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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    European journal of nutrition 26 (1987), S. 125-137 
    ISSN: 1436-6215
    Keywords: vitamin C ; functions ; kinetics ; pool ; saturation ; requirements ; RDA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Medicine
    Description / Table of Contents: Zusammenfassung Die Bedeutung von Vitamin C für den menschlichen Organismus wird aus den wichtigen Funktionen ersichtlich, an denen das Vitamin beteiligt ist, wie zum Beispiel Kollagen- und Karnitinsynthesen. In neuerer Zeit entdeckt wurde seine Rolle bei der Noradrenalinsynthese, der Inaktivierung von freien Radikalen sowie der Verhinderung der Nitrosaminbildung. Die Vielfalt dieser Vitamin-C-abhängigen Funktionen läßt erkennen, daß die Bedarfsfestsetzung für Vitamin C nicht nur die Verhütung der Mangelkrankheit Skorbut anvisieren, sondern auch berücksichtigen sollte, daß alle diese Funktionen jederzeit genügend Vitamin C zur Verfügung haben müßten, um optimal reagieren zu können. Das Konzept der Gewebesättigung kommt diesem Ziel am nächsten. Studien mit einem kinetischen Modell haben ergeben, daß eine Sättigung mit täglicher Einnahme von 100 mg Vitamin C bei Nichtrauchern und von 140 mg bei Rauchern eintritt, Mengen, die als optimale Werte gelten können. Bei verschiedenen Krankheiten dürfte der Bedarf höher sein; die genauen Mengen müssen jedoch erst noch ermittelt werden.
    Notes: Summary The importance of vitamin C is reflected in its multifunctional roles which include participation in collagen and carnitine syntheses, promotion of iron absorption and the more recently discovered participation in noradrenaline synthesis, inactivation of free radical chain reactions, prevention of N-nitroso compound formation and more. Given the many extra-antiscorbutic functions of the vitamin, the Recommended Dietary Allowances (RDA) should not just prevent deficiency disease but should aim at providing sufficient amounts for all vitamin C-dependent functions to operate at full capacity. The concept of vitamin C tissue saturation is best able to meet this demand. The use of kinetic models has shown that the body pool is saturated with a daily intake of 100 mg vitamin C in non-smokers and 140 mg in smokers, amounts that may be regarded as optimal RDA values. Certain disease states may be accompanied by still higher vitamin C requirements but the exact amounts are not yet known.
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  • 2
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    Colloid & polymer science 266 (1988), S. 958-964 
    ISSN: 1435-1536
    Keywords: a-Se colloids ; photoadsorption ; kinetics ; activation energy ; compensation effect
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract In this study, a model is developed to explain in microscopic terms the results obtained from thermally activated photoadsorption experiments in a-Se colloids. The observed compensation effect can be described for two different cases. At low efficiency adsorption, the process is controlled by the potential at the boundary layer. In the high efficiency adsorption case, the process is controlled by diffusion transport.
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  • 3
    ISSN: 1435-1536
    Keywords: Phospholipid bilayer ; kinetics ; laser temperature jump ; phase transition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The iodine-laser temperature-jump technique has been used to investigate the main phase transition in single shell vesicles of dimyristoylphosphatidylcholine. The probe molecules DPH and TMA-DPH were incorporated into the lipid bilayer and laserT-jump experiments with turbidity and flourescence polarization detection were performed. We found three well separated relaxation processes between 5 μs and 10 ms. The relaxation signals showed strong cooperativity in the relaxation times as well as in their corresponding amplituedes. We attributed the relaxation to the formation and dissolution of clusters of different order inside the bilayer.
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  • 4
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    Colloid & polymer science 265 (1987), S. 58-64 
    ISSN: 1435-1536
    Keywords: Polymerisation ; emulsion ; styrene ; methylmethacrylate ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The dependence of emulsion polymerisation rates on a number of important parameters is considered. Attention is paid to the use of seeded emulsion systems for the evaluation of radical desorption coefficients (k o). Experimental conditions are shown to be important. When the average number of radicals per particle is low, large changes in the rate coefficient for chain termination do not have a large effect on the kinetics. With styrene and methylmethacrylate, radical re-absorption by the polymer particles is shown to be important and radical capture efficiences can be high. Consistency is established between the results of a number of workers and values fork o are shown to be lower than those calculated from chain transfer rates.
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  • 5
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    Acta biotheoretica 35 (1986), S. 77-106 
    ISSN: 1572-8358
    Keywords: Evolution ; nonequilibrium thermodynamics ; boundary conditions models ; initial conditions models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Proponents of two axioms of biological evolutionary theory have attempted to find justification by reference to nonequilibrium thermodynamics. One states that biological systems and their evolutionary diversification are physically improbable states and transitions, resulting from a selective process; the other asserts that there is an historically constrained inherent directionality in evolutionary dynamics, independent of natural selection, which exerts a self-organizing influence. The first, the Axiom of Improbability, is shown to be nonhistorical and thus, for a theory of change through time, acausal. Its perception of the improbability of living states is at least partially an artifact of closed system thinking. The second, the Axiom of Historically Determined Inherent Directionality, is supported evidentially and has an explicit historical component. Historically constrained dynamic populations are inherently nonequilibrium systems. It is argued that living, evolving systems, when considered to be historically constrained nonequilibrium systems, do not appear improbable at all. Thus, the two axioms are not compatible. Instead, the Axiom of Improbability is considered to result from an unjustified attempt to extend the contingent proximal actions of natural selection into the area of historical, causal explanations. It is thus denied axiomatic status, and the effects of natural selection are subsumed as an additional level of constraint in an evolutionary theory derived from the Axiom of Historically Determined Inherent Directionality.
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  • 6
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    Journal of solution chemistry 15 (1986), S. 221-229 
    ISSN: 1572-8927
    Keywords: Ultrasonics ; kinetics ; aqueous solution ; triethylene glycol monobutyl ether
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The ultrasonic absorption from 6.5 to 220 MHz and velocities at 2.5 MHz have been measured in aqueous solution of triethylene glycol monobutyl ether as a function of concentration at 25°C. A single relaxational excess absorption, observed from 0.60 to 2.5 mol-dm−3, is attributed to a perturbation of an equilibrium associated with solute-solvent interaction. Rate constants for the forward and reverse processes have been determined from the concentration dependence of the relaxation frequency, and the influence on the water structure by an addition of the solute has been considered. Solution densities were also measured in order to obtain the expansivity of the solution. The standard volume and enthalpy changes of the reaction have been estimated from the concentration dependence of the maximum excess absorption per wave length. A linear relationship between the number of oxyethylene groups and the free energy change between bonded water and nonbonded water is established.
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  • 7
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    Cellular and molecular life sciences 41 (1985), S. 1080-1082 
    ISSN: 1420-9071
    Keywords: Evolution ; evolutionary rate ; stasis ; brain ; encephalization ; body size ; fitness
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Constant evolutionary rates are possible only in verylarge populations, where natural selection does not exhaust varition because mutation supplies fresh variability. In a small population where a small number of genes influence an integrated system like brain and body size which have an allometric relationship, variation is removed rapidly under natural selection, This occurs even when the final fitness of the population is not optimal.
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  • 8
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    Cellular and molecular life sciences 43 (1987), S. 202-205 
    ISSN: 1420-9071
    Keywords: Evolution ; substrate specificity ; serological homologies ; flavone biosynthesis ; Silene ; glycosyltransferases
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The variation in flavone glycosylation patterns inSilene is the result of the expression of six genetic loci, which control either the presence of allozymes differing in substrate specificity or isozymes regulated differently during development. Serological studies showed that at least three of these six loci are evolutionarily related. The genetic mechanisms leading to these complicated variation patterns and the role of this polymorphism for the plant in its interaction with the environment are discussed.
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  • 9
    ISSN: 1432-0983
    Keywords: psbA ; Cyanelle ; Cyanophora paradoxa ; Evolution ; Sequence analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The psbA gene is part of the reaction center of photosystem II in cyanobacteria and the plastids of higher plants. Its primary sequence is highly conserved among all species investigated so far and its sequence shows homologies with the L and M subunits of the reaction center of photosynthetic bacteria. We have analyzed the psbA homolog from a eukaryotic alga, Cyanophora paradoxa, where the gene is encoded on cyanelle DNA. These cyanelles are surrounded by a murein sacculus and resemble cyanobacteria in many other characteristics, although they are genuine organelles that functionally replace plastids. Analysis of the gene revealed a psbA protein identical in length (360 codons) with the cyanobacterial counterpart. The overall sequence identity is, however, more pronounced between cyanelle psbA and the shorter (353 amino acids) psbA product found in higher plants. These data strongly support the postulated bridge position of cyanelles between chloroplasts and free-living cyanobacteria.
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  • 10
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    Current genetics 10 (1986), S. 931-941 
    ISSN: 1432-0983
    Keywords: T. aestivum ; Chloroplast DNA ; Repeat DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Low-stringency hybridisation between recombinant plasmids representing the complete T. aestivum chloroplast genome has revealed small repeated DNA segments dispersed through the molecule. Thirty-two repeated DNA segments were detected, and they could be divided into 12 unrelated sets; no repeat was detected as multiple copies. The longest of the small repeats mapped just within the large inverted repeat in spinach and mung-bean ctDNAs. It was found to have been duplicated after the divergence of a cereal progenitor to generate a third, dispensible copy, 0.2 kbp downstream of rbcL. In maize at least, this copy has also become integrated, with rbcL, in the mitochondrial genome. Another of the repeats is thought to have mediated a chloroplast DNA inversion (Howe 1985). Thus the diverse collection of small repeats probably represents some consequences and causes of past recombination events as well as a mechanism for further intramolecular ctDNA recombination. Their possible significance in the restructuring and evolution of chloroplast genomes is discussed.
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  • 11
    ISSN: 1432-0983
    Keywords: Wheat chloroplast DNA ; Repeated sequences ; Ribosomal protein genes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Some dispersed repeated sequences and their flanking regions from wheat and maize ctDNAs have been characterized. Two sets of wheat ctDNA repeats were found to be the chloroplast ribosomal protein genesrpl2 andrpl23, plus nonfunctional segments of them, designatedrpl2′ andrpl23′. Pairwise comparisons were made between the wheatrp123 andrpl23′, and the maizerp123′ sequences. The precise patterns of homology suggest that the divergence of the wheat and maize nonfunctional (rpl23′) sequences is being retarded by nonreciprocal recombination, biased by selection for individuals with functional (rpl23) sequences. The implied involvement of these sequences in mechanisms of homologous recombination, and therefore in the creation and spread of new ctDNA variants, is discussed.
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  • 12
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    Current genetics 15 (1989), S. 99-106 
    ISSN: 1432-0983
    Keywords: Yeast ; Isoleucyl-tRNA synthetase ; Isoleucine ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The isoleucyl-tRNA synthetase gene (ILS1) from the yeast Saccharomyces cerevisiae was cloned and sequenced. This gene was initially cloned because it cross-hybridizated to what is now presumed to be the isoleucyl-tRNA synthetase gene (cupC) from the protozoan Tetrahymena hhermophila. The ILS1 gene was determined to be 1,072 amino acids in length. A comparison with a recently published sequence of ILS1 1 from another laboratory (Englisch et al. 1987) was made and differences noted. Two promoter elements were detected, one for general amino acid control and one for constitutive transcription. A heat shock protein (hsp70) gene (probably SSA3) was found 237 by upstream from the ILS1 translation start site. The ILS1 amino acid sequence was compared to isoleucyl-tRNA synthetases from other organisms, as well as to valyl-, leucyl- and methionyl-tRNA synthetases. Regions of conservation between these enzymes were found.
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  • 13
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    Current genetics 15 (1989), S. 221-229 
    ISSN: 1432-0983
    Keywords: Chloroplast DNA ; Chlorophyll a/c alga ; Evolution ; Ribosomal operon
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary There are almost no data describing chloroplast genome organization in chromophytic (chlorophyll a/c) plants. In this study chloroplast ribosomal operon placement and gene organization has been determined for the golden-brown alga Olisthodiscus luteus. Ribosomal RNA genes are located on the chloroplast DNA inverted repeat structure. Nucleotide sequence analysis, demonstrated that in contrast to the larger spacer regions in land plants, the 16S–23S rDNA spacer of O. luteus is only 265 by in length. This spacer contains tRNAIle and tRNAAla genes which lack introns and are separated by only 3 bp. The sequences of the tRNA genes and 16S and 23S rDNA termini flanking the spacer were examined to determine homology between O. luteus, chlorophytic plant chloroplast DNA, and prokaryotes.
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  • 14
    ISSN: 1432-0983
    Keywords: Comparative restriction site mapping ; Gene mapping ; Deletions and additions ; Chloroplast genome ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The chloroplast genomes from the interfertile green algae Chlamydomonas eugametos and C. moewusii have been compared in their overall sequence organization. Physical mapping of Aval, BstEII and EcoRI restriction sites on the C. moewusii chloroplast genome revealed that this 292 kilobase-pair (kbp) genome is 49 kbp larger than the C. eugametos genome. Heterologous fragment hybridizations indicated the same order of common sequence elements on the two algal genomes. Almost all of the 49 kbp size difference is accounted for by the presence of two large extra sequences in C. moewusii: a 21 kbp sequence in the inverted repeat and a 5.8 kbp sequence in the single copy-region bordering the 16S ribosomal RNA (rRNA) genes. In addition to these two major deletion/addition differences, 42 restriction site and fragment length differences (ranging from 100 to 500 base pairs) were mapped on the two algal genomes. Surprisingly, the greatest density of these differences was found to be confined within the inverted repeat, one of the most conserved regions of land plant chloroplast genomes.
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  • 15
    ISSN: 1432-0983
    Keywords: Physarum polycephalum ; rRNA ; Sequence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The nucleotide sequence of the Physarum polycephalum small subunit ribosomal RNA (SSU rRNA) gene has been determined. Sequence data indicate that the mature 19S SSU rRNA is 1,964 nucleotides long. A complete secondary structure model for P. polycephalum SSU rRNA has been constructed on the basis of the Escherichia coli 16S rRNA model and data from comparative analyses of 28 different eukaryotic sequences. A “four-helix” model is presented for the central domain variable region. This model can be applied both to vertebrate and most lower eukaryotic SSU rRNAs. The increased size of P. polycephalum SSU rRNA relative to the smaller SSU rRNAs from such other lower eukaryotes, as Dictyostelium, Tetrahymena or Saccharomyces is due mainly to three G+C-rich insertions found in two regions known to be of variable length in eukaryotes. In a phylogenetic tree constructed from pairwise comparisons of eukaryotic SSU rRNA sequences, the acellular myxomycete P. polycephalum is seen to diverge before the appearance of the cellular mycomycete Dictyostelium discoideum.
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  • 16
    ISSN: 1432-0983
    Keywords: Evolution ; Sequence comparison ; RUBISCO ; Transit peptide
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have isolated and characterized a full-length cDNA clone encoding the precursor of the small subunit (pSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase (RUBISCO) from the green alga, Chlamydomonas moewusii. Comparison with the C. reinhardtii rbcS1 gene sequence reveals that both small subunit (SS) coding regions are 75% homologous and that their predicted mature polypeptide chains are each composed of 140 amino acids. In contrast, their transit peptides appear to be divergent. We also show that transcription of the C. moewusii rbcS gene(s) which generates a 1,230 and a 930 base mRNA species are light-stimulated/or accumulated during the light period of the cell cycle. Finally, the SS polypeptide sequences of fifteen different photosynthetic organisms are compared; this analysis reveals at least five well-conserved polypeptide domains.
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  • 17
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    Journal of molecular evolution 25 (1987), S. 141-150 
    ISSN: 1432-1432
    Keywords: 20S particle ; Prosome ; Evolution ; Small cytoplasmic RNAs ; Heat shock proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have purified and characterized a particle sedimenting at 20S from the postribosomal fraction of yeast, wheat germ,Drosophila melanogaster tissue culture cells, chicken embryo fibroblasts, rabbit reticulocyte lysate, and HeLa cells. Most of the protein constituents of the 20S particle have molecular weights of 20–35 kd and differ between species; however, some do have similar molecular weights and isoelectric points, suggesting they are related. Several low-molecular-weight RNAs, distinct from tRNAs, co-purify with the particle isolated from all these species and show increasingly more complex patterns ascending the arbitrary order from yeast to human (yeast, plant, insect, bird, and mammals). InDrosophila, we present evidence that these small RNAs are tightly associated with this 20S structure.
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  • 18
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    Journal of molecular evolution 28 (1988), S. 98-112 
    ISSN: 1432-1432
    Keywords: rRNA ; Evolution ; Sequence comparison ; Parsimony ; Bootstrap
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Sequences of small subunit (SSU) and large subunit (LSU) ribosomal RNA genes from archaebacteria, eubacteria, and the nucleus, chloroplasts, and mitochondria of eukaryotes have been compared in order to identify the most conservative positions. Aligned sets of these positions for both SSU and LSU rRNA have been used to generate tree diagrams relating the source organisms/organelles. Branching patterns were evaluated using the statistical bootstrapping technique. The resulting SSU and LSU trees are remarkably congruent and show a high degree of similarity with those based on alternative data sets and/or generated by different techniques. In addition to providing insights into the evolution of prokaryotic and eukaryotic (nuclear) lineages, the analysis reported here provides, for the first time, an extensive phylogeny of the mitochondrial lineage.
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  • 19
    ISSN: 1432-1432
    Keywords: Aspergillus nidulans ; 5S rRNA ; Pseudogenes ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary AllAspergillus nidulans 5S rRNA pseudogenes known so far are the result of integration of an approx. 0.2-kbp-long DNA sequence into the 5S rRNA genes. This sequence, called block C, is present in at least five copies in theA. nidulans genome and seems to be associated either with 5S rRNA genes or pseudogenes. In contrast to the 78% sequence conservation of the C-block in pseudogenes, the truncated 5′ halves of the pseudogenes are very highly conserved (96.9–100%). We postulate that the 5S rRNA pseudogenes are still a subject of concerted evolution. The C-block sequence shows similarity to the switch region of the mouse heavy chain immunoglobulin gene. A characteristic motif GGGTGAG is repeated several times in both sequences; the sequence conservation is 63%.
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  • 20
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    Journal of molecular evolution 28 (1989), S. 175-184 
    ISSN: 1432-1432
    Keywords: Sheep ; Globin genes ; Evolution ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Domestic sheep have two common alleles at the adult β-globin locus,β A andβ B. Here we report the structure of the β-globin locus of A-haplotype sheep. The locus consists of 12 genes, organized as a triplicated 4-gene set: 5′ ∈I-∈II-ΨβI-βC-∈III-∈IV-ΨβII-βA-∈V-∈VI-ΨβIII-βF 3′. This arrangement is identical to that of the closely related goat locus. Sheep with the B haplotype have a locus arrangement consisting of a duplicated four-gene set, lacking the βC gene as well as three other genes present in A sheep and goats. In order to understand the evolutionary history of the B sheep locus, we have sequenced the βB gene from these sheep, and the βB gene from A-haplotype sheep, and compared the sequences to those of the sheep βA, goat βC, and βA, and cow adult β genes. Our results indicate that the βB gene has diverged recently from the βA gene, and therefore the βB locus structure may have resulted from a recent deletion from a triplicated locus.
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  • 21
    ISSN: 1432-1432
    Keywords: Evolution ; Multiple sequence alignment ; NTP binding ; Phylogenetic analysis ; Positive-strand RNA viruses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary NTP-motif, a consensus sequence previously shown to be characteristic of numerous NTP-utilizing enzymes, was identified in nonstructural proteins of several groups of positive-strand RNA viruses. These groups include picorna-, alpha-, and coronaviruses infecting animals and como-, poty-, tobamo-, tricorna-, hordei-, and furoviruses of plants, totalling 21 viruses. It has been demonstrated that the viral NTP-motif-containing proteins constitute three distinct families, the sequences within each family being similar to each other at a statistically highly significant level. A lower, but still valid similarity has also been revealed between the families. An overall alignment has been generated, which includes several highly conserved sequence stretches. The two most prominent of the latter contain the socalled “A” and “B” sites of the NTP-motif, with four of the five invariant amino acid residues observed within these sequences. These observations, taken together with the results of comparative analysis of the positions occupied by respective proteins (domains) in viral multidomain proteins, suggest that all the NTP-motif-containing proteins of positive-strand RNA viruses are homologous, constituting a highly diverged monophyletic group. In this group the “A” and “B” sites of the NTP-motif are the most conserved sequences and, by inference, should play the principal role in the functioning of the proteins. A hypothesis is proposed that all these proteins posses NTP-binding capacity and possibly NTPase activity, performing some NTP-dependent function in viral RNA replication. The importance of phylogenetic analysis for the assessment of the significance of the occurrence of the NTP-motif (and of sequence motifs of this sort in general) in proteins is emphasized.
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  • 22
    ISSN: 1432-1432
    Keywords: Tropomyosin ; Differential splicing ; Evolution ; Isochore ; Codon usage ; Sequence convergence ; Functional constraints
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned and determined the nucleotide sequence of a complementary DNA (cDNA) encoded by a newly isolated human tropomyosin gene and expressed in liver. Using the leastsquare method of Fitch and Margoliash, we investigated the nucleotide divergences of this sequence and those published in the literature, which allowed us to clarify the classification and evolution of the tropomyosin genes expressed in vertebrates. Tropomyosin undergoes alternative splicing on three of its nine exons. Analysis of the exons not involved in differential splicing showed that the four human tropomyosin genes resulted from a duplication that probably occurred early, at the time of the amphibian radiation. The study of the sequences obtained from rat and chicken allowed a classification of these genes as one of the types identified for humans. The divergence of exons 6 and 9 indicates that functional pressure was exerted on these sequences, probably by an interaction with proteins in skeletal muscle and perhaps also in smooth muscle; such a constraint was not detected in the sequences obtained from nonmuscle cells. These results have led us to postulate the existence of a protein in smooth muscle that may be the counterpart of skeletal muscle troponin. We show that different kinds of functional pressure were exerted on a single gene, resulting in different evolutionary rates and different convergences in some regions of the same molecule. Codon usage analysis indicates that there is no strict relationship between tissue types (and hence the tRNA precursor pool) and codon usage. G+C content is characteristic of a gene and does not change significantly during evolution. These results are in good agreement with an isochore composition of the genome, and thus suggest a similar chromosomal environment in chicken, rat, and human.
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  • 23
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    Journal of molecular evolution 27 (1988), S. 291-297 
    ISSN: 1432-1432
    Keywords: P1 P2 protamines ; Evolution ; Regulatory sequence ; Primordial sequence ; Similarity ; Alignment
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary With the recent availability of the primary structural data for the trout, bovine, and mouse protamine genes, a detailed comparison of their structures has been made. This has revealed extensive conservation of potentially biologically significant regions. An inverse correlation is apparent between gene copy number and the number of sequence-distinct protamines synthesized with the number of CP-box-like (CCYPCCC) putative transcription modulating sequences situated 5′ to these genes. A common nucleotide sequence 5′ to the CP-box-like putative transcription modulating sequence(s) at the end of a common region has been identified. It is postulated that this is the testis-specific protamine P1 transcription regulator sequence. Evidence based on sequence similarity is also provided for the existence of a primordial protamine gene and a scheme for the evolution of vertebrate protamine genes is proposed.
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  • 24
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    Journal of molecular evolution 29 (1989), S. 28-39 
    ISSN: 1432-1432
    Keywords: Transposable elements ; Zea mays ; Evolution ; Inverted repeats
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The Robertson's Mutator stock of maize exhibits a high mutation rate due to the transposition of theMu family of transposable elements. All characterizedMu elements contain similar ≈200-bp terminal inverted repeats, yet the internal sequences of the elements may be completely unrelated. Non-Mutator stocks of maize have a 20–100-fold lower mutation rate relative to Mutator stocks, yet they contain multiple sequences that hybridize to theMu terminal inverted repeats. Most of these sequences do not cohybridize to internal regions of previously clonedMu elements. We have cloned two such sequences from the maize line B37, a non-Mutator inbred line. These sequences, termedMu4 andMu5, have an organization characteristic of transposable elements and possess ≈200-bpMu terminal inverted repeats that flank internal DNA, which is unrelated to other clonedMu elements.Mu4 andMu5 are both flanked by 9-bp direct repeats as has been observed for otherMu elements. However, we have no direct evidence that they have recently transposed because they have not been found in known genes. Although the internal regions ofMu4 andMu5 are not related by sequence similarity, both elements share an unusual structural feature: the terminal inverted repeats extend more than 100 bp internally fromMu-similar termini. The distribution of these elements in maize lines and related species suggests thatMu elements are an ancient component of the maize genome. Moreover, the structure of theMu termini and the fact thatMu termini are found flanking different internal sequences leads us to speculate thatMu termini once may have been capable of transposing as independent entities.
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  • 25
    ISSN: 1432-1432
    Keywords: Xenopus tropicalis ; Xenopus borealis ; Globin cDNAs ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Globin mRNAs ofXenopus borealis andXenopus tropicalis have been cloned and sequenced. The nucleotide and derived amino acid sequences were compared with each other and with already available data fromXenopus laevis. This analysis rendered clear evidence that the common ancestor ofX. laevis andX. borealis, but not ofX. tropicalis, had lost one amino acid of the β-globins prior to a genome duplication event that preceded the segregation of the former two species. Replacement-site substitutions were used to calculate a rough time scale of genome duplication and species segregation. The results suggest an ancient separation between theX. laevis and theX. tropicalis groups occurring approximately 110–120 million years ago. Analysis of the amino acid chains demonstrated various alterations. However, some functional domains, like heme-binding sites andα1β2 contact sites, were subject to a high degree of conservation, indicating the existence of functional constraints on them also in the genusXenopus.
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  • 26
    ISSN: 1432-1432
    Keywords: Symbiosis ; Plant mitochondria ; 5S RNA ; Evolution ; Purple bacteria
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    Notes: Summary The complete nucleotide sequences of 5S ribosomal RNAs fromRhodocyclus gelatinosa, Rhodobacter sphaeroides, andPseudomonas cepacia were determined. Comparisons of these 5S RNA sequences show that rather than being phylogenetically related to one another, the two photosynthetic bacterial 5S RNAs share more sequence and signature homology with the RNAs of two nonphotosynthetic strains.Rhodobacter sphaeroides is specifically related toParacoccus denitrificans andRc. gelatinosa is related toPs. cepacia.These results support earlier 16S ribosomal RNA studies and add two important groups to the 5S RNA data base. Unique 5S RNA structural features previously found inP. denitrificans are present also in the 5S RNA ofRb. sphaeroides; these provide the basis for subdivisional signatures. The immediate consequence of our obtaining these new sequences is that we are able to clarify the phylogenetic origins of the plant mitochondrion. In particular, we find a close phylogenetic relationship between the plant mitochondria and members of the alpha subdivision of the purple photosynthetic bacteria, namely,Rb. sphaeroides, P. denitrificans, andRhodospirillum rubrum.
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  • 27
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    Journal of molecular evolution 22 (1985), S. 91-94 
    ISSN: 1432-1432
    Keywords: Primitive atmosphere ; Self-organization ; Evolution ; Prebiological chemistry ; Primordial soup ; Oparin thesis
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    Topics: Biology
    Notes: Summary A recently proposed model for the origin of prebiotic progenitors of life in particles suspended in a primitive, specially organized atmosphere is considered critically. It is concluded that the physical and chemical framework of the new hypothesis conflicts with the conditions necessary for the evolution of the progenitors of life in the atmosphere of the early Earth. Therefore this model seems not to be a reasonable alternative to the Oparin thesis.
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  • 28
    ISSN: 1432-1432
    Keywords: Nucleotide sequence ; Evolution ; Methanogens ; Extreme halophiles ; Eubacteria ; Eukaryotes
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    Notes: Summary The sequence of the small-subunit rRNA from the thermoacidophilic archaebacteriumSulfolobus solfataricus has been determined and compared with its counterparts from halophilic and methanogenic archaebacteria, eukaryotes, and eubacteria. TheS. solfataricus sequence is specifically related to those of the other archaebacteria, to the exclusion of the eukaryotic and eubacterial sequences, when examined either by evolutionary distance matrix analyses or by the criterion of minimum change (maximum parsimony). The archaebacterial 16S rRNA sequences all conform to a common secondary structure, with theS. solfataricus structure containing a higher proportion of canonical base pairs and fewer helical irregularities than the rRNAs from the mesophilic archaebacteria.S. solfataricus is unusual in that its 16S rRNA-23S rRNA intergenic spacer lacks a tRNA gene.
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  • 29
    ISSN: 1432-1432
    Keywords: Actin-coding regions ; Sequence divergence ; Conversion ; Codon usage ; Evolution
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    Notes: Summary We have determined the sequences of three recombinant cDNAs complementary to different mouse actin mRNAs that contain more than 90% of the coding sequences and complete or partial 3′ untranslated regions (3′UTRs): pAM 91, complementary to the actin mRNA expressed in adult skeletal muscle (αsk actin); pAF 81, complementary to an actin mRNA that is accumulated in fetal skeletal muscle and is the major transcript in adult cardiac muscle (αc actin); and pAL 41, identified as complementary to a β nonmuscle actin mRNA on the basis of its 3′UTR sequence. As in other species, the protein sequences of these isoforms are highly (〉93%) conserved, but the three mRNAs show significant divergence (13.8–16.5%) at silent nucleotide positions in their coding regions. A nucleotide region located toward the 5′ end shows significantly less divergence (5.6–8.7%) among the three mouse actin mRNAs; a second region, near the 3′ end, also shows less divergence (6.9%), in this case between the mouse β and αsk actin mRNAs. We propose that recombinational events between actin sequences may have homogenized these regions. Such events distort the calculated evolutionary distances between sequences within a species. Codon usage in the three actin mRNAs is clearly different, and indicates that there is no strict relation between the tissue type, and hence the tRNA precursor pool, and codon usage in these and other muscle mRNAs examined. Analysis of codon usage in these coding sequences in different vertebrate species indicates two tendencies: increases in bias toward the use of G and C in the third codon position in paralogous comparisons (in the order αc), and in orthologous comparisons (in the order chicken 〈 rodent 〈 man). Comparison of actin-coding sequences between species was carried out using the Perler method of analysis. As one moves backward in time, changes at silent sites first accumulate rapidly, then begin to saturate after −(30–40) million years (MY), and actually decrease between −400 and −500 MY. Replacements or silent substitutions therefore cannot be used as evolutionary clocks for these sequences over long periods. Other phenomena, such as gene conversion or isochore compartmentalization, probably distort the estimated divergence time.
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  • 30
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    Journal of molecular evolution 25 (1987), S. 248-254 
    ISSN: 1432-1432
    Keywords: Intervening sequence ; Evolution ; Archaebacteria
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    Notes: Summary Nucleotide sequences of four tRNA genes from the archaebacteriumSulfolobus solfataricus have been determined. Based upon DNA sequence analysis, three of the four genes contain presumptive intervening sequences (introns) in their anticodon loops. The three introns can form similar, but not identical, secondary structures. The cleavage site at the 3′ end of all three introns occurs in a three-base bulge loop. All four genes lack an encoded 3′ CCA terminus and are flanked by A+T-rich DNA sequences. Two of the genes are located on antiparallel DNA strands, with their 3′ termini separated by 414 bp of sequence. Including two previously published sequences, a total of five introns have now been detected among sixS. solfataricus tRNA genes. Occurrence of introns at corresponding locations in both archaebacterial and eukaryotic tRNA genes suggests that the intron/exon form of gene structure predates the evolutionary divergence of the archaebacteria and the eukaryotes.
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  • 31
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    Journal of molecular evolution 25 (1987), S. 261-269 
    ISSN: 1432-1432
    Keywords: Fimbriae ; Pili ; Protein structure ; Microbial phylogeny ; Evolution
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    Topics: Biology
    Notes: Summary We have analyzed and compared the amino acid sequences of the type 4 fimbrial subunits fromPseudomonas aeruginosa, Moraxella bovis, M. nonliquefaciens, Bacteroides nodosus, Neisseria gonorrhoeae, andN. meningitidis. We propose a consensus sequence for the highly conserved aminoterminal regions of these proteins. In the variable regions, a domain corresponding to an epitope common toN. gonorrhoeae andN. meningitidis fimbriae is conserved, both in sequence and in environment, in fimbrial subunits fromB. nodosus. The subunits fromM. bovis andP. aeruginosa do not show any homologies to this sequence. In all of the subunits, the carboxy-terminal half of the molecule consists of a series of fairly hydrophobic domains. The last three domains, two of which include the cysteines of the disulfide bridge inN. gonorrhoeae, P. aeruginosa, andM. bovis, are more or less conserved in sequence in all of the proteins including that ofB. nodosus. We propose that these conserved hydrophobic regions, which have the potential to form a series of beta-sheets, form a structural framework around which more variable hydrophilic sequences determining immunological profile are arranged. The evolutionary relationships of the contemporary proteins and the distribution of type 4 fimbriae are also discussed.
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  • 32
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    Journal of molecular evolution 26 (1987), S. 274-283 
    ISSN: 1432-1432
    Keywords: Cardiotoxin ; Circular dichroism ; Cytotoxin ; Evolution ; Protein
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    Notes: Summary In order to analyze the evolutionary behavior of the cobra venom cytotoxins, their probable tertiary structure was predicted using computer graphics. The 41 amino acid sequences known show that the major evolutionary changes have taken place in two particularly exposed areas of the molecular surface. In each area, neighboring residue positions seem to have evolved interdependently, but there is no obvious interdependence between the two areas. Indeed, the relative evolution of these two areas prompts a subdivision of the sequence set into four groups. According to the known cytotoxin circular dichroism spectra, one of these four groups could be characterized by a difference in molecular secondary structure. Sine the two variable areas have functional associations, it is suggested that their evolution may be governed by a target with several similar binding sites.
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  • 33
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    Journal of molecular evolution 26 (1987), S. 341-346 
    ISSN: 1432-1432
    Keywords: Evolution ; tRNA ; Recognition sites ; Statistics
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    Notes: Summary A compilation of known tRNA, and tRNA gene sequences from archaebacteria, eubacteria, and eukaryotes permits the construction of tRNA cloverleafs which show conserved structural elements for each tRNA family. Positions conserved across the three kingdoms are thought to represent archetypical features of tRNAs which preceded the divergence of these kingdoms.
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  • 34
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    Journal of molecular evolution 27 (1988), S. 17-28 
    ISSN: 1432-1432
    Keywords: Actin genes ; Evolution ; 5′ and 3′ untranslated regions
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    Notes: Summary We have sequenced the coding and leader regions, as well as part of the 3′ untranslated region, of aXenopus borealis type 1 cytoskeletal actin gene [defined according to the arrangement of acidic residues at the N-terminus; Vandekerckhove et al. (1981) J Mol Biol 152:413–426]. The encoded amino acid sequence is the same as the avian and mammalian β (type 1) cytoskeletal actins, except for an isoleucine at position 10 (as found in the mammalian γ cytoskeletal actins), and an extra amino acid, alanine, after the N-terminal methionine. Five introns were found, in the same positions as those of the rat and chicken β-actin genes. The 5′ and 3′ untranslated regions resemble those of the human γ (type 8) cytoskeletal actin gene more closely than the mammalian β genes. Primer extension showed that this type 1 gene is transcribed in ovary and tadpole. Sequencing of primer extension products demonstrated two additional mRNA species inX. borealis, encoding type 7 and 8 isoforms. This contrasts with the closely related speciesXenopus laevis, where type 4, 5, and 8 isoforms have been found. The type 7 isoform has not previously been found in any other species. The mRNAs of theX. borealis type 1 and 8 andX. laevis type 5 and 8 isoforms contain highly homologous leaders. TheX. borealis type 7 mRNA has no leader homology with the other mRNA species and, unlike them, has no extra N-terminal alanine codon. The evolutionary implications of these data are discussed.
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  • 35
    ISSN: 1432-1432
    Keywords: Histone genes ; Sea stars ; Echinoderms ; Evolution
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    Notes: Summary The arrangement of core histone genes and their transcriptional polarity has been determined for three species of sea stars (Pisaster ochraceus, P. brevispinus, andDermasterias imbricata) representing two orders which diverged over 500 million years ago. Each species has approximately 500 core histone cluster repeats per haploid genome. The close phylogenetic relationship between thePisaster species is evident from the correspondence of restriction sites in the repeat element, identical arrangement of core histones, and high degree of sequence homology in both the coding and spacer regions of the H3 gene. TheDermasterias repeat has the same gene order and transcriptional polarity of core histones, but its restriction map is significantly different. Moreover, theDermasterias H3 gene has the same amino acid sequence, but in comparison toPisaster nucleotide sequences, shows a high level of silent substitutions. Analyses of the nucleotide sequence of the 5′ and 3′ regions surrounding the H3 gene from each species demonstrate the presence of appropriately spaced consensus and processing signal segments. The 3′ spacer segment of theDermasterias H4 gene contains an unusual, threefold tandemly repeated, 21-nucleotide, AT-rich sequence. No similar sequence is seen in theP. brevispinus H4 3′ region, but these two species show a striking regularity of distribution of five different homologous oligomers in the 3′ spacer.
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  • 36
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    Journal of molecular evolution 27 (1988), S. 102-108 
    ISSN: 1432-1432
    Keywords: Hemopexin ; Evolution ; Gene structure ; Recombination ; Sequence homology
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    Notes: Summary The human hemopexin gene was isolated and its structure determined. The gene spans approximately 12 kb and is interrupted by nine introns. When the intron/exon pattern was examined with respect to the polypeptide segments they encode, a direct correspondence between exons and the 10 repeating units in the protein was observed. The introns are not randomly placed; they fall in the middle of the region of amino acid sequence homology in strikingly similar locations in 6 of the 10 units and in a symmetrical position in the two halves of the coding sequence. These features strongly support the hypothesis that the gene evolved through intron-mediated duplications of a primordial sequence to a five-exon cluster. A more recent gene duplication led to the present-day gene organization.
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  • 37
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    Journal of molecular evolution 29 (1989), S. 52-62 
    ISSN: 1432-1432
    Keywords: Genome organization ; Evolution ; Plant virus ; RNA recombination ; Sequence similarity
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    Notes: Summary The relationships of genome organization among elongated (rod-shaped and filamentous) plant viruses have been analyzed. Sequences in coding and noncoding regions of barley stripe mosaic virus (BSMV) RNAs 1, 2, and 3 were compared with those of the monopartite RNA genomes of potato virus X (PVX), white clover mosaic virus (WClMV), and tobacco mosaic virus, the bipartite genome of tobacco rattle virus (TRV), the quadripartite genome of beet necrotic yellow vein virus (BNYVV), and icosahedral tricornaviruses. These plant viruses belong to a supergroup having 5′-capped genomic RNAs. The results suggest that the genomic elements in each BSMV RNA are phylogenetically related to those of different plant RNA viruses. RNA 1 resembles the corresponding RNA 1 of tricornaviruses. The putative proteins encoded in BSMV RNA 2 are related to the products of BNYVV RNA 2, PVX RNA, and WClMV RNA. Amino acid sequence comparisons suggest that BSMV RNA 3 resembles TRV RNA 1. Also, it can be proposed that in the case of monopartite genomes, as a rule, every gene or block of genes retains phylogenetic relationships that are independent of adjacent genomic elements of the same RNA. Such differential evolution of individual elements of one and the same viral genome implies a prominent role for gene reassortment in the formation of viral genetic systems.
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  • 38
    ISSN: 1432-1432
    Keywords: Carcinoembryonic antigen ; Evolution ; Gene family ; Human ; Rat ; Synonymous substitutions ; Silent molecular clock ; Evolutionary trees
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    Notes: Summary Various rodent and primate DNAs exhibit a stronger intra- than interspecies cross-hybridization with probes derived from the N-terminal domain exons of human and rat carcinoembryonic antigen (CEA)-like genes. Southern analyses also reveal that the human and rat CEA gene families are of similar complexity. We counted at least 10 different genes per human haploid genome. In the rat, approximately seven to nine different N-terminal domain exons that presumably represent different genes appear to be present. We were able to assign the corresponding genomic restriction endonuclease fragments to already isolated CEA gene family members of both human and rat. Highly similar subgroups, as found within the human CEA gene family, seem to be absent from the rat genome. Hybridization with an intron probe from the human nonspecific cross-reacting antigen (NCA) gene and analysis of DNA sequence data indicate the conservation of noncoding regions among CEA-like genes within primates, implicating that whole gene units may have been duplicated. With the help of a computer program and by calculating the rate of synonymous substitutions, evolutionary trees have been derived. From this, we propose that an independent parallel evolution, leading to different CEA gene families, must have taken place in, at least, the primate and rodent orders.
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  • 39
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    Journal of molecular evolution 29 (1989), S. 180-187 
    ISSN: 1432-1432
    Keywords: Divergence ; Mitochondrial DNA ; Molecular evolution ; Constraints ; Two-parameter model ; Evolutionary distance ; Evolution ; Mutation ; Neutral space ; Variable positions
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    Notes: Summary Selective constraints on DNA sequence change were incorporated into a model of DNA divergence by restricting substitutions to a subset of nucleotide positions. A simple model showed that both mutation rate and the fraction of nucleotide positions free to vary are strong determinants of DNA divergence over time. When divergence between two species approaches the fraction of positions free to vary, standard methods that correct for multiple mutations yield severe underestimates of the number of substitutions per site. A modified method appropriate for use with DNA sequence, restriction site, or thermal renaturation data is derived taking this fraction into account. The model also showed that the ratio of divergence in two gene classes (e.g., nuclear and mitochondrial) may vary widely over time even if the ratio of mutation rates remains constant. DNA sequence divergence data are used increasingly to detect differences in rates of molecular evolution. Often, variation in divergence rate is assumed to represent variation in mutation rate. The present model suggests that differing divergence rates among comparisons (either among gene classes or taxa) should be interpreted cautiously. Differences in the fraction of nucleotide positions free to vary can serve as an important alternative hypothesis to explain differences in DNA divergence rates.
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  • 40
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    Journal of molecular evolution 29 (1989), S. 233-245 
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Salmonids ; Nucleotide sequence ; Transitions ; Transversions ; Evolution
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    Notes: Summary Sequence comparisons were made from 2214 bp of mitochondrial DNA cloned from six Pacific salmonid species. These sequences include the genes for ATPase subunit 6, cytochrome oxidase subunit 3, NADH dehydrogenase subunit 3, NADH dehydrogenase subunit 4L, tRNAGLY, and tRNAARG. Variation is found at 338 silent and 12 nonsilent positions of protein coding genes and 10 positions in the two tRNA sequences. A single 3-bp length difference was also detected. In all pairwise comparisons the sequence divergence observed in the fragment was higher than that previously predicted by restriction enzyme analysis of the entire molecule. The inferred evolutionary relationship of these species is consistent between methods. The distribution of silent variation shows a complex pattern with greatly reduced variation at the junctions of genes. The variation in the tRNA sequences is concentrated in the DHU loop. The close relationship of these species and extensive sequence analyzed allows for an analysis of the spectrum of substitutions that includes the frequencies of all 12 possible substitutions. The observed spectrum of substitutions is related to potential pathways of spontaneous substitution. The salmonid sequences show an extremely high ratio of silent to replacement substitutions. In addition the amino acid sequences of the four proteins coded in this fragment show a consistently high level of identity with theXenopus sequences. Taken together these data are consistent with a slower rate of amino acid substitution among the cold-blooded vertebrates when compared to mammals.
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  • 41
    ISSN: 1432-1432
    Keywords: α-Conotoxin ; α-Neurotoxin ; Erabutoxin b ; Evolution ; Venom
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    Topics: Biology
    Notes: Summary α-neurotoxins from elapid snake venoms andα-conotoxins from marine snails bind specifically and with high affinity to nicotinic cholinoceptors. Although both types of toxin are polypeptides, there is more than a fourfold difference in size between the two and no clear sequence homology is evident. A systematic computer search of the three-dimensional structure of erabutoxin b (anα-neurotoxin from the false sea snakeLaticauda semifasciata) was performed to identify the locality that most closely matched the amino acid compositions of the smallerα-conotoxins (from the marine snailsConus magus andConus geographus). The area of greatest similarity centered on residue position 25 of erabutoxin b, a locale that is conserved throughout the snakeα-neurotoxins and their homologues. Six Proteins unrelated to erabutoxin b were compared to theα-conotoxins to show that the extent of the erabutoxin b/α-conotoxin match was too high to be coincidental. Homologues of erabutoxin b, namelyα-cobratoxin fromNaja naja siamensis and cytotoxin VII4 fromNaja mossambica mossambica, were also analyzed. The extent of the matching with theα-conotoxins decreased in the series erabutoxin b〉α-cobratoxin〉cytotoxin VII4, and this also relates the order of similarity to the pharmacological properties of theα-conotoxins. Theα-conotoxin-like area of the snakeα-neurotoxins is peripheral to the site previously considered important for binding to the cholinoceptor, even though it seems to represent the focus of evolutionary convergence between the two types of neurotoxin. The area of resemblance does, however, have strong associations with the conformational behavior of the snake toxins. Hence, the outcome of this study has important consequences for the current ideas on snakeα-neurotoxin structure/activity relationships and the evolutionary origins of neurotoxicity.
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  • 42
    ISSN: 1432-1432
    Keywords: Evolution ; 5S Ribosomal RNA sequences ; Arthropoda ; Secondary structure
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    Notes: Summary 5S Ribosomal RNA sequences have proven to be useful tools in the study of evolutionary relationships among species. However, in reviewing previously published trees constructed from alignments of metazoan 5S RNAs, we noticed several discrepancies with classical evolutionary views. One such discrepancy concerned the phylum Arthropoda, where a crustacean,Artemia salina, seemed to be evolutionarily very remote from four insects. The cause of this phenomenon was studied by determining the 5S RNA sequences of additional arthropods, viz.Limulus polyphemus, Eurypelma californica, Lasiodora erythrocythara, Areneus diadematus, Daphnia magna, Ligia oceanica, Homarus gammarus, Cancer pagurus, Spirobolus sp.,Locusta migratoria, andTenebrio molitor. A tree was then constructed from a dissimilarity matrix by a clustering method known as weighted pair grouping. Application of a correction for unequal evolutionary rates improved the apparent evolutionary position of the arthropods and of some other metazoan species. However, neither the uncorrected nor the corrected tree permitted a completely acceptable reconstruction of metazoan evolution. We presume that this phenomenon is due to random deviations in the evolutionary rate of 5S RNA.
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  • 43
    ISSN: 1432-1432
    Keywords: Glycoprotein ; Evolution ; Ribonuclease
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    Notes: Summary The glycosylation characteristics of the digestive enzyme ribonuclease are summarized. The evolutionary role of this posttranslational modification is discussed and evidence is presented that selection has much influence on the presence or absence of carbohydrate in glycoproteins and on the positions of the carbohydrate attachment sites.
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  • 44
    ISSN: 1432-1432
    Keywords: Ribosomal RNAs ; Cross-hybridization ; Hybridization yield ; Fractional hybridization ; Hybridization homology ; Phylogenetic tree ; Phylogeny ; Evolution ; Archaebacteria
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    Notes: Summary Ribosomal RNAs of 17 species of archaebacteria were hybridized to corresponding and non-corresponding nitrocellulose bound DNAs. The temperature stability of these hybrids and the amount of bound rRNA were determined. A formula was derived to correct the hybridization yields for the different genome lengths and numbers of rRNA operons per genome. This correction made it possible to determine hybridization homologies, as functions of velocity constants, which could then be used in a similar way as sequence homologies. The results were consistent with those from 16S rRNA total sequence data. No correlation was found between the hybridization homologies and the temperature stabilities of the hybrids. This new method is faster and simpler than the method based on total 16S rRNA sequence determination although it provides less total information. Its application to archaebacterial phylogeny has shown theThermococcales to represent a third branch of the kingdom beside the branch of the methanogens + halophiles, and that of theThermoproteales + Sulfolobales. The method has also provided a detailed description of the phylogeny of theSulfolobales showing their origin within theThermoproteales.
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  • 45
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    Journal of molecular evolution 24 (1987), S. 228-235 
    ISSN: 1432-1432
    Keywords: 5S RNA ; Correspondence analysis ; Multivariate statistics ; Evolution ; Phylogeny
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    Topics: Biology
    Notes: Summary Correspondence analysis (a form of multivariate statistics) applied to 74 5S ribosomal RNA sequences indicates that the sequences are interrelated in a systematic, nonrandom fashion. Aligned sequences are represented as vectors in a 5N-dimensional space, where N is the number of base positions in the 5S RNA molecule. Mutually orthogonal directions (called factor axes) along which intersequence variance is greatest are defined in this hyperspace. Projection of the sequences onto planes defined by these factorial directions reveals clustering of species that is suggestive of phylogenetic relationships. For each factorial direction, correspondence analysis points to regions of “importance”, i.e., those base positions at which the systematic changes occur that define that particular direction. In effect, the technique provides a rapid determination of group-specific signatures. In several instances, similarities between sequences are indicated that have only recently been inferred from visual base-to-base comparisons. These results suggest that correspondence analysis may provide a valuable starting point from which to uncover the patterns of change underlying the evolution of a macromolecule, such as 5S RNA.
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  • 46
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    Journal of molecular evolution 24 (1987), S. 236-251 
    ISSN: 1432-1432
    Keywords: 28S rRNA ; RNA secondary structure ; Evolution ; Ribosome ; Translation
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    Topics: Biology
    Notes: Summary We have determined the secondary structure of the human 28S rRNA molecule based on comparative analysis of available eukaryotic cytoplasmic and prokaryotic large-rRNA gene sequences. Examination of large-rRNA sequences of both distantly and closely related species has enabled us to derive a structure that accounts both for highly conserved sequence tracts and for previously unanalyzed variable-sequence tracts that account for the evolutionary differences in size among the large rRNAs. Human 28S rRNA is composed of two different types of sequence tracts: conserved and variable. They differ in composition, degree of conservation, and evolution. The conserved regions demonstrate a striking constancy of size and sequence. We have confirmed that the conserved regions of large-rRNA molecules are capable of forming structures that are superimposable on one another. The variable regions contain the sequences responsible for the 83% increase in size of the human large-rRNA molecule over that ofEscherichia coli. Their locations in the gene are maintained during evolution. They are G+C rich and largely nonhomologous, contain simple repetitive sequences, appear to evolve by frequent recombinational events, and are capable of forming large, stable hairpins. The secondary-structure model presented here is in close agreement with existing prokaryotic 23S rRNA secondary-structure models. The introduction of this model helps resolve differences between previously proposed prokaryotic and eukaryotic large-rRNA secondary-structure models.
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  • 47
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    Journal of molecular evolution 25 (1987), S. 15-19 
    ISSN: 1432-1432
    Keywords: β-Turns ; Secondary structures ; Chirality ; Genetic code ; Biosynthetic pathways ; Evolution
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    Topics: Biology
    Notes: Summary The physicochemical properties of β-turns suggest their biological importance prior to the formation of the genetic code. These properties include ones potentially affecting the preference for eitherl- ord-amino acids. The abundance of certain amino acids in β-turns is correlated with their assignment to a small, well-defined part of the genetic code and with their role as metabolic precursors for other amino acids. It is proposed that in the prebiotic environment, β-turns became objects of selection that influenced the evolution of the genetic code and biosynthetic pathways for amino acids.
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  • 48
    ISSN: 1432-1432
    Keywords: Balbiani rings ; Evolution ; Immunological detection ; Nucleotide sequence ; 3′ End
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    Notes: Summary Two cDNA clones representing the 3′-end regions of BR1 and BR2 75S mRNA were obtained fromChironomus pallidivittatus. The regular structure characterizing the core of these genes, consisting of tandemly arranged repeat units, changes into a more irregular structure toward the 3′ end. Distal to a standard type of repeat unit with a characteristic excess of positive charges, a new type of repeat with a high, negative charge density is interspersed among parts of the standard unit. The last 111 amino acids before the stop codon represent a unique region distinctly different in amino acid composition from upstream regions, and include two partially homologous hydrophobic regions. Sequence comparison of 3′-end regions from clones representing BR1 and BR2 genes indicates striking sequence conservation in the unique part of the region. Analysis of the level of silent site divergence shows that the homology increases in the 3′ direction up to the polyadenylation site. That the unique region is retained as a part of the secreted protein is shown by Western blotting.
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  • 49
    ISSN: 1432-1432
    Keywords: Histone genes ; Echinoderms ; Maternal mRNA ; Development ; Evolution
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    Topics: Biology
    Notes: Summary The organization and maternal expression of histone genes differ greatly between the two echinoderm classes represented by the sea stars and sea urchins. We have isolated and characterized a 5.3-kb genomic DNA fragment encoding core histone genes in the sea starPisaster ochraceus. The majority of histone genes are organized as tandem repeats of the 5.3-kb fragment, which is present in as many as 700 copies per haploid genome. The identity, precise location, and transcriptional polarity of individual core histone genes within the repeat were determined by DNA sequence analyses. The gene order in the sea star (H2B, H2A, H4, H3) is different from that in sea urchins (H2B, H3, H2A, H4). What is remarkable is the low level of maternal histone mRNA inP. ochraceus eggs relative to that in sea urchins. This observation supports a recent suggestion that major changes in mode of gene expression, rather than in gene organization or copy number, can be correlated with major events in echinoderm evolution.
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  • 50
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    Journal of molecular evolution 25 (1987), S. 81-88 
    ISSN: 1432-1432
    Keywords: Glutathione ; Evolution ; Phototrophic microorganisms ; Oxygen toxicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Of the many roles ascribed to glutathione (GSH) the one most clearly established is its role in the protection of higher eucaryotes against oxygen toxicity through destruction of thiol-reactive oxygen byproducts. If this is the primary function of GSH then GSH metabolism should have evolved during or after the evolution of oxygenic photosynthesis. That many bacteria do not produce GSH is consistent with this view. In the present study we have examined the low-molecular-weight thiol composition of a variety of phototrophic microorganisms to ascertain how evolution of GSH production is related to evolution of oxygenic photosynthesis. Cells were extracted in the presence of monobromobimane (mBBr) to convert thiols to fluorescent derivatives, which were analyzed by highpressure liquid chromatography. Significant levels of GSH were not found in the green bacteria (Chlorobium thiosulfatophilum andChloroflexus aurantiacus). Substantial levels of GSH were present in the purple bacteria (Chromatium vinosum, Rhodospirillum rubrum, Rhodobacter sphaeroides, andRhodocyclus gelatinosa), the cyanobacteria [Anacystis nidulans, Microcoleus chthonoplastes S.G., Nostoc muscorum, Oscillatoria amphigranulata, Oscillatoria limnetica, Oscillatoria sp. (Stinky Spring, Utah),Oscillatoria terebriformis, Plectonema boryanum, andSynechococcus lividus], and eucaryotic algae (Chlorella pyrenoidsa, Chlorella vulgaris, Euglena gracilis, Scenedesmus obliquus, andChlamydomonas reinhardtii). Other thiols measured included cysteine, γ-glutamylcysteine, thiosulfate, coenzyme A, and sulfide; several unidentified thiols were also detected. Many of the organisms examined also exhibited a marked ability to reduce mBBr to syn-(methyl,methyl)bimane, an ability that was quenched by treatment with 2-pyridyl disulfide or 5,5′-bisdithio-(2-nitrobenzoic acid) prior to reaction with mBBR. These observations indicate the presence of a reducing system capable of electron transfer to mBBr and reduction of reactive disulfides. The distribution of GSH in phototrophic eubacteria indicates that GSH synthesis evolved at or around the time that oxygenic photosynthesis evolved.
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  • 51
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    Microchimica acta 94 (1988), S. 277-278 
    ISSN: 1436-5073
    Keywords: kinetics ; FT-IR ; temporal resolution
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    Topics: Chemistry and Pharmacology
    Notes: Abstract A system for performing gas-phase rapid scanning Fourier transform infrared time-resolved Spectrometry (FT-IR/TRS) has been evaluated. This technique can be applied to the study of the lifetimes and reactivity of transient species and can provide detailed information regarding reaction rate constants. Temperature-jump experiments have been initiated and preliminary results are presented.
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  • 52
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    Microchimica acta 94 (1988), S. 323-328 
    ISSN: 1436-5073
    Keywords: FTIR spectroscopy ; kinetics ; polymers ; rheo-optics ; variable-temperature measurements
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    Topics: Chemistry and Pharmacology
    Notes: Abstract The rapid-scanning capability of FTIR instrumentation has revitalized the field of vibrational spectroscopy in polymer research and will be discussed with reference to the study of polyurethane kinetics, the temperature dependence of hydrogen bonding in polyamide 6 and strain-induced crystallization in a polydimethylsiloxane elastomer.
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  • 53
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    Cellular and molecular life sciences 41 (1985), S. 1563-1564 
    ISSN: 1420-9071
    Keywords: Cytosine deaminase ; kinetics ; pyrophosphate ; orotidine monophosphate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary The maximal velocity of the reaction (Vmax) and the half-saturation constant (K0.5) values of theS. typhimurium cytosine deaminase were altered in the presence of its effectors, pyrophosphate and orotidine monophosphate. From the kinetics of orotidine monophosphate inhibition of cytosine deaminase, it was characterized as a mixed-type noncompetitive inhibitor.
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  • 54
    ISSN: 1420-9071
    Keywords: Evolution ; receptors ; plant hormones
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  • 55
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    Oecologia 72 (1987), S. 69-76 
    ISSN: 1432-1939
    Keywords: Cabbage butterfly ; Pieris rapae ; Evolution ; Adaptation ; Colonisation
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    Topics: Biology
    Notes: Summary Australian and U.K. Pieris rapae differ markedly in their oviposition behaviour; U.K. females produce a more aggregated egg distribution, and lay their eggs more quickly, than do Australian females. The adaptive reason for this divergence probably lies in the relative costs of increased flight time (more costly in the U.K.) and increased local crowding (more costly in Australia). There is also a strong relationship between juvenile developmental rate (at constant temperature) and oviposition behaviour, but the form of this relationship differed between the two populations. The adaptive reasons for the link between developmental rate and behaviour is not clear. It may be that this link represents the tip of the iceberg; i.e. that physiological, developmental, and behabioral characters all co-vary in ways and for reasons that we do not yet understand.
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  • 56
    ISSN: 1432-0983
    Keywords: Crithidia fasciculata ; rRNA ; Sequence ; Evolution
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    Topics: Biology
    Notes: Summary We present the cloning and sequence analysis of the nuclear-encoded Crithidia fasciculata small subunit (SSU) rRNA gene, the longest (2,206 bp) such gene yet characterized by direct sequence analysis. Much of the sequence can be folded to fit a phylogenetically conserved secondary structure model, with the additional length of this gene being accommodated within discrete variable domains that are present in eukaryotic SSU rRNAs. On the basis of sequence comparisons, we conclude that Crithidia contains the most highly diverged SSU rRNA described to date among the eukaryotes, and therefore represents one of the earliest branchings within the eukaryotic primary kingdom.
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  • 57
    ISSN: 1432-0983
    Keywords: ATP synthase β ; Selective constraint ; mtDNA ; Evolution
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    Topics: Biology
    Notes: Abstract We have cloned and sequenced human and bovine cDNAs for the β subunit of the ATP synthase (ATP-synß), a nuclear DNA (nDNA) encoded oxidative phosphorylation (OXPHOS) gene. The two cDNAs were found to share 99% amino acid homology and 94% nucleotide homology. The evolutionary rate of ATPsynß was then compared with that of two mitochondrial DNA (mtDNA) ATP synthase genes (ATPase 6 and 8), seven other mtDNA OXPHOS genes, and a number of nuclear genes. The synonymous substitution rate for ATPsynß proved to be 1.9 × 10−9 substitutions per site per year (substitutions × site−1 × year−1) (SSY). This is less than 1/2 that of the average nDNA gene, 1/12 the rate of ATPase 6 and 8, and 1/17 the rate of the average mtDNA gene. The synonymous and replacement substitution rates were used to calculate a new parameter, the “selective constraint ratio”. This revealed that even the most variable mtDNA protein was more constrained than the average nDNA protein. Thus, the high substitution mutation rate and strong selective constraints of mammalian mtDNA proteins suggest that mtDNA mutations may result in a disproportionately large number of human hereditary diseases of OXPHOS.
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  • 58
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    European journal of clinical pharmacology 29 (1985), S. 251-253 
    ISSN: 1432-1041
    Keywords: paracetamol ; antacids ; acetaminophen ; bioavailability ; kinetics
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    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary The effect of two antacids on the bioavailability of paracetamol has been investigated in 12 young healthy volunteers. Following a random cross over design, each subject swallowed, on three separate occasions, one weak apart, 500 mg paracetamol alone, or together with two different aluminium hydroxide, magnesium hydroxide preparations (Dimalan and Maalox). Plasma paracetamol levels were measured by HPLC. The bioavailability of paracetamol was not altered by either antacid, but they both delayed the time to peak plasma concentration (0.85 h; 1.43 h; 1.25 h, without antacid, with Dimalan and with Maalox respectively). The peak plasma concentration was not affected by concurrent antacid administration.
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  • 59
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    European biophysics journal 16 (1989), S. 321-325 
    ISSN: 1432-1017
    Keywords: Sodium currents ; inactivation ; kinetics ; channel gating
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    Topics: Biology , Physics
    Notes: Abstract The time constant of the process producing the delay in Na inactivation development as determined by the two pulse method (τdelay) was extracted and compared to that of the slowest Na activation process τ3 for the I Na during the conditioning pulse of that same determination. τdelay and two pulse inactivation τc values were computer generated using a nonlinear least squares algorithm. τh and single pulse inactivation τh values were independently generated for each determination also with the aid of the computer using the same non-linear least squares algorithm. In one determination at 2 mV, τc was 4.68 and τdelay 0.494 ms while τh was 4.70 and τ3 0.491 ms for a τc/τh of 0.996 and a τdelay/τ3 of 1.006. Mean τdelay/τ3 from five determinations in four axons, both Cs and K perfused, and spanning a potential range of-27 to 2mV was 1.068. The precursor process to inactivation is channel opening. Some fraction of channels presumably inactivate via another route where prior channel opening is not required.
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  • 60
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    European journal of clinical pharmacology 28 (1985), S. 163-169 
    ISSN: 1432-1041
    Keywords: indomethacin ; platelet aggregation ; prostanoids ; plasma concentration ; arachidonic acid ; thromboxane B2 ; 6-keto-prostaglandin F1α ; kinetics
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    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary A single oral dose of indomethacin 1 mg/kg was given to 6 male and 6 female volunteers. The formation of thromboxane B2 (TXB2) and 6-ketoprostaglandin F1α (6-keto-PGF1α) in clotting whole blood was measured by radioimmunoassay, and platelet aggregation induced by archidonic acid (AA) was measured with a plasma aggregometer. The results were related to the concomitant plasma concentration of indomethacin. The maximum plasma concentration ranged between 3.24 and 8.11 µg/ml and the elimination half-life between 4 and 11 h. Formation of the prostanoids was reversibly inhibited, with maximum suppression when the drug concentration in plasma exceeded 0.5–1.0 µg/ml; the IC50 was approximately 0.1 µg/ml. Platelet aggregation was also reversibly inhibited. The correlation between the formation of prostanoids and the different phases of the aggregatory response to exogenous AA is discussed.
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  • 61
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    European journal of clinical pharmacology 29 (1986), S. 529-534 
    ISSN: 1432-1041
    Keywords: pethidine ; epidural injections ; pain scores ; kinetics ; spinal cord
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    Topics: Chemistry and Pharmacology , Medicine
    Notes: Summary Twenty-one patients who had undergone total hip replacement were randomly assigned to one of three groups in order to compare a single dose of 1 mg/kg of pethidine im (I) and 20 mg (II) or 60 mg of extradural pethidine (III) in a double-blind design. The degree of analgesia, the adverse effects, and the kinetics were studied for 18 h. Pain was monitored using a visual analogue scale (VAS). Supplementary doses of oxycodone if required were given no earlier than 0.75 h after pethidine. Plasma concentrations of pethidine were measured with gas chromatography mass spectrometry (GCMS). Hypoalgesia to pin prick test was evaluated. Low pain scores were observed in the extradural groups between 0.25 and 1.5 h after the dose. A significant difference in pain score compared with the im group was found after the higher extradural dose only between 0.5 and 1 h (p〈0.05). The area under the curve (AUC) of pain score versus time (0–18 h) was not significantly different between groups. The recorded adverse effects were minor in all three groups. The terminal half-lives and plasma clearances of pethidine, and the time to peak concentration were not different between the groups. Single patients in the extradural groups showed hypoalgesia to pin prick in parallel to the effect. The present study shows that extradural pethidine produces shortlived analgesia, in contrast to the long-lasting effect of morphine found in other studies.
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  • 62
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    European biophysics journal 13 (1986), S. 343-353 
    ISSN: 1432-1017
    Keywords: Lipid/cholesterol ; phase transition ; kinetics ; second order transition ; pressure jump relaxation
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    Topics: Biology , Physics
    Notes: Abstract Lipid bilayers and monolayers composed of dimyristoylphosphatidic acid (DMPA) and cholesterol were characterized by differential scanning calorimetry and film balance measurements. Increasing cholesterol content decreases the bilayer phase transition temperature and enthalpy in a manner similar to that observed before for other lipid/cholesterol systems. In monomolecular films at the air-water interface cholesterol exhibits the well known condensing effect in the liquid-expanded phase, while the liquid-condensed phase is less affected. As with the bilayer phase transition, the transition temperature and change in area at the liquid-condensed to liquid-expanded phase transition, as measured from isobars at 25 dynes/cm, decreases with increasing cholesterol content. The kinetics of the phase transition of DMPA/cholesterol bilayers were measured using the pressure jump relaxation technique with optical detection. Three relaxation times were observed. The relaxation times and amplitudes pass through maximum values at the transition midpoint. With increasing cholesterol content the maximum values of the relaxation times decrease but not in a linear fashion. The time constants display an intermediate maximum at ca. 10% to 12 mol% cholesterol. This observation is discussed in terms of a possible change in the nature of the phase transition from first-order with phase separation to a continuous second-order transition. The dependence of the relaxation amplitudes on cholesterol content gave evidence for nucleation being the rate limiting step for the transition in this particular system.
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  • 63
    ISSN: 1432-072X
    Keywords: Sporomusa ; Sporomusa ovata ; Sporomusa sphaeroides ; Selenomonas ruminantium ; Megasphoera elsdenii ; Phylogeny of Gram-positive eubacteria ; Evolution ; 16S rRNA cataloguing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In order to determine the phylogenetic relationships of representatives of three Gram-negative genera, Sporomusa, Selenomonas, and Megasphaera, the 16S ribosomal RNAs were compared by oligonucleotide cataloguing. Surprisingly, Sporomusa ovata, S. sphaeroides, Selenomonas ruminantium, and Megasphaera elsdenii do not group with any of the 200 Gram-negative eubacterial species investigated so far by this method but show a distinct although remote relationship to Gram-positive eubacteria of the “Clostridium subdivision”. The presence of Gram-negative species within the radiation of the cluster defined by Gram-positive cubacteria reduces the significance the Gram-positive staining behaviour plays in taxonomic and phylogenetic studies. It furthermore supports previous findings showing the Gram-negative and phototrophic species Heliobacterium chlorum to be a member of the Clostridium-Bacillus cluster. The presence of Gram-negative endospore-containing Sporomusa species among the 16S rRNA cluster of Gram-positive endospore-forming eubacteria allow speculations about the evolutionary origin of Gram-positive eubacteria.
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    Archives of microbiology 151 (1989), S. 454-458 
    ISSN: 1432-072X
    Keywords: Photosynthesis ; Photosynthetic bacteria ; Evolution ; Bacteriochlorophyll ; Reaction centres ; Light harvesting
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract 1) A number of overlapping clones have been isolated from a Rhodobacter sphaeroides gene bank. Following conjugative gene transfer from Escherichia coli these clones restore a wild type phenotype to several mutants unable to synthesise bacteriochlorophyll. 2) The insert DNA was analysed by restriction mapping and together the clones form the basis of the first restriction map of the 45 kb photosynthetic gene cluster of Rb. sphaeroides. 3) This cluster is bounded on one side by puh A encoding the reaction centre H polypeptide and on the other by the puf operon encoding reaction centre L and M apoproteins and light harvesting LH1 and polypeptides. 4) DNA fragments from the 45 kb cluster were used to probe genomic DNA from other photosynthetic bacteria. Using heterologous hybridisation conditions, a significant degree of homology is shown between Rb. sphaeroides and these other bacteria, suggesting close evolutionary links with Rb. capsulatus in particular.
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  • 65
    ISSN: 1432-072X
    Keywords: Eubacteria ; Evolution ; Extreme thermophile ; Thermotoga
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    Topics: Biology
    Notes: Abstract Three new strains of eubacterial hyperthermophiles were isolated from continental solfataric springs at Lac Abbé (Djibouti, Africa). Due to their morphology, lipids, and RNA polymerases they belong to the genus Thermotoga. Strains LA4 and LA10 are closely related to Thermotoga neapolitana found up to now only in the marine environment. Strain LA 3 differs from Thermotoga maritima and Thermotoga neapolitana in significant physiological and molecular properties. It is described as the new species Thermotoga thermarum.
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  • 66
    ISSN: 1432-072X
    Keywords: Evolution ; Nif genes ; Nitrogen fixation ; Nitrogenase ; Nucleotide sequence ; Phylogeny ; Rhizobium ; 16S rRNA cataloguing
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    Topics: Biology
    Notes: Abstract It was known that nitrogenase genes and proteins are well conserved even though they are present in a large variety of phylogenetically diverse nitrogen fixing bacteria. This has lead to the speculation, among others, that nitrogen fixation (nif) genes were spread by lateral gene transfer relatively late in evolution. Here we report an attempt to test this hypothesis. We had previously established the complete nucleotide sequences of the three nitrogenase genes from Bradyrhizobium japonicum, and have now analyzed their homologies (or the amino acid sequence homologies of their gene products) with corresponding genes (and proteins) from other nitrogen fixing bacteria. There was a considerable sequence conservation which certainly reflects the strict structural requirements of the nitrogenase iron-sulfur proteins for catalytic functioning. Despite this, the sequences were divergent enough to classify them into an evolutionary scheme that was conceptually not different from the phylogenetic positions, based on 16S rRNA homology, of the species or genera harboring these genes. Only the relation of nif genes of slow-growing rhizobia (to which B. japonicum belongs) and fast-growing rhizobia was unexpectedly distant. We have, therefore, performed oligonucleotide cataloguing of their 16S rRNA, and found that there was indeed only a similarity of S AB=0.53 between fast- and slowgrowing rhizobia. In conclusion, the results suggest that nif genes may have evolved to a large degree in a similar fashion as the bacteria which carry them. This interpretation would speak against the idea of a recent lateral distribution of nif genes among microorganisms.
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  • 67
    ISSN: 1432-072X
    Keywords: Evolution ; Eubacteria ; Thermophile ; Anaerobe ; Thermotoga maritima
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    Topics: Biology
    Notes: Abstract A novel type of bacterium has been isolated from various geothermally heated locales on the sea floor. The organisms are strictly anaerobic, rod-shaped, fermentative, extremely thermophilic and grow between 55 and 90°C with an optimum of around 80°C. Cells show a unique sheath-like structure and monotrichous flagellation. By 16S rRNA sequencing they clearly belong to the eubacteria, although no close relationship to any known group could be detected. The majority of their lipids appear to be unique in structure among the eubacteria. Isolate MSB8 is described as Thermotoga maritima, representing the new genus Thermotoga.
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  • 68
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    Archives of microbiology 150 (1988), S. 56-60 
    ISSN: 1432-072X
    Keywords: Fumarate reduction ; Quinones ; Rhodospirillaceae ; Phototrophic bacteria ; Evolution ; Taxonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nineteen established and one undesignated species of the Rhodospirillaceae were examined for fumarate reduction in connection with their quinone systems. The fumarate reductase activity with reduced methyl viologen (MVH) or FMNH2 as electron donor was found in membrane (chromatophore) preparations from phototrophically grown cells of all species containing menaquinone (MK) and/or rhodoquinone. The species having ubiquinone as the sole quinone contained no fumarate reductase activity, except some Rhodobacter species showing the FMNH2-dependent activity. The MVH-fumarate reductase activity of the MK-type species was not inhibited by Triton X-100 or acetone treatment, suggesting the presence of a fumarate reductase reacting directly with MVH, while such an enzyme was absent in the MK-lacking strains, with few exceptions. The FMNH2-fumarate reduction system was abolished by a detergent or acetone extraction in all bacteria but differed much among species with different quinone types as to the response to respiratory inhibitors. These differences in fumarate-reducing properties and quinone systems among the phototrophic bacteria are discussed from evolutionary and taxonomic viewpoints.
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  • 69
    ISSN: 1432-072X
    Keywords: Eubacteria ; Evolution ; Extreme thermophile ; Thermotoga
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    Topics: Biology
    Notes: Abstract A second species of the extremely thermophilic, eubacterial genus Thermotoga is described as clearly distinguished from the type species Thermotoga maritima by physiological and phylogenetic criteria. It is named Thermotoga neapolitana.
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    Ecological research 2 (1987), S. 175-183 
    ISSN: 1440-1703
    Keywords: Egg size ; Evolution ; Hesperiidae ; Host specificity ; Leaf toughness
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    Topics: Biology
    Notes: Abstract The adaptive significance of egg size of skippers (Lepidoptera; Hesperiidae) in Japan was evaluated in relation to the leaf toughness of their major host grasses. The hesperids that fed on tougher grasses laid larger eggs. Hesperids that laid larger eggs were larger in body size, but lower in fecundity. They also had a wider host range. Thus, despite the lower fecundity, hesperids may benefit from large eggs by having a wider host range of larvae. Grass feeders had wider range of host plants than broadleaf feeders.
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    Plasma chemistry and plasma processing 5 (1985), S. 293-316 
    ISSN: 1572-8986
    Keywords: Plasma chemistry ; halocarbon decomposition ; kinetics
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    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Technology
    Notes: Abstract For the case of weak feed gas decomposition, where the concentration of CCl4 exceeds those of decomposition and built-up products, the emission of CCl* is shown to originate from dissociative excitation of CCl4. With electron concentration measured independently, the kinetics of CCl4 decomposition has been extracted from the time dependence of the CCl* intensity. Supported by EPR determinations of radical concentrations in rapidly flowing CCl4 and CCl4/O2 afterglows, the primary decomposition reaction is shown to be the electron impact dissociation into CCl3 and Cl. Its rate constant (k 1=4×10−8 cm3s−1) indicates strongly that dissociative electron attachment is the main reaction channel at least at r.f. power densities just above the threshold of a self-maintaining discharge. At extremely low mean electron energies the emission of a continuum is observed, which is tentatively ascribed to the radiative CCl3-Cl recombination.
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    Plasma chemistry and plasma processing 6 (1986), S. 429-436 
    ISSN: 1572-8986
    Keywords: Plasma ; laser ; diagnostics ; free radicals ; kinetics
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    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Technology
    Notes: Abstract The plasma of a pulse discharge (0.05 J/cm3) in methane at low pressure (200 Pa) is studied. The dynamics of formation and decay of C2(a3IIu, v″=0) is monitored using a stroboscopic laser absorption method. It was found that substantial amounts of C2, 1015 cm−3, arise with a 1-µs delay after the current pulse.
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    Plasma chemistry and plasma processing 8 (1988), S. 101-110 
    ISSN: 1572-8986
    Keywords: Plasma ; laser ; diagnostics ; hydrocarbons ; free radicals ; kinetics
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    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Technology
    Notes: Abstract The dynamics of the formation and decay of excited hydrogen during a pulse discharge in methane at a pressure of 200 Pa and energy density of 0.05 J/cm3 has been studied. The population of hydrogen in the n=2 state was monitored by the laser absorption method. The time constant of the decay of the excited hydrogen was measured to be 95±15 ns. The concentration of free electrons reached a maximum value of 7×1014 cm−3, and the time constant of their recombination was 220±50 ns. The formation of appreciable amounts of atomic hydrogen in the ground state during the discharge, H(n=1)〉1016 cm−3, was estimated on the basis of a kinetic model.
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  • 74
    ISSN: 1572-8986
    Keywords: Methane ; acetylene ; kinetics ; modeling
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    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Technology
    Notes: Abstract It is shown that it is basically possible to model plasma-chemical methane conversion using a kinetic concept regardless of the kind of plasma, i.e., the kind of activation. While the temporal plasma-chemical decomposition of methane is controlled by a first-order rate equation, the temporal product formation can be described by a set of first-order consecutive reactions. Prolonged portions of constant product concentrations in the temporal product formation curves were explained by the assumption of an equilibrium between forward and reverse reactions. The modeling revealed the special role of the re-formation of dissociated molecules.
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    Molecular and cellular biochemistry 86 (1989), S. 65-70 
    ISSN: 1573-4919
    Keywords: Hex A ; Hex B ; N-acetyl-glucosaminidases ; kinetics ; thermodynamic transitions ; ion-exchangers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Summary The kinetic and thermodynamic properties of N-acetyl-β-D-glucosaminidase A (Hex A) and N-acetyl-β-D-D-glucosaminidase β (Hex B) from goat testes were investigated in free and bound (after binding them on ion-exchangers such as DEAE- or CM-cellulose respectively) forms. The optimum pH of free Hex A and Hex B was at 4.2 and 5.4, whereas the bound forms showed the optimum pH at 4.0 and 5.2 respectively. While apparent Km of free and bound Hex A (0.8 and 1.0 mM respectively) did not differ, the Km of Hex B increased when bound on CM-cellulose (Km of free Hex B = 0.96 mM versus bound Hex B = 1.6 mM). Though the free Hex A was more thermo-labile than the free Hex B, both isozymes, on insoluble matrices decayed at faster rates on heating. Activation analysis revealed that the energy of activation (E infa supo ) for transition state of free Hex B (81 Kcal deg−1 mole−1) did not differ from E infa supo of bound Hex B. On the other hand, E infa supo of free Hex A declined from 77.2 to 71.1 Kcal deg−1 mole−1 when heat transitions were carried out in free and bound state respectively. Thermodynamic analysis suggested a change in entropy of activation (ΔS*) of free Hex A and Hex B as 200 and 211 eu respectively. While ΔS* of Hex B did not change after heat transitions, ΔS* of Hex A was 182.5 eu.
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  • 76
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    Biochemical genetics 23 (1985), S. 859-876 
    ISSN: 1573-4927
    Keywords: allozyme ; Cnidaria ; cline ; isozyme ; kinetics ; Metridium senile ; phosphoglucomutase ; polymorphism ; variation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract The phosphoglucomutase (Pgm) locus from populations of the sea anemone Metridium senile has three alleles in natural populations from the northeastern coast of North America. Two of the alleles exhibit clinal variation north of Cape Cod, suggesting a possible association of allele frequency with environmental temperature. This clinal pattern is reproducible and stable over at least brief periods of time. The allozymes encoded by each of the six Pgm genotypes have been partially purified and characterized. The symmetrical pH optimum for V max is pH 7.5; the apparent K m (K m app ) of glucose-1-phosphate declines monotonically as the pH increases from 6.5 to 8.5. There are no pronounced differences in heat stabilities of PGM produced by various genotypes, nor are there significant differences in specific activities. There are no differences in the sensitivity of V max to temperature. K m app values are very low for all genotypes, ranging from about 2 to 12 µm, depending upon the temperature. K m app of glucose-1-phosphate declines as the temperature is raised for all genotypes, whether the pH is held constant or allowed to vary with the temperature. Under certain conditions, there are small significant differences among genotypes in K m app values, but there is no systematic pattern to these differences. The present data provide no biochemical explanation for the maintenance of the Pgm cline by selection for functional differences under different thermal regimes.
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  • 77
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    Oxidation of metals 26 (1986), S. 139-155 
    ISSN: 1573-4889
    Keywords: oxidation ; Co-Cr-Ti alloys ; kinetics ; scale morphology
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Cobalt-based alloys containing 3,5,10,15, and 20% Cr with 1 and 3% Ti were oxidized at 1000°C in slowly flowing oxygen gas. In general, titanium additions decreased the oxidation rate with the most pronounced effect being observed at the 10% Cr level. Titanium accelerated the formation of Cr2O3 layers at the metal-oxide interface. Faceted CrxTiyOz spinel particles were found at the metal-oxide interface which varied in composition according to microprobe results. There was no evidence of spalling on the Co-Cr-Ti alloys studied in contrast to the severe spalling normally encountered in Ni-Cr-Ti alloys. Distinct morphological differences existed on the outer CoO layer of the 1% Ti alloys in comparison to the O and 3% Ti alloys.
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  • 78
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    Oxidation of metals 26 (1986), S. 417-430 
    ISSN: 1573-4889
    Keywords: cyclic carburization-oxidation ; carbides ; austenite ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Several austenitic heat-resistant steels were exposed to alternating periods of carburization at 1273 K [a c= 1,po2〈10−28 atm] and oxidation at 973°K [a c≈ O,po2 = 0.2 atm]. In all cases the depth of internal carbide precipitation increased with cumulative carburization time. It was found that the carburization rates of high nickel content alloys were unaffected by intermittent oxidation cycles, whereas the low nickel, high iron content alloys experienced a reduction in carburization rate subsequent to oxidation treatment. The latter group of alloys formed external scales of chromium-rich M7C3 which were shown by sulfur tracing experiments to be gas permeable. It was concluded, therefore, that oxidation of these materials led to blockage of cracks and holes in the scales, thereby decreasing the surface carbon activity and hence the carburization rate. High nickel, low iron alloys formed external scales of chromium-rich M7C3 covered by Cr3C2. These scales were shown to have very low gas permeabilities. It was concluded that the carbon activity at the surface of these alloys was controlled by scale-alloy equilibration, and was therefore not affected by brief periods of oxidation. The pattern of carbide scale formation is qualitatively consistent with the thermodynamics of the Fe-Cr-C system.
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  • 79
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    Molecular and cellular biochemistry 86 (1989), S. 171-179 
    ISSN: 1573-4919
    Keywords: porcine glucokinase ; purification ; kinetics ; sulfhydryl-related states
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract Porcine hepatic glucokinase (ATP: D-hexose 6-phosphotransferase EC 2.7.1.1) has been purified by a modification of the procedure for its purification from rats. However, difficulties were encountered with endogenous proteases and the reliability of a source for porcine livers. The molecular weight has been determined to be 60 400 ± 1400 by sodium dodecyl sulfate, polyacrylamide gel electrophoresis. The enzyme has been characterized kinetically. The parameter values, S 0.5 (glucose) and Hill coefficient (nH) are 2.4 mM and 1.9 respectively under sulfhydryl-reducing conditions. The enzyme undergoes the two sulfhydryl-related decays of its activity previously observed in the enzyme isolated from rat (Tippett PS, Neet KE: Arch Biochem Biophys 222:285–298, 1983). The enzyme is inhibited by palmitoyl-CoA, K i (apparent) = 1.0 µM, nH = 1.8; this concentration of inhibitor is significantly below its critical micelle concentration. Physically and kinetically glucokinase isolated from pig is similar to the enzyme isolated from rat. The porcine system provides a second source for isolation and further characterization of this important and unusual enzyme.
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  • 80
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    Oxidation of metals 25 (1986), S. 1-28 
    ISSN: 1573-4889
    Keywords: sulfidation ; yttrium ; duplex-sulfide scales ; lamellar sulfides ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The sulfidation of Ni-10Cr-5Al, Ni-20Cr-5Al, and Ni-50Cr-5Al, and of the same alloys containing 1% Y, was studied in 0.1 atm sulfur vapor at 700°C. The sulfidation process followed linear kinetics for all the alloys except Ni-50Cr-5Al-1Y, and possibly Ni-50Cr-5Al, which followed the parabolic law. The reaction rates decreased with increasing chromium content in alloys without yttrium, and the addition of yttrium reduced the rates by at least a factor of two for the alloys containing 10 and 20% Cr and by an order of magnitude for Ni-50Cr-5Al. Alloys containing 10 and 20% Cr (with and without yttrium) formed duplex scales consisting of an outer layer of NiS1.03 and an inner lamellar layer of a very fine mixture of Cr2S3 and A12O3 in a matrix of NiS1.03. The two alloys containing 50% Cr formed only a compact layer of Cr2S3, which was brittle and spalled during cooling. The lamellae in the duplex scales were parallel to the specimen surface and bent around corners. The lamellae were thicker than those on Ni-Al binary alloys. The lamellae were also thicker in scales on the 20% Cr alloy than on the 10% Cr alloy. The presence of yttrium refined the lamellae and increased the lamellae density near the scale/metal interface in the 10% alloy, but in the 20% Cr alloy the lammellae were thicker and more closely spaced. Platinum markers were found in the inner portion of the exterior NiS1.03 layer close to the lamellar zone. A counter-current diffusion mechanism is proposed involving outward cation diffusion and inward sulfur diffusion, although diffusion was not rate controlling for alloys containing 10 and 20% Cr. Auger analysis of scales formed on Ni-50Cr-1Y showed an even distribution of yttrium throughout the layer of Cr2S3, suggesting that some yttrium dissolved in the sulfide. The reduced sulfidation rate of samples containing yttrium is explained by the possible dissolution of yttrium as a donor. The presence of Y4+ would then decrease the concentration of interstitial chromium ions in the N-type layer of Cr2S3, which would decrease the reaction rate.
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    Oxidation of metals 23 (1985), S. 207-235 
    ISSN: 1573-4889
    Keywords: stainless steel ; duplex oxide ; kinetics ; growth rates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The nature of the first-formed oxide on 20% Cr/25% Ni/Nb stabilized steel during exposure to CO2 at high and low temperatures has been determined by surface analytical techniques. These results together with a consideration of gas/solid interactions show that the oxide produced may be determined by kinetics or thermodynamic factors, and a diagram is presented to show that rhombohedral Cr2O3 or spinel may be the oxide first formed. Under most standard conditions, a mixed spinel oxide is formed initially, and the subsequent growth of a duplex oxide is analyzed in terms of a solid-state reaction in which the spinel oxide is reduced to Cr2O3 at the metal/oxide interface. Diffusion control of growth by either spinel or Cr2O3 is incorporated in new equations describing the kinetics of oxidation, and weight-gain predictions are tested against experimental observations.
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  • 82
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    Oxidation of metals 32 (1989), S. 225-240 
    ISSN: 1573-4889
    Keywords: Hot corrosion ; nickel ; TGA ; kinetics ; mechanism
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The accelerated oxidation of pure nickel in the presence of a molten carbonate mixture has been studied in O2 and CO2-containing atmospheres. The oxidation rate of nickel with carbonate coatings was at least four orders of magnitude faster than that without salt coatings. The extent of oxidation, in terms of unit area weight gain, depended on both the amount of carbonate mixture coatings and the gas atmosphere. The unit area weight gain due to oxidation increased with increasing amounts of salt coatings up to a certain value. These observations suggest that the termination of nickel oxidation results from the exhaustion of either the salt coatings or metallic nickel. Porous and particulate oxide products were observed from scanning electron microscopic (SEM) examinations. The energy-dispersive analysis of x-rays (EDAX) shows that no salt remains on the specimen surface after the oxidation experiment.
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  • 83
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    Molecular and cellular biochemistry 76 (1987), S. 45-54 
    ISSN: 1573-4919
    Keywords: DNA methyltransferase ; hemimethylated DNA ; kinetics ; affinity chromatography ; (rat liver)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Notes: Abstract DNA substrate analogs were constructed from poly(dC-dG), M13, and XP12 DNA which do not contain a mixture of types of methylation sites. These were used to distinguish different kinetic mechanisms for maintenance and de novo methylation using a highly purified rat liver DNA (cytosine-5)-methyltransferase (DMase−) preparation. De novo methylation on single (ss) and double-stranded (ds) DNA was found to obey Michaelis-Menten kinetics while methylation of hemimethylated sites showed differences depending on size of the hemimethylated region. On long stretches analogous to maintenance methylation of newly replicated DNA, saturation could not be achieved and the kinetics showed non-ideal positive cooperative kinetics, while short stretches showed non-Michaelis-Menten kinetics and rapid saturation. Two types of DMase-DNA complexes could be distinguished by means of affinity chromatography on DNA-agarose matrices and in preincubation assays. The later complex, which is engaged in methyl group turnover, exhibited enhanced stability. The competitiveness of variously configured DNAs was found to parallel the stability of complex formation, e.g., ss, hemi- and ds DNA, respectively. In studies utilizing 5-bromodeoxyuridine, the thymine analog left the basic reaction mechanisms unchanged but increased the km and S0.5 while reducing the velocity of these reactions.
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  • 84
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    Oxidation of metals 28 (1987), S. 237-258 
    ISSN: 1573-4889
    Keywords: Steel oxidation ; duplex scale ; steam ; activation energy ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The kinetics of the oxidation of ferrous alloys in steam (10–60 kPa) at 450–550°C have been studied by measuring both the rate of hydrogen emission and the amount of metal oxidized. Excellent agreement has been found between the amount of metal oxidized calculated from both the total mass of hydrogen produced in the reaction and the thickness of the oxide layer formed; rate constants calculated from the rate of hydrogen emission, the mass of hydrogen produced as the reaction proceeds, and the oxide formed agree within experimental error. The rate of oxidation of a 9%Cr-1%Mo alloy at 501°C was found to be independent of the partial pressure of the steam. For this alloy, the activation energy agreed with literature values obtained at higher temperatures and pressures. The effect of the chromium and silicon content on the oxidation rates is compared. The rate constants are compared with theoretical calculations, assuming that the rate is determined by diffusion of iron in the magnetite lattice. For the 9%Cr-1%Mo alloy, the parabolic rate constant and activation energy are in excellent agreement with values calculated using Wagner's theory. The experimental rate constants are greater for the alloys containing smaller amounts of chromium; diffusion of iron along magnetite grain boundaries may be the dominant mechanism.
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  • 85
    ISSN: 1573-4889
    Keywords: Ni-base alloy IN 617 ; reactor helium ; oxidation ; carburization ; decarburization ; kinetics ; mechanisms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Application of the technical nickel-base alloy IN 617 in the primary circuit of the high-temperature gas-cooled reactor is limited essentially by the chemical reactions with the impurities (CO, CO2, H2, CH4, H2O) in the helium coolant. The interactions of the alloy with the reactive impurities in different helium-base gases were investigated by thermogravimetry in a gas-tight microbalance and by simultaneous measurement of the changes in gas composition by a continuous sensitive mass spectrometric analysis. The results demonstrate that the set of six reaction equations deduced in part 1 can be applied to describe the corrosion of the alloy. The occurrence of the various reactions is determined essentially by temperature. For the case of a standardized helium gas (HHT-He), three temperature regions can be distinguished. Below a critical temperature (about 1105 K), the presence of CO can cause simultaneous oxidation and carburization. Above this temperature, this reaction does not reverse itself. Rather, oxidation by CO2 and H2O takes place that shows, after a transient period, the same kinetics observed in undiluted oxygen-containing gases. At temperatures above about 1205 K, decarburization of the alloy accompanied by the production of CO takes place, leading to severe destruction of the carbide microstructure and, therefore, limiting the applicability of the material.
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    Oxidation of metals 30 (1988), S. 185-200 
    ISSN: 1573-4889
    Keywords: austenitic steels ; oxidation resistance ; protective αA12O3 film ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The cyclical oxidation behavior of an austenitic stainless steel (24% Ni, 10% Cr, 5% Al, and balance Fe) has been evaluated in the temperature range 800–1300°C. The effects of trace elements such as S, Y, Zr, and Ti on the oxidation of the austenitic stainless steel have also been evaluated. The results indicate that Fe-Ni-Cr-Al stainless steels exhibit superior oxidation resistance up to 1300°C due to the formation of a very adherent and thin film of α-Al2O3.
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  • 87
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    The protein journal 8 (1989), S. 529-548 
    ISSN: 1573-4943
    Keywords: carmin ; association-dissociation ; denaturation ; reaggregation ; kinetics ; reversibility ; hydrophobic interaction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract The effect of a decrease inpH on the structural integrity of carmin has been monitored by a variety of biophysical techniques. The protein undergoes initial dissociation up topH 3.5–4.0 without any significant denaturation. Below thispH the process of dissociation and denaturation appears to be simultaneous. Further, in thepH range of 2.5–1.6 the protein reassociates to probably a different polymer resulting from possibly, an entropically driven hydrophobic interaction. The process of dissociation appears to be reversible to a large extent. The process of denaturation appears to be governed by the kinetic path that the denatured protein molecule follows either by a sudden decrease inpH or through a gradual decrease inpH. These results are interpreted while keeping in view the oligomeric and globular structure of carmin at neutralpH. The results would help in understanding of structure-function relationship of the protein and its role in hydrogen ion bindingin vivo.
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  • 88
    ISSN: 1573-4943
    Keywords: lactate dehydrogenase isoenzymes ; lactate-to-pyruvate reaction ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract In order to evaluate the functional differences that may exist in human lactate dehydrogenase (LDH) isoenzymes widely used for clinical examination the kinetic and thermodynamic properties of the lactate to pyruvate reaction that they catalize were examined. Small but significant differences in the kinetic properties of the three isoenzymes were observed. The difference in the rate constants might affect the activity measurement of the individual isoenzyme as the initial velocity for the L-P reaction catalyzed will not be the same for an equal amount of enzyme. Equilibrium constants for the overall reaction in the presence and absence of pyruvate have been determined. On the basis of transition-state theory, the standard enthalpy and free-energy changes for formation of ternary activated complex were positive, while the standard entropy change was negative. Although the standard free-energy change was the same for activation by the three isoenzymes, the enthalpy and entropy changes for the LDH-3-catalyzed reaction were different from the respective values for others. A large positive value for the free-energy change and a negative value for the entropy change indicated unfavorable production of the activated complex (K infeq. sup╪ =1.89×10-16). The enzyme appears to stabilize and retain the activated complex until it dissociates into the products.
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  • 89
    ISSN: 1432-2048
    Keywords: Acetabularia ; Acicularia ; Chlorophyta ; Chloroplast genome ; Dasycladaceae ; Evolution ; Ribulose-1,5-bisphosphate carboxylase (conservatism)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In contrast to other plants the plastid genome of Acetabularia is larger in size and shows a high degree of variability. This study on the chloroplast-encoded large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase demonstrates that strongly conserved areas also exist in the plastid genome of the Dasycladaceae. Searching for differences in the amino acid sequence of the large subunit from Acetabularia mediterranea and Acicularia schenckii, proteolytic peptides which differ in their elution behaviour in reverse-phase high-performance liquid chromatography were sequenced. Only six amino acids were found to be exchanged in the large subunit from these two species. Since these two species diverged approx. 150 million years ago, these results imply that 0.84 amino-acid exchanges per 100 amino acids have occurred in 108 years, underlining the strong conservatism of the large subunit.
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  • 90
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    The journal of membrane biology 90 (1986), S. 67-87 
    ISSN: 1432-1424
    Keywords: cotransport ; kinetics ; reaction kinetic model ; dual isotherm ; random binding ; slip
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Solute uptake in many cells is characterized by a series of additive Michaelis-Menten functions. Several explanations for these kinetics have been advanced: unstirred layers, transport across more than one membrane, effects of solute concentration on membrane potential, numerous carrier systems. Although each of these explanations might suffice for individual cases, none provides a comprehensive basis for interpretation of the kinetics. The most common mechanism of solute absorption involves cotransport of solute with a driver ion. A model is developed in which solute and driver ion bind randomly to a membrane-bound carrier which provides a single transmembrane pathway for transport. The kinetic properties of the model are explored with particular reference to its capacity to generate additive Michaelian functions for initial rate measurements of isotopic solute influx. In accord with previous analysis of ordered binding models (Sanders, D., Hansen, U.-P., Gradmann, D., Slayman, C.L. (1984)J. Membrane Biol. 77:123), the conventional assumption that transmembrane transit rate-limits transport has not been applied. Random binding carriers can exhibit single or multiple Michaelian kinetics in response to changing substrate concentration. These kinetics include high affinity/low velocity and low affinity/high velocity phases (so-called “dual isotherms”) which are commonly observed in plant cells. Other combinations of the Michaelis parameters can result incis-(substrate) inhibition. Despite the generality of the random binding scheme and the complexity of the underlying rate equation, a number of predictive and testable features emerge. If external driver ion concentration is saturating, single Michaelian functions always result and increasing internal substrate concentration causes uncompetitive inhibition of transport. Numerical analysis of the model in conditions thought to resemble those in many experiments demonstrates that small relative differences in a few key component rate constants of the carrier reaction cycle are instrumental in generation of dual isotherms. The random binding model makes the important prediction that the contributions of the two isotherms show opposing dependence on external concentration of driver ion as this approaches saturation. In the one case in which this dependence has been examined experimentally, the model provides a good description of the data. Charge translocation characteristics of the carrier can be determined from steady-state kinetic data on the basis of the response of substrate flux to modulation of internal driver ion concentration. The application of the model to dual isotherm kinetics is discussed in relation to “slip” models of cotransport, in which the carrier is assumed to have the capability to transport substrate alone or with the driver ion. A method for distinguishing between the two models is suggested on the basis of measurement of charge/solute transport stoichiometry as a function of external driver ion concentration.
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    Journal of mathematical biology 21 (1985), S. 299-306 
    ISSN: 1432-1416
    Keywords: Evolution ; punctuated equilibria ; projection pursuit ; Brownian motion ; pattern recognition
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract The evolution of a species can be viewed as a trajectory in multidimensional space. What we perceive is only a low dimensional projection from the total dimensionality necessary to fully describe a species. Motivated by the phenomenon of punctuated equilibria, it is shown that there are projections of gradualistic evolution which will have a punctuated character. However, whether our eyes and minds would choose such a projection of the total phenotype is not resolved.
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    Journal of mathematical biology 25 (1987), S. 393-409 
    ISSN: 1432-1416
    Keywords: Evolution ; Evolutionary stable states ; Games theory ; Linear programming ; Convex polyhedra ; Linear complementarity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract The problem of finding an Evolutionary Stable Strategy (ESS) for an animal species is defined. It is shown how such strategies are a subset of the equilibrium solutions for a particular non-zero sum game. These equilibrium solutions are then shown to arise from the vertices of a particular convex polyhedron. A method of finding these equilibrium solutions through the vertices and then the ESS solutions is given. This is illustrated by a number of numerical examples taken from the literature. Finally an alternative approach based on solving a Linear Complementarity Problem is discussed.
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    Journal of mathematical biology 26 (1988), S. 347-357 
    ISSN: 1432-1416
    Keywords: Transposable elements ; Evolution ; Branching processes ; Population genetics ; Mobile genetic elements
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    Topics: Biology , Mathematics
    Notes: Abstract A discrete-time multitype branching process model is presented for the evolution of transposable elements in haploid populations. An individual is classified as type i if it possesses i copies of the TE, i⩾0. The general model incorporates copy-dependent selection and transposition, and recursion relations are derived for the distribution of the number of individuals of the various types. The asymptotic relative proportions of individuals of the different types is studied in the neutral case. The behavior of this equilibrium distribution is examined for various patterns of regulated transposition and deletion.
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  • 94
    ISSN: 1432-1424
    Keywords: sodium ; pyruvate ; transport ; proximal tubule ; kinetics ; kidney
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary The experiments reported in this paper aim at characterizing the carboxylic acid transport, the interactions of pyruvate and citrate with their transport sites and specificity. The study of these carriers was performed using isotopic solutes for the influx measurements in brush-border membrane vesicles under zerotrans conditions where the membrane potential was abolished with KCl preloading with valinomycin or equilibrium exchange conditions and Δψ=0. Under zerotrans condition and Δψ=0, the influence of pyruvate concentrations on its initial rates of transport revealed the existence of two families of pyruvate transport sites, one with a high affinity for pyruvate (K t =88 μm) and a low affinity for sodium (K t =57.7mm) (site I), the second one with a low affinity for pyruvate (K t =6.1mm) and a high affinity for sodium (K t =23.9mm) (site II). The coupling factor [Na]/[pyruvate] stoichiometry were determined at 0.25mm and 8mm pyruvate and estimated at 1.8 for site I, and 3 when the first and the second sites transport simultaneously. Under chemical equilibrium (Δψ≅0) single isotopic labeling, transport kinetics of pyruvate carrier systems have shown a double interaction of pyruvate with the transporter; the sodium/pyruvate stoichiometry also expressed according to a Hill plot representation wasn=1.7. The direct method of measuring Na+/pyruvate stoichiometry from double labeling kinetics and isotopic exchange, for a time course, gives an=1.67. Studies of transport specificity, indicate that the absence of inhibition of lactate transport by citrate and the existence of competitive inhibition of lactate and citrate transports by pyruvate leads to the conclusion that the low pyruvate affinity site can be attributed to the citrate carrier (tricarboxylate) and the high pyruvate affinity site to the lactate carrier (monocarboxylate).
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    The journal of membrane biology 108 (1989), S. 253-261 
    ISSN: 1432-1424
    Keywords: Chara ; Cl− ; cotransport ; reaction kinetic model ; pH ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary H+-coupled transport in plant and fungal cells is relatively insensitive to external pH (pH o ). H+-coupled Cl− transport at the plasma membrane ofChara corallina was studied to explore the phenomena responsible for this insensitivity. Raising pH o from a control value of 7.5 to 9.0 results in a modest (2.5-fold) decline inJ max and increase inK m . Further increase in pH o results in a selective increase inJ max, in accordance with predictions from a reaction kinetic model of the transport system (Sanders, D., Hansen, U.-P., 1981.J. Membrane Biol. 58:139–153). Increase in cytosolic Cl− concentration ([Cl−] c ) also results in a selective decrease inJ max at pH o =7.5. Quantitative kinetic modeling of the results is not possible if it is assumed that the sole effect of pH o isvia mass action on the binding of external H+ to a transport site. If, instead, the dependence of cytosolic pH (pH c ) on pH o (Smith, F.A., 1984,J. Exp. Bot. 35:1525–1536) is taken into account along with the dependence of Cl− influx on pH c (Sanders, D., 1980,J. Membrane Biol. 53:129–141), then the observed modest changes in Michaelis parameters can be accommodated by a reaction kinetic model. The quantitative parameters of the model yield respective pK a s of the internal and external H+-binding sites=7.85 and 7.2, respective dissociation constants of the internal and external Cl−-binding sites=160 and 40 μm, and an additional, kinetically transparent, H+-binding site with a pK a 〉8.0. The quantitative model independently predicts the response ofJ max andK m to acidic conditions. The results are discussed in terms of the general physiological requirement that fluxes through H+-coupled transport systems are relatively insensitive to environmental variation in pH o . It is proposed that (i) the weak (but finite) dependence of pH c on pH o , coupled with (ii) the strong dependence of H+-coupled transport on pH c are instrumental in endowing H+-coupled transport systems with a relative insensitivity to variation in pH o . This hypothesis might also explain why pH c in plants and fungi is not acutely controlled with respect to variation of pH o .
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  • 96
    Electronic Resource
    Electronic Resource
    Springer
    The journal of membrane biology 110 (1989), S. 57-65 
    ISSN: 1432-1424
    Keywords: fluorescence ; water transport ; vasopressin ; kidney collecting tubule ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Water transport across the mammalian collecting tubule is regulated by vasopressin-dependent water channel insertion into and retrieval from the cell apical membrane. The time course of osmotic water permeability (P f ) following addition and removal of vasopressin (VP) and 8-Br-cAMP was measured continuously by quantitative fluorescence microscopy using an impermeant fluorophore perfused in the lumen. Cortical collecting tubules were subjected to a 120 mOsm bath-to-lumen osmotic gradient at 37°C with 10–15 nl/min lumen perfusion and 10–20 ml/min bath exchange rate. With addition of VP (250 μU/ml), there was a 23±3 sec (sem,n=16) lag in whichP f did not change, followed by a rise inP f (initial rate 1.4±0.2×10−4 cm/sec2) to a maximum of 265±10×10−4 cm/sec. With addition of 8-Br-cAMP (0.01–1mm) there was an 11±2 sec lag. For [8-Br-cAMP]=0.01, 0.1 and 1mm, the initial rate ofP f increase following the lag was (units 10−4 cm/sec2): 1.1±0.1, 1.2±0.1 and 1.7±0.3. MaximumP f was (units 10−4 cm/sec): 64±4, 199±9 and 285±11. With removal of VP,P f decreased to baseline (12×10−4 cm/sec) with aT 1/2 of 18 min; removal of 0.1 and 1mm 8-Br-cAMP gaveT 1/2 of 4 and 8.5 min. These results demonstrate (i) a brief lag in theP f response, longer for stimulation by VP than by 8-Br-cAMP, representing the transient build-up of biochemical intermediates proximal to the water channel insertion step, (ii) similar initialdP f /dt (water channel insertion) over a wide range of [8-Br-cAMP] and steady-stateP f values, and (iii) more rapidP f decrease with removal of 8-Br-cAMP than with VP. These pre-steady-state results define the detailed kinetics of the turn-on and turn-off of tubuleP f and provide kinetic evidence that the rate-limiting step for turn-on ofP f is not the step at which VP regulates steady-stateP f . If water channel insertion is assumed to be the rate-limiting step in the turn-on ofP f , these results raise the possibility that water channels must be activated following insertion into the apical membrane.
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  • 97
    ISSN: 1432-1424
    Keywords: charybdotoxin ; erythrocytes ; iodination ; kinetics ; peptides ; potassium channels ; scorpions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary Two charybdotoxin peptides were purified from venom of the Israeli scorpion,Leiurus quinquestriatus hebraeus. Microsequencing of the most abundant toxin, ChTX-Lq1, revealed identity with the 37-residue peptide previously sequenced by Gimenez-Gallego et al. [Gimenez-Gallego, G., et al.,Proc. Natl. Acad. Sci. USA 85:3329–3333 (1988)]. Sequence data on the minor peptide, ChTX-Lq2, showed substantial homology to ChTX-Lq1 with differences observed at eight positions. These two charybdotoxin sequences, along with that of noxiustoxin, define a distinct family of scorpion peptide toxins with activity against K+ channels. Both charybdotoxin homologs inhibited Ca2+-dependent K+ efflux from human erythrocytes with similar potency,K 0.5∼-40nm. In planar bilayer assays of single K(Ca) channels from rat muscle, ChTX-Lq1 and ChTX-Lq2 blocked with intrinsicK d's of 1.3 and 43nm, respectively, in the presence of 50mm external KCl. A new application of dwell-time histogram analysis of single-channel blocking events was used to characterize the kinetic homogeneity of toxin samples and the blocking kinetics of ChTX derivatives. The lower blocking affinity of ChTX-Lq2 was the combined result of a faster dissociation rate and a slower association rate as compared to ChTX-Lq1. The blocking activity of two mono-iodinated derivatives of ChTX-Lq1 was also analyzed. Blocked dwell-time histograms of the iodinated peptides were characterized by predominately brief (0.2–2 sec) blocking events in comparison to the native toxin (20 sec). Histogram analysis revealed that mono-iodination of ChTX-Lq1 impairs blocking activity by adverse effects on both dissociation and association rate constants. Frequency density histograms of single channel blocking events provide a sensitive assay of toxin purity suitable for quantitating structure-activity relationships of charybdotoxin derivatives.
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  • 98
    Electronic Resource
    Electronic Resource
    Springer
    The journal of membrane biology 102 (1988), S. 225-234 
    ISSN: 1432-1424
    Keywords: erythrocytes ; valinomycin ; protonophore ; CCCP ; permeability ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary A transport model for translocation of the protonophore CCCP across the red cell membrane has been established and cellular CCCP binding parameters have been determined. The time course of the CCCP redistribution across the red cell membrane, following a jump in membrane potential induced by valinomycin addition, has been characterized by fitting values of preequilibrium extracellular pHvs. time to the transport model. It is demonstrated, that even in the presence of valinomycin, the CCCP-anion is “well behaved,” in that the translocation can be described by simple electrodiffusion. The translocation kinetics conform to an Eyring transport model, with a single activation energy barrier, contrary to translocation across lipid bilayers, that is reported to follow a transport model with a plateau in the activation energy barrier. The CCCP anion permeability across the red cell membrane has been calculated to be close to 2.0×10−4 cm/sec at 37°C with small variations between donors. Thus the permeability of CCCP in the human red cell membrane deviates from that found in black lipid membranes, in which the permeability is found to be a factor of 10 higher.
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  • 99
    Electronic Resource
    Electronic Resource
    Springer
    Journal of classification 2 (1985), S. 29-39 
    ISSN: 1432-1343
    Keywords: Taxonomy ; Evolution ; Judgment ; Species ; Genus
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mathematics
    Notes: Abstract Relative frequency of genera as a function of number of species per genus is plotted for six eighteenth-century classifications: Linnaeus' classifications of animals, plants, minerals, and diseases, and Sauvages' classifications of plants and diseases. The distributions for animals and plants form positively skewed hollow curves similar but not identical to those found in modern biological classifications and predicted by mathematical models of evolution. The distributions for minerals and diseases, however, are more nearly symmetric and convex. The difference between the eighteenth-century and modern classifications of animals and plants probably reflects psychological properties of the taxonomists' judgments; but the difference between the classifications of animals and plants and those of minerals and diseases reflects evolutionary properties of the materials classified, since all six classifications were constructed by the same taxonomists using the same methods. Consequently, the observable effects of evolution are strong enough to be detected in classifications constructed before the acceptance of evolutionary theory; and traditional classifications can contain substantial scientific information despite their reliance on incompletely understood processes of judgment.
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  • 100
    Electronic Resource
    Electronic Resource
    Springer
    Theoretical and applied genetics 69 (1985), S. 463-474 
    ISSN: 1432-2242
    Keywords: Multiline varieties ; Disease control ; “Dirty crop” approach ; Evolution ; Pathogens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A general model for the evolution of pathogen populations on mixtures or multilines is developed. This model is used to extend previous analyses of the effects of the widespread cultivation of multilines on the evolution of virulence in obligate parasites to mixtures of lines carrying different numbers of resistance genes. It is concluded that the composition of an equilibrium pathogen population growing on a multiline may vary within wide limits and the prinicipal determinant of its composition is the number of components in the multiline and the resistance genes they carry. Other factors of importance are (i) the relative contribution made by each host class (with different numbers of resistance genes) to the pathogen spore pool each generation; (ii) the levels of ‘stabilizing selection’ against unnecessary virulence genes; and (iii) the way in which unnecessary genes for virulence combine to reduce pathogen fitness. Conditions for the fixation of avirulent biotypes in the pathogen population and the evolution of a pathogen superrace are given for multilines of various compositions.
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