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  • 1
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    Springer Nature | Springer
    Publication Date: 2024-04-05
    Description: This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications. The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes. The book’s respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory. Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.
    Keywords: Microbial Genetics and Genomics ; Evolutionary Biology ; Genetics and Population Dynamics ; Microbial Ecology ; Human Genetics ; Genetics and Genomics ; Comparative genomics ; Metagenomics ; Microbial Population Analysis ; Pangenome Profile ; Supra-Genome Analysis ; Adaptive Evolution ; Computational Tools ; Bioinformatic Genomics ; Core Dispensable Genome ; Selection, Recombination, Composition ; Acquired Resistance ; Bacterial Species Concept ; Genomic Diversity ; Bacterial Ecology, Microevolution ; Open Access ; Pan-metagenomics ; Pan-microbiomics ; Pan-epigenome ; Gene Transfer ; Pan-phenomes ; Microbiology (non-medical) ; Genetics (non-medical) ; Evolution ; Applied mathematics ; Ecological science, the Biosphere ; Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSG Microbiology (non-medical) ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAJ Evolution ; thema EDItEUR::P Mathematics and Science::PB Mathematics::PBW Applied mathematics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere ; thema EDItEUR::M Medicine and Nursing::MF Pre-clinical medicine: basic sciences::MFN Medical genetics ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (non-medical)
    Language: English
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  • 2
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    Oxford University Press
    Publication Date: 2024-04-05
    Description: This collection of essays explores the metaphysical thesis that the living world is not ontologically made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organized as an interdependent hierarchy of processes, which are stabilized and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be looked for in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritize processes over things, and it suggests that the central explanandum of biology is not change but rather stability—or, more precisely, stability attained through constant change. This multicontributor volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies and employ a process perspective to cast new light on a number of traditional philosophical problems such as identity, persistence, and individuality.
    Keywords: explanation ; identity ; individuality ; metaphysics of science ; organism ; persistence ; philosophy of biology ; process ontology ; substance ontology ; symbiosis ; Evolution ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences
    Language: English
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  • 3
    ISSN: 1570-7458
    Keywords: Rhopalosiphum maidis ; Zea mays ; induced plant volatiles ; repellence ; (E)-β-farnesene ; alarm pheromone ; plant insect interactions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract When maize plants, Zea mays L., are mechanically damaged and the damaged sites are treated with caterpillar regurgitant, the plants will release a specific blend of volatiles. It is known that these volatiles can be attractive to natural enemies of herbivores. We hypothesise that the plant volatiles constitute part of the induced plant defence and that herbivores will be affected by the odours as well. In laboratory and semi-field studies this hypothesis was tested for the aphid Rhopalosiphum maidis (Fitch) (Rhynchota, Sternorrhyncha, Aphididae). In a Y-tube olfactometer significantly more aphids chose the odour of healthy, undamaged maize seedlings when tested against clean air or plants treated with regurgitant. Clean air was chosen more often when tested next to the odour of treated plants. This apparently repellent effect of the odour of treated plants was significant for winged aphids, but not for the wingless aphids. In field experiments aphids were released in the centre of circles of eight potted maize plants. Four plants in each circle were damaged and treated with caterpillar regurgitant while the other plants were left unharmed. At different intervals after aphid release, the number of aphids was counted on each plant. Significantly fewer winged and wingless aphids were found back on treated plants than on healthy plants. We suggest that herbivores may be repelled by the odours because they could indicate that: 1) the plant has initiated the production of toxic compounds; 2) potential competitors are present on the plant; 3) the plant is attractive to parasitoids and predators. Aphids may be particularly sensitive to induced maize volatiles because one of the major compounds emitted by the plant is (E)-β-farnesene, which is a common alarm pheromone for aphids. Collections and analyses of the odours emitted by crushed R. maidis confirmed that it too emits (E)-β-farnesene when stressed. The results are discussed in context of plant defence strategies and their possible exploitation for the control of pest insects.
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  • 4
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    Springer
    Entomologia experimentalis et applicata 89 (1998), S. 119-124 
    ISSN: 1570-7458
    Keywords: maize ; Zea mays ; Helicoverpa zea ; antibiosis ; flavonoids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The corn earworm (Helicoverpa zea Boddie) is an important pest of corn (Zea mays L.), and its larvae sometimes cause severe ear damage to hybrids grown in the southeastern United States. The antibiotic compound isoorientin is present in silks of some corn inbreds at a concentration that is harmful to corn earworm larvae. The inbred T218, which produces biologically active levels of this compound (〈2.0% dry weight), was evaluated in hybrid combination with two other non-isoorientin producing inbreds to determine the mode of isoorientin inheritance in corn silks. Silk masses from individual ears of each parent, the F1, F2, first backcrosses, F3 families and selfed BC1 families were evaluated in 1994 and 1995 for isoorientin concentration. Reversed-phase high performance liquid chromatography (HPLC) was used to make chemical determinations. Segregation ratios in the F2, first backcross to T218, F3 families and selfed BC1 families were tested. The tests were conclusive in the identification of a single recessive gene controlling high isoorientin concentration in the silks of inbred T218. Some evidence for modifiers exists, in that there was a statistically nonsignificant trend for more plants than expected to occur in the low isoorientin concentration classes. Development of inbreds with a high concentration of the simply inherited isoorientin in their silks will add to the arsenal of compounds available in corn silks to combat damage to corn by corn earworm larvae.
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  • 5
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    Entomologia experimentalis et applicata 90 (1999), S. 313-322 
    ISSN: 1570-7458
    Keywords: Coleoptera ; Coccinellidae ; Coleomegilla maculata ; Euphorbiaceae ; Acalypha ostryaefolia ; Zea mays ; dispersal ; predator
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The polyphagous predator, Coleomegilla maculata (DeGeer) (Coleoptera: Coccinellidae), commonly oviposits on the native weed, Acalypha ostryaefolia Riddell (Euphorbiaceae), in and around Kentucky sweet corn fields. Cannibalism of eggs by C. maculata adults and larvae is drastically lower on A. ostryaefolia than on nearby sweet corn plants. We examined ovipositional preference of C. maculata for A. ostryaefolia plants or sweet corn plants, dispersal of larvae from A. ostryaefolia plants, capability for dispersal of larvae across bare soil (e.g., to nearby plants), ability of larvae to climb from ground level up A. ostryaefolia plants or sweet corn plants, and effect of A. ostryaefolia borders adjacent to sweet corn plots on C. maculata population density in sweet corn. The ovipositional preference study revealed that C. maculata laid more eggs on A. ostryaefolia than on corn. First-instar C. maculata that hatched from egg clusters on A. ostryaefolia dispersed predominantly by falling, rather than crawling, to the ground. Glandular trichomes on A. ostryaefolia petioles and stems apparently inhibited intraplant movement of first instars, resulting in those larvae falling directly from leaves to the ground. Some first instars were capable of moving at least 8 m across bare soil in 24 h. From the ground, significantly more first instars climbed sweet corn plants than climbed A. ostryaefolia plants. Significantly more larvae were present in sweet corn plots bordered by A. ostryaefolia plants than in sweet corn plots without an A. ostryaefolia border. These findings show that physical attributes of companion plants can significantly influence natural enemy populations on crop plants by affecting interplant dispersal of natural enemies.
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  • 6
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    Entomologia experimentalis et applicata 71 (1994), S. 177-180 
    ISSN: 1570-7458
    Keywords: aflatoxin ; Carophilus ; Zea mays ; corn ; plant resistance ; Coleoptera ; Nitidulidae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
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  • 7
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    Entomologia experimentalis et applicata 72 (1994), S. 17-23 
    ISSN: 1570-7458
    Keywords: plant varietal resistance ; armyworm ; Spodoptera exempta ; leaf extracts ; Zea mays ; feeding deterrent ; toxicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Maize (Zea mays L.) leaf tissue of cv Bastille and cv Michoacan 12 was extracted with n-hexane. The extracts were bioassayed against 5th instar African armyworm,Spodoptera exempta (Walker)(Lepidoptera: Noctuidae), by feeding the larvae on agar based media or sucrose impregnated glass fibre discs. The hexane extract of the ‘resistant’ cv Bastille exhibited feeding deterrency and toxicity which were not shown by the ‘susceptible’ cv Michoacan 12. The hexane extract of cv Bastille was adsorbed onto silica gel, the solution filtered off and the adsorbed component taken up into ethyl acetate. Bioassay of these fractions indicated that the toxic and deterrent action was retained in the ethyl acetate fraction. Preparative thin layer chromatography of the ethyl acetate fraction isolated two biologically active constituents. These were both growth inhibitors and lethal by ingestion to the 5th instar African armyworm. Implications for resistance in maize varieties to insect pests are discussed.
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  • 8
    ISSN: 1572-8358
    Keywords: Animal cognition ; Evolution ; Representation ; Computation ; Significance ; Phenomenology ; Autonomy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A distinction is made between two definitions of animal cognition: the one most frequently employed in cognitive sciences considers cognition as extracting and processing information; a more phenomenologically inspired model considers it as attributing to a form of the outside world a significance, linked to the state of the animal. The respective fields of validity of these two models are discussed along with the limitations they entail, and the questions they pose to evolutionary biologists are emphasized. This is followed by a presentation of a general overview of what might be the study of the evolution of knowledge in animals.
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  • 9
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    Entomologia experimentalis et applicata 77 (1995), S. 315-321 
    ISSN: 1570-7458
    Keywords: Insecta ; Helicoverpa zea ; Zea mays ; resistance inheritance ; joint scaling test ; additive-dominance model
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The corn earworm,Helicoverpa zea (Boddie), is a perennial economic pest of field crops in the United States. Maize,Zea mays L., is the major host crop promoting the build-up of devastating corn earworm populations that limit full production of cotton, soybean, peanut, and grain sorghum. Resistance to the corn earworm in maize and in particular sweet maize, would provide an environmentally safe, economical method of control for this pest insect. Antibiotic effects of corn silks on this insect are: small larvae, extended developmental period, and reduced fecundity. Silks from individual maize plants of resistant and susceptible lines and progeny in six generations consisting of parents (P1, P2), F1, F2, and backcrosses BC1.1 (F1 × P1) and BC1.2 (F1 × P2) from each of four crosses were used to determine the genetic basis of the antibiotic resistance of silks to the corn earworm. In the cross of Zapalote Chico × PI340856, genes controlling resistance in the silks to the corn earworm larvae are dominant in PI340856 to those in Zapalote Chico. The cross of Zapalote Chico × GT114 involves parents differing in degree of resistance, and possibly differing for the genetic mechanism by which the resistance is inherited. The inheritance of resistance may involve non-additive (dominance and epistasis) genetic variance. A digenic 6-parameter model indicated (1) the resistance in this cross is controlled by more than one pair of genes and (2) some or all of the genes interact to cause non-allelic interaction. Thus, the resistance in this cross may be controlled by both dominant and recessive genes. The resistance of Zapalote Chico × CI64, an intermediate inbred, is influenced by additive gene effects. The digenic model adequately predicts all generation means of the cross of GT3 × PI340856 except for the F1. Thus, it appears that the additive-dominance model is not satisfactory for this cross involving susceptible and resistant parents. Generation mean analysis indicates that resistance to silk-feeding by corn earworm larvae is under genetic control, but gene action differs from one type of cross to another.
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  • 10
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    Monatshefte für Chemie 125 (1994), S. 1033-1039 
    ISSN: 1434-4475
    Keywords: Prebiotic peptide formation ; Evolution ; Clay catalysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Description / Table of Contents: Zusammenfassung Die Fähigkeit von Tonmineralien der Montmorillonitklasse zur Katalyse von Peptidbildungsreaktionen aus Aminosäuren in wäßriger Lösung wurde am Beispiel von Glyzin und Kupfer sowie Kalzium und Morillonit untersucht. Experimente mit Verdampfungszyklen haben gezeigt, daß kleinere Mengen von Di- und Tripeptiden aus der Aminosäure gebildet werden. Die weitere Polymerisation von Dipeptiden hingegen scheint wesentlich leichter in diesem Reaktionssystem zu verlaufen als der Anfangsschritt der Bildung des Dipeptides. Eine mögliche Rolle von Tonmineralien in der präbiotischen Peptidevolution kann daher in der Verlängerung von Peptidketten gesehen werden. Kupferionen in der Tonmatrix zeigen keinerlei Vorteile gegenüber den üblichen Kalziumionen, die in natürlichem Montmorillonit vorkommen.
    Notes: Summary The ability of montmorillonite clay minerals for catalyzing peptide formation from amino acids in aqueous solution has been investigated using glycine and Cu2+ and Ca2+ containing montmorillonites as reaction systems. Evaporation cycle experiments showed that minor amounts of di- and tripeptide are formed from the amino acid. Further polymerization of dipeptide, however, seems to be more favoured by this reaction system than the initial step of dipeptide formation, and a possible role of clays in prebiotic peptide evolution could be seen therefore in the prolongation of peptide chains. Cu2+ ions in the clay matrix did not show any advantage over the usual Ca2+ ions embedded in natural montmorillonite.
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  • 11
    ISSN: 1433-4909
    Keywords: Key words Thermococcus ; Pyrococcus ; Thermophilic ; Phosphofructokinase ; Evolution ; ADP ; Glycolysis ; ATP
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The ADP-dependent phosphofructokinase (PFK) from Thermococcus zilligii has been purified 950 fold; it had a specific activity of 190 U mg−1. The enzyme required Mg2+ ions for optimal activity and was specific for ADP. The forward reaction kinetics were hyperbolic for both cosubstrates (pH optimum of 6.4), and the apparent K m values for ADP and fructose-6-phosphate were 0.6 mM (apparent V max of 243 U mg−1) and 1.47 mM (apparent V max of 197 U mg−1), respectively. Significantly, the enzyme is indicated to be nonallosteric but was slightly activated by some monovalent cations including Na+ and K+. The protein had a subunit size of 42.2 kDa and an estimated native molecular weight of 66 kDa (gel filtration). Maximal reaction rates for the reverse reaction were attained at pH 7.5–8.0, and the apparent K m values for fructose-1,6-bisphosphate and AMP were 0.56 mM (apparent V max of 2.9 U mg−1) and 12.5 mM, respectively. The biochemical characteristics of this unique ADP-dependent enzymatic activity are compared to ATP and pyrophosphate-dependent phosphofructokinases.
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  • 12
    ISSN: 1433-4909
    Keywords: Key wordsNatronomonas pharaonis ; Natronobacteria ; Archaea ; Serine protease ; Chymotrypsinogen ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A protease of a molecular mass of approximately 30 kDa was isolated and purified from the haloalkaliphilic archaeon Natronomonas (formerly Natronobacterium) pharaonis. The enzyme hydrolyzed synthetic peptides, preferentially at the carboxyl terminus of phenylalanine or leucine, as well as large proteins. Hydrolysis occurred over the range of pH from 6 to 12, with an optimum at pH 10. The temperature optimum was 61°C. The enzyme was nearly equally active over the range of salt concentration from 0.5 to 4 M (NaCl or KCl). A strong cross-reaction with a polyclonal antiserum against human chymotrypsin was observed. Enzymatic activity was inhibited by typical serine protease inhibitors. There was significant homology between N-terminal and internal sequences from autolytic fragments and the sequence of bovine chymotrypsinogen B; the overall amino acid composition was similar to that of vertebrate chymotrypsinogens. Evidence for a zymogen-like processing of the protease was obtained. Cell extracts from other halobacteria exhibited similar proteolytic activity and immunoreactivity. The data suggested a widespread distribution of a chymotrypsinogen B-like protease among halo- and haloalkaliphilic Archaea.
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  • 13
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    Entomologia experimentalis et applicata 54 (1990), S. 29-36 
    ISSN: 1570-7458
    Keywords: Zea mays ; corn ; host plant resistance ; phenolics ; flavonoids ; hydroxamic acids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Description / Table of Contents: Résumé Les réactions de larves et adultes du nitidulidé C. hemipterus (L.), vecteur de champignons produisant la mycotoxine, aux composés phénoliques caractéristiques, aux flavonoïdes et aux acides hydroxamiques, métabolites secondaires qui provoquent la résistance du maïs (Zea mays L.) ont été examinées au cours d'expériences avec et sans choix. L'alimentation des adultes et des larves est généralement réduite par les acides coumarique et férulique et par la 6-méthoxy-2-benzoxazolinone dans des expériences sans choix; les insectes évitent généralement les aliments qui contiennent ces produits. Quoi qu'il en soit, les larves préfèrent consommer d'autres aliments contenant les autres phénoliques ou flavonoïdes examinés. Les adultes sont plus inconstants dans leur choix alimentaires, mais préfèrent souvent des aliments contenant de la quercetine. Ainsi, des programmes de sélection orientés contre les principaux ravageurs comme Heliothis zea (Boddie) ou Ostrinia nubilalis (Hübner), impliquant la sélection de plantes à teneur élevée en acides phénolique ou hydroxamique, augmentant probablement aussi la résistance aux nitidulidés.
    Notes: Abstract Selected secondary metabolites produced by maize (Zea mays L.) were tested for effects on larvae and adults of the dried-fruit beetle [Carpophilus hemipterus (L.)] in no-choice and choice assays. Feeding by adults and larvae was significantly reduced by ferulic acid and 6-methoxy-2-benzoxazolinone (MBOA) in no-choice assays. In choice assays, larvae and adults generally preferred diets with trans-cinnamic acid, quercetin, rutin, and thymol, but were repelled by diets with either ferulic acid or MBOA.
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  • 14
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    Journal for general philosophy of science 21 (1990), S. 309-328 
    ISSN: 1572-8587
    Keywords: Evolution ; evolutionäre Erkenntnistheorie ; Organismus ; Autonomie ; Abbildungskritik
    Source: Springer Online Journal Archives 1860-2000
    Topics: Philosophy , Nature of Science, Research, Systems of Higher Education, Museum Science
    Notes: Summary The concept of evolutionary epistemology has been critically discussed by philosophers who have mainly pointed to unacceptable philosophical tenets (cf. Vittorio Hösle, this Journal, Vol. 19 (1988), pp. 348–377). However, as most philosophers are extremely reluctant to critically treat the biological theories on which the ideas of evolutionary epistemology are based, the invalid concepts of adaption escaped their critical scrutiny. Therefore the influence of preconceived biological theories on the biological basis of evolutionary epistemology and the distorting consequences on the philosophical level could not be elaborated. The following context sketches a new view of organismic reasoning and its impact on evolutionary aspects of epistemology. The basic theorem of adaptation is shown to be unacceptable and invalid if organisms are conceived as autonomous entities which can only evolve according to their specific internal organismic properties.
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  • 15
    ISSN: 1432-1211
    Keywords: Key words Antigen processing ; Evolution ; Cell surface molecules ; Mhc ; Class I antigens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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  • 16
    ISSN: 1432-1211
    Keywords: Key words NRAMP ; Fish ; Carp ; Evolution ; Expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The mouse Lsh/Ity/Bcg locus regulates natural resistance to intracellular pathogens, and the Nramp1 gene was isolated as its candidate. Nramp is part of a small family of at least two genes, Nramp1 and Nramp2. In the present study, a full-length cDNA for carp NRAMP has been isolated and characterized. Nucleotide and predicted amino acid sequence analysis indicate that the carp NRAMP encodes a 548 amino acid membrane protein with 12 putative transmembrane domains, two N-linked glycosylation sites, and an evolutionarily conserved consensus transport motif. The peptide sequence identity among carp and human NRAMP2 is 78%, and 65% with human NRAMP1. Reverse transcription-polymerase chain reaction revealed that carp NRAMP is ubiquitously expressed. Phylogenetic analysis, using neigbor-joining, showed that the carp NRAMP protein clustered together with mammalian NRAMP2 proteins.
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  • 17
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    Immunogenetics 50 (1999), S. 301-308 
    ISSN: 1432-1211
    Keywords: Key words T-cell receptors ; Variable region genes ; Evolution ; Phylogeny ; Diversity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of γδ T-cells in their peripheral T-cell populations. The "γδ low" group of species includes humans and mice, in which γδ T-cells constitute very limited portion of the T-cell population. The "γδ high" group includes sheep, cattle, rabbits, and chicken, in which γδ T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the γδ low species have a high degree of diversity of TCR-V genes, while γδ high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes.
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  • 18
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    Immunogenetics 50 (1999), S. 329-335 
    ISSN: 1432-1211
    Keywords: Key words Marsupials ; Light chains ; Variable regions ; IGK ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  A full-length and several partial cDNAs encoding IGK light chains from the marsupial South American opossum, Monodelphis domestica, were isolated and characterized. Using these clones as a starting point, the expressed IGKV repertoire was sampled by anchored polymerase chain reaction using an IGKC-specific primer. Based on nucleotide sequences of twenty unique, expressed IGKV-J combinations, there are at least four IGKV families and two J segments. Southern blot analysis revealed each IGK-V family contains multiple gene segments totaling at least thirty-five IGKV in the opossum genome. No evidence for particular, recurrent IGKV-J combinations in the opossum IGK repertoire was seen, rather the V-J combinations appeared random and diverse. Each of the four IGKV families appear more closely related to V segments from placental mammals than to each other, suggesting the duplication of the IGKV families prior to the separation of marsupials and placental mammals more than one-hundred-million years ago. Overall, the complexity of opossum light chain V segments appears greater than that found in the heavy chain, and light chains are likely to contribute significantly to Ig diversity in this species.With this report, the homologues encoding all three classes of eutherian Ig chains, IGH, IGL, and IGK, have been described in a non-placental mammal.
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  • 19
    ISSN: 1432-1211
    Keywords: Key words MHC ; MIC ; Nonhuman primates ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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  • 20
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    Immunogenetics 49 (1999), S. 295-302 
    ISSN: 1432-1211
    Keywords: Key words Major histocompatibility complex ; Class II ; Antigen processing ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract  Proper peptide presentation by major histocompatibility complex (MHC)-encoded class II antigens is dependent on the products of the MHC DM loci. We identified the rabbit orthologues (RLA-DMA and -DMB) of human HLA-DMA and -DMB and found that they have 76.9% and 78.8% identity with HLA-DMA and -DMB, respectively. Like classical class II MHC genes, RLA-DM genes are more closely related to human HLA-DM genes than to mouse H2-DM. Among the DM family, there is a high degree of variability at the amino terminus of the DMa chains, and length variability in the cytoplasmic tails of both DMα and DMβ. The rabbit DM genes are coexpressed with class II genes in lymphoid tissues, as are the DM genes of other mammals. The RLA-DM locus maps to the class II region of the rabbit MHC, and is flanked by the DP and DOB loci. Despite having some similarities to class II genes of bony fishes, the DM family represents a separate branch of the MHC class II family.
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  • 21
    ISSN: 1432-1211
    Keywords: Key words Mhc ; Class II A ; Cichlid ; Fish ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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  • 22
    ISSN: 1432-1211
    Keywords: Key words Beta2-microglobulin ; Evolution ; Sturgeon ; cDNA ; Genomic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
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  • 23
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    Mycorrhiza 4 (1993), S. 1-4 
    ISSN: 1432-1890
    Keywords: Tropics ; Mycotrophy ; Spore dispersal ; Community composition ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract This article introduces reports concerning the occurrence of mycorrhizae on epiphytes in Costa Rica, Ethiopia, Venezuela, Malaysia, and Mexico. Association of vesicular-arbuscular mycorrhizal fungi with the roots of epiphytes is not well known. Vesicular-arbuscular mycorrhizal fungi (VAM) do occur in the canopy, but are uncommon except in certain sites and host taxa. Occurrence of VAM on epiphytes may be constrained by mineral nutrient availability and spatial heterogeneity in the canopy. Nevertheless, epiphytes present unique opportunities to study influences of mycorrhizae on vascular plant community composition and on the evolution of mycorrhizal associations.
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  • 24
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    Mycorrhiza 5 (1994), S. 119-124 
    ISSN: 1432-1890
    Keywords: Key words Glomus mosseae ; Manganese uptake ; Root exudation ; Manganese reduction ; Mycorrhizal effect ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The influence of rhizosphere microorganisms and vesicular-arbuscular (VA) mycorrhiza on manganese (Mn) uptake in maize (Zea mays L. cv. Tau) plants was studied in pot experiments under controlled environmental conditions. The plants were grown for 7 weeks in sterilized calcareous soil in pots having separate compartments for growth of roots and of VA mycorrhizal fungal hyphae. The soil was left either uninoculated (control) or prior to planting was inoculated with rhizosphere microorganisms only (MO-VA) or with rhizosphere microorganisms together with a VA mycorrhizal fungus [Glomus mosseae (Nicol and Gerd.) Gerdemann and Trappe] (MO+VA). Mycorrhiza treatment did not affect shoot dry weight, but root dry weight was slightly inhibited in the MO+VA and MO-VA treatments compared with the uninoculated control. Concentrations of Mn in shoots decreased in the order MO-VA〉MO+VA〉control. In the rhizosphere soil, the total microbial population was higher in mycorrhizal (MO+VA) than nonmycorrhizal (MO-VA) treatments, but the proportion of Mn-reducing microbial populations was fivefold higher in the nonmycorrhizal treatment, suggesting substantial qualitative changes in rhizosphere microbial populations upon root infection with the mycorrhizal fungi. The most important microbial group taking part in the reduction of Mn was fluorescent Pseudomonas. Mycorrhizal treatment decreased not only the number of Mn reducers but also the release of Mn-solubilizing root exudates, which were collected by percolation from maize plants cultivated in plastic tubes filled with gravel quartz sand. Compared with mycorrhizal plants, the root exudates of nonmycorrhizal plants had two fold higher capacity for reduction of Mn. Therefore, changes in both rhizosphere microbial population and root exudation are probably responsible for the lower acquisition of Mn in mycorrhizal plants.
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  • 25
    ISSN: 1432-1890
    Keywords: Glomus mosseae ; Zea mays ; Mineral uptake ; Root exudation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Maize (Zea mays L. cv. Alize) plants were grown in a calcareous soil in pots divided by 30-μm nylon nets into three compartments, the central one for root growth and the outer ones for hyphal growth. Sterle soil was inoculated with either (1) rhizosphere microorganisms other than vesicular-arbuscular mycorrhizal (VAM) fungi, (2) rhizosphere microorganisms together with a VAM fungus [Glomus mosseae (Nicol. and Gerd.) Gerdemann and Trappel], or (3) with a gamma-irradiated inoculum as control. Plants were grown under controlled-climate conditions and harvested after 3 or 6 weeks. VAM plants had higher shoot∶root ratios than non-VAM plants. After 6 weeks, the concentrations of P, Zn and Cu in roots and shoots had significantly increased with VAM colonization, whereas Mn concentrations had significantly decreased. Root exudates were collected on agar sheets placed on the interface between root and hyphal compartments. Six-week-old VAM and non-VAM plants had similar root exudate compositions of 72–73% reducing sugars, 17–18% phenolics, 7% organic acids and 3% amino acids. In another experiment in which root exudates were collected on agar sheets with or without antibiotics, the amounts of amino acids and carbohydrates recovered were similar in VAM and non-VAM plants. However, threeto sixfold higher amounts of carbohydrates, amino acids and phenolics were recovered when antibiotics were added to the agar sheets. Thus, the high microbial activity in the rhizosphere and on the rhizoplane limits the exudates recovered from roots.
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  • 26
    ISSN: 1432-1890
    Keywords: Key words Glomus mosseae ; Zea mays ; Mineral uptake ; Root exudation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  Maize (Zea mays L. cv. Alize) plants were grown in a calcareous soil in pots divided by 30-μm nylon nets into three compartments, the central one for root growth and the outer ones for hyphal growth. Sterile soil was inoculated with either (1) rhizosphere microorganisms other than vesicular-arbuscular mycorrhizal (VAM) fungi, (2) rhizosphere microorganisms together with a VAM fungus [Glomus mosseae (Nicol. and Gerd.) Gerdemann and Trappel], or (3) with a gamma-irradiated inoculum as control. Plants were grown under controlled-climate conditions and harvested after 3 or 6 weeks. VAM plants had higher shoot : root ratios than non-VAM plants. After 6 weeks, the concentrations of P, Zn and Cu in roots and shoots had significantly increased with VAM colonization, whereas Mn concentrations had significantly decreased. Root exudates were collected on agar sheets placed on the interface between root and hyphal compartments. Six-week-old VAM and non-VAM plants had similar root exudate compositions of 72–73% reducing sugars, 17–18% phenolics, 7% organic acids and 3% amino acids. In another experiment in which root exudates were collected on agar sheets with or without antibiotics, the amounts of amino acids and carbohydrates recovered were similar in VAM and non-VAM plants. However, three- to sixfold higher amounts of carbohydrates, amino acids and phenolics were recovered when antibiotics were added to the agar sheets. Thus, the high microbial activity in the rhizosphere and on the rhizoplane limits the exudates recovered from roots.
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  • 27
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    Biology and fertility of soils 18 (1994), S. 228-230 
    ISSN: 1432-0789
    Keywords: Fine root ; Root litter ; Biofertiliser ; Leucaena leucocephala ; Trigonella foenum-graecum ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The efficacy ofLeucaena leucocephala root litter as a natural biological fertiliser was assessed usingZea mays as a test plant. Up to 8% of the fine roots of the plants constituted root litter. This fine root litter was better than that ofTrigonella foenum-graecum at increasing the growth and productivity ofZea mays. The root litter increased the growth of maize shoots more than the growth of roots. This appears to be a general phenomenon when plant nutrients are insufficient, as in the present study.
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  • 28
    ISSN: 1432-0789
    Keywords: Arbuscular mycorrhiza ; Limed silty loam Heavy metals ; Pb-Zn smelter ; Root colonization Spore numbers ; Tolerance ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The bioavailability of heavy metals (Cd, Zn, Pb, Cu) and the abundance of arbuscular mycorrhiza (AM) were studied in two agricultural fields close to a Pb-Zn smelter and three fields outside the pollution zone all cultivated with maize (Zea mays L.). Metal extractability with ethylenediaminetetraacetic acid (EDTA)-NH4OAc and Ca(NO3)2, plant metal uptake, and mycorrhizal parameters (spore number, root colonization) were assessed at two growth stages (six-leaf and maturity). Despite regular liming, the availability of Cd, Zn, and Pb was markedly higher in the two metal-polluted fields than in the three uncontaminated fields. However, the AM abundance was not correlated with metal availability. Root colonization and spore numbers in the metal polluted fields were relatively high, though at plant maturity the former was significantly lower than in one of the uncontaminated fields. The very low AM abundance in the two other unpolluted fields was related to other factors, particular soil and plant P status and soil pH. AM root colonization did not substantially prevent plant metal accumulation, since the metal concentrations in maize grown on the polluted fields strongly exceeded normal values, and for Cd and Pb reached the limits of toxicity for animal feed.
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  • 29
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    Biology and fertility of soils 25 (1997), S. 163-168 
    ISSN: 1432-0789
    Keywords: Key words Arbuscular mycorrhiza ; Ectomycorrhiza ; Benomyl ; Colonization ; External hyphae ; Field study ; Glomales ; Zea mays ; Pisolithus tinctorius
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Arbuscular mycorrhizal (AM) grasses compete for nutrients with ectomycorrhizal (EM) pine in the southeastern United States. Our objective was to determine if benomyl could be used to selectively inhibit the function of AM and thereby reduce grass competition in the field. The effects of Benlate (active ingredient: benomyl) in the greenhouse and field were evaluated. No effect was observed on pine inoculated with Pisolithus tinctorius in the greenhouse. Colonized root length of benomyl-treated Zea mays L. plants inoculated with Glomus sp. in the greenhouse remained static over time and the response was not dose dependent at concentrations of 0, 20, 60 and 150kg benomyl ha–1 equivalent. In contrast, colonization of nontreated plants increased over time. In the field, a minimal reduction of grass colonization was observed following four applications of benomyl ranging from 5 to 20kgha–1. We conclude that benomyl can successfully inhibit development of AM fungi under controlled conditions in the greenhouse with no inhibitory effects on the EM fungus P. tinctorius; however, in the field several factors may interfere with the effect of benomyl on AM fungi. These factors include: (a) the presence of ground cover which obstructs penetration of the fungicide to the soil, (b) timing of application in relation to mycorrhizal development, and (c) the application method of benomyl, a soil drench being preferable to a foliar spray.
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  • 30
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    Biology and fertility of soils 9 (1990), S. 110-118 
    ISSN: 1432-0789
    Keywords: Kuehneltiella terricola gen. nov., sp. nov. ; Soil ciliates ; Colpodidae ; Systematics ; Evolution ; Australia
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The morphology and biology of the colpodid ciliate Kuehneltiella terricola gen. nov., sp. nov. has been investigated using living organisms, various silver impregnation methods, and scanning electron microscopy. The new species has been isolated in soil from central Australia and might be endemic to this continent. The new genus Kuehneltiella differs from its nearest relative, Bresslaua, in having a right oral polykinetid composed of a single row of dikinetids. A reinvestigation of Lynn's slides of Bresslaua insidiatrix showed that, contrary to the statement of Lynn (1979), this species has a typic colpodid right oral polykinetid, i.e., composed of many short, disordered kineties. A brief review of the literature suggests that simple, single-rowed, right oral polykinetids are apomorphic in the colpodids s. str. Further, this special character has obviously evolved independently several times within the class Colpodea and even within the colpodids s. str. An illustrated key to the genera of the family Colpodidae is provided.
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  • 31
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    Biology and fertility of soils 9 (1990), S. 95-100 
    ISSN: 1432-0789
    Keywords: Assulina-Valkanovia ; Testacea ; Polymorphism ; Genotypes ; Evolution ; Spruce forest ; Sphagnum
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Summary The taxonomy and evolution of the Assulina-Valkanovia complex were investigated in a spruce forest soil which included a Sphagnum plot (GDR, Thuringia). In both habitats Assulina muscorum occurred in two colour forms (brown and colourless) and four shapes. A quantified phenospectrum from Assulina muscorum was obtained. The four shapes were distributed differently between the brown and the colourless forms in Sphagnum and soil. The shell measurements showed statistically significant differences between the brown and the colourless forms. Even between the two brown populations there were some significant differences. Each of the four shape types of brown and of colourless Assulina can be kept in clonal cultures for some time. However, without selection, single cultures eventually revert to mixed types. The four shape types show different degrees of stability. These colour and shape forms are genotypes, which can also occur for short periods in the natural habitats. The brown populations in Sphagnum and in the soil were dominated by different shape types during the period of investigation. Valkanovia elegans cannot be distinguished from Assulina muscorum type 4, but Valkanovia can inhabit both upper and lower soil horizons, whereas Assulina and its forms lives exclusively in the upper horizon (litter). Valkanovia from the lower horizon is constant in clonal culture. The conclusion of the present investigation is that there are stable and unstable constellations within a changeable genome, which give asexual groups both a taxonomic structure and a continuum of forms. Selection can increase stability, by polygenic control of features.
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  • 32
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    Biology and fertility of soils 23 (1996), S. 161-165 
    ISSN: 1432-0789
    Keywords: Key words ANI ; Baythroid ; Cyfluthrin ; Insecticide ; 15N ; Nitrification ; N uptake ; Synthetic pyrethroid ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A pot experiment was conducted to compare the uptake and dry matter production potential of NH+ 4 and NO– 3 and to study the effect of Baythroid, a contact poison for several insect pests of agricultural crops, on growth and N uptake of maize (Zea mays L.). Nitrogen was applied as (15NH4)2SO4, K15NO3, or 15NH4NO3 and in one treatment Baythroid was combined with 15NH4NO3. Source of N had, in general, a nonsignificant effect on dry matter and N yield, but uptake of NO– 3 was significantly higher than that of NH+ 4 when both N sources were applied together. Substantial loss of N occurred from both the sources, with NH+ 4 showing greater losses. Baythroid was found to have a significant positive effect on dry matter yield of both root and shoot; N yield also increased significantly. Uptake of N from both the applied and native sources increased significantly in the presence of Baythroid and a substantial added nitrogen interaction (ANI) was determined. The positive effect of Baythroid was attributed to: (1) a prolonged availability of NH+ 4 due to inhibition of nitrification, (2) an increased availability of native soil N through enhanced mineralization, and (3) an enhanced root proliferation.
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  • 33
    ISSN: 1432-0789
    Keywords: Soil carbon ; Crop rotation ; Legumes ; Cover crop ; Nitrogen fertilization ; Microbial biomass ; Soil health ; Gossypium hirsutum ; Zea mays ; Trifolium incarnatum ; Glycine max
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The “Old Rotation” cotton experiment was designed to aid farm managers in implementing rotation schemes that not only increase yield, but also improve soil quality. Six different crop rotation treatments were imposed since 1896. Rotations were: IA, cotton (Gossypium hirsutum L.) grown every year without a winter legume and without N fertilization; IB, cotton grown every year with a winter legume and without N fertilization; IC, cotton grown every year without a winter legume and with 134 kg N as NH4NO3 ha-1 year-1; IIA, 2-year cotton-corn (Zea mays L.) rotation with a winter legume and without N fertilization; IIB, 2-year cotton-corn rotation with a winter legume and with 134 kg N ha-1 year-1 as NH4NO3; and III, 3-year cotton-corn- alternating soybean [Glycine max (L.) Merr.] or rye (Secale cereale L.) rotation with a winter legume and with 134 g N as NH4NO3 ha-1 year-1. Crimson clover (Trifolium incarnatum L.) was the winter legume cover crop. The 2-year cotton-corn rotation with a winter legume and with 134 kg N ha-1 year-1 (IIB) and the 3-year cotton-corn soybean/rye rotation with a winter legume and with 134 kg N ha-1 year-1 (III) had higher amounts of soil organic matter, soil microbial biomass C and crop yield than the other four treatments. The cotton grown every year without a winter legume or N fertilizer (IA) had a lower amount of soil organic matter, soil microbial biomass C and N and cotton seed yield than all other rotations. In 1988 and 1992 cotton seed and legume yield were correlated in positive, curvilinear relationships with soil organic matter (r 2 ranged from 0.72 to 0.87). In most months, soil microbial biomass C and N was lower in the cotton grown every year without winter legumes or fertilizer (IA) than the other five rotations. In 1994, microbial biomass C and the Cmic:Corg ratio correlated in positive, curvilinear relationships with seed cotton yield (r 2=0.87 and 0.98, respectively). After 99 years of management the “Old Rotation” cotton experiment indicates that winter legumes increase amounts of both C and N in soil, which ultimately contribute to higher cotton yields. Microbial biomass C and the Cmic:Corg ratio are poor predictors of annual crop yield but may be an accurate indicator of soil health and a good predictor of long-term crop yield.
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  • 34
    ISSN: 1432-0789
    Keywords: Key words Soil carbon ; Crop rotation ; Legumes ; Cover crop ; Nitrogen fertilization ; Microbial biomass ; Soil health ; Gossypium hirsutum ; Zea mays ; Trifolium ; incarnatum ; Glycine max
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The “Old Rotation” cotton experiment was designed to aid farm managers in implementing rotation schemes that not only increase yield, but also improve soil quality. Six different crop rotation treatments were imposed since 1896. Rotations were: IA, cotton (Gossypium hirsutum L.) grown every year without a winter legume and without N fertilization; IB, cotton grown every year with a winter legume and without N fertilization; IC, cotton grown every year without a winter legume and with 134 kg N as NH4NO3 ha–1 year–1; IIA, 2-year cotton-corn (Zea mays L.) rotation with a winter legume and without N fertilization; IIB, 2-year cotton-corn rotation with a winter legume and with 134 kg N ha–1 year–1 as NH4NO3; and III, 3-year cotton-corn- (alternating soybean [Glycine max (L.) Merr.] or rye (Secale cereale L.) rotation with a winter legume and with 134g N as NH4NO3 ha–1 year–1. Crimson clover (Trifolium incarnatum L.) was the winter legume cover crop. The 2-year cotton-corn rotation with a winter legume and with 134 kg N ha–1 year–1 (IIB) and the 3-year cotton-corn soybean/rye rotation with a winter legume and with 134 kg N ha–1 year–1 (III) had higher amounts of soil organic matter, soil microbial biomass C and crop yield than the other four treatments. The cotton grown every year without a winter legume or N fertilizer (IA) had a lower amount of soil organic matter, soil microbial biomass C and N and cotton seed yield than all other rotations. In 1988 and 1992 cotton seed and legume yield were correlated in positive, curvilinear relationships with soil organic matter (r 2 ranged from 0.72 to 0.87). In most months, soil microbial biomass C and N was lower in the cotton grown every year without winter legumes or fertilizer (IA) than the other five rotations. In 1994, microbial biomass C and the Cmic:Corg ratio correlated in positive, curvilinear relationships with seed cotton yield (r 2=0.87 and 0.98, respectively). After 99 years of management the “Old Rotation” cotton experiment indicates that winter legumes increase amounts of both C and N in soil, which ultimately contribute to higher cotton yields. Microbial biomass C and the Cmic:Corg ratio are poor predictors of annual crop yield but may be an accurate indicator of soil health and a good predictor of long-term crop yield.
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  • 35
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    Biology and fertility of soils 25 (1997), S. 142-146 
    ISSN: 1432-0789
    Keywords: Key words Denitrification ; Tillage systems ; Maize ; Zea mays ; Hot spots ; Denitrifying populations ; N2O emission
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Denitrification losses show an irregular pattern through the year, often being caused by climatic conditions and management practices. The objectives of the present work were to quantify denitrification losses and to determine the influence of tillage system on the factors that control denitrification in fertilized soils. The modal profile of the soil was an Vertic Argiudoll, clay loam texture, located in Buenos Aires province, Argentina. The treatments were: (a) fertilized, (b) incorporated fertilization and (c) without fertilization for both no tillage and conventional tillage systems. Chambers were placed in the field to measure denitrification. In this clayish soil the estimated mean values of accumulated denitrification during the crop cycle (90 days) were 0.190kgNha–1 for conventional tillage and 0.350kgNha–1 for no tillage. In treatments with no tillage, losses by denitrification were approximately twice those of conventional tillage. These differences were also evidenced by the number of microorganisms, which were significantly higher (P〈〉;5%) for no tillage on all dates, except for at flowering. The increase at flowering coincided with the period of highest rainfall and consequently the highest water contents in the soil. The highest denitrification losses, except for sowing, were measured when soil moisture content was more than 30% (v/v). Denitrification increased in conjunction with an increase in the availability of carbon that is consumed by the heterotrophic microorganisms (including the denitrifiers).
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  • 36
    ISSN: 1432-0789
    Keywords: Key wordsAlternaria alternata ; Arbuscular mycorrhizas ; Fusarium equiseti ; Glomus mosseae ; Lactuca sativa ; Lettuce ; Maize ; Saprophytic fungi ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The effect of inoculation with the saprophytic fungi Alternaria alternata or Fusarium equiseti on maize (Zea mays) and lettuce (Lactuca sativa) with or without arbuscular mycorrhizal (AM) colonization by Glomus mosseae was studied in a greenhouse trial. Plant dry weights of non-AM-inoculated maize and lettuce were unaffected by the presence of A. alternata and F. equiseti. In contrast, A. alternata and F. equiseti decreased plant dry weights and mycorrhization when inoculated to the rhizosphere before G. mosseae. The saprophytic fungi inoculated 2 weeks after G. mosseae did not affect the percentage of root length colonized by the AM endophyte, but did affect its metabolic activity assessed as succinate dehydrogenase activity. Although F. equiseti inoculated at the same time as G. mosseae did not affect mycorrhization of maize roots, its effect on AM colonization of lettuce roots was similar to that with A. alternata. In the rhizosphere of both plants, the population of saprophytic fungi decreased significantly, but was not affected by the presence of G. mosseae. Our results suggest that there may have been a direct effect of the saprophytic fungi on the mycorrhizal fungi in the extramatrical phase of the latter, and when the AM fungus was established in the root the AM fungus was less affected by the saprophytic fungi.
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  • 37
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    Biology and fertility of soils 20 (1995), S. 57-62 
    ISSN: 1432-0789
    Keywords: Nitrogen use ; Nitrogen fertilizer recovery ; Zea mays ; Phaseolus vulgaris ; Vigna unguiculata ; Nitrogen fixation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Locally suitable cultivars of maize, beans, and cowpeas were grown in field experiments for four seasons in semi-arid Kenya. For three seasons, the dry matter production and grain yield of maize and beans were not increased by N fertilizer additions up to 120 kg N ha-1. Fertilizer recoveries measured by 15N isotope dilution techniques were low, less than 20%. Inoculated and uninoculated beans failed to fix N2. By contrast the cowpea derived 50% of its N from fixation, equivalent to 197 kg N ha-1. The N content of the grain generally exceeded 40 kg N ha-1, and the N content of the seeds from the grain legumes were greater than those from the cereals. Large inputs of N fertilizer or N by fixation are required if maize-grain legume cropping system in semiarid Kenya are to be sustained in the long term.
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  • 38
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    Biology and fertility of soils 23 (1996), S. 161-165 
    ISSN: 1432-0789
    Keywords: ANI ; Baythroid ; Cyfluthrin ; Insecticide ; 15N ; Nitrification ; N uptake ; Synthetic pyrethroid ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract A pot experiment was conducted to compare the uptake and dry matter production potential of NH inf4 sup+ and NO inf3 sup- and to study the effect of Baythroid, a contact poison for several insect pests of agricultural crops, on growth and N uptake of maize (Zea mays L.). Nitrogen was applied as (15NH4)2SO4, K15NO3, or 15NH4NO3 and in one treatment Baythroid was combined with 15NH4NO3. Source of N had, in general, a nonsignificant effect on dry matter and N yield, but uptake of NO inf3 sup- was significantly higher than that of NH inf4 sup+ when both N sources were applied together. Substantial loss of N occurred from both the sources, with NH inf4 sup+ showing greater losses. Baythroid was found to have a significant positive effect on dry matter yield of both root and shoot; N yield also increased significantly. Uptake of N from both the applied and native sources increased significantly in the presence of Baythroid and a substantial added nitrogen interaction (ANI) was determined. The positive effect of Baythroid was attributed to: (1) a prolonged availability of NH inf4 sup+ due to inhibition of nitrification, (2) an increased availability of native soil N through enhanced mineralization, and (3) an enhanced root proliferation.
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  • 39
    ISSN: 1432-0789
    Keywords: Key words Corn stubble decomposition ; N-fertilization ; Carbon light fraction ; Humic acids ; Microbial activity ; Zea mays
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The variation in stubble decomposition due to fertilizer incorporation was determined in a typical Argiudoll of the Argentinian rolling pampas. The experiment was conducted for 15 years, which included a no till system under maize (Zea mays L.) and a soybean rotation (Glycine max) with 0 and 45kg N ha–1 nitrogen fertilization treatments, called NFS and FS, respectively. A higher proportion of residues with a high N content was found in the FS plots. The different substrate quality proved to be the regulating factor for mineralization. This activity was indicated by the increase in soil microbial activity and soil carbon light fraction in FS compared to NFS. This carbon light fraction mineralizes rapidly but does not contribute to the most stable components, which are related to synthesis and polymerization of humic acids. No significant differences in humic acid content were found.
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  • 40
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    Biology and fertility of soils 24 (1997), S. 266-273 
    ISSN: 1432-0789
    Keywords: Key words Green manure ; Lime ; K deficiency ; Oxisol ; Sweet corn ; Zea mays ; Mn toxicity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Effects of local green manure (GM) and lime on soil productivity in a low-input agricultural system were evaluated by growing three successive crops of sweet corn (Zea mays) on an acid Oxisol (Typic acrorthox, Togitogiga series) in Western Samoa. The soil was amended with coral lime at 0, 5, and 10Mgha–1 and with cowpea GM at 0, 7.5, and 15Mgha–1. Commercial NPK fertilizers at 50kgha–1 each of N, P, and K were included for comparison. The amendments were applied only once prior to planting of the first crop. Response parameters measured included nutrient composition of leaves at tasseling and grain yield of each crop, and selected soil chemical properties at each planting. Yields of the first crop were nearly tripled with GM additions and doubled with lime additions. Such yield increases were caused mainly by better K nutrition and to a lesser extent by enhanced P nutrition. Yields of subsequent crops were much lower than those of the first, and the declines were much steeper for the GM treatments than for the lime treatments. Thus, the enhancement effect on K nutrition did not last beyond one crop. Poor growth of the second and third crops was caused by K deficiency; probably coupled with Mn toxicity. Significant yield reductions were found when Mn-to-K ratios in leaves exceeded 0.010. As for effects on soil, soil pH was increased significantly by lime but only slightly by GM. Given the variable charge property of this Oxisol, each unit pH increase corresponds to a cation exchange capacity (CEC) increase of 5cmolckg–1. Having greater CEC, the amended soil retained K more effectively, thereby causing yield increases, especially of the first corn crop, which required at least 0.75cmolckg–1 of exchangeable soil K or 7% of CEC for adequate growth.
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  • 41
    ISSN: 1432-0819
    Keywords: Key wordsZoned magma body ; Chemical variation ; ash-flow sheets ; Tephra sequence ; Differentiation ; time constraints ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract The Rainier Mesa ash-flow is a large (1200 km3), 11.6 My old, chemically zoned unit that ranges in composition from 55 to 76% SiO2– one of the largest chemical ranges ever observed in a large volume ash-flow sheet. Two chemical trends occur in this sheet, a low silica (55–66% SiO2) and a high silica (〉66% SiO2) trend. Ninety per cent of the Rainier Mesa sheet occurs in the high silica trend. Immediately beneath the Rainier Mesa sheet is a thick tephra sequence. The chemical variation of this sequence is nearly equivalent to the high silica portion of the Rainier Mesa ash-flow sheet (about 66–78% SiO2). Throughout the tephra sequence numerous small ash-flow layers occur, and each ash-flow layer is chemically zoned from more evolved at the base to less evolved at the top. This is consistent with having been erupted from a zoned magma body. The lowest silica tephra units are at the base of the sequence and the highest silica units are at the top – that is, the large-scale chemical trend of the entire sequence is opposite to that of the individual ash-flow layers. These ash-flow layers are of very small volume. The tephra sequence provides a unique record of the incremental development of the zoned, high silica portion of the Rainier Mesa magma body.
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  • 42
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    Bulletin of volcanology 59 (1997), S. 161-170 
    ISSN: 1432-0819
    Keywords: Key words Structure ; Evolution ; Uplift ; Geodetic modeling ; Alban Hills
    Source: Springer Online Journal Archives 1860-2000
    Topics: Geosciences
    Notes: Abstract  The Alban Hills, a Quaternary volcanic center lying west of the central Apennines, 15–25 km southeast of Rome, last erupted 19 ka and has produced approximately 290 km3 of eruptive deposits since the inception of volcanism at 580 ka. Earthquakes of moderate intensity have been generated there at least since the Roman age. Modern observations show that intermittent periods of swarm activity originate primarily beneath the youngest features, the phreatomagmatic craters on the west side of the volcano. Results from seismic tomography allow identification of a low-velocity region, perhaps still hot or partially molten, more than 6 km beneath the youngest craters and a high-velocity region, probably a solidified magma body, beneath the older central volcanic construct. Thirty centimeters of uplift measured by releveling supports the contention that high levels of seismicity during the 1980s and 1990s resulted from accumulation of magma beneath these craters. The volume of magma accumulation and the amount of maximum uplift was probably at least 40×106 m3 and 40 cm, respectively. Comparison of newer levelings with those completed in 1891 and 1927 suggests earlier episodes of uplift. The magma chamber beneath the western Alban Hills is probably responsible for much of the past 200 ka of eruptive activity, is still receiving intermittent batches of magma, and is, therefore, continuing to generate modest levels of volcanic unrest. Bending of overburden is the most likely cause of the persistent earthquakes, which generally have hypocenters above the 6-km-deep top of the magma reservoir. In this view, the most recent uplift and seismicity are probably characteristic and not precursors of more intense activity.
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  • 43
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    Current genetics 17 (1990), S. 223-227 
    ISSN: 1432-0983
    Keywords: Orotidine-5′-phosphate decarboxylase ; Cephalosporium acremonium ; Recombinant DNA ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned the Cephalosporium acremonium pyr4 gene by cross-hybridization with the equivalent gene from Neurospora crassa, the closest relative from which this gene is available. The C. acremonium pyr4 gene complements an E. coli pyrF mutant lacking orotidine-5′-phosphate decarboxylase (OMPdecase), and most probably does not contain introns. Maxicell analysis in E. coli shows that it encodes a 46 kDa polypeptide. The C. acremonium OMPdecase contains a highly conserved pentadecapeptide characteristic for this category of enzyme. Extensive sequence comparison suggests an important role of this region in enzymatic activity.
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  • 44
    ISSN: 1432-0983
    Keywords: Trypanosomes ; RNA polymerase ; Transcription ; Evolution ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have sequenced the genes encoding te largest subunits of the three classes of DNA-dependent RNA polymerases of Trypanosoma brucei. The nucleotide and deduced amino acid sequences were compared and aligned with the corresponding sequences of other eukaryotes. Phylogenetic relationships were subsequently calculated with a distant matrix, a bootstrapped parsimony and a maximum-likelihood method. These independent calculations resulted in trees with very similar topologies. The analyses show that all the largest subunits of T. brucei are evolutionarily distant members within each of the three RNA polymerase classes. An early separation of the trypanosomal subunits from the eukaryotic lineage might from the fundamental basis for the unusual transcription process of this species. Finally, all dendrograms show a separate ramification for the largest subunit of RNA polymerase I, II and III. RNA polymerase II and/or III form a bifurcation with the archaebacterial lineage. RNA polymerase I, however, arises separately from the eubacterial β′ lineage. This suggests that the three eukaryotic RNA polymerase classes are not simply derived by two gene duplications of an ancestral gene with subsequent differentiation.
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  • 45
    ISSN: 1432-0983
    Keywords: Cyanophora paradoxa ; Ferredoxin-NADP+-oxidoreductase ; Protein-import ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Cyanophora paradoxa is an important model organism for the study of the transition from endocytobiontic cyanobacteria to factual eukaryotic cell organelles. The cyanelles of these organisms possess cyanobacterial, as well as plastidic, characteristics. Although the transfer of cyanellar proteins from cytosolic into cyanellar space has been shown, the process of translocation of a known protein across the peptidoglycan layer and the envelope membranes has not been characterized. In this study we demonstrate that a specific and obligate cyanelle protein —Ferredoxin-NADP+-oxidoreductase (FNR) — is coded on the nuclear genome, synthesized on 80S ribosomes and transported from the eukaryotic cell compartment into the cyanelles of Cyanophora paradoxa, an original intracellular host-guest relation. These results indicate a gene transfer from guest to host genome and support the view that, in spite of their cyanobacterial origin, cyanelles have been evolved to cell organelles comparable to plastids.
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  • 46
    ISSN: 1432-0983
    Keywords: Chloroplast DNA ; Junction between small single copy and inverted repeat regions ; Zea mays ; Grammineae ; ndhH gene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The junctions JSA and JSB between the two inverted repeat regions IRA and IRB and the small single copy region of the maize chloroplast DNA have been identified by DNA sequencing. The JSA junction coincides with the initiation codon of the ndhH gene which is encoded by the adjacent region of the small single copy region. A comparison with the plastomes of rice, rye, tobacco and liverwort shows that linkage of this junction with the ndhH gene is specific for gramminean species. The amino acid sequences deduced from the ndhH genes show conserved histidine and cysteine residues which are likely to form a metal-binding domain.
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  • 47
    ISSN: 1432-1432
    Keywords: Evolution ; κ-Casein ; Cytochrome b ; Artiodactyla ; Ruminantia ; Caprinae ; Capricornis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nucleotide sequences for the κ-casein precursor proteins have been determined from the genomic DNAs or hair roots of the Ruminantia. The coding regions, exons 2, 3, and 4, were amplified separately via the three kinds of PCRs and then directly sequenced. The primers were designed from the sequence of bovine κ-casein gene; they were applicable for the amplification of the κ-casein genes from the 13 species in the Ruminantia except exon 2 of the lesser mouse deer. These results permitted an easy phylogenetic analysis based on the sequences of an autosomal gene. A phylogenetic tree was constructed from the mature K-casein sequences and compared with the tree of the cytochrome b genes which were sequenced from the same individuals. The Cervidae (sika deer, Cervus nippon) were separated from the branch of the Bovidae on the tree of κ-casein genes with a relatively high confidence level of the bootstrap analysis, but included in the branch of the Bovidae on the tree of cytochrome b genes. The κ-casein tree indicated a monophyly of the subfamily Caprinae, although the internal branches were uncertain in the Caprinae. The tree based on the nucleotide sequences of cytochrome b genes clearly showed the relationships of the closely related species in the genus Capricornis consisting of serow (C. smatorensis), Japanese serow (C. crispus), and Formosan serow (C. swinhoei). These results would be explained by the difference of resolving power between the κ-casein and the cytochrome b sequences.
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  • 48
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    Journal of molecular evolution 43 (1996), S. 399-404 
    ISSN: 1432-1432
    Keywords: Asarum ; Dioscorea ; Angiosperms ; Evolution ; Legumins ; Seed proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Analysis of legumin-encoding cDNAs fromDioscorea caucasica Lipsky (Dioscoreaceae) and fromAsarum europaeum L. (Aristolochiaceae) shows that there is an especially methionine-rich legumin subfamily present in the lower angiosperm clades including the Monocotyledoneae. It is characterized by a methionine content of 3–4 mol% which is roughly triple the methionine proportion of most other legumins. These “MetR” legumins, if present, still have to be detected in the higher angiosperms including the important seed crops. Evolutionary analysis suggests that the MetR legumins are the result of a gene duplication allowing the differentiation of legumin genes according to their sulfur content. The duplication event must have taken place before the split into mono- and dicotyledonous plants but probably after the separation of angiosperms and gymnosperms.
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  • 49
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    Journal of molecular evolution 43 (1996), S. 685-689 
    ISSN: 1432-1432
    Keywords: Retroposons ; Integration targets ; Evolution
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    Topics: Biology
    Notes: Abstract Genomic DNA fragments generated by the reverse transcription of cellular RNA are called retroposons. Because they are flanked by short repeats, mammalian retroposons are believed to integrate at staggered chromosomal breaks. Recently, a significant sequence pattern associated with the integration of Alu and ID repeats was identified (Jurka 1996). It is represented by the 5′ TTAAAA consensus sequence around the 5′ ends of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary strand between 3′ AA and the following 3′ TTTT bases. The first four bases of the flanking repeats corresponding to the 3′ TTTT consensus sequence show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evidence for such base pairing based on correlated variations in nucleotide composition of different tail and target regions.
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  • 50
    ISSN: 1432-1432
    Keywords: Alleles ; Evolution ; Gene conversion ; Introns ; Nematode
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Globin genes from theCaenorhabditis speciesbriggsae andremanei were identified and compared with a previously describedC. elegans globin gene. The encoded globins share between 86% and 93% amino acid identity, with most of the changes in or just before the putative B helix.C. remanei was found to have two globin alleles,Crg1-1 andCrgl-2. The coding sequence for each is interrupted by a single intron in the same position. The exons of the two genes are only 1 % divergent at the nucleotide level and encode identical polypeptides. In contrast, intron sequence divergence is 16% and numerous insertions and deletions have significantly altered the size and content of both introns. Genetic crosses show thatCrg1-1 andCrgl-2 segregate as alleles. Homozygous lines for each allele were constructed and northern analysis confirmed the expression of both alleles. These data reveal an unusual situation wherein two alleles encoding identical proteins have diverged much more rapidly in their introns than the silent sites of their coding sequences, suggesting multiple gene conversion events.
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  • 51
    ISSN: 1432-1432
    Keywords: Evolution ; Expression patterns ; α-Amylase ; Glucose repression ; Starch induction ; Intra- and interspecific variation ; Drosophila ; Gene expression ; Regulatory genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Intraspecific variation of α-amylase activity in D. melanogaster and D. immigrans, which is distantly related to D. melanogaster, and interspecific variation of α-amylase activity in 18 Drosophila species were examined. The amount of intraspecific variation of α-amylase activities measured in terms of coefficient of variation in D. melanogaster and D. immigrans was one-half and one-tenth or less, respectively, of the interspecific variation in 18 Drosophila species. We also surveyed the response patterns of α-amylase activity to dietary carbohydrates at the larval and adult stages. The levels of α-amylase activity depended on both repression by dietary glucose (glucose repression) and induction by dietary starch (starch induction). In general, our data suggest that glucose repression was conserved among species at both stages while starch induction was mainly observed in larvae, although the degree of the response depended on species. In D. lebanonensis lebanonensis and D. serrata, larvae expressed electrophoretically different α-amylase variants (isozymes) from those of adult flies. These results may suggest that the regulatory systems responsible both for the response to environment and developmental expression are different among species in Drosophila.
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  • 52
    ISSN: 1432-1432
    Keywords: Soybean ; Ferritin ; Plant-animal ; Monocotyledons ; Dicotyledons ; Plastid ; Gene organization ; Evolution ; Intron
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Ferritin, a protein widespread in nature, concentrates iron −1011−1012-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soy-bean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.
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  • 53
    ISSN: 1432-1432
    Keywords: Evolution ; Multigene family ; Recombination ; Trypanosome ; Variant surface glycoprotein
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The surface of the parasitic protozoanTrypanosoma brucei spp. is covered with a dense coat consisting of a single type of glycoprotein molecule, the variant surface glycoprotein (VSG). There may be as many as 1,000 genes for VSG within the genome ofT. brucei, and the switch of expression from one to another is the phenomenon of antigenic variation. As an approach to understanding the evolution of VSG genes we have determined the genomic DNA sequences of the eight genes encoding the variant surface glycoprotein 117 (VSG) family. From these data we have observed a number of features concerning the relationships between these genes: (1) there is a region of high variability confined to the N-terminus of the coding sequence, and comparison of the sequences with the available X-ray diffraction crystal structures suggests that two of the most variable stretches within the N-terminal domain are present on surface-exposed loops, indicating a role for epitope selection in evolution of these genes; (2) the 29 nucleotides surrounding the splice acceptor site are absolutely conserved in all eight 117 VSG genes; (3) numerous insertion/deletion mutations are located within or immediately downstream of the C-terminal protein-coding sequences: (4) within 500 by downstream of the insertion/deletion mutations are one or two copies of a repeat motif highly homologous to the recombinogenic 76-bp repeat sequences present upstream of many VSG basic copy genes and the expression-linked copy.
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  • 54
    ISSN: 1432-1432
    Keywords: Metalloproteinase ; Disintegrin ; Evolution ; Venom ; Phylogeny ; Gene duplication
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolution of the Metalloproteinase Disintegrin Cysteine-rich (MDC) gene family and that of the mammalian Matrix-degrading Metalloproteinases (MMPs) are compared. The alignment of snake venom and mammalian MDC and MMP precursor sequences generated a phylogenetic tree that grouped these proteins mainly according to their function. Based on this observation, a common ancestry is suggested for mammalian and snake venom MDCs; it is also possible that gene duplication of the already-assembled domain structure, followed by divergence of the copies, may have significantly contributed to the evolution of the functionally diverse MDC proteins. The data also suggest that the structural resemblance of the zinc-binding motif of venom MDCs and MMPs may best be explained by common ancestry and conservation of the proteolytic motifs during the divergence of the proteins rather than through convergent evolution.
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  • 55
    ISSN: 1432-1432
    Keywords: Krebs cycle ; Evolution ; Metabolism ; Citric acid cycle ; Chemical design
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into asingle-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
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  • 56
    ISSN: 1432-1432
    Keywords: Histone H1° ; 3′ untranslated region ; Slippage ; Sequence simplicity ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The H1° gene has a long 3′ untranslated region (3′UTR) of 1,125 nucleotides in the rat and 1,310 in humans. Analysis of the sequences shows that they have features of simple DNA that suggest involvement of replication slippage in their evolution. These features include the length imbalance between the rat and human sequences; the abundance of single-base repeats, two-base runs and other simple motifs clustered along the sequence; and the presence of single-base repeat length polymorphisms in the rat and mouse sequences. Pairwise comparisons show numerous short insertions/deletions, often flanked by direct repeats. In addition, a proportion of short insertions/deletions results from length differences in conserved single-base repeats. Quantification of the sequence simplicity shows that simple sequences have been more actively incorporated in the human lineage than in the rodent lineage. The combination of insertions/deletions and nucleotide substitutions along the sequence gives rise to three main regions of homology: a highly variable central region flanked by more conserved regions nearest the coding region and the polyA addition site.
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  • 57
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    Journal of molecular evolution 30 (1990), S. 489-492 
    ISSN: 1432-1432
    Keywords: Actinomyces ; Phosphotransferase ; Aminoglycoside ; Phylogenetic tree ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The protein sequences of seven 3′-aminoglycoside phosphotransferases falling into the six identified types and three 6′-aminoglycoside phosphotransferases were analyzed to give a rooted phylogenetic tree. This tree supports the origin of these groups of enzymes in an ancestor closely related to the actinomycetes, and that horizontal transfer of the resistance genes occurred, possibly via transposons. The implications for genetic engineering of a novel antibiotic are discussed.
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  • 58
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Evolution ; Echinoderms ; Sea stars ; DNA sequence ; Mitochondrial proteins ; Mitochondrial tRNA genes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have cloned and sequenced over 9 kb of the mitochondrial genome from the sea starPisaster ochraceus. Within a continuous 8.0-kb fragment are located the genes for NADH dehydrogenase subunits 1, 2, 3, and 4L (ND1, ND2, ND3, and ND4L), cytochrome oxidase subunits I, II, and III (COI, COII, and COIII), and adenosine triphosphatase subunits 6 and 8 (ATPase 6 and ATPase 8). This large fragment also contains a cluster of 13 tRNA genes between ND1 and COI as well as the genes for isoleucine tRNA between ND1 and ND2, arginine tRNA between COI and ND4L, lysine tRNA between COII and ATPase 8, and the serine (UCN) tRNA between COIII and ND3. The genes for the other five tRNAs lie outside this fragment. The gene for phenylalanine tRNA is located between cytochrome b and the 12S ribosomal genes. The genes for tRNAglu and tRNAthr are 3′ to the 12S ribosomal gene. The tRNAs for histidine and serine (AGN) are adjacent to each other and lie between ND4 and ND5. These data confirm the novel gene order in mitochondrial DNA (mtDNA) of sea stars and delineate additional distinctions between the sea star and other mtDNA molecules.
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  • 59
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    Journal of molecular evolution 33 (1991), S. 68-75 
    ISSN: 1432-1432
    Keywords: DNA ; Genome size ; Repetitive DNA ; Amphibians ; Reptiles ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Many characters differentiate amphibian from reptilian genomes. The former have, on the average, larger and more variable genome sizes, a greater repetitive DNA percentage, and a higher interspersion level among DNAs with different degrees of repetitivity. Reptiles have more reduced and uniform genome sizes, a repetitive DNA percentage generally lower than 50%, and a lower interspersion level. Other differences can be observed in the chromosome banding and in the correlations between genome size and other morphometric and functional parameters of the cell. The differences found in amphibians and reptiles seem to indicate that in these two vertebrate classes there is a different tendency toward or tolerance of the accumulation and preservation of genetically dispensable DNA fractions. This might depend either on a different propensity toward genic amplification or on the appearance, in reptiles, of stricter and more efficient constraints regulating genome size.
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  • 60
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    Journal of molecular evolution 33 (1991), S. 133-141 
    ISSN: 1432-1432
    Keywords: Y-chromosome ; DNA ; Human ; Primate ; Evolution ; PUPPY sequence ; Alu element
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A Y-chromosomal DNA fragment has been isolated from a human Y-Charon 21A recombinant library. Evolutionary analysis of 1F5 indicates that the size and sequence of this fragment have been conserved in higher primates. Deletion mapping and in situ hybridization analysis have localized 1F5 to the middle euchromatic portion of the long arm of the human Y chromosome at Yq11.2. Sequence analysis revealed the presence of an atypical Alu element and two regions rich in polypyrimidine-polypurine residues.
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  • 61
    ISSN: 1432-1432
    Keywords: Bacteria ; Sugars ; Phosphotransferase system ; Transport proteins ; Evolution ; Sequence comparisons ; NADH dehydrogenase ; Mitochondria
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of 15 sugar permeases of the bacterial phosphoenolpyruvatedependent phosphotransferase system (PTS) were divided into four homologous segments, and these segments were analyzed to give phylogenetic trees. The permease segments fell into four clusters: the lactose-cellobiose cluster, the fructose-mannitol cluster, the glucose-N-acetylglucosamine cluster, and the sucrose-β-glucoside cluster. Sequences of the glucitol and mannose permeases (clusters 5 and 6, respectively) were too dissimilar to establish homology with the other permeases, but short regions of statistically significant sequence similarities were noted. The functional and structural relationships of these permease segments are discussed. Some of the homologous PTS permeases were found to exhibit sufficient sequence similarity to subunits 4 and 5 of the eukaryotic mitochondrial NADH dehydrogenase complex to suggest homology. Moreover, subunits 4 and 5 of this complex appeared to be homologous to each other, suggesting that these PTS and mitochondrial proteins comprise a superfamily. The integral membrane subunits of the evolutionarily divergent mannose PTS permease, the P and M subunits, exhibited limited sequence similarity to subunit 6 of the mitochondrial F1F0-ATPase and subunit 5b of cytochrome oxidase, respectively. These results suggest that PTS sugar permeases and mitochondrial proton-translocating proteins may be related, although the possibility of convergent evolution cannot be ruled out.
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  • 62
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    Journal of molecular evolution 30 (1990), S. 60-71 
    ISSN: 1432-1432
    Keywords: Cysteine endopeptidase ; Cysteine proteinase ; Inhibitor ; Cystatin ; Kininogen ; Evolution ; Amino acid sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have examined the amino acid sequences of a number of proteins that have been suggested to be related to chicken cystatin, a protein from chicken egg white that inhibits cysteine proteinases. On the basis of statistical analysis, the following proteins were found to be members of the cystatin superfamily: human cystatin A, rat cystatin A(α), human cystatin B, rat cystatin B(β), rice cystatin, human cystatin C, ox colostrum cystatin, human cystatin S, human cystatin SA, human cystatin SN, chicken cystatin, puff adder cystatin, human kininogen, ox kininogen, rat kininogen, rat T-kininogens 1 and 2, human α2HS-glycoprotein, and human histidine-rich glycoprotein. Fibronectin is shown not to be a member of this superfamily, and the c-Ha-ras oncogene protein p21(Val-12) probably is not a member also. It was convenient to divide members of the superfamily into four types on the basis of the presence of one, two, or three copies of cystatin-like segments and the presence or absence of disulfide bonds. Evolutionary dendrograms were calculated by three methods, and from these we have constructed a scheme depicting the sequence of events in the evolution of these proteins. We suggest that about 1000 million years ago a precursor containing disulfide loops appeared, and that all disulfide-containing cystatins are derived from this. We follow the evolution of the proteins of the superfamily along four main lineages, with special attention to the part that duplication of segments has played in the development of the more complex molecules.
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    Journal of molecular evolution 37 (1993), S. 426-434 
    ISSN: 1432-1432
    Keywords: Primate ; Evolution ; Protamine ; Polymerase chain reaction ; Sperm proteins
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    Topics: Biology
    Notes: Abstract Protamine P1 genes have been sequenced by PCR amplification and direct DNA sequencing from 9 primates representing 5 major families, Cebidae (new world monkeys), Cercopithecidae (old world monkeys), Hylobatidae (gibbons), Pongidae (gorilla, orangutan, and chimpanzee), and Hominidae (human). In this recently diverged group of primates these genes are clearly orthologous but very variable, both at the DNA level and in their expressed amino acid sequences. The rate of variation amongst the protamine Pls indicates that they are amongst the most rapidly diverging polypeptides studied. However, some regions are conserved both in primates and generally in other placental mammals. These are the 13 N-terminal residues (including a region of alternating serine and arginine residues (the motif SRSR, res. 10–13) susceptible to Ser phosphorylation), a tract of six Arg residues (res. 24–29) in the center of the molecule, and a six-residue region (RCCRRR, res. 39–44), consisting of a pair of cysteines flanked by arginines. Detailed consideration of nearest neighbor matrices and trees based on maximum parsimony indicates that PI genes from humans, gorillas, and chimpanzees are very similar. The amino acid and nucleotide differences between humans and gorillas. are fewer than those between humans and chimpanzees. This finding is at variance with data from DNA-DNA hybridization and extensive globin and mitochondrial DNA sequences which place human and chimpanzee as closest relatives in the super family, Hominoidea. This may be related to the fact that protamine Pls are expressed in germ line rather than somatic cells. In contrast to the variability of the exon regions of the protamine P1 genes, the sequence of the single intron is highly conserved.
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  • 64
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    Journal of molecular evolution 38 (1994), S. 1-17 
    ISSN: 1432-1432
    Keywords: HSP70 ; Heat shock ; Evolution ; Phylogeny ; Yeast ; Multigene family ; Subcellular compartmentalization
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    Topics: Biology
    Notes: Abstract Eukaryotic genomes encode multiple 70-kDa heat-shock proteins (HSP70s). The Saccharomyces cerevisiae HSP70 family is comprised of eight members. Here we present the nucleotide sequence of the SSA3 and SSB2 genes, completing the nucleotide sequence data for the yeast HSP70 family. We have analyzed these yeast sequences as well as 29 HSP70s from 24 additional eukaryotic and prokaryotic species. Comparison of the sequences demonstrates the extreme conservation of HSP70s; proteins from the most distantly related species share at least 45% identity and more than one-sixth of the amino acids are identical in the aligned region (567 amino acids) among all proteins analyzed. Phylogenetic trees constructed by two independent methods indicate that ancient molecular and cellular events have given rise to at least four monophyletic groups of eukaryotic HSP70 proteins. Each group of evolutionarily similar HSP70s shares a common intracellular localization and is presumed to be comprised of functional homologues; these include heat-shock proteins of the cytoplasm, endoplasmic reticulum, mitochondria, and chloroplasts. HSP70s localized in mitochondria and plastids are most similar to the DnaK HSP70 homologues in purple bacteria and cyanobacteria, respectively, which is consistent with the proposed prokaryotic origin of these organelles. The analyses indicate that the major eukaryotic HSP70 groups arose prior to the divergence of the earliest eukaryotes, roughly 2 billion years ago. In some cases, as exemplified by the SSA genes encoding the cytoplasmic HSP70s of S. cerevisiae, more recent duplication events have given rise to subfamilies within the major groups. The S. cerevisiae SSB proteins comprise a unique subfamily not identified in other species to date. This subfamily appears to have resulted from an ancient gene duplication that occurred at approximately the same time as the origin of the major eukaryotic HSP70 groups.
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  • 65
    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Evolution ; Hybrid dysgenesis ; I elements ; Transposons
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    Notes: Summary There are two categories of strains inDrosophila melanogaster with respect to the I-R system of hybrid dysgenesis. The inducer strains contain particular transposable elements named I factors. They are not present in the strains of the other category called reactive (R) strains. Defective I elements are present in the pericentromeric regions of both categories of strains. This last subfamily of I sequences has not yet been described in detail and little is known about its origin. In this paper, we report that the defective I elements display an average of 94% of sequence identity with each other and with the transposable I factor. The results suggest that they cannot be the progenitors of the present day I factors, but that each of these two subfamilies started to evolve independently several million years ago. Furthermore, the sequence comparison of these I elements with an active I factor fromDrosophila teissieri provides useful information about when the deleted I elements became immobilized.
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  • 66
    ISSN: 1432-1432
    Keywords: Repetitive DNA ; Tandem repeats ; Sequence analysis ; Recombination ; Isolated populations ; Evolution
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    Notes: Abstract The satellite DNA family pDoP102 is species specific for the cave cricket Dolichopoda schiavazzii, an endemic species of mainland and insular Tuscany. It consists of numerous tandemly arranged repeats, 102 bp in length, and evolved most probably after cladogenesis of D. schiavazzii from the D. baccettii-aegilion group within the last 2.3 ± 0.8 million years. A sequence comparison of 31 clones (53 repetition units) from three isolated populations reveals a very high degree of sequence homogeneity within the species with no evidence for any specific population features. This appears to be in contrast to the results of allozyme analyses which account for a relatively old evolutionary divergence of the Elba island population from the mainland ones. Since the assumption of actual gene flow and recent colonization is rejected, the observed sequence homogeneity is hypothesized to be maintained by recombination processes preventing fixation of newly introduced mutations on pDoP102 sequence clusters.
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  • 67
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    Journal of molecular evolution 32 (1991), S. 296-303 
    ISSN: 1432-1432
    Keywords: Prebiotic chemistry ; Primordial soup ; Oparin hypothesis ; Evolution ; Impact catastrophism
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    Notes: Summary In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical evolution may not have occurred continuously because planetesimals and asterioids impacted the Earth many times during the first billion years, may have sterilized the Earth, and required the process to start over. A rapid process of chemical evolution may have been required in order that life appeared at or before 3.5 billion years ago. Thus, a setting favoring rapid chemical evolution may be required. A chemical evolution hypothesis set forth by Woese in 1979 accomplished prebiotic reactions rapidly in droplets in giant atmospheric reflux columns. However, in 1985 Scherer raised a number of objections to Woese's hypothesis and concluded that it was not valid. We propose a mechanism for prebiotic chemistry in clouds that satisfies Scherer's concerns regarding the Woese hypothesis and includes advantageous droplet chemistry. Prebiotic reactants were supplied to the atmosphere by comets, meteorites, and interplanetary dust or synthesized in the atmosphere from simple compounds using energy sources such as ultraviolet light, corona discharge, or lightning. These prebiotic monomers would have first encountered moisture in cloud drops and precipitation. We propose that rapid prebiotic chemical evolution was facilitated on the primordial Earth by cycles of condensation and evaporation of cloud drops containing clay condensation nuclei and nonvolatile monomers. For example, amino acids supplied by, or synthesized during entry of, meteorites, comets, and interplanetary dust would have been scavenged by cloud drops containing clay condensation nuclei. Polymerization would have occurred within cloud systems during cycles of condensation, freezing, melting, and evaporation of cloud drops. We suggest that polymerization reactions occurred in the atmosphere as in the Woese hypothesis, but life originated in the ocean as in the Oparin-Haldane hypothesis. The rapidity with which chemical evolution could have occurred within clouds accommodates the time constraints suggested by recent astrophysical theories.
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    Journal of molecular evolution 32 (1991), S. 415-420 
    ISSN: 1432-1432
    Keywords: Drosophila melanogaster ; Drosophila virilis ; mastermind ; Gene comparison ; Repetitive sequences ; Homopolymers ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Themastermind gene ofDrosophila melanogaster encodes a novel, highly repetitive nuclear protein required for neural development. To identify functionally important regions we have initiated an interspecific comparison of the gene inDrosophila virilis. Mastermind transcription and genomic organization are similar in both species and sequence analysis reveals significant conservation in a major cluster of charged amino acids. In contrast, extensive variation is noted in homopolymer domains that immediately flank the acidic cluster. Distinct patterns of evolutionary change can be identified: the major difference between unique regions are occasional amino acid substitutions whereas the repetitive areas are characterized by numerous large in-frame insertions/deletions and a nearly threefold higher rate of amino acid replacement. Conservation of the acidic domain suggests that it has an important functional role whereas the hypervariable homopolymer regions appear to be under less selective constraints than adjacent unique areas.
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  • 69
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    Journal of molecular evolution 36 (1993), S. 448-457 
    ISSN: 1432-1432
    Keywords: Retrovirus ; HIV ; CD4 ; Minus strand ; Alternate reading frame ; Frameshift ; Divergence ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A local sequence similarity of HIV envelope proteins (gp120 and gp41) to immunoglobulins suggests that a mimicry phenomenon may form the basis of the HIV-cell membrane interaction and of HIV-induced autoimmune reaction. We explored the hypothesis of any deeper relationship between HIV env proteins and immunoglobulin family members. An overall DNA sequence similarity between gp41 coding region of env gene and the HIV-receptor CD4 gene was observed and a 14-base-long oligonucleotide, almost unique in the GenBank, was found in gp41 and CD4 genes. The alignment of env gene to CD4 gene and to 84 different sequences showed a significantly higher homology score and a nonrandom similarity in the CD4-env alignment. A significant similarity was also found between the env protein and the sequence encoded by an alternate reading frame of CD4 gene. Our observations suggest that gp41 coding region might have a different origin than the gp120 coding region of the env gene, and that a divergent evolution might link gp41 to CD4 or immunoglobulin family members. In this study the analysis of alternate-reading-frame products is also proposed as a novel approach to investigate evolutionary links and structure-function relationships.
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    Journal of molecular evolution 35 (1992), S. 156-180 
    ISSN: 1432-1432
    Keywords: DNA damage ; DNA repair ; Chromatin ; Evolution ; Nucleosomes ; Nuclear matrix ; Active genes ; Z-DNA ; Sperm ; Mutation ; Molecular clock
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    Topics: Biology
    Notes: Summary Some evolutionary consequences of different rates and trends in DNA damage and repair are explained. Different types of DNA damaging agents cause nonrandom lesions along the DNA. The type of DNA sequence motifs to be preferentially attacked depends upon the chemical or physical nature of the assaulting agent and the DNA base composition. Higher-order chromatin structure, the nonrandom nucleosome positioning along the DNA, the absence of nucleosomes from the promoter regions of active genes, curved DNA, the presence of sequence-specific binding proteins, and the torsional strain on the DNA induced by an increased transcriptional activity all are expected to affect rates of damage of individual genes. Furthermore, potential Z-DNA, H-DNA, slippage, and cruciform structures in the regulatory region of some genes or in other genomic loci induced by torsional strain on the DNA are more prone to modification by genotoxic agents. A specific actively transcribed gene may be preferentially damaged over nontranscribed genes only in specific cell types that maintain this gene in active chromatin fractions because of (1) its decondensed chromatin structure, (2) torsional strain in its DNA, (3) absence of nucleosomes from its regulatory region, and (4) altered nucleosome structure in its coding sequence due to the presence of modified histones and HMG proteins. The situation in this regard of germ cell lineages is, of course, the only one to intervene in evolution. Most lesions in DNA such as those caused by UV or DNA alkylating agents tend to diminish the GC content of genomes. Thus, DNA sequences not bound by selective constraints, such as pseudogenes, will show an increase in their AT content during evolution as evidenced by experimental observations. On the other hand, transcriptionally active parts may be repaired at rates higher than inactive parts of the genome, and proliferating cells may display higher repair activities than quiescent cells. This might arise from a tight coupling of the repair process with both transcription and replication, all these processes taking place on the nuclear matrix. Repair activities differ greatly among species, and there is a good correlation between life span and repair among mammals. It is predicted that genes that are transcriptionally active in germ-cell lineages have a lower mutation rate than bulk DNA, a circumstance that is expected to be reflected in evolution. Exception to this rule might be genes containing potential Z-DNA, H-DNA, or cruciform structures in their coding or regulatory regions that appear to be refractory to repair. This study supports the molecular clock hypothesis when applied to one gene within a group of related species and contends that evolutionary rates might vary between genes and gene segments not only as a result of differences in selective constraints but also as a result of differences in the rate of damage minus rate of repair among different segments of chromatin DNA.
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    Journal of molecular evolution 40 (1995), S. 570-577 
    ISSN: 1432-1432
    Keywords: Alternate reading frames ; Evolution ; Overlapping frames ; Homology search ; Primary sequence analysis ; Polycistronic genes
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    Topics: Biology
    Notes: Abstract Hypothetical Products from Noncoding Frames (i.e., HyPNoFs) are hypothetical, not-coded proteins, translated from alternate reading frames (i.e., coding+1 and coding+2) of cDNAs. HyPNoFs of CD4, PKC, oncostatin, bcl-2 proto-oncogene, tumor suppressor p53, cystic fibrosis transmembrane regulator (CFTR), and tumor necrosis factors a and β were searched as query sequences vs the SWISS-PROT data bank. Homology searches carried out revealed that hypothetical products (i.e., HyPNoFs) may share high similarity with real protein products actually coded. Sequence similarity of hypothetical products to real proteins is sometimes very high, suggesting common conformational features, according to the Sander and Schneider cutoff value. This finding supports the hypothesis that eukaryotic DNA, currently considered to be monocistronic, might occasionally have polycistronic regions, carrying different protein messages on overlapping frames. As yet, polycistronic genes have been observed in viral genomes only. The presence of polycistronic regions in eukaryotic genes is likely reminiscent of an ancient strategy, rather than a present feature of the genome in eukaryotes. These data suggest that thorough investigation of HyPNoFs is likely to improve our ability to trace genes' evolution and to investigate structure-function relationships of protein and DNA sequences.
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  • 72
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    Journal of molecular evolution 40 (1995), S. 601-607 
    ISSN: 1432-1432
    Keywords: Prolamine ; Sperm proteins ; Evolution ; Mammals
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    Topics: Biology
    Notes: Abstract Prolamine P1 genes have been sequenced following PCR amplification from 11 mammals representing five major mammalian orders: Rodentia (rat and guinea pig), Carnivora (cat and bear), Proboscidea (elephant), Perissodactyla (horse), and Artiodactyla (camel, deer, elk, moose, and gazelle). The predicted amino acid sequence for these genes together with previously reported sequences results in a data set of 25 different P1 genes and 30 different P1 amino acid sequences. The alignment of all these sequences reveals that prolamines are amongst the most rapidly diverging proteins studied. In spite of the large number of differences there are conserved motifs that are also common to birds such as the N-terminal ARYR followed by the triple alternating SRSRSR phosphorylation site. The central region contains 3 arginine clusters consisting of 5–6 arginines each. The C-terminus appears to be the most variable region of the protamines. Overall the molecular evolution of P1 genes is in agreement with the expected species evolution supporting that these genes have evolved vertically.
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    Journal of molecular evolution 36 (1993), S. 545-554 
    ISSN: 1432-1432
    Keywords: Echinoderms ; Evolution ; Phylogeny ; mtDNA ; Mitochondrial gene arrangements
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    Notes: Summary Previous analyses have demonstrated that, among the echinoderms, the sea star (class: Asteroidea) mitochondrial genome contains a large inversion in comparison to the mitochondrial DNA of sea urchins (class: Echinoidea). Polymerase chain reaction amplification, DNA cloning, and sequencing have been used to examine the relationships of the brittle stars (class: Ophiuroidea) and sea cucumbers (class: Holothuroidea) to the sea stars and sea urchins. The DNA sequence of the regions spanning potential inversion junctions in both brittle stars and sea cucumbers has been determined. This study has also revealed a highly modified tRNA cluster in the ophiuroid mitochondrial genome. Our data indicate mitochondrial gene arrangement patterns that group the sea cucumbers with sea urchins and sea stars with brittle stars. This use of molecular characters clarifies the relationships among these classes.
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    Journal of molecular evolution 39 (1994), S. 489-495 
    ISSN: 1432-1432
    Keywords: Repetitive sequences ; Sequence variability ; Evolution ; Heterochromatin ; DNA curvature
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    Notes: Abstract Two highly abundant satellite DNAs comprise 36% of the Tenebrio obscurus (Tenebrionidae, Coleoptera) genome. They are designated as satellite I and satellite II with the monomer length of 344 and 142 base pairs (bp), respectively. Both satellites differ in their nucleotide (nt) sequences, but the frequency of point mutations, well-conserved length of monomer variants, stretches of shared mutations characteristic for the process of gene conversion, and distribution of both satellites in regions of centromeric heterochromatin of all chromosomes indicate that the same evolutionary processes act on both of them with the same, or similar, rate. While satellite I shares no sequence similarity with any other known nt sequence, satellite II is 79.7% homologous with the highly abundant satellite from closely related Tenebrio molitor. Difference in the frequency of point mutations and absence of shared mutations indicating gene conversion strongly suggest that in these two closely related species mutational processes affecting satellite DNAs seem to be changed. Retarded electrophoretic mobility, due to sequence-induced curvature of DNA helix axis, was observed for T. obscurus satellite II, but not for satellite I. Although evolutionary processes act with different rates in T. obscurus and T. molitor satellites the monomer length and sequence-induced curvature are well preserved in both 142-bp satellites, as well as in, at the nt sequence level completely divergent, Palorus ratzeburgii (Tenebrionidae) satellite, indicating potential importance of these parameters in their evolution.
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  • 75
    ISSN: 1432-1432
    Keywords: Snake venom ; Bothrops ; Phospholipase ; Myotoxin ; Evolution ; cDNA ; Gene duplication ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The sequence coding for a snake venom phospholipase A2 (PLA2), BJUPLA2, has been cloned from a Bothrops jararacussu venom gland cDNA library. The cDNA sequence predicts a precursor containing a 16-residue signal peptide followed by a molecule of 122 amino acid residues with a strong sequence similarity to group II snake venom PLA2's. A striking feature of the cDNA is the high sequence conservation of the 5′ and 3′ untranslated regions in cDNAs coding for PLA2's from a number of viper species. The greatest sequence variation was observed between the regions coding for the mature proteins, with most substitutions occurring in nonsynonymous sites. The phylogenetic tree constructed by alignment of the amino acid sequence of BJUPLA2 with group II PLA2's in general groups them according to current taxonomical divisions and/or functional activity. It also suggests that gene duplications may have occurred at a number of different points during the evolution of snake venom group II PLA2's.
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    Journal of molecular evolution 41 (1995), S. 238-246 
    ISSN: 1432-1432
    Keywords: Cellular slime molds ; Animals ; Fungi ; Plantae ; Maximum-likelihood method ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The phylogenetic position of Dictyostelium inferred from 18S rRNA data contradicts that from protein data. Protein trees always show the close affinity of Dictyostelium with animals, fungi, and plants, whereas in 18S rRNA trees the branching of Dictyostelium is placed at a position before the massive radiation of protist groups including the divergence of the three kingdoms. To settle this controversial issue and to determine the correct position of Dictyostelium, we inferred the phylogenetic relationship among Dictyostelium and the three kingdoms Animalia, Fungi, and Plantae by a maximum-likelihood method using 19 different protein data sets. It was shown at the significance level of 1 SE that the branching of Dictyostelium antedates the divergence of Animalia and Fungi, and Plantae is an outgroup of the Animalia-Fungi-Dictyostelium clade.
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    Journal of molecular evolution 41 (1995), S. 293-298 
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
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    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to theDrosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in themontium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling speciesD. auraria, D. triauraria, andD. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental speciesD. bicomuta, D. serrata, andD. birchii, as well as in the Afrotropical speciesD. diplacantha andD. seguyi. The complete separation of the genes is observed in the Indian speciesD. kikkawai andD. jambulina and in the Afrotropical speciesD. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among themontium species are discussed.
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    Journal of molecular evolution 41 (1995), S. 293-298 
    ISSN: 1432-1432
    Keywords: β-tubulin ; Evolution ; Gene cluster ; Gene dispersion ; Drosophila montium subgroup
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The β1-, β2-, and β3-tubulin genes have been mapped by in situ hybridization on the polytene chromosomes of 11 selected species (15 strains) belonging to the Drosophila montium subgroup. Although the hybridization pattern among the strains of the same species does not differ, this pattern is significantly different among the species. The β-tubulin genes in the montium subgroup seem to be organized in a cluster, or in a semi-cluster, or are completely dispersed. The clustered arrangement is found in the North-Oriental sibling species D. auraria, D. triauraria, and D. quadraria. The semi-clustered arrangement, wherein the β1 and β2 genes are located at the same locus while β3 is at a different one, appears in the South-Oriental species D. bicomuta, D. serrata, and D. birchii, as well as in the Afrotropical species D. diplacantha and D. seguyi. The complete separation of the genes is observed in the Indian species D. kikkawai and D. jambulina and in the Afrotropical species D. vulcana. Based on the above results, a possible mode of evolution of the β-tubulin genes in the montium subgroup is attempted. In addition, phylogenetic relationships among the montium species are discussed.
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  • 79
    ISSN: 1432-1432
    Keywords: Giardia ; Trichomonas ; CDK ; CDC ; Unicellular ; Metazoa ; Evolution
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    Notes: Abstract Cyclin-dependent kinase (CDK) and cell division control (CDC2) sequences are strongly conserved among eukaryotes and may complement the use of other sequence families in eukaryotic phylogenetic inference. We synthesized degenerate PCR primers to amplify the catalytic region of CDK homologs in representatives of the earliest available lineages of eukaryotes. CDK family sequence-based, maximum-likelihood distance measurements with neighbor joining, and Fitch-Margoliash least-squares analyses produced unrooted dendrograms that included protists, yeasts, and higher eukaryotes. Bootstrap confidence estimates supported CDK-based phylogenetic groupings among the protists, fungi, and vertebrates although resolution within these groups was often insignificant. However, Trichomonas vaginalis and Giardia lamblia exhibited two of the most divergent CDK-like sequences consistent with rRNA-phylogenetic inference of early divergence of these eukaryotic lineages. In the evolution from unicellular to multicellular organisms, a constellation of amino acid residues aligning with the human, CDK N-terminal β sheet may have undergone abrupt replacement.
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  • 80
    ISSN: 1432-1432
    Keywords: Lens ; Crystallin ; Squid ; Chicken ; Gene ; Regulation ; AP-1 ; Evolution
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Abstract Previous experiments have shown that the minimal promoters required for function of the squid SL20-1 and SL11 crystallin genes in transfected rabbit lens epithelial cells contain an overlapping AP-1/antioxidant responsive element (ARE) upstream of the TATA box. This region resembles the PL-1 and PL-2 elements of the chicken βB 1-cry stallin promoter which are essential for promoter function in transfected primary chicken lens epithelial cells. Here we demonstrate by site-directed mutagenesis that the AP-1/ARE sequence is essential for activity of the squid SL20-1 and SL11 promoters in transfected embryonic chicken lens cells and fibroblasts. Promoter activity was higher in transfected lens cells than in fibroblasts. Electrophoretic mobility shift and DNase protection experiments demonstrated the formation of numerous complexes between nuclear proteins of the embryonic chicken lens and the AP-1/ARE sequences of the squid SL20-1 and SL11 crystallin promoters. One of these complexes comigrated and cross-competed with that formed with the PL-1 element of the chicken βB1-crystallin promoter. This complex formed with nuclear extracts from the lens, heart, brain, and skeletal muscle of embryonic chickens and was eliminated by competition with a consensus AP-1 sequence. The nonfunctional mutant AP-1/ ARE sequences did not compete for complex formation. These data raise the intriguing possibility that entirely different, nonhomologous crystallin genes of the chicken and squid have convergently evolved a similar cis-acting regulatory element (AP-1/ARE) for high expression in the lens.
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    Journal of molecular evolution 41 (1995), S. 813-832 
    ISSN: 1432-1432
    Keywords: Phylogeny ; Evolution ; Carbamoylphosphate synthetase ; Dihydroorotase ; Aspartate transcarbamoylase ; Intron ; Exon ; Arginine biosynthesis ; Pyrimidine biosynthesis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Carbamoylphosphate is a common intermediate in the metabolic pathways leading to the biosynthesis of arginine and pyrimidines. The amino acid sequences of all available proteins that catalyze the formation of carbamoylphosphate were retrieved from Genbank and aligned to estimate their mutual phylogenetic relations. In gram-negative bacteria carbamoylphosphate is synthesized by a two-subunit enzyme with glutamiriase and carbamoylphosphate synthetase (CPS) activity, respectively. In gram-positive bacteria and lower eukaryotes this two-subunit CPS has become dedicated to arginine biosynthesis, while in higher eukaryotes the two subunits fused and subsequently lost the glutaminase activity. The CPS dedicated to pyrimidine synthesis is part of a multifunctional enzyme (CPS II), encoding in addition dihydroorotase and aspartate transcarbamoylase. Evidence is presented to strengthen the hypothesis that the two “kinas” subdomains of all CPS isozymes arose from a duplication of an ancestral gene in the progenote. A further duplication of the entire CPS gene occurred after the divergence of the plants and before the divergence of the fungi from the eukaryotec root, generating the two isoenzymes involved in either the synthesis of arginine or that of pyrimidines. The mutation rate was found to be five- to tenfold higher after the duplication than before, probably reflecting optimization of the enzymes for their newly acquired specialized function. We hypothesize that this duplication arose from a need for metabolic channeling for pyrimidine biosynthesis as it was accompanied by the tagging of the CPS gene with the genes for dihydroorotase and aspartate transcarbamoylase, and as the duplication occurred independently also in gram-positive bacteria. Analysis of the exon-intron organization of the two “kinase” subdomains in CPS I and II suggests that ancient exons may have comprised approx. 19 amino acids, in accordance with the prediction of the “intron-early” theory.
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  • 82
    ISSN: 1432-1432
    Keywords: Ribonuclease ; Gene duplication ; Evolution ; Ruminants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Phylogenetic analysis, based on the primary structures of mammalian pancreatic-type ribonucleases, indicated that gene duplication events, which occurred during the evolution of ancestral ruminants, gave rise to the three paralogous enzymes present in the bovine species. Herein we report data that demonstrate the existence of the orthologues of the bovine pancreatic, seminal, and cerebral ribonucleases coding sequences in the genomes of giraffe and sheep. The “seminal” sequence is a pseudogene in both species. We also report an analysis of the transcriptional expression of ribonuclease genes in sheep tissues. The data presented support a model for positive selection acting on the molecular evolution of ruminant ribonuclease genes.
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  • 83
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    Journal of molecular evolution 30 (1990), S. 333-346 
    ISSN: 1432-1432
    Keywords: Protamine ; Evolution ; Nuclear protein ; DNA condensation ; Sperm proteins
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The availability of the amino acid sequence for nine different mammalian P1 family protamines and the revised amino acid sequence of the chicken protamine galline (Oliva and Dixon 1989) reveals a much close relationship between mammalian and avian protamines than was previously thought (Nakano et al. 1976). Dot matrix analysis of all protamine genes for which genomic DNA or cDNA sequence is available reveals both marked sequence similarities in the mammalian protamine gene family and internal repeated sequences in the chicken protamine gene. The detailed alignments of the cis-acting regulatory DNA sequences shows several consensus sequence patterns, particularly the conservation of a cAMP response element (CRE) in all the protamine genes and of the regions flanking the TATA box, CAP site, N-terminal coding region, and polyadenylation signal. In addition we have found a high frequency of the CA dinucleotide immediately adjacent to the CRE element of both the protamine genes and the testis transition proteins, a feature not present in other genes, which suggests the existence of an extended CRE motif involved in the coordinate expression of protamine and transition protein genes during spermatogenesis. Overall these findings suggest the existence of an avian-mammalian P1 protamine gene line and are discussed in the context of different hypotheses for protamine gene evolution and regulation.
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  • 84
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    Journal of molecular evolution 30 (1990), S. 409-424 
    ISSN: 1432-1432
    Keywords: Phylogeny ; Tetrapods ; Morphology ; Cladistics ; Divergence ; Evolution ; Amphibians ; Reptiles ; Birds ; Mammals
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The phylogeny of the major groups of tetrapods (amphibians, reptiles, birds, and mammals) has until recently been poorly understood. Cladistic analyses of morphological data are producing new hypotheses concerning the relationships of the major groups, with a focus on the identification of monophyletic groups. Molecular phylogenies support some of these views and dispute others. Geological dates of the major evolutionary branching points are recalculated on the basis of the cladograms and new fossil finds.
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  • 85
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    Journal of molecular evolution 32 (1991), S. 24-30 
    ISSN: 1432-1432
    Keywords: Short sequence distribution ; Sequence constraints ; Averaged sequence ; Sequence structure ; Asymmetric nucleotide sequences ; GC content ; Evolution ; Evolutionary constraints
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The data from a genomic library can be sorted into the frequencies of every possible tetranucleotide in the sequence. This tabulation, a short sequence distribution, contains the frequency of occurrence of the 256 tetranucleotides and thus seems to serve as a vehicle for averaging sequence information. Two such distributions can be readily compared by correlation. Reported here are correlations (Spearmanr s) of the distributions from all of the genomic libraries in GenBank 44.0 with sizes equal to or larger than that ofSalmonella typhimurium, except for the data for mouse and humans. All of the organisms examined showed highly significant correlations between the two DNA strands (not the complementarity expected from base pairing). Of 155 comparisons between libraries, 132 showed significant correlations at the 99% confidence level. Application of the correlation coefficients as a similarity matrix clustered most organisms in a phenogram in a pattern consistent with other hypotheses. This suggests a highly conserved pattern underlying all other genetic information in cellular DNA and affecting both DNA strands, perhaps caused by interaction with conserved factors necessary for DNA packaging.
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  • 86
    ISSN: 1432-1432
    Keywords: Lagomorphs ; Rabbit ; Mitochondrial DNA ; Heteroplasmy ; Restriction site polymorphism ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A characterization was conducted on mitochondrial DNA (mtDNA) molecules extracted separately from 107 European rabbits (Oryctolagus cuniculus) both wild and domestic, 13 European hares (Lepus capensis), and 1 eastern cottontail (Sylvilagus floridanus). Experimentally this study took into account restriction site polymorphism, overall length variation of the noncoding region, and numbers of repeated sequences. Nucleotide divergences indicate that the mtDNAs from the three species derived from a common ancestor some 6–8 million years (Myr) ago. Every animal appeared heteroplasmic for a set of molecules with various lengths of the noncoding region and variable numbers of repeated sequences that contribute to them. This systematic heteroplasmy, most probably generated by a rate of localized mtDNA rearrangements high enough to counterbalance the cellular segregation of rearranged molecules, is a shared derived character of leporids. The geographic distribution of mtDNA polymorphism among wild rabbit populations over the western European basin shows that two molecular lineages are represented, one in southern Spain, the second over northern Spain, France, and Tunisia. These two lineages derived from a common ancestor some 2 Myr ago. Their present geographical distribution may be correlated to the separation of rabbits into two stocks at the time of Mindel glaciation. Finally the distribution of mtDNA diversity exhibits a mosaic pattern both at inter- and intrapopulation levels.
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  • 87
    ISSN: 1432-1432
    Keywords: Aspergillus ; 5S rRNA genes ; 5S rRNA pseudogenes ; Evolution
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    Topics: Biology
    Notes: Summary We have cloned and determined the nucleotide sequence of 18 DNA fragments hybridizing to 5S rRNA from twoAspergillus species-A. wentii andA. awamori. Four of the analyzed sequences were pseudogenes. The gene sequences of these two species were very similar and differed fromAspergillus nidulans at both constant and microheterogeneous sites.
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  • 88
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    Journal of molecular evolution 33 (1991), S. 464-469 
    ISSN: 1432-1432
    Keywords: Evolution ; tRNA ; Ribosome ; Peptide bond ; Catalytic RNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Continuation of early evolutionary bonding between tRNAs would provide a solution to residence time problems between peptidyl-tRNA and mRNA. It could also improve the speed of peptide bond formation by holding the amino acid close to the growing peptide. The tRNA clover leaf structure would allow each tRNA to from a TΨC(GA)-loop bond to one side and a D-loop bond to the other, hence fixing itself within a group of tRNAs, all attached to the mRNA. This can be developed into a system for peptide elongation in which bonds are made and broken in an ordered sequence, with each step triggering the next. This leads to a model system that fits with some recent propsals for a three-site ribosome.
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  • 89
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    Journal of molecular evolution 34 (1992), S. 78-84 
    ISSN: 1432-1432
    Keywords: Urate oxidase ; Evolution ; Mechanism of inactivation ; Mutations ; Hominoids
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Summary Urate oxidase was lost in hominoids during primate evolution. The mechanism and biological reason for this loss remain unknown. In an attempt to address these questions, we analyzed the sequence of urate oxidase genes from four species of hominoids: human (Homo sapiens), chimpanzee (Pan troglodytes), orangutan (Pongo pygmaeus), and gibbon (Hylobates). Two nonsense mutations at codon positions 33 and 187 and an aberrant splice site were found in the human gene. These three deleterious mutations were also identified in the chimpanzee. The nonsense mutation at codon 33 was observed in the orangutan urate oxidase gene. None of the three mutations was present in the gibbon; in contrast, a 13-bp deletion was identified that disrupted the gibbon urate oxidase reading frame. These results suggest that the loss of urate oxidase during the evolution of hominoids could be caused by two independent events after the divergence of the gibbon lineage; the nonsense mutation at codon position 33 resulted in the loss of urate oxidase activity in the human, chimpanzee, and orangutan, whereas the 13-bp deletion was responsible for the urate oxidase deficiency in the gibbon. Because the disruption of a functional gene by independent events in two different evolutionary lineages is unlikely to occur on a chance basis, our data favor the hypothesis that the loss of urate oxidase may have evolutionary advantages.
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  • 90
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    Journal of molecular evolution 40 (1995), S. 482-486 
    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetase ; Computer analysis ; Evolution ; Genetic code ; tRNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract tRNA sequences were analyzed for sequence features correlated with known classes of aminoacyl-tRNA synthetase enzymes. The tRNAs were searched for distinguishing nucleotides anywhere in their sequences. The analyses did not find nucleotides predictive of synthetase class membership. We conclude that such nucleotides never existed in tRNA sequences or that they existed and were lost from many of the tRNA sequences during evolution.
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  • 91
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    Journal of molecular evolution 40 (1995), S. 476-481 
    ISSN: 1432-1432
    Keywords: Aminoacylation ; Aminoacyl-tRNA synthetases ; tRNA ; GluRS ; GlnRS ; Glutamate ; Glutamine ; Evolution ; Mischarging
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Aminoacyl-tRNA for protein synthesis is produced through the action of a family of enzymes called aminoacyl-tRNA synthetases. A general rule is that there is one aminoacyl-tRNA synthetase for each of the standard 20 amino acids found in all cells. This is not universal, however, as a majority of prokaryotic organisms and eukaryotic organelles lack the enzyme glutaminyl-tRNA synthetase, which is responsible for forming Gln-tRNAGln in eukaryotes and in Gram-negative eubacteria. Instead, in organisms lacking glutaminyl-tRNA synthetase, Gln-tRNAGln is provided by misacylation of tRNAGln with glutamate by glutamyl-tRNA synthetase, followed by the conversion of tRNA-bound glutamate to glutamine by the enzyme Glu-tRNAGln amidotransferase. The fact that two different pathways exist for charging glutamine tRNA indicates that ancestral prokaryotic and eukaryotic organisms evolved different cellular mechanisms for incorporating glutamine into proteins. Here, we explore the basis for diverging pathways for aminoacylation of glutamine tRNA. We propose that stable retention of glutaminyl-tRNA synthetase in prokaryotic organisms following a horizontal gene transfer event from eukaryotic organisms (Lamour et al. 1994) was dependent on the evolving pool of glutamate and glutamine tRNAs in the organisms that acquired glutaminyl-tRNA synthetase by this mechanism. This model also addresses several unusual aspects of aminoacylation by glutamyl- and glutaminyl-tRNA synthetases that have been observed.
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  • 92
    ISSN: 1432-1432
    Keywords: Aminoacyl-tRNA synthetases ; tRNA ; Genetic code ; RNA world ; Evolution
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    Notes: Abstract Two aspects of the evolution of aminoacyl-tRNA synthetases are discussed. Firstly, using recent crystal structure information on seryl-tRNA synthetase and its substrate complexes, the coevolution of the mode of recognition between seryl-tRNA synthetase and tRNAser in different organisms is reviewed. Secondly, using sequence alignments and phylogenetic trees, the early evolution of class 2 Amnoacyl-tRNA synthetases is traced. Arguments are presented to suggest that synthetases are not the oldest of protein enzymes, but survived as RNA enzymes during the early period of the evolution of protein catalysts. In this view, the relatedness of the current synthetases, as evidenced by the division into two classes with their associated subclasses, reflects the replacement of RNA synthetases by protein synthetases. This process would have been triggered by the acquisition of tRNA 3′ end charging activity by early proteins capable of activating small molecules (e.g., amino acids) with ATP. If these arguments are correct, the genetic code was essentially frozen before the protein synthetases that we know today came into existence. Correspondence to: S. Cusack
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  • 93
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    Journal of molecular evolution 35 (1992), S. 253-260 
    ISSN: 1432-1432
    Keywords: Protein-coding sequences ; DNA sequences ; Evolution ; Evolutionary rates ; Rate heterogeneity ; Maximum likelihood ; Statistical testing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary A codon-based approach to estimating the number of variable sites in a protein is presented. When first and second positions of codons are assumed to be replacement positions, a capture-recapture model can be used to estimate the number of variable codons from every pair of homologous and aligned sequences. The capture-recapture estimate is compared to a maximum likelihood estimate of the number of variable codons and to previous approaches that estimate the number of variable sites (not codons) in a sequence. Computer simulations are presented that show under which circumstances the capture-recapture estimate can be used to correct biases in distance matrices. Analysis of published sequences of two genes, calmodulin and serum albumin, shows that distance corrections that employ a capture-recapture estimate of the number of variable sites may be considerably different from corrections that assume that the number of variable sites is equal to the total number of positions in the sequence.
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  • 94
    ISSN: 1432-1432
    Keywords: Evolution ; Teleostei ; Clupea harengus ; Esox lucius ; Fish ; Polymerase chain reaction ; Calcium binding
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ependymins represent the predominant protein constituents in the cerebrospinal fluid of many teleost fish and they are synthesized in meningeal fibroblasts. Here, we present the ependymin sequences from the herring (Clupea harengus) and the pike (Esox lucius). A comparison of ependymin homologous sequences from three different orders of teleost fish (Salmoniformes, Cypriniformes, and Clupeiformes) revealed the highest similarity between Clupeiformes and Cypriniformes. This result is unexpected because it does not reflect current systematics, in which Clupeiformes belong to a separate infradivision (Clupeomorpha) than Salmoniformes and Cypriniformes (Euteleostei). Furthermore, in Salmoniformes the evolutionary rate of ependymins seems to be accelerated mainly on the protein level. However, considering these inconstant rates, neither neighbor joining trees nor DNA parsimony methods gave any indication that a separate euteleost infradivision exists.
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  • 95
    ISSN: 1432-1432
    Keywords: Ribonuclease ; Evolution ; Gene duplication ; Ruminants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Mammalian pancreatic ribonucleases form a family of homologous proteins that has been extensively investigated. The primary structures of these enzymes were used to derive phylogenetic trees. These analyses indicate that the presence of three strictly homologous enzymes in the bovine species (the pancreatic, seminal, and cerebral ribonucleases) is due to gene duplication events which occurred during the evolution of ancestral ruminants. In this paper we present evidence that confirms this finding and that suggests an overall structural conservation of the putative ribonuclease genes in ruminant species. We could also demonstrate that the sequences related to ox ribonuclease coding regions present in genomic DNA of the giraffe species are the orthologues of the bovine genes encoding the three ribonucleases mentioned above.
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  • 96
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    Journal of molecular evolution 37 (1993), S. 71-76 
    ISSN: 1432-1432
    Keywords: Evolution ; Catalase ; Phylogenetic tree
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Heme-containing catalase sequences from 20 different organisms representing prokaryotes, fungi, animals, and plants have been compiled for phylogenetic reconstruction. Phylogenies based on distance and parsimony analysis show that fungal and animal catalases can be derived from one ancestor, whereas bacterial catalases fail to form a monophyletic group. Plant catalases appear to form a second class of catalases that arose independently from a possible prokaryotic ancestor.
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  • 97
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    Journal of molecular evolution 39 (1994), S. 13-21 
    ISSN: 1432-1432
    Keywords: Y chromosome ; Great ape ; Human ; Evolution ; DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Nine newly described single-copy and lowcopy-number genomic DNA sequences isolated from a flow-sorted human Y chromosome library were mapped to regions of the human Y chromosome and were hybridized to Southern blots of male and female great ape genomic DNAs (Gorilla gorilla, Pan troglodytes, Pongo pygmaeus). Eight of the nine sequences mapped to the euchromatic Y long arm (Yq) in humans, and the ninth mapped to the short arm or pericentromeric region. All nine of the newly identified sequences and two additional human Yq sequences hybridized to restriction fragments in male but not female genomic DNA from the great apes, indicating Y chromosome localization. Seven of these 11 human Yq sequences hybridized to similarly-sized restriction endonuclease fragments in all the great ape species analyzed. The five human sequences that mapped to the most distal subregion of Yq (deletion of which region is associated with spermatogenic failure in humans) were hybridized to Southern blots generated by pulsed-field gel electrophoresis. These sequences define a region of approximately 1 Mb on human Yq in which HpaII tiny fragment (HTF) islands appear to be absent. The conservation of these human Yq sequences on great ape Y chromosomes indicates a greater stability in this region of the Y than has been previously described for most anonymous human Y chromosomal sequences. The stability of these sequences on great ape Y chromosomes seems remarkable given that this region of the Y does not undergo meiotic recombination and the sequences do not appear to encode genes for which positive selection might occur.
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  • 98
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    Journal of molecular evolution 41 (1995), S. 996-1005 
    ISSN: 1432-1432
    Keywords: Repetitive DNA ; Tandem repeats ; Sequence analysis ; Phylogenetic tree ; Silent repeats ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Two different satellite DNAs exist in the genus Cucurbita which are different with respect to repeat length (350 by and 170 bp), array size, and sequence homogenization. Whereas the 350-bp satellite DNA is prominent and very homogeneous in all species investigated except for C. maxima and C. lundelliana, the 170-bp satellite is rather evenly distributed in all species. In C. maxima and C. lundelliana the 350-bp satellite is present only in small amounts, but detectable by the sensitive PCR method. These repeats are also very homogeneous, reflecting a silent stage of satellite DNA. In contrast, the 170-bp satellite DNA is intra- and interspecifically heterogeneous. It is striking that the species with no detectable amount of 350-bp satellite contain 170-bp satellite DNA clusters with the highest degree of homogeneity. The evolution of satellite DNA repeats within cultivated and wild species in the genus Cucurbita is elucidated using the sequence data of both satellite DNAs from all species investigated. The value of satellite DNA for phylogenetic analysis between closely related species is discussed.
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  • 99
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    Journal of molecular evolution 40 (1995), S. 120-126 
    ISSN: 1432-1432
    Keywords: Simple repetitive DNA ; Microsatellites ; Unstable triplets ; Database ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Simple repeats composed of tandemly repeated units 1–6 nucleotides (nt) long have been extracted from a selected set of primate genomic DNA sequences. Of the 501 theoretically possible, different types of repeats only 67 were present in the analyzed database in at least two different size ranges over 12 nt. They include all simple repeats known to be polymorphic in the primate genome. A list of moderately expanding and nonexpanding oligonucleotide patterns has also been included. Furthermore, we have compiled statistical data with emphasis on the overall variability of the most abundant 67 types of repeats. We have demonstrated that the expandability of at least some simple repeats may be affected by the overall base composition and by flanking sequences. In particular, the occurrence of tandemly repeated CAG and GCC triplets in exons positively correlates with their G+C content. We also noted that in the vicinity of Alu sequences tetrameric repeats are more abundant than in the total genomic DNA. This paper can be used as a comprehensive guide in identification of the most abundant and potentially polymorphic simple repeats. It is also of broader significance as a step toward understanding the contribution of flanking sequences and the overall sequence composition to variability of simple repeats.
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  • 100
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    Journal of molecular evolution 41 (1995), S. 457-466 
    ISSN: 1432-1432
    Keywords: Seed storage proteins ; Legumin ; Gene structure ; Evolution ; Gymnosperms ; Ginkgo biloba
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Legumin-like seed storage proteins have been intensively studied in crop plants. However, little is known about the molecular evolution of these proteins and their genes and it was assumed that they originated from an ancestral gene that already existed at the beginning of angiosperm evolution. We have evidence for the ubiquitous occurrence of homologous proteins in gymnosperms as well. We have characterized the major seed storage globulin from Ginkgo biloba by amino acid sequencing, which reveals clear homology to legumin-like proteins from angiosperms. The Ginkgo legumin is encoded by a gene family; we describe two of its members. The promoter regions contain sequence motifs which are known to function as regulatory elements involved in seed-specific expression of angiosperm legumins, although the tissues concerned are different in gymnosperms and angiosperms. The Ginkgo legumin gene structure is divergent from that of angiosperms and suggests that the evolution of legumin genes implicated loss of introns. From our data and from functional approaches recently described it becomes obvious that the posttranslational processing site of legumin precursors is less conserved than hitherto assumed. Finally, we present a phylogenetic analysis of legumin encoding sequences and discuss their utility as molecular markers for the reconstruction of seed plant evolution.
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