conservative lineage. PMID:26766238

  1. Codon optimization and expression of irisin in Pichia pastoris GS115.

    PubMed

    Duan, Huikun; Wang, Haisong; Ma, Baicheng; Jiang, Pingzhe; Tu, Peipei; Ni, Zaizhong; Li, Xiaodan; Li, Miao; Ma, Xiaofeng; Wang, Bin; Wu, Ri; Li, Minggang

    2015-08-01

    Irisin is a novel hormone which is related to many metabolic diseases. In order to illuminate the function and therapeutic effect of irisin, gaining active irisin is necessary. In this work, a codon-optimized irisin gene was designed according to Pichia pastoris synonymous codon usage bias and cloned into the pPIC9K expression vector. Sequencing result indicating that the sequence of irisin was consistent with the modified irisin and the irisin was in frame with α-factor secretion signal ATG. The plasmid pPIC9K-irisin was transformed into GS115 P. pastoris cells through electroporation. The positive transformants were screened on MD medium and analyzed by PCR. Five recombinant GS115/pPIC9K-irisin strains were obtained, but only one strain expressed irisin successfully. SDS-PAGE and Western blot were used to assess the expression level and purity of irisin. The irisin was also simply purified and the effect of pH value, methanol concentration and induction time on the production of irisin was investigated. The results showed that the best conditions of irisin expression were as follows: pH 6.0, 2.0% methanol and induction for 96 h. This work laid the basis for further investigation into the therapeutic and pharmacological effects of irisin, as well as development of irisin-based therapy. PMID:25931394

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

    PubMed Central

    Yu, Ping; Yan, Yuan; Gu, Qing; Wang, Xiangyang

    2013-01-01

    The mature cDNA of endochitinase from Trichoderma viride sp. was optimised based on the codon bias of Pichia pastoris GS115 and synthesised by successive PCR; the sequence was then transformed into P. pastoris GS115 via electroporation. The transformant with the fastest growth rate on YPD plates containing 4 mg/mL G418 was screened and identified. This transformant produced 23.09 U/mL of the recombinant endochitinase, a 35% increase compared to the original strain bearing the wild-type endochitinase cDNA. The recombinant endochitinase was sequentially purified by ammonia sulphate precipitation, DE-52 anion-exchange chromatography and Sephadex G-100 size-exclusion chromatography. Thin-layer chromatography indicated that the purified endochitinase could hydrolyse chito-oligomers or colloidal chitin to generate diacetyl-chitobiose (GlcNAc)2 as the main product. This study demonstrates (1) a means for high expression of Trichoderma viride sp. endochitinase in P. pastoris using codon optimisation and (2) the preparation of chito-oligomers using endochitinase. PMID:24154717

  3. Ribosome collisions and translation efficiency: optimization by codon usage and mRNA destabilization.

    PubMed

    Mitarai, Namiko; Sneppen, Kim; Pedersen, Steen

    2008-09-26

    Individual mRNAs are translated by multiple ribosomes that initiate translation with an interval of a few seconds. The ribosome speed is codon dependent, and ribosome queuing has been suggested to explain specific data for translation of some mRNAs in vivo. By modeling the stochastic translation process as a traffic problem, we here analyze conditions and consequences of collisions and queuing. The model allowed us to determine the on-rate (0.8 to 1.1 initiations/s) and the time (1 s) the preceding ribosome occludes initiation for Escherichia coli lacZ mRNA in vivo. We find that ribosome collisions and queues are inevitable consequences of a stochastic translation mechanism that reduce the translation efficiency substantially on natural mRNAs. The cells minimize collisions by having its mRNAs being unstable and by a highly selected codon usage in the start of the mRNA. The cost of mRNA breakdown is offset by the concomitant increase in translation efficiency. PMID:18619977

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

    PubMed Central

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

    2013-01-01

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

  5. Marked high density lipoprotein deficiency due to apolipoprotein A-I Tomioka (codon 138 deletion).

    PubMed

    Wada, Masamichi; Iso, Tatsuya; Asztalos, Bela F; Takama, Noriaki; Nakajima, Tadashi; Seta, Yukihiro; Kaneko, Katsumi; Taniguchi, Yasuhiro; Kobayashi, Hideo; Nakajima, Katsuyuki; Schaefer, Ernst J; Kurabayashi, Masahiko

    2009-11-01

    We report a novel apolipoprotein A-I (apoA-I) mutation identified in a 64-year-old patient with marked plasma high density lipoprotein (HDL) cholesterol (4 mg/dl) and apoA-I (5mg/dl) deficiency, prior myocardial infarction, and moderate corneal opacities. Coronary angiography revealed extensive atherosclerosis in all three major vessels. Genomic DNA sequencing of the proband revealed a homozygous novel deletion of two successive adenine residues in codon 138 in the apoA-I gene, resulting in a frameshift mutation at amino acid residues 138-178, which we have designated as apoA-I Tomioka. His elder brother was also homozygous for apoA-I Tomioka with marked HDL cholesterol and apoA-I deficiency, but had no clinical evidence of coronary heart disease. Other family members including three siblings and two sons were heterozygous for the mutation, and had approximately 50% of normal plasma HDL cholesterol, and apoA-I. Analysis of apoA-I-containing HDL particles by two-dimensional gel electrophoresis revealed undetectable apoA-I HDL particles in the homozygotes, while in heterozygotes, the mean concentrations of apoA-I in large alpha-1 and very small prebeta-1 HDL subpopulations were significantly decreased at about 35% of normal. Thus, apoA-I Tomioka, a novel deletion mutation in codon 138 of the apoA-I gene, is the causative defect in this case of HDL deficiency. PMID:19473658

  6. Expression, purification and identification of Pla a1 in a codon-optimized Platanus pollen allergen.

    PubMed

    Liu, Yun; Sun, Xiuzhen; Wang, Guizuo; Tao, Ailin; Wu, Yuanyuan; Li, Manxiang; Shi, Hongyang; Xie, Mei

    2015-08-01

    The present study aimed to express, purify and identify the major allergen gene, Pla a1, in Platanus pollen. According to previous studies, the major gene sequences of the Pla a1 allergen were obtained and codon optimization and synthesis of the genome were performed using DNAStar software. Following binding of the target gene fragment and the pET-44a vector, the JM109 cells were transfected to produce positive clones. The vectors were then transformed into Escherichia coli Rosetta cells to induce the expression of the target protein. The exogenous protein was purified using affinity chromatography and was identified by western blot analysis. Pla a1, the major allergen protein in Platanus pollen, was successfully isolated and this exogenous protein was purified using affinity chromatography. The present study was the first, to the best of our knowledge, to obtain expression of the allergen recombinant protein, Pla a1, fused with a Strep-TagII via codon optimization and provided the basis for the preparation of allergens with high purity, recombinant hypoallergenic allergens and allergen nucleic acid vaccines. PMID:25902014

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

    PubMed

    Rosandić, Marija; Glunčić, Matko; Paar, Vladimir

    2013-01-21

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

  8. 3' UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons.

    PubMed

    Boehm, Volker; Haberman, Nejc; Ottens, Franziska; Ule, Jernej; Gehring, Niels H

    2014-10-23

    Nonsense-mediated mRNA decay (NMD) degrades different classes of mRNAs, including transcripts with premature termination codons (PTCs). The NMD factor SMG6 initiates degradation of substrate mRNAs by endonucleolytic cleavage. Here, we aim to delineate the cascade of NMD-activating events that culminate in endocleavage. We report that long 3' UTRs elicit SMG6-mediated endonucleolytic degradation. The presence of an exon-junction complex (EJC) within the 3' UTR strongly stimulates endocleavage in a distance-independent manner. The interaction of SMG6 with EJCs is not required for endocleavage. Whereas the core NMD component UPF2 supports endonucleolytic decay of long 3' UTR mRNAs, it is mostly dispensable during EJC-stimulated endocleavage. Using high-throughput sequencing, we map endocleavage positions of different PTC-containing reporter mRNAs and an endogenous NMD substrate to regions directly at and downstream of the termination codon. These results reveal how messenger ribonucleoprotein (mRNP) parameters differentially influence SMG6-executed endonucleolysis and uncover central characteristics of this phenomenon associated with translation termination. PMID:25310981

  9. Codon optimization, expression, purification, and functional characterization of recombinant human IL-25 in Pichia pastoris.

    PubMed

    Liu, Yushan; Wu, Chengsheng; Wang, Jinyu; Mo, Wei; Yu, Min

    2013-12-01

    Interleukin (IL)-25 (also known as IL-17E) is a distinct member of the IL-17 cytokine family which induces IL-4, IL-5, and IL-13 expression and promotes pathogenic T helper (Th)-2 cell responses in various organs. IL-25 has been shown to have crucial role between innate and adaptive immunity and also a key component of the protection of gastrointestinal helminthes. In this study, to produce bioactive recombinant human IL-25 (rhIL-25), the cDNA of mature IL-25 was performed codon optimization based on methylotropic yeast Pichia pastoris codon bias and cloned into the expression vector pPICZαA. The recombinant vector was transformed into P. pichia strain X-33 and selected by zeocin resistance. Benchtop fermentation and simple purification strategy were established to purify the rhIL-25 with about 17 kDa molecular mass. Functional analysis showed that purified rhIL-25 specifically bond to receptor IL-17BR and induce G-CSF production in vitro. Further annexin V-FITC/PI staining assay indicated that rhIL-25 induced apoptosis in two breast cancer cells, MDA-MB-231 and HBL-100. This study provides a new strategy for the large-scale production of bioactive IL-25 for biological and therapeutic applications. PMID:24100683

  10. A population-specific HTR2B stop codon predisposes to severe impulsivity.

    PubMed

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

    2010-12-23

    Impulsivity, describing action without foresight, is an important feature of several psychiatric diseases, suicidality and violent behaviour. The complex origins of impulsivity hinder identification of the genes influencing it and the diseases with which it is associated. Here we perform exon-focused sequencing of impulsive individuals in a founder population, targeting fourteen genes belonging to the serotonin and dopamine domain. A stop codon in HTR2B was identified that is common (minor allele frequency > 1%) but exclusive to Finnish people. Expression of the gene in the human brain was assessed, as well as the molecular functionality of the stop codon, which was associated with psychiatric diseases marked by impulsivity in both population and family-based analyses. Knockout of Htr2b increased impulsive behaviours in mice, indicative of predictive validity. Our study shows the potential for identifying and tracing effects of rare alleles in complex behavioural phenotypes using founder populations, and indicates a role for HTR2B in impulsivity. PMID:21179162

  11. Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.

    PubMed

    Matsumoto, Tomotaka; John, Anoop; Baeza-Centurion, Pablo; Li, Boyang; Akashi, Hiroshi

    2016-06-01

    A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estimated α) considerably larger than its true value. Nonstationary evolution (changes in population size, selection, or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, α-hat < α. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating α. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with α-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees. PMID:26873577

  12. Codon optimization for high level expression of human bone morphogenetic protein-2 in Escherichia coli.

    PubMed

    Retnoningrum, Debbie S; Pramesti, H T; Santika, P Y; Valerius, O; Asjarie, S; Suciati, T

    2012-08-01

    Codons in the open reading frame (ORF) encoding for human bone morphogenetic protein-2 (hBMP-2) were optimized to reach high level expression in Escherichia coli. The optimization was done by the computer programs DNA works and DNA Star according to Thermodynamically Balanced Inside Out (TBIO) approach. The ORF consisting of 342 base pairs (bp) was assembled using two-steps Polymerase Chain Reaction, cloned into a pGEM-T vector with a mutation rate of 6.38 bp per kb and transformed into E. coli JM109. After a DNA sequence confirmation, mutation-free ORF was subcloned into pET32b and transformed into E. coli BL21(DE3). The rhBMP-2 was produced as a thioredoxin-his-tag fusion protein at relatively high level, approximately 60% of total intracellular proteins as inclusion bodies (IB), with a yield of 1.39 g per liter culture. Solubilization of IB gave soluble monomer rhBMP-2 with a recovery of 13.6% and refolding of soluble rhBMP-2 produced dimeric forms with a yield of 8.7%. The size and identity of the purified rhBMP-2 was confirmed by nano-LC-MS/MS2 analysis. Our work demonstrates for the first time that by using TBIO approach, a codon-optimized ORF encoding for rhBMP-2 protein can be expressed at high level in E. coli expression system. PMID:22691543

  13. Calibration of radionuclide calibrators in Canadian hospitals

    SciTech Connect

    Santry, D.C.

    1986-01-01

    The major user of radioactive isotopes in Canada is the medical profession. Because of this a program has been initiated at the National Research Council of Canada (NRCC) to assist the nuclear medicine community to determine more accurately, the rather large amounts of radioactive materials administered to patients either for therapeutic or medical diagnostics. Since radiation exposure to the human body has deleterious effects, it is important for the patient that the correct amount of radioactive material is administered to minimize the induction of a fatal cancer at a later time. Hospitals in many other countries have a legal requirement to have their instruments routinely calibrated and have previously entered into intercomparisons with other hospitals or their national standards laboratories. In Canada, hospitals and clinics can participate on a voluntary basis to have the proper operation of measuring devices (radionuclide calibrators in particular) examined through intercomparisons. The program looks primarily at laboratory performance. This includes not only the instrument's performance but the performance of the individual doing the procedure and the technical procedure or method employed. In an effort to provide personal assistance to those having problems, it is essential that the comparisons should be pertinent to the daily work of the laboratory and that the most capable technologist not be selected to carry out the assay.

  14. OPTIMUM FREQUENCY OF CALIBRATION MONITORING

    EPA Science Inventory

    The paper develops an algorithm by which to compute the optimal frequency of calibration monitoring to minimize the total cost of analyzing a set of samples and the required calibration standards. Optimum calibration monitoring is needed because of the high cost and calibration d...

  15. Probable Carbonate Fossilization Processes Within Dead Sea Microbial Remains

    NASA Technical Reports Server (NTRS)

    Morris, P. A.; Wentworth, S. J.; Thomas-Keprta, K. L.; Allen, C. C.; McKay, D. S.

    2001-01-01

    Microbial fossilization processes in the Dead Sea is primarily associated with the calcium cation. The putative fossilized microbes do not represent the reported living microbial population. Additional information is contained in the original extended abstract.

  16. Psychophysical contrast calibration

    PubMed Central

    To, Long; Woods, Russell L; Goldstein, Robert B; Peli, Eli

    2013-01-01

    Electronic displays and computer systems offer numerous advantages for clinical vision testing. Laboratory and clinical measurements of various functions and in particular of (letter) contrast sensitivity require accurately calibrated display contrast. In the laboratory this is achieved using expensive light meters. We developed and evaluated a novel method that uses only psychophysical responses of a person with normal vision to calibrate the luminance contrast of displays for experimental and clinical applications. Our method combines psychophysical techniques (1) for detection (and thus elimination or reduction) of display saturating nonlinearities; (2) for luminance (gamma function) estimation and linearization without use of a photometer; and (3) to measure without a photometer the luminance ratios of the display’s three color channels that are used in a bit-stealing procedure to expand the luminance resolution of the display. Using a photometer we verified that the calibration achieved with this procedure is accurate for both LCD and CRT displays enabling testing of letter contrast sensitivity to 0.5%. Our visual calibration procedure enables clinical, internet and home implementation and calibration verification of electronic contrast testing. PMID:23643843

  17. STIS Calibration Pipeline

    NASA Astrophysics Data System (ADS)

    Hulbert, S.; Hodge, P.; Lindler, D.; Shaw, R.; Goudfrooij, P.; Katsanis, R.; Keener, S.; McGrath, M.; Bohlin, R.; Baum, S.

    1997-05-01

    Routine calibration of STIS observations in the HST data pipeline is performed by the CALSTIS task. CALSTIS can: subtract the over-scan region and a bias image from CCD observations; remove cosmic ray features from CCD observations; correct global nonlinearities for MAMA observations; subtract a dark image; and, apply flat field corrections. In the case of spectral data, CALSTIS can also: assign a wavelength to each pixel; apply a heliocentric correction to the wavelengths; convert counts to absolute flux; process the automatically generated spectral calibration lamp observations to improve the wavelength solution; rectify two-dimensional (longslit) spectra; subtract interorder and sky background; and, extract one-dimensional spectra. CALSTIS differs in significant ways from the current HST calibration tasks. The new code is written in ANSI C and makes use of a new C interface to IRAF. The input data, reference data, and output calibrated data are all in FITS format, using IMAGE or BINTABLE extensions. Error estimates are computed and include contributions from the reference images. The entire calibration can be performed by one task, but many steps can also be performed individually.

  18. Calibration Under Uncertainty.

    SciTech Connect

    Swiler, Laura Painton; Trucano, Timothy Guy

    2005-03-01

    This report is a white paper summarizing the literature and different approaches to the problem of calibrating computer model parameters in the face of model uncertainty. Model calibration is often formulated as finding the parameters that minimize the squared difference between the model-computed data (the predicted data) and the actual experimental data. This approach does not allow for explicit treatment of uncertainty or error in the model itself: the model is considered the %22true%22 deterministic representation of reality. While this approach does have utility, it is far from an accurate mathematical treatment of the true model calibration problem in which both the computed data and experimental data have error bars. This year, we examined methods to perform calibration accounting for the error in both the computer model and the data, as well as improving our understanding of its meaning for model predictability. We call this approach Calibration under Uncertainty (CUU). This talk presents our current thinking on CUU. We outline some current approaches in the literature, and discuss the Bayesian approach to CUU in detail.

  19. GTC Photometric Calibration

    NASA Astrophysics Data System (ADS)

    di Cesare, M. A.; Hammersley, P. L.; Rodriguez Espinosa, J. M.

    2006-06-01

    We are currently developing the calibration programme for GTC using techniques similar to the ones use for the space telescope calibration (Hammersley et al. 1998, A&AS, 128, 207; Cohen et al. 1999, AJ, 117, 1864). We are planning to produce a catalogue with calibration stars which are suitable for a 10-m telescope. These sources will be not variable, non binary and do not have infrared excesses if they are to be used in the infrared. The GTC science instruments require photometric calibration between 0.35 and 2.5 microns. The instruments are: OSIRIS (Optical System for Imaging low Resolution Integrated Spectroscopy), ELMER and EMIR (Espectrógrafo Multiobjeto Infrarrojo) and the Acquisition and Guiding boxes (Di Césare, Hammersley, & Rodriguez Espinosa 2005, RevMexAA Ser. Conf., 24, 231). The catalogue will consist of 30 star fields distributed in all of North Hemisphere. We will use fields containing sources over the range 12 to 22 magnitude, and spanning a wide range of spectral types (A to M) for the visible and near infrared. In the poster we will show the method used for selecting these fields and we will present the analysis of the data on the first calibration fields observed.

  20. A miniature remote deadweight calibrator

    NASA Astrophysics Data System (ADS)

    Supplee, Frank H., Jr.; Tcheng, Ping

    A miniature, computer-controlled, deadweight calibrator was developed to remotely calibrate a force transducer mounted in a cryogenic chamber. This simple mechanism allows automatic loading and unloading of deadweights placed onto a skin friction balance during calibrations. Equipment for the calibrator includes a specially designed set of five interlocking 200-milligram weights, a motorized lifting platform, and a controller box taking commands from a microcomputer on an IEEE interface. The computer is also used to record and reduce the calibration data and control other calibration parameters. The full-scale load for this device is 1,000 milligrams; however, the concept can be extended to accommodate other calibration ranges.

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

    NASA Astrophysics Data System (ADS)

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

    2000-03-01

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

  2. Calibration of fossil scleraxonian Southern Ocean deep-sea corals for U-series dating

    NASA Astrophysics Data System (ADS)

    Gutjahr, M.; Vance, D.; Hoffmann, D.; Hillenbrand, C.; Kuhn, G.

    2008-12-01

    The deep Southern Ocean has been pinpointed as candidate reservoir capable of storing the additional respired carbon that was drawn from the atmosphere during the Last Glacial Maximum compared with the present-day. In this context the determination of deep ocean ventilation ages is a commonly applied tool, potentially identifying radiocarbon depletion in glacial deep water and enhanced ocean stratification. In order to derive deep-sea ventilation ages most studies to date have used either radiocarbon age differences between paired planktic and benthic foraminifera samples or coupled U-Th and radiocarbon dates obtained from aragonitic deep-sea corals. Results from both these approaches are, however, as yet very scarce for the Southern Ocean. We present calendar ages for a set of deep-sea scleraxonian corals from the Marie Byrd Seamounts in the Amundsen Sea sector of the Southern Ocean (~123°W, ~69°S, 2500 m to 1430 m water depth) employing the 230Th/U-dating method. The aim of our study is to evaluate whether these calcitic octocorals can be used for ventilation age determinations. Our corals have significantly lower uranium concentrations than aragonitic deep-sea corals, ranging from 80 to 250 ng/g. Most corals of Holocene age reproduced the present-day seawater 234U/238U. Pre-Holocene corals, however, show a systematic enrichment of 234U, leading to slightly elevated deglacial initial 234U/238U and significantly higher 234U/238U for ~MIS5 sub-samples. These corals also appear to grow very slowly, on the order of only few μm/year, making it essential to sample as little coral material as possible for combined 230Th/U- and radiocarbon dating purposes. One coral, sampled at high-resolution in various sections returned ages that scatter around 10 ka BP and the early deglaciation, though several significantly older ages were obtained as well. The present-day (234U/238U) ACT in different sections of this coral is very homogenous (1.155 ± 0.003) and more or less independent of apparent age, suggesting effective preferential 234U diffusion throughout the coral. Strikingly this composition is also higher than the present-day seawater (234U/238U) ACT of 1.147. We show the apparent 230Th/U coral ages and 234U/238U results alongside coral major and trace element ratios obtained by laser ablation along selected transects, to better characterize U diffusion pathways and mechanisms, to identify internal diagenetic alteration rims and to evaluate the presence of coral paleo- surfaces.

  3. Research and development entitled smart structures for fossil energy applications

    SciTech Connect

    Claus, R.O.

    1990-12-01

    Two different fiber optic sensors were considered for use in ceramic cross flow filters. The intensity-based sensor was tested with a great degree of success. Even with a computerized data acquisition system, the intensity-based sensor was unable to achieve the resolution of the Fabry-Perot sensor. Another drawback of the intensity sensor is the hysteresis behavior observed over cyclic variation of temperature. We have determined that extrinsic Fabry-Perot fiber optic sensors can be used to measure thermal strains in ceramic cross-flow filters with accuracies of 0.1 {mu}m/m. The single ended approach of the reflective Fabry-Perot sensors is well suited for high thermal strain measurements; the results obtained show that the output of the fiber sensor tracks the temperature changes exactly as expected and shows no noticeable time lag between the measurand and the output signal. Sapphire fibers were manufactured with silica claddings and their spectral attenuation was measured. An intensity based sensor using sapphire fibers was fabricated and its performance calibrated. The success of the Fabry-Perot sensor has proved that such fiber optic sensors are ideally suited for smart structures'' in fossil energy applications. 11 refs., 43 figs.

  4. Reconstructing palaeoclimatic variables from fossil pollen using boosted regression trees: comparison and synthesis with other quantitative reconstruction methods

    NASA Astrophysics Data System (ADS)

    Salonen, J. Sakari; Luoto, Miska; Alenius, Teija; Heikkilä, Maija; Seppä, Heikki; Telford, Richard J.; Birks, H. John B.

    2014-03-01

    We test and analyse a new calibration method, boosted regression trees (BRTs) in palaeoclimatic reconstructions based on fossil pollen assemblages. We apply BRTs to multiple Holocene and Lateglacial pollen sequences from northern Europe, and compare their performance with two commonly-used calibration methods: weighted averaging regression (WA) and the modern-analogue technique (MAT). Using these calibration methods and fossil pollen data, we present synthetic reconstructions of Holocene summer temperature, winter temperature, and water balance changes in northern Europe. Highly consistent trends are found for summer temperature, with a distinct Holocene thermal maximum at ca 8000-4000 cal. a BP, with a mean Tjja anomaly of ca +0.7 °C at 6 ka compared to 0.5 ka. We were unable to reconstruct reliably winter temperature or water balance, due to the confounding effects of summer temperature and the great between-reconstruction variability. We find BRTs to be a promising tool for quantitative reconstructions from palaeoenvironmental proxy data. BRTs show good performance in cross-validations compared with WA and MAT, can model a variety of taxon response types, find relevant predictors and incorporate interactions between predictors, and show some robustness with non-analogue fossil assemblages.

  5. Targetless Camera Calibration

    NASA Astrophysics Data System (ADS)

    Barazzetti, L.; Mussio, L.; Remondino, F.; Scaioni, M.

    2011-09-01

    In photogrammetry a camera is considered calibrated if its interior orientation parameters are known. These encompass the principal distance, the principal point position and some Additional Parameters used to model possible systematic errors. The current state of the art for automated camera calibration relies on the use of coded targets to accurately determine the image correspondences. This paper presents a new methodology for the efficient and rigorous photogrammetric calibration of digital cameras which does not require any longer the use of targets. A set of images depicting a scene with a good texture are sufficient for the extraction of natural corresponding image points. These are automatically matched with feature-based approaches and robust estimation techniques. The successive photogrammetric bundle adjustment retrieves the unknown camera parameters and their theoretical accuracies. Examples, considerations and comparisons with real data and different case studies are illustrated to show the potentialities of the proposed methodology.

  6. Automatic beamline calibration procedures

    SciTech Connect

    Corbett, W.J.; Lee, M.J.; Zambre, Y.

    1992-03-01

    Recent experience with the SLC and SPEAR accelerators have led to a well-defined set of procedures for calibration of the beamline model using the orbit fitting program, RESOLVE. Difference orbit analysis is used to calibrate quadrupole strengths, BPM sensitivities, corrector strengths, focusing effects from insertion devices, and to determine the source of dispersion and coupling errors. Absolute orbit analysis is used to locate quadrupole misalignments, BPM offsets, or beam loss. For light source applications, the photon beam source coordinates can be found. The result is an accurate model of the accelerator which can be used for machine control. In this paper, automatable beamline calibration procedures are outlined and illustrated with recent examples. 5 refs.

  7. Calibration Systems Final Report

    SciTech Connect

    Myers, Tanya L.; Broocks, Bryan T.; Phillips, Mark C.

    2006-02-01

    The Calibration Systems project at Pacific Northwest National Laboratory (PNNL) is aimed towards developing and demonstrating compact Quantum Cascade (QC) laser-based calibration systems for infrared imaging systems. These on-board systems will improve the calibration technology for passive sensors, which enable stand-off detection for the proliferation or use of weapons of mass destruction, by replacing on-board blackbodies with QC laser-based systems. This alternative technology can minimize the impact on instrument size and weight while improving the quality of instruments for a variety of missions. The potential of replacing flight blackbodies is made feasible by the high output, stability, and repeatability of the QC laser spectral radiance.

  8. Fossil energy waste management. Technology status report

    SciTech Connect

    Bossart, S.J.; Newman, D.A.

    1995-02-01

    This report describes the current status and recent accomplishments of the Fossil Energy Waste Management (FE WM) projects sponsored by the Morgantown Energy Technology Center (METC) of the US Department of Energy (DOE). The primary goal of the Waste Management Program is to identify and develop optimal strategies to manage solid by-products from advanced coal technologies for the purpose of ensuring the competitiveness of advanced coal technologies as a future energy source. The projects in the Fossil Energy Waste Management Program are divided into three types of activities: Waste Characterization, Disposal Technologies, and Utilization Technologies. This technology status report includes a discussion on barriers to increased use of coal by-products. Also, the major technical and nontechnical challenges currently being addressed by the FE WM program are discussed. A bibliography of 96 citations and a list of project contacts is included if the reader is interested in obtaining additional information about the FE WM program.

  9. Diatoms: a fossil fuel of the future.

    PubMed

    Levitan, Orly; Dinamarca, Jorge; Hochman, Gal; Falkowski, Paul G

    2014-03-01

    Long-term global climate change, caused by burning petroleum and other fossil fuels, has motivated an urgent need to develop renewable, carbon-neutral, economically viable alternatives to displace petroleum using existing infrastructure. Algal feedstocks are promising candidate replacements as a 'drop-in' fuel. Here, we focus on a specific algal taxon, diatoms, to become the fossil fuel of the future. We summarize past attempts to obtain suitable diatom strains, propose future directions for their genetic manipulation, and offer biotechnological pathways to improve yield. We calculate that the yields obtained by using diatoms as a production platform are theoretically sufficient to satisfy the total oil consumption of the US, using between 3 and 5% of its land area. PMID:24529448

  10. FOSSIL RIDGE WILDERNESS STUDY AREA, COLORADO.

    USGS Publications Warehouse

    DeWitt, Ed; Kluender, Steven E.

    1984-01-01

    The Fossil Ridge Wilderness Study Area, approximately 20 mi northeast of Gunnison in central Colorado, was studied and its mineral-resource potential assessed. Portions of the study area have substantiated resource potential for gold, silver, copper, lead, zinc, molybdenum, uranium, thorium, rare-earth elements, and high-calcium limestone. Much of the area has a probable resource potential for the preceeding commodities as well as for tin. Various other elements are found in anomalous concentrations within the study area, but there is likelihood for their occurrence in amounts sufficient to constitute resources. Exploration, especially for molybdenum, gold, and uranium, has been active in the past and is expected to continue in the future. No potential for fossil fuel resources was identified in this study.

  11. 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

  12. CRISPRi-Manipulation of Genetic Code Expansion via RF1 for Reassignment of Amber Codon in Bacteria

    PubMed Central

    Zhang, Bo; Yang, Qi; Chen, Jingxian; Wu, Ling; Yao, Tianzhuo; Wu, Yiming; Xu, Huan; Zhang, Lihe; Xia, Qing; Zhou, Demin

    2016-01-01

    The precise engineering of proteins in bacteria via the amber codon has been hampered by the poor incorporation of unnatural amino acid (UAA). Here we explored the amber assignment as a sense codon for UAA by CRISPRi targeting release factor 1 (RF1). Scanning of RF1 gene with sgRNAs identified target loci that differentiate RF1 repressions. Quantitation of RF1 repressions versus UAA incorporation indicated an increasing interrelation with the amber reassignment maximized upon RF1 knockdown to ~30%, disclosing the beneficial role of RF1 in amber assignment. However, further RF1 repression reversed this trend resulting from the detrimental effects on host cell growth, disclosing the harmful aspect of RF1 in reassignment of the amber codon. Our data indicate RF1 as a switch manipulating genetic code expansion and pave a direction via CRISPRi for precise engineering and efficient production of proteins in bacteria. PMID:26818534

  13. K-ras mutation at codon 12 in stage I pancreatic adenocarcinoma: analysis by laser capture microdissection and direct sequencing.

    PubMed

    Chang, M C; Chang, Y T; Wu, M S; Shun, C T; Tien, Y W; Lin, J T

    2001-05-01

    Pancreatic ductal adenocarcinoma has been reported to carry a rate mutation high in codon 12 of the K-ras oncogene. To avoid the pitfalls of conventional methods of tissue dissection that might affect the sensitivity and specificity of detecting K-ras mutation, laser capture microdissection (LCM) technique was used. Pancreatic adenocarcinoma tissues were obtained from 15 patients who underwent Whipple's procedure. Selected tissues procured by LCM were analyzed by direct sequencing after polymerase chain reaction amplification of K-ras sequences at codon 12. K-ras mutation was noted in nine patients. All mutations showed G to A substitution at codon 12. The mutational pattern (GGT to GAT) is similar in both western and eastern reports. LCM is a feasible method to effectively obtain pure tumor cells from a surgical specimen. It remains to be determined whether this low mutation rate is a result of relatively early stage of disease or different carcinogenesis in different geographic regions. PMID:11432318

  14. The NEMO Mutation Creating the Most-Upstream Premature Stop Codon Is Hypomorphic Because of a Reinitiation of Translation

    PubMed Central

    Puel, Anne; Reichenbach, Janine; Bustamante, Jacinta; Ku, Cheng-Lung; Feinberg, Jacqueline; Döffinger, Rainer; Bonnet, Marion; Filipe-Santos, Orchidée; Beaucoudrey, Ludovic de; Durandy, Anne; Horneff, Gerd; Novelli, Francesco; Wahn, Volker; Smahi, Asma; Israel, Alain; Niehues, Tim; Casanova, Jean-Laurent

    2006-01-01

    Amorphic mutations in the NF-κB essential modulator (NEMO) cause X-dominant incontinentia pigmenti, which is lethal in males in utero, whereas hypomorphic mutations cause X-recessive anhidrotic ectodermal dysplasia with immunodeficiency, a complex developmental disorder and life-threatening primary immunodeficiency. We characterized the NEMO mutation 110_111insC, which creates the most-upstream premature translation termination codon (at codon position 49) of any known NEMO mutation. Surprisingly, this mutation is associated with a pure immunodeficiency. We solve this paradox by showing that a Kozakian methionine codon located immediately downstream from the insertion allows the reinitiation of translation. The residual production of an NH2-truncated NEMO protein was sufficient for normal fetal development and for the subsequent normal development of skin appendages but was insufficient for the development of protective immune responses. PMID:16532398

  15. Problematic microscopic trace (?) fossils, Oligocene, Slovakia

    NASA Astrophysics Data System (ADS)

    Mikuláš, R.; Boorová, D.; Holcová, K.

    2013-05-01

    Meioscopic to microscopic capsules found in reddish, probably marine or brackish shales (Oligocene, Pannonian Basin; South Slovakia) are interpreted as possible trace fossils. They may represent burrows of meioscopic in-fauna. Ferruginous walls of the capsules appeared very probably as late as during diagenesis; however, the (possibly organic) matrix had to exist before the diagenetic processes. Other discussed explanations (inorganic "ironstones"; coprolites) are not plausible.

  16. Identifying Fossil Bacteria in Martian Materials

    NASA Technical Reports Server (NTRS)

    Westall, F.; McKay, D. S.; Gibson, E. K., Jr.

    1999-01-01

    Within the next decade, robotic missions are going to Mars with the search for evidence for extant and extinct life as at least one of the mission objectives. Moreover, the first Martian samples will be returned to Earth in 2008. It is therefore imperative that we can be certain that we can identify life in Martian rocks. In this paper we will not be discussing extant life but will concentrate on fossil life.

  17. Precambrian ``fossil'' Vermiforma is a tectograph

    SciTech Connect

    Seilacher, A.; Meschede, M.; Bolton, E.W.; Luginsland, H.

    2000-03-01

    Vermiforma antiqua Cloud 1976, once celebrated as the earliest animal fossil of the US, is actually a tectonic artifact. The main argument is that the congruence and equal orientation of multiple patterns on the same bedding plane are incompatible with swaying worm bodies of worm burrows. As shown by analog and numerical simulations, these structures can be explained as tracks of particles that broke out from the base of an overlying turbidite and became rolled between beds during bed-to-bed shearing.

  18. Adaptation, plant evolution, and the fossil record

    NASA Technical Reports Server (NTRS)

    Knoll, A. H.; Niklas, K. J.

    1987-01-01

    The importance of adaptation in determining patterns of evolution has become an important focus of debate in evolutionary biology. As it pertains to paleobotany, the issue is whether or not adaptive evolution mediated by natural selection is sufficient to explain the stratigraphic distributions of taxa and character states observed in the plant fossil record. One means of addressing this question is the functional evaluation of stratigraphic series of plant organs set in the context of paleoenvironmental change and temporal patterns of floral composition within environments. For certain organ systems, quantitative estimates of biophysical performance can be made on the basis of structures preserved in the fossil record. Performance estimates for plants separated in time or space can be compared directly. Implicit in different hypotheses of the forces that shape the evolutionary record (e.g. adaptation, mass extinction, rapid environmental change, chance) are predictions about stratigraphic and paleoenvironmental trends in the efficacy of functional performance. Existing data suggest that following the evolution of a significant structural innovation, adaptation for improved functional performance can be a major determinant of evolutionary changes in plants; however, there are structural and development limits to functional improvement, and once these are reached, the structure in question may no longer figure strongly in selection until and unless a new innovation evolves. The Silurian-Devonian paleobotanical record is consistent with the hypothesis that the succession of lowland floodplain dominants preserved in the fossil record of this interval was determined principally by the repeated evolution of new taxa that rose to ecological importance because of competitive advantages conferred by improved biophysical performance. This does not seem to be equally true for Carboniferous-Jurassic dominants of swamp and lowland floodplain environments. In these cases

  19. Fossil dust shells around luminous supergiants

    NASA Technical Reports Server (NTRS)

    Stothers, R.

    1975-01-01

    The observed frequency with which infrared excesses appear in F, G, and K supergiants of luminosity class Ia supports the idea that these excesses arise in a 'fossil' circumstellar dust shell that was formed during a prior M-super-giant phase of evolution. The required leftward evolution of the star on the H-R diagram would then imply that the Ledoux, rather than the Schwarzschild, criterion for convective mixing is the correct criterion to use in stellar evolution calculations.

  20. Iterative Magnetometer Calibration

    NASA Technical Reports Server (NTRS)

    Sedlak, Joseph

    2006-01-01

    This paper presents an iterative method for three-axis magnetometer (TAM) calibration that makes use of three existing utilities recently incorporated into the attitude ground support system used at NASA's Goddard Space Flight Center. The method combines attitude-independent and attitude-dependent calibration algorithms with a new spinning spacecraft Kalman filter to solve for biases, scale factors, nonorthogonal corrections to the alignment, and the orthogonal sensor alignment. The method is particularly well-suited to spin-stabilized spacecraft, but may also be useful for three-axis stabilized missions given sufficient data to provide observability.

  1. Autonomous Phase Retrieval Calibration

    NASA Technical Reports Server (NTRS)

    Estlin, Tara A.; Chien, Steve A.; Castano, Rebecca; Gaines, Daniel M.; Doubleday, Joshua R.; Schoolcraft, Josua B.; Oyake, Amalaye; Vaughs, Ashton G.; Torgerson, Jordan L.

    2011-01-01

    The Palomar Adaptive Optics System actively corrects for changing aberrations in light due to atmospheric turbulence. However, the underlying internal static error is unknown and uncorrected by this process. The dedicated wavefront sensor device necessarily lies along a different path than the science camera, and, therefore, doesn't measure the true errors along the path leading to the final detected imagery. This is a standard problem in adaptive optics (AO) called "non-common path error." The Autonomous Phase Retrieval Calibration (APRC) software suite performs automated sensing and correction iterations to calibrate the Palomar AO system to levels that were previously unreachable.

  2. Regulation of the Escherichia coli tna operon: nascent leader peptide control at the tnaC stop codon.

    PubMed Central

    Konan, K V; Yanofsky, C

    1997-01-01

    Expression of the tryptophanase (tna) operon of Escherichia coli is regulated by catabolite repression and by tryptophan-induced transcription antitermination at Rho-dependent termination sites in the leader region of the operon. Tryptophan induction is dependent on translation of a short leader peptide coding region, tnaC, that contains a single, crucial tryptophan codon. Recent studies suggest that during induction, the TnaC leader peptide acts in cis on the translating ribosome to inhibit its release at the tnaC stop codon. In the present study we use a tnaC-UGA-'lacZ construct lacking the tnaC-tnaA spacer region to analyze the effect of TnaC synthesis on the behavior of the ribosome that translates tnaC. The tnaC-UGA-'lacZ construct is not expressed significantly in the presence or absence of inducer. However, it is expressed in the presence of UGA suppressors, or when the structural gene for polypeptide release factor 3 is disrupted, or when wild-type tRNATrP is overproduced. In each situation, tnaC-UGA-'lacZ expression is reduced appreciably by the presence of inducing levels of tryptophan. Replacing the tnaC UGA stop codon with a sense codon allows considerable expression, which is also reduced, although to a lesser extent, by the addition of tryptophan. Inhibition by tryptophan is not observed when Trp codon 12 of tnaC is changed to a Leu codon. Overexpression of tnaC in trans from a multicopy plasmid prevents inhibition of expression by tryptophan. These results support the hypothesis that the TnaC leader peptide acts in cis to alter the behavior of the translating ribosome. PMID:9045840

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

    PubMed Central

    Sanz, Miguel Angel

    2015-01-01

    Translation initiation of alphavirus subgenomic mRNA (sgmRNA) can occur in the absence of several initiation factors (eIFs) in infected cells; however, the precise translation mechanism is still poorly understood. In this study, we have examined the mechanism of initiation and AUG selection in Sindbis virus (SINV) sgmRNA. Our present findings suggest that sgmRNA is translated via a scanning mechanism, since the presence of a hairpin structure before the initiation codon hampers protein synthesis directed by this mRNA. In addition, translation is partially recovered when an in-frame AUG codon is placed upstream of this hairpin. This scanning process takes place without the participation of eIF4A and active eIF2. These results, combined with our findings through modifying the SINV sgmRNA leader sequence, do not support the possibility of a direct initiation from the start codon without previous scanning, or a shunting mechanism. Moreover, studies carried out with sgmRNAs containing two alternative AUG codons within a good context for translation reveal differences in AUG selection which are dependent on the cellular context and the phosphorylation state of eIF2α. Thus, initiation at the additional AUG is strictly dependent on active eIF2, whereas the genuine AUG codon can start translation following eIF2α inactivation. Collectively, our results suggest that SINV sgmRNA is translated by a scanning mechanism without the potential participation of crucial eIFs. A model is presented that explains the mechanism of initiation of mRNAs bearing two alternative initiation codons. PMID:25404563

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

    PubMed

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

    2015-01-01

    Translation initiation of alphavirus subgenomic mRNA (sgmRNA) can occur in the absence of several initiation factors (eIFs) in infected cells; however, the precise translation mechanism is still poorly understood. In this study, we have examined the mechanism of initiation and AUG selection in Sindbis virus (SINV) sgmRNA. Our present findings suggest that sgmRNA is translated via a scanning mechanism, since the presence of a hairpin structure before the initiation codon hampers protein synthesis directed by this mRNA. In addition, translation is partially recovered when an in-frame AUG codon is placed upstream of this hairpin. This scanning process takes place without the participation of eIF4A and active eIF2. These results, combined with our findings through modifying the SINV sgmRNA leader sequence, do not support the possibility of a direct initiation from the start codon without previous scanning, or a shunting mechanism. Moreover, studies carried out with sgmRNAs containing two alternative AUG codons within a good context for translation reveal differences in AUG selection which are dependent on the cellular context and the phosphorylation state of eIF2α. Thus, initiation at the additional AUG is strictly dependent on active eIF2, whereas the genuine AUG codon can start translation following eIF2α inactivation. Collectively, our results suggest that SINV sgmRNA is translated by a scanning mechanism without the potential participation of crucial eIFs. A model is presented that explains the mechanism of initiation of mRNAs bearing two alternative initiation codons. PMID:25404563

  5. Are Solar Wind Reconnection Events Fossil Sites?

    NASA Astrophysics Data System (ADS)

    Vu, H. X.; Karimabadi, H.; Scudder, J. D.; Roytershteyn, V.; Daughton, W. S.; Gosling, J. T.; Egedal, J.

    2010-12-01

    Studies of reconnection in the solar wind led by Gosling and collaborators have revealed surprising results that are posing serious challenges to current theoretical understanding of the reconnection process. This include observations of prolonged quasi-steady reconnection, low magnetic shear angles, and no real bulk heating (i.e., full thermalization rather than appearance of heating due to two beams) or substantial particle acceleration. In contrast, the theoretical expectations have been that reconnection leads to significant bulk heating and particle acceleration. Similarly, recent full particle simulations indicate that reconnection is generally time dependent. We have recently re-examined this apparent discrepancy between observations and theory and propose a resolution to these puzzling observations based on the concept of fossil reconnection site. We have performed large scale 2D fully kinetic simulations of reconnection to very long times to gain an understanding of reconnection structure as they would be seen in the observations. We find that reconnection weakens in time and approaches an asymptotic state which we refer to as fossil state. The properties of the fossil reconnection state explain several of the puzzling aspects of the observations. The implications of these findings for studies of solar wind reconnection are discussed.

  6. Exploring macroevolution using modern and fossil data.

    PubMed

    Benton, Michael J

    2015-07-01

    Macroevolution, encompassing the deep-time patterns of the origins of modern biodiversity, has been discussed in many contexts. Non-Darwinian models such as macromutations have been proposed as a means of bridging seemingly large gaps in knowledge, or as a means to explain the origin of exquisitely adapted body plans. However, such gaps can be spanned by new fossil finds, and complex, integrated organisms can be shown to have evolved piecemeal. For example, the fossil record between dinosaurs and Archaeopteryx has now filled up with astonishing fossil intermediates that show how the unique plexus of avian adaptations emerged step by step over 60 Myr. New numerical approaches to morphometrics and phylogenetic comparative methods allow palaeontologists and biologists to work together on deep-time questions of evolution, to explore how diversity, morphology and function have changed through time. Patterns are more complex than sometimes expected, with frequent decoupling of species diversity and morphological diversity, pointing to the need for some new generalizations about the processes that lie behind such patterns. PMID:26063844

  7. Fossil avian eggshell preserves ancient DNA

    PubMed Central

    Oskam, Charlotte L.; Haile, James; McLay, Emma; Rigby, Paul; Allentoft, Morten E.; Olsen, Maia E.; Bengtsson, Camilla; Miller, Gifford H.; Schwenninger, Jean-Luc; Jacomb, Chris; Walter, Richard; Baynes, Alexander; Dortch, Joe; Parker-Pearson, Michael; Gilbert, M. Thomas P.; Holdaway, Richard N.; Willerslev, Eske; Bunce, Michael

    2010-01-01

    Owing to exceptional biomolecule preservation, fossil avian eggshell has been used extensively in geochronology and palaeodietary studies. Here, we show, to our knowledge, for the first time that fossil eggshell is a previously unrecognized source of ancient DNA (aDNA). We describe the successful isolation and amplification of DNA from fossil eggshell up to 19 ka old. aDNA was successfully characterized from eggshell obtained from New Zealand (extinct moa and ducks), Madagascar (extinct elephant birds) and Australia (emu and owl). Our data demonstrate excellent preservation of the nucleic acids, evidenced by retrieval of both mitochondrial and nuclear DNA from many of the samples. Using confocal microscopy and quantitative PCR, this study critically evaluates approaches to maximize DNA recovery from powdered eggshell. Our quantitative PCR experiments also demonstrate that moa eggshell has approximately 125 times lower bacterial load than bone, making it a highly suitable substrate for high-throughput sequencing approaches. Importantly, the preservation of DNA in Pleistocene eggshell from Australia and Holocene deposits from Madagascar indicates that eggshell is an excellent substrate for the long-term preservation of DNA in warmer climates. The successful recovery of DNA from this substrate has implications in a number of scientific disciplines; most notably archaeology and palaeontology, where genotypes and/or DNA-based species identifications can add significantly to our understanding of diets, environments, past biodiversity and evolutionary processes. PMID:20219731

  8. Exploring macroevolution using modern and fossil data

    PubMed Central

    Benton, Michael J.

    2015-01-01

    Macroevolution, encompassing the deep-time patterns of the origins of modern biodiversity, has been discussed in many contexts. Non-Darwinian models such as macromutations have been proposed as a means of bridging seemingly large gaps in knowledge, or as a means to explain the origin of exquisitely adapted body plans. However, such gaps can be spanned by new fossil finds, and complex, integrated organisms can be shown to have evolved piecemeal. For example, the fossil record between dinosaurs and Archaeopteryx has now filled up with astonishing fossil intermediates that show how the unique plexus of avian adaptations emerged step by step over 60 Myr. New numerical approaches to morphometrics and phylogenetic comparative methods allow palaeontologists and biologists to work together on deep-time questions of evolution, to explore how diversity, morphology and function have changed through time. Patterns are more complex than sometimes expected, with frequent decoupling of species diversity and morphological diversity, pointing to the need for some new generalizations about the processes that lie behind such patterns. PMID:26063844

  9. Tool making, hand morphology and fossil hominins

    PubMed Central

    Marzke, Mary W.

    2013-01-01

    Was stone tool making a factor in the evolution of human hand morphology? Is it possible to find evidence in fossil hominin hands for this capability? These questions are being addressed with increasingly sophisticated studies that are testing two hypotheses; (i) that humans have unique patterns of grip and hand movement capabilities compatible with effective stone tool making and use of the tools and, if this is the case, (ii) that there exist unique patterns of morphology in human hands that are consistent with these capabilities. Comparative analyses of human stone tool behaviours and chimpanzee feeding behaviours have revealed a distinctive set of forceful pinch grips by humans that are effective in the control of stones by one hand during manufacture and use of the tools. Comparative dissections, kinematic analyses and biomechanical studies indicate that humans do have a unique pattern of muscle architecture and joint surface form and functions consistent with the derived capabilities. A major remaining challenge is to identify skeletal features that reflect the full morphological pattern, and therefore may serve as clues to fossil hominin manipulative capabilities. Hominin fossils are evaluated for evidence of patterns of derived human grip and stress-accommodation features. PMID:24101624

  10. Tool making, hand morphology and fossil hominins.

    PubMed

    Marzke, Mary W

    2013-11-19

    Was stone tool making a factor in the evolution of human hand morphology? Is it possible to find evidence in fossil hominin hands for this capability? These questions are being addressed with increasingly sophisticated studies that are testing two hypotheses; (i) that humans have unique patterns of grip and hand movement capabilities compatible with effective stone tool making and use of the tools and, if this is the case, (ii) that there exist unique patterns of morphology in human hands that are consistent with these capabilities. Comparative analyses of human stone tool behaviours and chimpanzee feeding behaviours have revealed a distinctive set of forceful pinch grips by humans that are effective in the control of stones by one hand during manufacture and use of the tools. Comparative dissections, kinematic analyses and biomechanical studies indicate that humans do have a unique pattern of muscle architecture and joint surface form and functions consistent with the derived capabilities. A major remaining challenge is to identify skeletal features that reflect the full morphological pattern, and therefore may serve as clues to fossil hominin manipulative capabilities. Hominin fossils are evaluated for evidence of patterns of derived human grip and stress-accommodation features. PMID:24101624

  11. Effect of the nucleotides surrounding the start codon on the translation of foot-and-mouth disease virus RNA.

    PubMed

    Ma, X X; Feng, Y P; Gu, Y X; Zhou, J H; Ma, Z R

    2016-06-01

    As for the alternative AUGs in foot-and-mouth disease virus (FMDV), nucleotide bias of the context flanking the AUG(2nd) could be used as a strong signal to initiate translation. To determine the role of the specific nucleotide context, dicistronic reporter constructs were engineered to contain different versions of nucleotide context linking between internal ribosome entry site (IRES) and downstream gene. The results indicate that under FMDV IRES-dependent mechanism, the nucleotide contexts flanking start codon can influence the translation initiation efficiencies. The most optimal sequences for both start codons have proved to be UUU AUG(1st) AAC and AAG AUG(2nd) GAA. PMID:27265464

  12. Elevation of the Yields of Very Long Chain Polyunsaturated Fatty Acids via Minimal Codon Optimization of Two Key Biosynthetic Enzymes.

    PubMed

    Xia, Fei; Li, Xueying; Li, Xinzheng; Zheng, Desong; Sun, Quanxi; Liu, Jiang; Li, Yaxiao; Hua, Jinping; Qi, Baoxiu

    2016-01-01

    Eicosapentaenoic acid (EPA, 20:5Δ5,8,11,14,17) and Docosahexaenoic acid (DHA, 22:6Δ4,7,10,13,16,19) are nutritionally beneficial to human health. Transgenic production of EPA and DHA in oilseed crops by transferring genes originating from lower eukaryotes, such as microalgae and fungi, has been attempted in recent years. However, the low yield of EPA and DHA produced in these transgenic crops is a major hurdle for the commercialization of these transgenics. Many factors can negatively affect transgene expression, leading to a low level of converted fatty acid products. Among these the codon bias between the transgene donor and the host crop is one of the major contributing factors. Therefore, we carried out codon optimization of a fatty acid delta-6 desaturase gene PinD6 from the fungus Phytophthora infestans, and a delta-9 elongase gene, IgASE1 from the microalga Isochrysis galbana for expression in Saccharomyces cerevisiae and Arabidopsis respectively. These are the two key genes encoding enzymes for driving the first catalytic steps in the Δ6 desaturation/Δ6 elongation and the Δ9 elongation/Δ8 desaturation pathways for EPA/DHA biosynthesis. Hence expression levels of these two genes are important in determining the final yield of EPA/DHA. Via PCR-based mutagenesis we optimized the least preferred codons within the first 16 codons at their N-termini, as well as the most biased CGC codons (coding for arginine) within the entire sequences of both genes. An expression study showed that transgenic Arabidopsis plants harbouring the codon-optimized IgASE1 contained 64% more elongated fatty acid products than plants expressing the native IgASE1 sequence, whilst Saccharomyces cerevisiae expressing the codon optimized PinD6 yielded 20 times more desaturated products than yeast expressing wild-type (WT) PinD6. Thus the codon optimization strategy we developed here offers a simple, effective and low-cost alternative to whole gene synthesis for high expression of

  13. Elevation of the Yields of Very Long Chain Polyunsaturated Fatty Acids via Minimal Codon Optimization of Two Key Biosynthetic Enzymes

    PubMed Central

    Zheng, Desong; Sun, Quanxi; Liu, Jiang; Li, Yaxiao; Hua, Jinping

    2016-01-01

    Eicosapentaenoic acid (EPA, 20:5Δ5,8,11,14,17) and Docosahexaenoic acid (DHA, 22:6Δ4,7,10,13,16,19) are nutritionally beneficial to human health. Transgenic production of EPA and DHA in oilseed crops by transferring genes originating from lower eukaryotes, such as microalgae and fungi, has been attempted in recent years. However, the low yield of EPA and DHA produced in these transgenic crops is a major hurdle for the commercialization of these transgenics. Many factors can negatively affect transgene expression, leading to a low level of converted fatty acid products. Among these the codon bias between the transgene donor and the host crop is one of the major contributing factors. Therefore, we carried out codon optimization of a fatty acid delta-6 desaturase gene PinD6 from the fungus Phytophthora infestans, and a delta-9 elongase gene, IgASE1 from the microalga Isochrysis galbana for expression in Saccharomyces cerevisiae and Arabidopsis respectively. These are the two key genes encoding enzymes for driving the first catalytic steps in the Δ6 desaturation/Δ6 elongation and the Δ9 elongation/Δ8 desaturation pathways for EPA/DHA biosynthesis. Hence expression levels of these two genes are important in determining the final yield of EPA/DHA. Via PCR-based mutagenesis we optimized the least preferred codons within the first 16 codons at their N-termini, as well as the most biased CGC codons (coding for arginine) within the entire sequences of both genes. An expression study showed that transgenic Arabidopsis plants harbouring the codon-optimized IgASE1 contained 64% more elongated fatty acid products than plants expressing the native IgASE1 sequence, whilst Saccharomyces cerevisiae expressing the codon optimized PinD6 yielded 20 times more desaturated products than yeast expressing wild-type (WT) PinD6. Thus the codon optimization strategy we developed here offers a simple, effective and low-cost alternative to whole gene synthesis for high expression of

  14. Consequences of Secondary Calibrations on Divergence Time Estimates.

    PubMed

    Schenk, John J

    2016-01-01

    Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates. PMID:26824760

  15. Consequences of Secondary Calibrations on Divergence Time Estimates

    PubMed Central

    Schenk, John J.

    2016-01-01

    Secondary calibrations (calibrations based on the results of previous molecular dating studies) are commonly applied in divergence time analyses in groups that lack fossil data; however, the consequences of applying secondary calibrations in a relaxed-clock approach are not fully understood. I tested whether applying the posterior estimate from a primary study as a prior distribution in a secondary study results in consistent age and uncertainty estimates. I compared age estimates from simulations with 100 randomly replicated secondary trees. On average, the 95% credible intervals of node ages for secondary estimates were significantly younger and narrower than primary estimates. The primary and secondary age estimates were significantly different in 97% of the replicates after Bonferroni corrections. Greater error in magnitude was associated with deeper than shallower nodes, but the opposite was found when standardized by median node age, and a significant positive relationship was determined between the number of tips/age of secondary trees and the total amount of error. When two secondary calibrated nodes were analyzed, estimates remained significantly different, and although the minimum and median estimates were associated with less error, maximum age estimates and credible interval widths had greater error. The shape of the prior also influenced error, in which applying a normal, rather than uniform, prior distribution resulted in greater error. Secondary calibrations, in summary, lead to a false impression of precision and the distribution of age estimates shift away from those that would be inferred by the primary analysis. These results suggest that secondary calibrations should not be applied as the only source of calibration in divergence time analyses that test time-dependent hypotheses until the additional error associated with secondary calibrations is more properly modeled to take into account increased uncertainty in age estimates. PMID:26824760

  16. Stop codon recognition in the early-diverged protozoans Giardia lamblia and Trichomonas vaginalis.

    PubMed

    Chai, Baofeng; Li, Cui; Yu, Jingfei; Hao, Yanrong; Guo, Ping; Shen, Quan

    2015-07-01

    Two classes of polypeptide release factors (RFs) are responsible for maintaining accuracy in translation termination; however, their detailed mechanism of action and evolutionary history of these factors remain elusive. The structure and function of RFs vary in bacteria and eukaryotes, a fact that is suggestive of evolutionary changes in the translation termination system. Giardia lamblia (Diplomonada) and Trichomonas vaginalis (Parabasalia) are considered as early-diverged eukaryotes. The class II release factor, eRF3, of Giardia (Gl-eRF3) appears to have only one domain that corresponds to EF-1α and lacks the N-terminal domain, similar to that of eRF3 of other organisms. In the present study, we show that the chimeric molecules Gl/Sc eRF1 and Tv/Sc eRF1, which are composed of the N-terminal domain of Gl-eRF1 or Tv-eRF1, fused to the core domain (M and C domain) of Saccharomyces cerevisiae eRF1 (Sc-eRF1), resulting in loss of the RF properties of the N-terminal domain. This suggests that the conformation of eRF1 for stop codon recognition in Giardia and Trichomonas varies from the eRF1s of other eukaryotes, including ciliates and yeast. Further studies using intra-N-terminal chimeras of eRF1 indicated that the combination of the GTS loop and NIKS motif from Gl-eRF1 and the Y-C-F motif from Sc-eRF1within the N terminal domain of hybrid eRF1 could restore UGA, but not UAG and UGA recognition. In contrast, the combination of the GTS loop and the NIKS motif of Sc-eRF1 and the Y-C-F motif of Gl-eRF1 could restore UAG and UAA recognition, but not UGA recognition. Thus, these results confirm the findings of previous studies that three motifs in eRF1 are necessary for discrimination of the three bases of stop codons. The NIKS motif is responsible for recognition of the first two bases of UAA and UAG, and the Y-C-F motif identifies the second base of UGA by Gl-eRF1. Amino acid residue substitutions in Gl/Sc-eRF1 by corresponding residues of Sc-eRF1 could change and even

  17. Age and metallicity gradients in fossil ellipticals

    NASA Astrophysics Data System (ADS)

    Eigenthaler, P.; Zeilinger, W. W.

    2013-05-01

    Context. Fossil galaxy groups are speculated to be old and highly evolved systems of galaxies that formed early in the universe and had enough time to deplete their L∗ galaxies through successive mergers of member galaxies, building up one massive central elliptical, but retaining the group X-ray halo. Aims: Considering that fossils are the remnants of mergers in ordinary groups, the merger history of the progenitor group is expected to be imprinted in the fossil central galaxy (FCG). We present for the first time radial gradients of single-stellar population (SSP) ages and metallicites in a sample of FCGs to constrain their formation scenario. We also measure line-strength gradients for the strongest absorption features in these galaxies. Methods: We took deep spectra with the long-slit spectrograph ISIS at the William Herschel Telescope (WHT) for six FCGs. The obtained spectra are fit with Pegase HR SSP models within the full-spectrum fitting package ULySS yielding SSP ages and metallicities of the stellar populations. We measure radial gradients of SSP ages and metallicities along the major axes. Lick indices are measured for the strongest absorption features to determine line-strength gradients and compare with the full-spectrum fitting results. Results: Our sample comprises some of the most massive galaxies in the universe exhibiting an average central velocity dispersion of σ0 = 271 ± 28 km s-1. Metallicity gradients are throughout negative with comparatively flat slopes of ∇[Fe/H] = -0.19 ± 0.08 while age gradients are found to be insignificant (∇age = 0.00 ± 0.05). All FCGs lie on the fundamental plane, suggesting that they are virialised systems. We find that gradient strengths and central metallicities are similar to those found in cluster ellipticals of similar mass. Conclusions: The comparatively flat metallicity gradients with respect to those predicted by monolithic collapse (∇Z = -0.5) suggest that fossils are indeed the result of

  18. The surprising negative correlation of gene length and optimal codon use - disentangling translational selection from GC-biased gene conversion in yeast

    PubMed Central

    2011-01-01

    Background Surprisingly, in several multi-cellular eukaryotes optimal codon use correlates negatively with gene length. This contrasts with the expectation under selection for translational accuracy. While suggested explanations focus on variation in strength and efficiency of translational selection, it has rarely been noticed that the negative correlation is reported only in organisms whose optimal codons are biased towards codons that end with G or C (-GC). This raises the question whether forces that affect base composition - such as GC-biased gene conversion - contribute to the negative correlation between optimal codon use and gene length. Results Yeast is a good organism to study this as equal numbers of optimal codons end in -GC and -AT and one may hence compare frequencies of optimal GC- with optimal AT-ending codons to disentangle the forces. Results of this study demonstrate in yeast frequencies of GC-ending (optimal AND non-optimal) codons decrease with gene length and increase with recombination. A decrease of GC-ending codons along genes contributes to the negative correlation with gene length. Correlations with recombination and gene expression differentiate between GC-ending and optimal codons, and also substitution patterns support effects of GC-biased gene conversion. Conclusion While the general effect of GC-biased gene conversion is well known, the negative correlation of optimal codon use with gene length has not been considered in this context before. Initiation of gene conversion events in promoter regions and the presence of a gene conversion gradient most likely explain the observed decrease of GC-ending codons with gene length and gene position. PMID:21481245

  19. SAR calibration: A technology review

    NASA Technical Reports Server (NTRS)

    Larson, R. W.; Politis, D. T.; Shuchman, R. A.

    1983-01-01

    Various potential applications of amplitude-calibrated SAR systems are briefly described, along with an estimate of calibration performance requirements. A review of the basic SAR calibration problem is given. For background purposes and to establish consistent definition of terms, various conventional SAR performance parameters are reviewed along with three additional parameters which are directly related to calibrated SAR systems. Techniques for calibrating a SAR are described. Included in the results presented are: calibration philosophy and procedures; review of the calibration signal generator technology development with results describing both the development of instrumentation and internal calibration measurements for two SAR systems; summary of analysis and measurements required to determine optimum retroreflector design and configuration for use as a reference for the absolute calibration of a SAR system; and summary of techniques for in-flight measurements of SAR antenna response.

  20. Primer on multivariate calibration

    SciTech Connect

    Thomas, E.V. )

    1994-08-01

    In analytical chemistry, calibration is the procedure that relates instrumental measurements to an analyte of interest. Typically, instrumental measurements are obtained from specimens in which the amount (or level) of the analyte has been determined by some independent and inherently accurate assay (e.g., wet chemistry). Together, the instrumental measurements and results from the independent assays are used to construct a model that relates the analyte level to the instrumental measurements. The advent of high-speed digital computers has greatly increased data acquisition and analysis capabilities and has provided the analytical chemist with opportunities to use many measurements - perhaps hundreds - for calibrating an instrument (e.g., absorbances at multiple wave-lengths). To take advantage of this technology, however, new methods (i.e., multivariate calibration methods) were needed for analyzing and modeling the experimental data. The purpose of this report is to introduce several evolving multivariate calibration methods and to present some important issues regarding their use. 30 refs., 7 figs.