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  • Articles: DFG German National Licenses  (17)
  • Analytical Chemistry and Spectroscopy  (11)
  • Codon usage  (6)
  • 1
    Electronic Resource
    Electronic Resource
    Codon usage and base composition inRickettsia prowazekii (1996)
    Springer
    Journal of molecular evolution 42 (1996), S. 525-536 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Mutation bias ; Rickettsia prowazekii
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Codon usage and base composition in sequences from the A + T-rich genome ofRickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21R. prowazekii proteins with that of a homologous set of proteins fromEscherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests thatR. prowazekii has around 800 genes and that 60–70% of the genome may be coding.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02352282
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  • 2
    Electronic Resource
    Electronic Resource
    Selection pressures on codon usage in the complete genome of bacteriophage T7 (1985)
    Springer
    Journal of molecular evolution 21 (1985), S. 150-160 
    Details
    ISSN: 1432-1432
    Keywords: Bacteriophage T7 ; DNA sequence analysis ; Codon usage ; Molecular evolution ; Synonymous codons ; RNY codons ; Restriction sites ; tRNA ; Pretermination codons
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We searched the complete 39,936 base DNA sequence of bacteriophage T7 for nonrandomness that might be attributed to natural selection. Codon usage in the 50 genes of T7 is nonrandom, both over the whole code and among groups of synonymous codons. There is a great excess of purineany base-pyrimidine (RNY) codons. Codon usage varies between genes, but from the pooled data for the whole genome (12,145 codons) certain putative selective constraints can be identified. Codon usage appears to be influenced by host tRNA abundance (particularly in highly expressed genes), tRNA-mRNA interactions (one such interaction being perhaps responsible for maintaining the excess of RNY codons) and a lack of short palindromes. This last constraint is probably due to selection against host restriction enzyme recognition sites; this is the first report of an effect of this kind on codon usage. Selection against susceptibility to mutational damage does not appear to have been involved.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100089
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  • 3
    Electronic Resource
    Electronic Resource
    An evolutionary perspective on synonymous codon usage in unicellular organisms (1986)
    Springer
    Journal of molecular evolution 24 (1986), S. 28-38 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Synonymous substitution rate ; Codon Adaptation Index ; Enterobacterial genes ; G+C content ; Theoretical models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Observed patterns of synonymous codon usage are explained in terms of the joint effects of mutation, selection, and random drift. Examination of the codon usage in 165Escherichia coli genes reveals a consistent trend of increasing bias with increasing gene expression level. Selection on codon usage appears to be unidirectional, so that the pattern seen in lowly expressed genes is best explained in terms of an absence of strong selection. A measure of directional synonymous-codon usage bias, the Codon Adaptation Index, has been developed. In enterobacteria, rates of synonymous substitution are seen to vary greatly among genes, and genes with a high codon bias evolve more slowly. A theoretical study shows that the patterns of extreme codon bias observed for someE. coli (and yeast) genes can be generated by rather small selective differences. The relative plausibilities of various theoretical models for explaining nonrandom codon usage are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099948
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  • 4
    Electronic Resource
    Electronic Resource
    Molecular evolution of bacteriophages: Discrete patterns of codon usage in T4 genes are related to the time of gene expression (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 13-22 
    Details
    ISSN: 1432-1432
    Keywords: Transfer RNAs ; Codon usage ; Bacteriophage T4
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Patterns of codon usage in certain coliphages are adapted to expression inEscherichia coli. Bacteriophage T4 may be an exception to test the rule, as it produces eight tRNAs with specificities that are otherwise rare inE. coli. A database of all known T4 DNA sequences has been compiled, comprising 174 genes and a total of 115 kb (approximately 70% of the T4 genome). Codon usage has been examined in all T4 genes; some of these are known to be expressed before, and some after, the production of phage tRNAs. The results show two different patterns of codon usage: by comparison with the early genes, the late genes exhibit a shift in preference toward those codons recognized by the phage-encoded tRNAs. The T4 tRNAs translate A-ending codons, and it is possible that the phage acquired the tRNA genes because the mutation bias of the T4 DNA polymerase forces the T4 genome toward A+T-richness.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100191
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  • 5
    Electronic Resource
    Electronic Resource
    Evolution of the recA gene and the molecular phylogeny of bacteria (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 399-407 
    Details
    ISSN: 1432-1432
    Keywords: Enterobacteria ; Proteobacteria ; Molecular phylogenetics ; recA gene ; RecA protein ; G + C content ; Codon usage
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The DNA sequences of the recA gene from 25 strains of bacteria are known. The evolution of these recA gene sequences, and of the derived RecA protein sequences, is examined, with special reference to the effect of variations in genomic G + C content. From the aligned RecA protein sequences, phylogenetic trees have been drawn using both distance matrix and maximum parsimony methods. There is a broad concordance between these trees and those derived from other data (largely 16S ribosomal RNA sequences). There is a fair degree of certainty in the relationships among the “Purple” or Proteobacteria, but the branching pattern between higher taxa within the eubacteria cannot be reliably resolved with these data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178869
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  • 6
    Electronic Resource
    Electronic Resource
    Mammalian gene evolution: Nucleotide sequence divergence between mouse and rat (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 441-456 
    Details
    ISSN: 1432-1432
    Keywords: Molecular clocks ; Rodents ; Genome evolution ; G + C content ; Codon usage ; Dinucleotide mutation effects
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract As a paradigm of mammalian gene evolution, the nature and extent of DNA sequence divergence between homologous protein-coding genes from mouse and rat have been investigated. The data set examined includes 363 genes totalling 411 kilobases, making this by far the largest comparison conducted between a single pair of species. Mouse and rat genes are on average 93.4% identical in nucleotide sequence and 93.9% identical in amino acid sequence. Individual genes vary substantially in the extent of nonsynonymous nucleotide substitution, as expected from protein evolution studies; here the variation is characterized. The extent of synonymous (or silent) substitution also varies considerably among genes, though the coefficient of variation is about four times smaller than for nonsynonymous substitutions. A small number of genes mapped to the X-chromosome have a slower rate of molecular evolution than average, as predicted if molecular evolution is “male-driven.” Base composition at silent sites varies from 33% to 95% G + C in different genes; mouse and rat homologues differ on average by only 1.7% in silent-site G + C, but it is shown that this is not necessarily due to any selective constraint on their base composition. Synonymous substitution rates and silent site base composition appear to be related (genes at intermediate G + C have on average higher rates), but the relationship is not as strong as in our earlier analyses. Rates of synonymous and nonsynonymous substitution are correlated, apparently because of an excess of substitutions involving adjacent pairs of nucleotides. Several factors suggest that synonymous codon usage in rodent genes is not subject to selection.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00178874
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  • 7
    Electronic Resource
    Electronic Resource
    Automated probe mass spectrometry (1989)
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 18 (1989), S. 733-737 
    Details
    ISSN: 0887-6134
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method of fully automating the analysis of routine samples using probe introduction techniques has been designed and developed. Unattended 24 h operation has dramatically increased the ability to process large numbers of samples and has freed much of an operator's time to perform other tasks.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bms.1200180915
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  • 8
    Electronic Resource
    Electronic Resource
    Routine clinical determination of carotene, vitamin E, vitamin A, 25-hydroxy vitamin D3 and trans-vitamin K1 in human serum by straight phase HPLC (1987)
    New York, NY : Wiley-Blackwell
    Biomedical Chromatography 2 (1987), S. 79-88 
    Details
    ISSN: 0269-3879
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: A universal extraction procedure is described for fat-soluble vitamins in human serum. Methods are presented for routine quantitative analysis by isocratic straight phase HPLC with UV-detection of (α + β)-carotene, vitamin E. (α-tocopherol) and vitamin A (all-trans-retinol) in one single run, and of vitamin K1 (trans-phylloquinone) and 25-hydroxy vitamin D3 after sample clean-up using disposable reversed-phase cartridges. The limits of detection, precisions and selectivities of the developed assays are shown to be satisfactory after more than three years' experience. The routine clinical determination of fat-soluble vitamins can be performed in less than 5 mL of serum. Analyses of external quality control and randomly taken outpatient samples are shown to be of great value in assessing laboratory performance.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bmc.1130020209
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  • 9
    Electronic Resource
    Electronic Resource
    Measurement of (C13)arginine incorporation into apolipoprotein B-100 in very low density lipoproteins and low density lipoproteins in normal subjects using (13C)sodium bicarbonate infusion and isotope ratio mass spectrometry (1990)
    Chichester : Wiley-Blackwell
    Biological Mass Spectrometry 19 (1990), S. 459-464 
    Details
    ISSN: 1052-9306
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: We describe a new stable isotope technique for the in vivo study of hepatic plasma protein synthesis in humans. The method involves the infusion of (13C)sodium bicarbonate for 1 h and the measurement of the isotopic enrichment of (13C)arginine in newly synthesized apolipoprotein B of very low density lipoproteins (VLDL-apoB) and low density lipoproteins (LDL-apoB) in blood samples taken over a 5-6 h period from the commencement of the infusion. Isotope ratio mass spectrometry was utilized to measure 13CO2 enrichment following hydrolysis of these proteins and conversion of the guanidinium carbon of arginine in the hydrolysate to carbon dioxide by sequential incubation with arginase and urease. The method is capable of measuring isotopic enrichment as low as 0.001 at. % excess (APE) with a precision of 1.2%. In both subjects studied, the (13C)arginine of VLDL-apoB reached enrichments of 0.2 APE and that of the arginine of LDL-apoB, 0.03 APE. Incorporation of labeled arginine into LDL-apoB was demonstrable at 60-90 min. The new technique is safe and is applicable to the study of the hepatic biosynthesis of a wide range of plasma proteins.
    Additional Material: 5 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/bms.1200190803
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  • 10
    Electronic Resource
    Electronic Resource
    Femtosecond coherence spectroscopy of heme proteins (1996)
    New York, NY [u.a.] : Wiley-Blackwell
    Biospectroscopy 2 (1996), S. 301-309 
    Details
    ISSN: 1075-4261
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Physics
    Notes: Femtosecond pump-probe experiments are used to study the photophysics and photochemistry of heme proteins on ultrafast time scales. Using electronic relaxation measurements combined with reaction-driven coherence signals, we determine that, after the photoexcitation of myoglobin (Mb)NO, the bond-breaking time is on the order of the electronic dephasing time (∼ 20 fs) and the electronic ground state of deoxy Mb appears on a time scale of 80 ± 30 fs. This latter time scale is linked to the Fe-His bond compression (TFe-His/2 ∼ 75 fs), which is initiated by the photolytic depletion of electron density from the antibonding dz2 orbital. The subsequent depression of the dx2-y2 orbital energy, and its population as the iron moves out of plane, leads to the formation of the S = 2 electronic ground state and drives the doming of the heme (Tdome/4 ∼ 100 fs). Thus, the initial stage of heme doming is completed in TFe-His/2 + Tdome/4 ∼ 180 fs. Samples of hemoglobin (Hb)NO display a strong coherent Fe-His stretching vibration at 230 cm-1, which appears immediately (∼ 200 fs) after photodissociation. The data also show a lower-frequency component at 95 cm-1, which we assign to heme doming. The reaction driven coherence of HbNO is observed to be much stronger than the impulsively stimulated Raman coherence of Hb, as might be expected, based on the large relative displacement between reactant and product equilibrium position. The Raman coherence of deoxy Mb is also studied as a function of temperature. As the temperature decreases from 290 to 10 K, the amplitude of the 370 cm-1 mode increases while the amplitude of the 220 cm-1 Fe-His stretching mode decreases. Finally, we report preliminary observations of the first Raman coherences in samples of another heme protein, cytochrome P450. © 1996 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
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