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  • Saccharomyces cerevisiae  (307)
  • Evolution
  • Springer  (553)
  • Frontiers Media SA  (2)
  • Taylor & Francis  (2)
  • Annual Reviews
  • Blackwell Publishing Ltd
  • 2020-2024  (5)
  • 2005-2009
  • 1990-1994  (421)
  • 1980-1984  (131)
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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)
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  • 2
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    Taylor & Francis | CRC Press
    Publication Date: 2024-04-05
    Description: This book focuses on the amphibian, Xenopus, one of the most commonly used model animals in the biological sciences. Over the past 50 years, the use of Xenopus has made possible many fundamental contributions to our knowledge in cell biology, developmental biology, molecular biology, and neurobiology. In recent years, with the completion of the genome sequence of the main two species and the application of genome editing techniques, Xenopus has emerged as a powerful system to study fundamental disease mechanisms and test treatment possibilities. Xenopus has proven an essential vertebrate model system for understanding fundamental cell and developmental biological mechanisms, for applying fundamental knowledge to pathological processes, for deciphering the function of human disease genes, and for understanding genome evolution. Key Features Provides historical context of the contributions of the model system Includes contributions from an international team of leading scholars Presents topics spanning cell biology, developmental biology, genomics, and disease model Describes recent experimental advances Incorporates richly illustrated diagrams and color images Related Titles Green, S. L. The Laboratory Xenopus sp. (ISBN 978-1-4200-9109-0) Faber, J. & P. D. Nieuwkoop. Normal Table of Xenopus laevis (Daudin): A Systematical & Chronological Survey of the Development from the Fertilized Egg till the End of Metamorphosis (ISBN 978-0-8153-1896-5) Jarret, R. L. & K. McCluskey. The Biological Resources of Model Organisms (ISBN 978-1-0320-9095-5)
    Keywords: Developmental biology ; Genetics (non-medical) ; Evolution ; Ecological science, the Biosphere ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSC Developmental biology ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAK Genetics (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::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere
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  • 3
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    Taylor & Francis | CRC Press
    Publication Date: 2024-04-14
    Description: This book is an extended argument for abandoning the species rank. Instead, the author proposes that the rank of "species" be replaced by a pluralistic and multi-level view. In such a view, all clades including the smallest identifiable one would be named and studied within a phylogenetic context. What are currently called "species" represent different sorts of things depending on the sort of organisms and processes being considered. This is already the case, but is not formally recognized by those scientists using the species rank in their work. Adopting a rankless taxonomy at all levels would enhance academic studies of evolution and ecology and yield practical benefits in areas of public concern such as conservation. The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license. KEY FEATURES • Proposes the replacement of restrictive species concepts with a pluralistic view • Suggests abandoning the formal taxonomic rank of "species" • Considers zoological, botanical, and microbiological aspects of the species level • Deals with practical issues such as conservation, inventories, and field guides
    Keywords: Wildlife: general interest ; Botany and plant sciences ; Evolution ; Biology, life sciences ; thema EDItEUR::W Lifestyle, Hobbies and Leisure::WN Nature and the natural world: general interest::WNC Wildlife: general interest ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAJ Evolution ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences
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  • 4
    Publication Date: 2024-04-05
    Description: During their life cycle plants undergo a wide variety of morphological and developmental changes. Impinging these developmental processes there is a layer of gene, protein and metabolic networks that are responsible for the initiation of the correct developmental transitions at the right time of the year to ensure plant life success. New omic technologies are allowing the acquisition of massive amount of data to develop holistic and integrative analysis to understand complex processes. Among them, Microarray, Next-generation Sequencing (NGS) and Proteomics are providing enormous amount of data from different plant species and developmental stages, thus allowing the analysis of gene networks globally. Besides, the comparison of molecular networks from different species is providing information on their evolutionary history, shedding light on the origin of many key genes/proteins. Moreover, developmental processes are not only genetically programed but are also affected by internal and external signals. Metabolism, light, hormone action, temperature, biotic and abiotic stresses, etc. have a deep effect on developmental programs. The interface and interplay between these internal and external circuits with developmental programs can be unraveled through the integration of systematic experimentation with the computational analysis of the generated omics data (Molecular Systems Biology). This Research Topic intends to deepen in the different plant developmental pathways and how the corresponding gene networks evolved from a Molecular Systems Biology perspective. Global approaches for photoperiod, circadian clock and hormone regulated processes; pattern formation, phase-transitions, organ development, etc. will provide new insights on how plant complexity was built during evolution. Understanding the interface and interplay between different regulatory networks will also provide fundamental information on plant biology and focus on those traits that may be important for next-generation agriculture.
    Keywords: QK1-989 ; Q1-390 ; Plant Development ; Omics ; Molecular Systems Biology ; Evolution ; Gene Regulatory Networks ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PST Botany and plant sciences
    Language: English
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  • 5
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    Frontiers Media SA
    Publication Date: 2024-04-04
    Description: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact
    Keywords: Carrion ; Mass Mortality ; Organic Matter ; Decomposition ; Resource Subsidy ; Disturbance ; Pulse ; Necrobiome ; Evolution ; Food Webs ; thema EDItEUR::P Mathematics and Science::PD Science: general issues ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAF Ecological science, the Biosphere
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    European journal of nutrition 22 (1983), S. 205-212 
    ISSN: 1436-6215
    Keywords: Schwermetallwirkung ; Malatdehydrogenase ; Glutamatdehydrogenase ; Glycerinaldehyd-3-phosphatdehydrogenase ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Medicine
    Description / Table of Contents: Summary The difference between cadmium, zinc, lead, and mercury in regard of their effects on the activity of the enzymes tested is very slight. Concentrations higher than 10−5 M reduce significantly the activity of the enzymes, and concentrations of approximately 10−3 M inhibit it completely. An increase of the activity cannot be detected. The addition of combinations of cadmium, zinc, and lead results in a summing up of the toxic effects, whereas the interaction between mercury and the other three heavy metals shows a cumulative effect, which is appointed nearly completely by the heavy metal more toxic. The findings suggest that under in-vitro conditions there exists a direct interaction between the heavy metals and the enzymes.
    Notes: Zusammenfassung Die vier Schwermetalle Cadmium, Zink, Blei und Quecksilber unterscheiden sich in ihrer Wirkung auf die Aktivität der untersuchten Enzyme nur sehr wenig. Konzentrationen über 10−5 M vermindern die Enzymaktivität signifikant, und Konzentrationen von etwa 10−3 M unterbinden sie völlig. Eine Steigerung der Enzymaktivität läßt sich nicht feststellen. Die Zugabe von Cadmium-, Zink- und Bleikombinationen führt zu einer Addition der toxischen Effekte, während bei der Interaktion zwischen Quecksilber und den anderen drei Schwermetallen die Gesamtwirkung fast ausschließlich durch das stärker hemmende Schwermetall allein bestimmt wird. Die erhaltenen Ergebnisse lassen vermuten, daß es unter Invitro-Bedingungen zu einer direkten Wechselwirkung zwischen den Schwermetallen und den Enzymen kommt.
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  • 7
    Electronic Resource
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    Springer
    Acta biotheoretica 33 (1984), S. 35-50 
    ISSN: 1572-8358
    Keywords: Evolution ; falsification ; Darwinism ; philosophy of science
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract In this paper we discuss the epistemological positions of evolution theories. A sharp distinction is made between the theory that species evolved from common ancestors along specified lines of descent (here called “the theory of common descent”), and the theories intended as causal explanations of evolution (e.g. Lamarck's and Darwin's theory). The theory of common descent permits a large number of predictions of new results that would be improbable without evolution. For instance, (a) phylogenetic trees have been validated now; (b) the observed order in fossils of new species discovered since Darwin's time could be predicted from the theory of common descent; (c) owing to the theory of common descent, the degrees of similarity and difference in newly discovered properties of more or less related species could be predicted. Such observations can be regarded as attempts to falsify the theory of common descent. We conclude that the theory of common descent is an easily-falsifiable & often-tested & still-not-falsified theory, which is the strongest predicate a theory in an empirical science can obtain. Theories intended as causal explanations of evolution can be falsified essentially, and Lamarck's theory has been falsified actually. Several elements of Darwin's theory have been modified or falsified: new versions of a theory of evolution by natural selection are now the leading scientific theories on evolution. We have argued that the theory of common descent and Darwinism are ordinary, falsifiable scientific theories.
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  • 8
    ISSN: 1572-8773
    Keywords: catalase ; copper resistance ; pH-dependent growth ; Saccharomyces cerevisiae ; superoxide dismutase
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Abstract A strain of Saccharomyces cerevisiae has been adapted to increasing concentrations of copper at two different pH values. The growth curve at pH 5.5 is characterized by a time generation increasing with the amount of added copper. A significant decrease of cell volume as compared with the control is also observed. At pH 3 the cells grow faster than at pH 5.5 and resist higher copper concentrations (3.8 against 1.2 mm). Experimental evidence indicates that, after copper treatment, the metal is not bound to the cell wall, but is localized intracellularly. A significant precipitation of copper salts in the medium was observed only at pH 5.5. Increased levels of superoxide dismutase (SOD) activity were observed in copper-treated cells and which persisted after 20 subsequent inocula in a medium without added metal. On the contrary, catalase activity was not stimulated by copper treatment and, hence, not correlated with SOD levels. The mechanism of copper resistance, therefore, probably involves a persistent induction of SOD, but not of catalase, and it is strongly pH-dependent.
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  • 9
    Electronic Resource
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    Springer
    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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  • 10
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    Cellular and molecular life sciences 40 (1984), S. 1159-1161 
    ISSN: 1420-9071
    Keywords: Saccharomyces cerevisiae ; 5-trifluoromethyl-6-àzauracil ; yeast cell cultures ; cell division ; inhibition of
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary Cell division, as studied in asynchronous cultures of yeast cells, is sensitive to 5-trifluoromethyl-6-azauracil (F3CAzU). Under defined conditions (10 mmoles l−1 F3CAzU) this compound blocks immediately and completely the process of cell division. Using synchronized cells, the time-point at which division process of yeast cell can be inhibited by F3CAzU has been determined. The inhibitor effect of this compound is completely reversed by thymine, thymidine and uracil.
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  • 11
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    Cellular and molecular life sciences 48 (1992), S. 1162-1164 
    ISSN: 1420-9071
    Keywords: Polygodial ; warburganal ; antifungal activity ; Candida albicans ; Saccharomyces cerevisiae ; Pityrosporum ovale ; enhancing effect ; antioxidants ; vitamin C ; BHA ; anethole
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The antifungal activity of two drimane sesquiterpene dialdehydes, polygodial (1) and warburganal (2), alone and in combination with several other substances, was examined against three fungi,Candida albicans, Saccharomyces cerevisiae andPityrosporum ovale employing a broth dilution method. Anethole significantly synergized the activity of the two sesquiterpenoids againstC. albicans andS. cerevisiae however, it had only an, additive effect againstP. ovale. By contrast, two antioxidants, ascorbic acid (vitamin C) and BHA (butylated hydroxyanisole), noticeably enhanced the activity of the sesquiterpenoids againstP. ovale, but had no, effect againstC. albicans andS. cerevisiae.
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  • 12
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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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  • 13
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    Journal of industrial microbiology and biotechnology 7 (1991), S. 131-135 
    ISSN: 1476-5535
    Keywords: Saccharomyces cerevisiae ; Jerusalem artichoke ; High-fructose syrup ; Ethanol ; Immobilized yeast cells
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary The results from this study showed that Jerusalem artichoke juice can be used for the production of very enriched fructose syrup by selective conversion of glucose to ethanol in a continuous process using immobilized cells ofSaccharomyces cerevisiae ATCC 36859. The product contained up to 99% of the total carbohydrates as fructose compared to 76% in the feed. Using Jerusalem artichoke juice supplemented with some glucose a product was obtained with 7.5% w/v ethanol which made ethanol recovery economically favourable. It was found that some fructose was consumed in these continuous processes; the glucose/fructose conversion rate ratio was regulated by the glucose concentration in the product stream.
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  • 14
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    Journal of industrial microbiology and biotechnology 7 (1991), S. 181-189 
    ISSN: 1476-5535
    Keywords: Saccharomyces cerevisiae ; Torulaspora delbrueckii ; Aroma
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Summary Thirty-three fermentations of Pedro Ximénez grapes, collected in three degrees of ripeness, were carried out by inoculation with three types of inoculum: pure cultures ofSaccharomyces cerevisiae races and ofTorulaspora delbrueckii, indigenous yeasts, and mixed cultures of indigenous yeasts enriched with the pure cultures. By means of variance analysis 21 compounds were determined whose final concentrations in the wines significantly depended on the musts, the inocula or both. Eleven products that depended significantly on the inocula were subjected to a discriminant analysis in which most of the pure cultures gathered in a discriminant space area different from that occupied by the indigenous yeasts. The centroids corresponding to most of the mixed cultures were shifted to the central area of the discriminant space, moved away from their corresponding pure cultures and approached the indigenous yeasts. The results show a high similarity between the fermentations carried out with mixed cultures with the addedS. cerevisiae races and those fermentations carried out with the indigenous yeasts, with regard to those compounds which were significantly dependent on the inocula.
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  • 15
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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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  • 16
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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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  • 17
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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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  • 18
    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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  • 19
    ISSN: 1432-0983
    Keywords: 2-oxoglutarate dehydrogenase ; Saccharomyces cerevisiae ; rad52-mediated chromosome loss
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Ogd1 mutants of Saccharomyces cerevisiae are deficient in mitochondrial 2-oxoglutarate dehydrogenase activity; they cannot grow on glycerol and produce an increased amount of organic acids during growth on glucose as substrate. Using gamma ray-induced rad52-mediated chromosome loss the ogd1 mutation can be assigned to chromosome IX. Tetrad analysis of crosses between ogd1 and other markers on chromosome IX revealed that the OGD1 gene maps on the left arm of this chromosome 1.9 cM from his5.
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  • 20
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Orotate phosphoribosyl transferase ; Nucleotide sequence-5-phosphoribosyl 1-pyrophosphate (5PRPP)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Orotate phosphoribosyl transferase (OPRTase) catalyses the transformation of orotate to OMP in the pyrimidine pathway. In the yeast Saccharomyces cerevisiae, the URA5 gene is known to encode this enzyme activity. In this paper we present the cloning and sequencing of a yeast gene, named URA10, encoding a second OPRTase enzyme. Comparison of the predicted amino acid sequences between URA5 and URA10 genes shows more than 75% similarity. These sequences have also been compared to those of Escherichia coli, Podospora anserina, Sordaria macrospora and Dictyostelium discoideum. Remarkable similarities in the primary structure of these proteins have been found. Gene disruption experiments revealed that URA10 gene expression is responsible for the leaky phenotype of a ura5 mutant. Assays of OPRTase activity in extracts from ura5 and ura10 mutants indicate that the URA10 product contributes only 20% of the total activity found in wild type cells.
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  • 21
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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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  • 22
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Mutants ; Farnesyl diphosphate synthetase ; Ergosterol
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    Topics: Biology
    Notes: Summary Two yeast mutant strains auxotrophic for ergosterol and blocked in farnesyl diphosphate synthetase (EC 2.5.1.1) were isolated. Genetic analysis has shown that these mutant strains carry additional mutations in the ergosterol pathway besides erg20-1 and erg20-2 which affect FPP synthetase. The novel feature of these mutants is their ability to excrete prenyl alcohols (farnesol and geraniol). As geraniol is toxic for yeast cells, the above leaky mutations in FPP synthetase have to be associated with others in the sterol pathway, in order to slow down geraniol synthesis.
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  • 23
    ISSN: 1432-0983
    Keywords: Glucose oxidase ; Aspergillus ; Saccharomyces cerevisiae
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    Topics: Biology
    Notes: Summary We report the cloning of the Aspergillus niger glucose oxidase gene and its use to elevate glucose oxidase productivity in A. niger by increasing the gene dosage. In addition, the gene has been introduced into A. nidulans where it provides the novel capacity to produce glucose oxidase. A plasmid, in which DNA encoding the mature form of glucose oxidase was preceded by a Saccharomyces cerevisiae secretion signal, effected high-level production of extracellular glucose oxidase in this yeast.
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  • 24
    ISSN: 1432-0983
    Keywords: Trypanosomes ; RNA polymerase ; Transcription ; Evolution ; Phylogeny
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    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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  • 25
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; Saccharomyces cerevisiae ; Argininosuccinate lyase ; Sequence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The complete nucleotide sequence of the ARG7 gene, coding for argininosuccinate lyase (EC 4.3.2.1), in the fission yeast (Schizosaccharomyces pombe) has been determined. It consists of an open reading frame of 461 codons. The deduced protein has a molecular weight of 51 200 Da. The gene is devoid of introns which is confirmed by the fact that it is expressed in Escherichia coli after spontaneous insertion of a bacterial sequence probably bearing a prokaryotic promoter. A perfect “TATA” box is found at-72 and the major transcription initiation site in Saccharomyces cerevisiae is located at-11 as shown by primer extension experiments. Comparison of the S. pombe lyase with related proteins from other organisms reveals an important degree of conservation except in the carboxyterminal part of the polypeptide. Additionally, a deletion removing 66 amino acids of the carboxy terminus yields an enzyme exhibiting some biological activity. A unique 1500 b transcript was found in S. cerevisiae when the intact gene was present, but the deleted version of the gene gave rise to at least three transcripts of 1800, 2800 and 3900 b.
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  • 26
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Pyrimidine salvage pathway ; Semi-dominant mutants ; FUR1 ; Uracil phosphoribosyl transferase ; Regulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In Saccharomyces cerevisiae, the protein encoded by the FUR1 gene is absolutely required for the expression of uracil phosphoribosyl transferase activity. The occurrence of semi-dominant mutations for 5-fluorouracil-(5FU)-resistance at this locus led us to clone and sequence the semi-dominant fur 1–5 allele. A single point mutation, resulting in the substitution of arginine 134 for serine, is responsible for this mutant phenotype. The fur 1–5 allele is transcribed and expressed at the same level as the wild-type allele. But, in contrast with the wild-type, the UPR Tase activity of the fur 1–5 mutant strain is stimulated in vitro by UTP and does not, therefore, correspond to a loss of feedback of UPR Tase activity. We found that uracil, as a free base, induces a significative increase in transcription and UPR Tase activity in a wild-type strain as well as in uracil-overproducing mutants which principally explains the high efficiency of the pyrimidine salvage pathway in S. cerevisiae.
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  • 27
    ISSN: 1432-0983
    Keywords: Gene cloning ; Saccharomyces cerevisiae
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have carried out experiments aimed at explaining the observed variations in transformation frequencies when Saccharomyces cerevisiae or Saccharomyces carlbergensis are transformed with chimeric plasmids that contain one of 4 possible EcoRI fragments of the yeast 2-μm circle. These plasmids fall into 2 classes when used to transform 2 different yeast his3 auxotrophs, one (strain LL20) harbours indigenous 2-μm circle, and the other (strain YF233) is devoid of this plasmid. Hybrid plasmids containing either the 2.4 mega-dalton (mD) R-form EcoRI fragment (pYF88) or the l.4 mD L-form EcoRI fragment (pYF177) of 2-μm circle transform either of the two hosts at a high frequency (50,000 colonies per Mg in LL20 and 10,000 colonies per μg in YF233). Hybrid plasmids containing the 1.5 mD R-form EcoRI fragment (pYF87) or the 2.5 mD L-form EcoRI fragment (pYF178) of the 2-μm circle transform LL20 at a reduced frequency (6,000–16,000 colonies per μg) and YF233 at extremely low frequencies (1–5 colonies per μg). All plasmids retrieved from strain YF233 that had been transformed with pYF88 or pYF177 were identical to the original transforming plasmid. Of the plasmids retrieved from strain LL20 that had been transformed with pYF87 and pYF178, approximately half had acquired an extra copy of the 2-μm circle. Of the plasmids retrieved from strain LL20 that had been transformed with pYF88 and pYF177, an average of only approximately 13% had acquired an extra copy of 2-μm circle. Taken together, these observations indicate that the transformation of yeast by a plasmid lacking the ability to replicate (pYF87 and pYF1780) occurs by the recombinational acquisition of 1 copy of the host 2-μm circle, which serves to supply the incoming plasmid with missing essential sequences. A comparison of 2-μm circle DNA fragments carried by pYF88 and pYF177 indicates that the region of 2-μm circle required for high frequency transformation is a 1.2 mD segment that is common to the 2.4 mD R-form and 1.4 ml) L-form EcoRI fragments. This region extends from the EcoRI cut site adjacent to the PstI site, through to the end of the inverted repeat. However, the inverted repeat sequence alone is not sufficient to bestow high frequency transformation of yeast.
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  • 28
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    Current genetics 18 (1990), S. 401-403 
    ISSN: 1432-0983
    Keywords: Baking yeast ; Saccharomyces cerevisiae ; Dough leavening ; Benomyl
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary To investigate the leavening ability of yeast in dough, chromosome loss was induced by benomyl treatment in YOY1037, a diploid between a baking strain and a laboratory strain, and its effect on the leavening ability was studied. When benomyl-treated cells were spread on plates with a dye indicator for ploidy, about 20% of the visible colonies were stained dark blue or dark purple; the rest stained pale blue, similar to the diploid YOY1037. Strains showing the MATα phenotype, and non-galactose fermenting strains, apparently having lost particular chromosomes, were observed only in those with darkcoloured colonies. Strains with dark-coloured colonies showed a wider range of leavening ability than did those with pale-coloured colonies.
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  • 29
    ISSN: 1432-0983
    Keywords: Xylitol dehydrogenase gene ; Pichia stipitis ; Saccharomyces cerevisiae ; Xylose utilization
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    Notes: Summary A P. stipitis cDNA library in λgt11 was screened using antisera against P. stipitis xylose reductase and xylitol dehydrogenase, respectively. The resulting cDNA clones served as probes for screening a P. stipitis genomic library. The genomic XYL2 gene was isolated and the nucleotide sequence of the 1089 bp structural gene, and of adjacent non-coding regions, was determined. The XYL2 open-reading frame codes for a protein of 363 amino acids with a predicted molecular mass of 38.5 kDa. The XYL2 gene is actively expressed in S. cerevisiae transformants. S. cerevisiae cells transformed with a plasmid, pRD1, containing both the xylose reductase gene (XYL1) and the xylitol dehydrogenase gene (XYL2), were able to grow on xylose as a sole carbon source. In contrast to aerobic glucose metabolism, S. cerevisiae XYL1-XYL2 transformants utilize xylose almost entirely oxidatively.
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  • 30
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Centromere flanking sequences ; tRNA modification enzymes
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    Notes: Summary Transcriptional analysis of the region flanking the left boundary of the centromere of chromosome VI revealed the presence of a gene immediately adjacent to CEN6. The transcription of the gene is directed toward the centromere, and nucleotide sequence analysis showed that the coding region terminates only 50 bp away from CEN6. Our results extend to chromosome VI the observation that centromere-flanking regions of S. cerevisiae are transcriptionally active. Disruption of the coding region of the gene showed that its product, whilst not essential for cell viability, is important for normal cell growth. The gene has been termed DEG1 (DEpressed Growth rate). Comparison of the deduced amino acid sequence of DEG1 with a protein sequence databank revealed homology with the enzyme tRNA pseudouridine synthase I of E. coli.
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  • 31
    ISSN: 1432-0983
    Keywords: Mutagen hyper-resistance ; Nitrogen mustard ; Saccharomyces cerevisiae
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    Notes: Summary A screening of haploid yeast strains for enhanced resistance to nitrogen mustard (HN2) yielded a recessive mutant allele, hnm1, that conferred hyper-resistance (HYR) to HN2. Diploids, homo- or heterozygous for the HNM1 locus, exhibit normal wild-type like resistance while homozygosity for hnm1 leads to the phenotype HYR to HN2. The hnm1 mutation could be found in yeast strains proficient or deficient in different DNA repair systems. In these mostly HN2-sensitive haploid repair-deficient mutants, hnm1 acted as a partial suppressor of HN2 sensitivity. All isolated recessive mutations conferring hyper-resistance belonged to a single complementations group. The HYR to HN2 phenotype was maximally expressed in growing cells and was associated with reduced mutability by HN2. HNM1 most probably controls uptake of HN2 which would be impaired in the hnm1 mutants.
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  • 32
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; G418 resistance ; Gene cartridges ; Heterologous Gene expression
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    Notes: Summary Coding sequence cartridges for aminoglycoside phosphotransferase (APT) were isolated from bacterial transposon Tn903. When incorporated into a heterologous gene construction utilising the PGK1 promoter and terminator, the heterologous APT gene provided a G418-resistance determinant that functioned efficiently as a dominant marker for yeast in both multiple- and single-copy. Transformant colonies on selective medium appeared rapidly, within 36–48 h, and growth rate of the transformed cells was normal. A simple and highly sensitive radiolabelling assay for APT enzyme activity was developed for use with crude cell protein extracts. Enzyme activity units were equated to the amount of APT protein present in the cells, and the APT protein was shown to be stable in yeast. Heterologous APT expression was 130-fold reduced compared with homologous PGK1. This resulted from an estimated two-fold decrease in mRNA level and a 65-fold decrease in translation efficiency. The latter was unaffected by AUG sequence context change, but corresponded with a high frequency of minor codons in the APT-coding sequence. APT can be used as a semi-quantitative reporter of gene expression, whose useful features are in vivo detection via the G418-resistance phenotype and powerful cell-free assay.
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  • 33
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    Current genetics 2 (1980), S. 115-120 
    ISSN: 1432-0983
    Keywords: Galactose fermentation ; Saccharomyces cerevisiae ; Regulatory mutant
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    Notes: Summary A novel type of regulatory mutation for galactose metabolism in Saccharomyces cerevisiae is described. The mutation named gal11 was recessive, non-allelic to GAL4, GAL80, GAL2, or GAL3, and unlinked to the gene cluster of GAL1, GAL10, and GAL7. It caused a ‘coordinate’ reduction of galactokinase, galactose-1-P uridylyl transferase, and UDP-glucose 4-epimerase by a factor of more than 5, rendering the mutant cells galactose-nonfermenting. The effect of the mutation was manifested not only in cells grown on galactose but also in cells constitutively synthesizing the galactose-metabolizing enzymes.
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  • 34
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    Current genetics 19 (1991), S. 9-14 
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Mevalonate kinase ; Ergosterol
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    Topics: Biology
    Notes: Summary The nucleotide sequence of the ERG12 gene, encoding mevalonate kinase, from Saccharomyces cerevisiae is presented. The longest open reading frame may code for a protein containing 443 amino acids with a deduced relative molecular mass of 48 500. The analysis of the nucleotide sequence reveals a complete identity with the yeast gene RAR1, isolated elsewhere by complementation of a rar1 mutation involved in the stability of plasmids with weak ARS. In addition, we show that mevalonate kinase is not a rate-limiting enzyme; however its sensitivity to FFP could be a key regulatory mechanism in the sterol pathway of yeast.
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  • 35
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    Current genetics 2 (1980), S. 223-228 
    ISSN: 1432-0983
    Keywords: Transcriptional Units ; GAL Genes ; Saccharomyces cerevisiae ; UV mapping
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    Topics: Biology
    Notes: Summary The size of the transcriptional unit of the structural genes for three galactose-metabolizing enzymes which form a cluster on chromosome II in Saccharomyces cerevisiae was studied by the ultraviolet light (UV)-mapping technique. Thus the size of the primary transcripts of GAL7 for galactose-1-phosphate uridylyl transferase, GAL10 for uridine diphosphoglucose 4-epimerase, or GAL1 for galactokinase were estimated to be 0.81 x 106, 1.1 x 106, or 1.3 x 106 respectively. In the light of these data together with the known directions of transcription of the genes, we concluded that each of three genes was transcribed from its own promoter.
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  • 36
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Episomal plasmid ; Copy number control ; Plasmid maintenance ; Glycolytic enzyme levels
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    Topics: Biology
    Notes: Summary This study demonstrates how varying the promoter strength of an essential gene on a yeast 2μORI-STB YEp multicopy vector can influence vector copy levels. A phosphoglycerate kinase gene (PGK) on this plasmid was made essential for fermentative growth by transformation into a pgk - yeast strain. When in these PGK- transformants the requirement for PGK expression was the sole selective criterion for plasmid maintenance, PGK promoter activity was inversely related to vector copy levels. Plasmids with an efficiently-transcribed PGK gene were maintained at approximately one copy per cell, whereas those lacking the UAS that normally directs high basal PGK transcription levels were present at up to 10–15 copies. All cultures of these PGK+ transformants contained only a low proportion of pgk - cells. Since mitotic loss of the plasmid arrests growth through loss of a functional PGK allele, PGK confers high stability to the YEp vector in such a pgk - genetic background. In this system YEp vector levels are probably influenced by PGK transcription because high expression of PGK is needed in rapid fermentative growth. Remarkably, low plasmid PGK promoter activity caused PGK mRNA levels slightly higher than those found in yeast with normal PGK regulation. A higher plasmid copy number is therefore not the only factor counteracting the effects of low PGK transcription, and it is possible that PGK mRNA becomes more stable in response to inefficient PGK transcription.
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  • 37
    ISSN: 1432-0983
    Keywords: Cyanophora paradoxa ; Ferredoxin-NADP+-oxidoreductase ; Protein-import ; Evolution
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    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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  • 38
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Sporulation ; Inessential genes ; Genome organization
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    Notes: Summary The SPR6 gene of Saccharomyces cerevisiae encodes a moderately abundant RNA that is present at high levels only during sporulation. The gene contains a long open reading frame that could encode a hydrophilic protein approximately 21 kDa in size. This protein is probably produced by the yeast, because the lacZ gene of Escherichia coli is expressed during sporulation when fused to SPR6 in the expected reading frame. SPR6 is inessential for sporulation; mutants that lack SPR6 activity sporulate normally and produce viable ascospores. Nonetheless, the SPR6 gene encodes a function that is relevant to sporulating cells; the wild-type allele can enhance sporulation in strains that are defective for several SPR functions. SPR6 is located on chromosome V, 14.4 centimorgans centromere-distal to MET6.
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  • 39
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Nucleo-mitochondrial interactions ; Mitochondrial status ; Lycorine
    Source: Springer Online Journal Archives 1860-2000
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    Notes: Summary In a previous paper we have shown that the alkaloid lycorine inhibits growth of rho +, mit - and rho -, strains of Saccharomyces cerevisiae, whereas strains devoid of mitochondrial DNA (rho o) are resistant to more than 200 μg/ml of the alkaloid. In this report we show that hypersuppressive petites are almost as resistant as rho o mutants, whereas isogenic rho - petites, which have retained tained longer segments of the genome, are sensitive to the drug.
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  • 40
    ISSN: 1432-0983
    Keywords: Schizosaccharomyces pombe ; Saccharomyces cerevisiae ; CaMV 35S promoter ; CaMV 35S terminator ; Heterologous expression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Complementation of fission yeast mutants by plant genomic libraries could be a promising method for the isolation of novel plant genes. One important prerequisite is the functioning of plant promoters and terminators in Schizosaccharomyces pombe and Saccharomyces cerevisiae. Therefore, we studied the expression of the bacterial β-glucuronidase (GUS) reporter gene under the control of the Cauliflower Mosaic Virus (CaMV) 35S promoter and 35S terminator. We show here that S. pombe initiates transcription at exactly the same start site as was reported for tobacco. The 35S CaMV terminator is appropriately recognized leading to a polyadenylated mRNA of the same size as obtained in plant cells transformed with the same construct. Furthermore, the GUS-mRNA is translated into fully functional GUS protein, as determined by an enzymatic assay. Interestingly, expression of the 35S promoter in the budding yeast S. cerevisiae was found to be only moderate and about hundredfold lower than in S. pombe. To investigate whether different transcript stabilities are responsible for this enormous expression difference in the two yeasts, the 35S promoter was substituted by the ADH (alcohol dehydrogenase) promoter from fission yeast. In contrast to the differential expression pattern of the 35S promoter, the ADH promoter resulted in equally high expression rates in both fission and budding yeast, comparable to the 35S promoter in S. pombe. Since the copy number of the 35S-GUS constructs differs only by a factor of two in the two yeasts, it appears that differential recognition of the 35S promoter is responsible for the different transcription rates.
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  • 41
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Mitochondria ; Intron-encoded proteins ; Recombination
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    Notes: Summary The respiratory competency of a yeast strain devoid of mitchondrial introns is quite normal. However, it may be asked whether intron-encoded proteins participate in metabolisms other than those of mitochondrial introns. Using strains without mitochondrial introns we have answered two questions. The first was: does the absence of intron-encoded proteins abolsh mitochondrial recombination? The second was: do mitochondrial introns and intron-encoded proteins play a part in mitochondrial DNA rearrangements induced by ethidium bromide (rho- production)? We have shown that the introns and intron-encoded proteins are not essential essential components of either phenomenon.
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  • 42
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    Current genetics 18 (1990), S. 23-27 
    ISSN: 1432-0983
    Keywords: Protein translocation ; Saccharomyces cerevisiae ; Peroxisomes ; Overexpression
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Import of proteins into organelles usually requires a cis-acting targeting signal. Analysis of various hybrid proteins, consisting of mouse DHFR and parts of catalase A from Saccharomyces cerevisiae, revealed that fusion proteins containing the N-terminal 126 amino acids, or less, of catalase A remain in the cytosol whereas fusion proteins containing 140, or more, N-terminal amino acids of catalase A form large aggregates inside the cell. These protein bodies, which lack a surrounding membrane, copurified with peroxisomes on cell fractionation. The peroxisomal targeting signal of catalase A does not reside at the C-terminus or at the N-terminus.
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  • 43
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    Journal of molecular evolution 16 (1980), S. 149-150 
    ISSN: 1432-1432
    Keywords: Exons ; Evolution ; Heme-binding proteins
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    Topics: Biology
    Notes: Summary It is known that globin genes contain three exons with the middle exon coding for a four-helical supersecondary structure responsible for heme binding. Since this portion of the globin peptide chain can be structurally superimposed onto the cytochromec and cytochromeb 5 chains (Argos and Rossmann 1979), it can be inferred that the cytochromec gene will contain only one coding sequence while the cytochromeb 5 gene will be composed of three exons as found in the globin gene.
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  • 44
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    Journal of molecular evolution 16 (1980), S. 211-267 
    ISSN: 1432-1432
    Keywords: Nucleic acids ; Proteins ; Natural selection ; Genetics ; Nonrandom molecular divergence ; Nonrandom REH theory ; Evolution ; mRNA ; DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary REH theory is extended by deriving the theoretical equations that permit one to analyze the nonrandom molecular divergence of homologous genes and proteins. The nonrandomicities considered are amino acid and base composition, the frequencies with which each of the four nucleotides is replaced by one of the other three, unequal usage of degenerate codons, distribution of fixed base replacements at the three nucleotide positions within codons, and distributions of fixed base replacements among codons. The latter two distributions turn out to dominate the accuracy of genetic distance estimates. The negative binomial density is used to allow for the unequal mutability of different codon sites, and the implications of its two limiting forms, the Poisson and geometric distributions, are considered. It is shown that the fixation intensity — the average number of base replacements per variable codon - is expressible as the simple product of two factors, the first describing the asymmetry of the distribution of base replacements over the gene and the second defining the ratio of the average probability that a codon will fix a mutation to the probability that it will not. Tables are given relating these features to experimentally observable quantities inα hemoglobin,β hemoglobin, myoglobin, cytochromec, and the parvalbumin group of proteins and to the structure of their corre-sponding genes or mRNAs. The principal results are (1) more accurate methods of estimating parameters of evolutionary interest from experimental gene and protein sequence data, and (2) the fact that change in gene and protein structure has been a much less efficient process than previously believed in the sense of requiring many more base replacements to effect a given structural change than earlier estimation procedures had indicated. This inefficiency is directly traceable to Darwinian selection for the nonrandom gene or protein structures necessary for biological function. The application of these methods is illustrated by detailed consideration of the rabbitα -andβ hemoglobin mRNAs and the proteins for which they code. It is found that these two genes are separated by about 425 fixed base replacements, which is a factor of two greater than earlier estimates. The replacements are distributed over approximately 114 codon sites that were free to accept base mutations during the divergence of these two genes.
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  • 45
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    Journal of molecular evolution 17 (1981), S. 31-42 
    ISSN: 1432-1432
    Keywords: Pea ; Mung bean ; Genome organization ; Evolution ; Amplification ; Repetitive DNA ; Single copy DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Essentially all of the sequences in the pea (Pisum sativum) genome which reassociate with single copy kinetics at standard (Tm -25°C) criterion follow repetitive kinetics at lower temperatures (about Tm-35°C). Analysis of thermal stability profiles for presumptive single copy duplexes show that they contain substantial mismatch even when formed at standard criterion. Thus most of the sequences in the pea genome which are conventionally defined as “single copy” are actually “fossil repeats” — that is, they are members of extensively diverged (mutuated) and thus presumably ancient families of repeated sequences. Coding sequences as represented by a cDNA probe prepared from poly-somal poly(A) + mRNA reassociate with single copy kinetics regardless of criterion and do not form mismatched duplexes. The coding regions thus appear to be composed of true single copy sequences but they cannot represent more than a few percent of the pea genome. Ancient diverged repeats are present, but not a prominent feature of the smaller mung bean (Vigna radiata) genome. An extension of a simple evolutionary model is proposed in which these and other differences in genome organization are considered to reflect different rates of sequence amplification or genome turnover during evolution. The model accounts for some of the differences between typical plant and animal genomes.
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  • 46
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    Journal of molecular evolution 17 (1981), S. 368-376 
    ISSN: 1432-1432
    Keywords: Evolution ; Phylogeny ; Maximum likelihood ; Parsimony ; Estimation ; DNA sequences
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    Topics: Biology
    Notes: Summary The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of the estimate of the tree.
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  • 47
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    Journal of molecular evolution 18 (1981), S. 15-17 
    ISSN: 1432-1432
    Keywords: Amino acid code ; Evolution ; Primitive codes ; Mitochondria
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    Notes: Summary Differences between mitochondrial codes and the universal code indicate that an evolutionary simplification has taken place, rather than a return to a more primitive code. However, these differences make it evident that the universal code is not the only code possible, and therefore earlier codes may have differed markedly from the previous code. The present universal code is probably a “frozen accident.” The change in CUN codons from leucine to threonine (Neurospora vs. yeast mitochondria) indicates that neutral or near-neutral changes occurred in the corresponding proteins when this code change took place, caused presumably by a mutation in a tRNA gene.
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  • 48
    ISSN: 1432-1432
    Keywords: Monomeric hemoglobins ; Dimeric hemoglobins ; Chironomus ; Antibodies ; Evolution ; Gene duplication
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    Notes: Summary The monomeric hemoglobins ofChironomus tentans andC. pallidivittatus have been isolated and separated into their respective components by gel chromatography on Sephadex G-75 and ion-exchange chromatography on DEAE-Sephacel. The amino acid compositions of the purified components are given. The sequence of the 30 N-terminal amino acid residues of one of the monomeric components (Hb I fromC. pallidivittatus) was determined and found to be identical in almost all of its parts with the monomeric hemoglobins ofC. thummi (CTT III and CTT IV). Antibodies against the monomeric hemoglobins Hb I and Hb IIc and the dimeric fraction were highly specific and no cross reaction between dimeric and monomeric hemoglobins could be demonstrated. The antibodies against the monomers crossreact with the monomeric hemoglobins CTT III and CTT IV ofC. thummi. Taken together with genetic data, the immunological results indicate that divergence of monomeric from dimeric forms was an early event in the evolution of the various hemoglobins inChironomus.
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  • 49
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    Journal of molecular evolution 30 (1990), S. 489-492 
    ISSN: 1432-1432
    Keywords: Actinomyces ; Phosphotransferase ; Aminoglycoside ; Phylogenetic tree ; Evolution
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    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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  • 50
    ISSN: 1432-1432
    Keywords: Mitochondrial DNA ; Evolution ; Echinoderms ; Sea stars ; DNA sequence ; Mitochondrial proteins ; Mitochondrial tRNA genes
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    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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  • 51
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    Journal of molecular evolution 19 (1982), S. 20-27 
    ISSN: 1432-1432
    Keywords: GU base pairing ; RNA replication ; Globular proteins ; Genetic code ; Evolution
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    Topics: Biology
    Notes: Summary It has previously been shown that the formation of GU base pairs in RNA copying processes leads to an accumulation of G and U in both strands of the replicating RNA, which results in a non-random distribution of base triplets. In the present paper, this distribution is calculated, and, using the χ2-test, a correlation between the distribution of triplets and the amino acid composition of the evolutionarily conservative interior regions of selected globular proteins is established. It is suggested that GU wobbling in early replication of RNA could have led to the observed amino acid composition of present-day protein interiors. If this hypothesis is correct, the GU wobbling must have been very extensive in the imprecisely replicating RNA, even reaching values close to the critical for stability of its double-helical structure. Implications of the hypothesis both for the evolution of the genetic code and of proteins are discussed.
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  • 52
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    Journal of molecular evolution 19 (1983), S. 203-213 
    ISSN: 1432-1432
    Keywords: Evolution ; Phylogenetic distribution ; Repetitive-dispersed DNAs ; Speciation ; Transposons
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    Notes: Summary We have examined the phylogenetic distribution of a spectrum ofDrosophila repetitive-dispersed DNAs ranging from structurally complex transposable elements to scrambled middle repetitive sequences. Our data suggest that unlike typical “genes” these DNAs are unstable components of the drosophilid genome. The unusual behavior of these repetitive-dispersed DNAs raises the possibility that this type of sequence may have an important role in the evolution of the family Drosophilidae.
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  • 53
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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
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    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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  • 54
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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
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    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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  • 55
    ISSN: 1432-1432
    Keywords: Bacteria ; Sugars ; Phosphotransferase system ; Transport proteins ; Evolution ; Sequence comparisons ; NADH dehydrogenase ; Mitochondria
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    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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  • 56
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    Journal of molecular evolution 15 (1980), S. 149-159 
    ISSN: 1432-1432
    Keywords: Genes ; REH theory ; Genetic distance ; Evolution ; mRNA ; Nucleic acids
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    Notes: Summary It is shown how REH theory in conjunction with mRNA or gene sequence data can be used to obtain estimates of the fixation intensity, the number of varions, and the total mutations fixed between homologous pairs of nucleic acids. These estimates are more accurate than those that can be derived from amino acid sequence data. The method is illustrated forα andβ hemoglobin genes and these improved estimates are compared with those made from the amino acid sequences for which those genes code. Significant differences are found between the estimates made by these two methods. For theβ hemoglobin gene sequences examined here, the fixation intensity is some-what less than the protein data had suggested, and the number of rations is considerably greater. Depending on the gene sequences examined, between 62 and 83% of the codons appear able to fix mutations during the divergences considered. This reflects the constraints of natural selection on acceptable mutations. The total number of base replacements separating the genes for human, mouse, and rabbitβ hemoglobin varies from 61 to 105 depending on the pair examined. Rabbitα andβ hemoglobin are separated by at least 290 fixed mutations. For such distantly related sequences estimates made from protein and mRNA data differ less, reflecting the higher quality of information from the many observed changes in primary structure. The effects of nonrandom gene structure on these evolutionary estimates and the fact that various genetic events are not equiprobable are discussed.
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  • 57
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    Journal of molecular evolution 21 (1984), S. 54-57 
    ISSN: 1432-1432
    Keywords: Mitochondrion ; Cytochrome C ; Rhodospirillaceae ; Endosymbiosis ; rRNA ; Evolution
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    Notes: Summary The comparative morphology and pigmentation of protists suggest that those with tubular mitochondrial cristae belong to a different lineage than those with lamellar cristae and that the evolutionary divergence might have been very early. We propose that the difference in cristal morphology is the result of separate origins of the mitochondria from endosymbionts related to the Rhodospirillaceae (purple nonsulfur bacteria) but differing in the morphology of their internal membranes. Comparisons of the cytochromes c of protists and the Rhodospirillaceae and of 16s rRNA T1 oligonucleotide catalogs in the Rhodospirillaceae do not contradict, and in fact provide support for, the idea. More extensive evidence may be lacking simply because cytochromes c have been studied in very few protists with tubular mitochondrial cristae.
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  • 58
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    Journal of molecular evolution 21 (1984), S. 72-75 
    ISSN: 1432-1432
    Keywords: Heat ; Rates of copy error ; Evolution
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    Notes: Summary Heat induces a number of premutational lesions (for example, the deamination of cytosine to uracil) in DNA and RNA. These kinds of errors occur in resting as well as replicating polynucleotides. However, an increase in temperature also raises the probability of copying error occurring in nucleic acids because of increased thermal noise in the replicative machinery. In most modern genetic systems, the majority of heat-induced lesions are efficiently repaired. It follows that the importance of heat-induced error increases as the effectiveness of repair declines. We show in this paper that the error rate of enzymatic polynucleotide copying is expected to increase monotonically with temperature. We also explore the effects of temperature variations on the early evolution of biological information transmission mechanisms.
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  • 59
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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
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    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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    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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    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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    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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  • 62
    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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  • 63
    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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  • 64
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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
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    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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    Journal of molecular evolution 36 (1993), S. 448-457 
    ISSN: 1432-1432
    Keywords: Retrovirus ; HIV ; CD4 ; Minus strand ; Alternate reading frame ; Frameshift ; Divergence ; Evolution
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    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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  • 67
    ISSN: 1432-1432
    Keywords: Thiolase ; Peroxisome evolution ; Bootstrap analysis ; Saccharomyces cerevisiae
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    Notes: Summary The thiolase family is a widespread group of proteins present in prokaryotes and three cellular compartments of eukaryotes. This fact makes this family interesting in order to study the evolutionary process of eukaryotes. Using the sequence of peroxisomal thiolase from Saccharomyces cerevisiae recently obtained by us and the other known thiolase sequences, a phylogenetic analysis has been carried out. It shows that all these proteins derived from a primitive enzyme, present in the common ancestor of eubacteria and eukaryotes, which evolved into different specialized thiolases confined to various cell compartments. The evolutionary tree obtained is compatible with the endosymbiotic theory for the origin of peroxisomes.
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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 36 (1993), S. 545-554 
    ISSN: 1432-1432
    Keywords: Echinoderms ; Evolution ; Phylogeny ; mtDNA ; Mitochondrial gene arrangements
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    Topics: Biology
    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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  • 71
    ISSN: 1432-1432
    Keywords: Lens ; Crystallin ; Squid ; Chicken ; Gene ; Regulation ; AP-1 ; Evolution
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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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  • 72
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    Journal of molecular evolution 17 (1981), S. 167-181 
    ISSN: 1432-1432
    Keywords: Evolution ; Genetics ; REH theory ; Mutations ; Natural selection ; Nucleic acids ; Proteins ; Paleogenetics
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    Notes: Summary We have independently repeated the computer simulations on which Nei and Tateno (1978) base their criticism of REH theory and have extended the analysis to include mRNAs as well as proteins. The simulation data confirm the correctness of the REH method. The high average value of the fixation intensity μ2 found by Nei and Tateno is due to two factors: 1) they reported only the five replications in which μ2 was high, excluding the forty-five replications containing the more representative data;and 2) the lack of information, inherent to protein sequence data, about fixed mutations at the third nucleotide position within codons, as the values are lower when the estimate is made from the mRNAs that code for the proteins. REH values calculated from protein or nucleic acid data on the basis of the equiprobability of genetic events underestimate, not overestimate, the total fixed mutations. In REH theory the experimental data determine the estimate T2 of the time average number of codons that have been free to fix mutations during a given period of divergence. In the method of Nei and Tateno it is assumed, despite evidence to the contrary, that every amino acid position may fix a mutation. Under the latter assumption, the measure X2 of genetic divergence suggested by Nei and Tateno is not tenable: values of X2 for theα hemoglobin divergences are less than the minimum number of fixed substitutions known to have occurred. Within the context of REH theory, a paradox, first posed by Zuckerkandl, with respect to the high rate of covarion turnover and the nature of general function sites in proteins is resolved.
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  • 73
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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
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    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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  • 74
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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
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    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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  • 75
    ISSN: 1432-1432
    Keywords: Archaebacteria ; Taxonomy ; Evolution ; DNA ; 16S rRNA ; Hybridization ; Phylogeny ; Thermoproteales
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    Notes: Summary DNAs from 16 species of archaebacteria including 6 novel isolates were hybridized with 16S rRNAs from 7 species representing different orders or groups of the urkingdom of archaebacteria. The yields, normalized for the number of genes perµg of DNA, and the temperature stabilities of all hybrids were determined and related to each other. A taxonomic tree constructed from such fractional stability data reveals the same major divisions as that derived from comparative cataloging of 16S rRNA sequences. The extreme halophiles appear however as a distinct order besides the three known divisions of methanogens. The methanogens, the halophiles andThermoplasma form one of two clearly recognizable branches of the archaebacterial urkingdom. The order represented bySulfolobus and the related novel orderThermoproteales form the other branch. Three novel genera,Thermoproteus, Desulfurococcus and the “stiff filaments” represent three families of this order. The extremely thermophilic methanogenMethanothermus fervidus belongs to theMethanobacteriales. SN1, a methanogen from Italy, appears as another species of the genusMethanococcus. Another novel methanogen, M3, represents a genus or family of the orderMethanomicrobiales.
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  • 76
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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
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    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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  • 77
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    Journal of molecular evolution 19 (1982), S. 80-86 
    ISSN: 1432-1432
    Keywords: Microtubules ; Tubulin ; Evolution
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    Notes: Summary Tubulin subunits have been isolated from a variety of protists and marine invertebrates. The sources were: sperm tails of a tunicate (Ciona intestinalis), an abalone (Haliotis rufescens) and a sea anemone (Tealia crassicornis), the gill cilia of a clam (Mercenaria mercenaria), the cilia of a ciliate (Tetrahymena pyriformis) and the cytoplasm of a slime mold (Physarum polycephalum). All the β-tubulins, as characterised by their electropherograms after limited proteolytic cleavage withStaphylococcus aureus protease, were fairly similar. In contrast, two markedly different peptide patterns were found for the α-tubulins of (a) metazoan axonemes and (b) protistan axonemes, plant axonemes and slime mold cytoplasm. Metazoan axonemal α-tubulin peptide patterns could be further divided into two similar but distinct subtypes which did not correlate with the taxonomic divisions of deuterostomia and protostomia, or to different tubulins within an axoneme, or to different tubulins of flagella and cilia. We have postulated that these small differences may be accounted for by a simple glutamicaspartic acid exchange at a particular position in the α-tubulin sequence. Identical peptide patterns were observed for sea urchin and sea anemone sperm tail tubulins, proving that the metazoan type of axonemal tubulin arose before the divergence of bilateral and radial symmetric organisms. The close similarity of the slime mold cytoplasmic α-tubulin peptide pattern to protistan and plant axonemal α-tubulin patterns suggests that the same type of tubulin might be used to form both axonemal and cytoplasmic types of microtubules in protists and plants. The large structural constraints imposed upon this tubulin molecule probably allowed very little change in its primary structure, thus explaining the similarity of tubulins from organisms which diverged at such an early time in eukaryote history. Duplication and modification of the tubulin gene may then have led to the development of specific axonemal and cytoplasmic microtubules during the evolution of the metazoa.
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  • 78
    ISSN: 1432-1432
    Keywords: Microbial phylogeny ; Evolution ; Aromatic biosynthesis ; Regulatory enzymes
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    Notes: Abstract Pseudomonad bacterial are a phylogenetically diverse assemblage of species named within contemporary genera that includePseudomonas, Xanthomonas andAlcaligenes. Thus far, five distinct rRNA homology groups (Groups I through V) have been established by oligonucleotide cataloging and by rRNA/DNA hybridization. A pattern of enzymic features of aromatic amino acid biosynthesis (enzymological patterning) is conserved at the level of rRNA homology, five distinct and unambiguous patterns therefore existing in correspondence with the rRNA homology groups. We sorted 87 pseudomonad strains into Groups (and Subgroups) by aromatic pathway patterning. The reliability of this methodology was tested in a blind study using coded cultures of diverse pseudomonad organisms provided by American Type Culture Collection. Fourteen of 14 correct assignments were made at the Group level (the level of rRNA homology), and 12 of 14 correct assignments were made at the finer-tuned Subgroup levels. Many strains of unknown rRNA-homology affiliation had been placed into tentative rRNA groupings based upon enzymological patterning. Positive confirmation of such strains as members of the predicted rRNA homology groups was demonstrated by DNA/rRNA hybridization in nearly every case. It seems clear that the combination of these molecular approaches will make it feasible to deduce the evolution of biochemical-pathway construction and regulation in parallel with the emerging phylogenies of microbes housing these pathways.
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  • 79
    ISSN: 1432-1432
    Keywords: mtDNA ; Gene mapping ; Evolution ; Yeasts
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    Notes: Summary Mapping of sequences specifying the large and small ribosomal RNAs and six polypeptides in the circular 23.7 kbp mitochondrial DNA ofSaccharomyces exiguus has shown that these genes have the same orientation and that a 5 gene cluster is common to this DNA and the 18.9 kbp mtDNA fromTorulopsis glabrata. Included in the preserved region are juxtaposed sequences specifying ATPase subunits 6 and 9 which have the same order and orientation as analogous genes in theEscherichia coli unc operon. The above data, together with knowledge that these two sequences are dispersed in larger yeast mtDNAs, leads us to suggest that larger forms are derived from a smaller ancestral molecule that would have had some resemblance to the mtDNAs ofS. exiguus andT. glabrata.
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    Journal of molecular evolution 19 (1983), S. 342-345 
    ISSN: 1432-1432
    Keywords: mtDNA ; Gene mapping ; Evolution ; Yeasts
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    Notes: Summary Analysis of gene order and orientation in the circular 18.9 kbp mitochondrial DNA molecule ofTorulopsis glabrata has shown that the eight large genic sequences have the same orientation and that a five gene cluster which runs — cytochrome b, cytochrome oxidase subunit 1, ATPase subunits 6 and 9 and cytochrome oxidase subunit 2 — is common to this DNA andSaccharomyces exiguus mtDNA (see accompanying paper).
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  • 81
    ISSN: 1432-1432
    Keywords: Lagomorphs ; Rabbit ; Mitochondrial DNA ; Heteroplasmy ; Restriction site polymorphism ; Evolution
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    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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  • 82
    ISSN: 1432-1432
    Keywords: Aspergillus ; 5S rRNA genes ; 5S rRNA pseudogenes ; Evolution
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    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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  • 83
    ISSN: 1432-1432
    Keywords: Yeast ; E. coli ; tRNA ; rRNA ; Sequence homologies ; Evolution ; Origins ; Coding mechanism
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    Notes: Summary Many tRNAs ofE. coli and yeast contain stretches whose base sequences are similar to those found in their respective rRNAs. The matches are too frequent and extensive to be attributed to coincidence. They are distributed without discernible pattern along and among the RNAs and between the two species. They occur in loops as well as in stems, among both conserved and non-conserved regions. Their distributions suggest that they reflect common ancestral origins rather than common functions, and that they represent true homologies.
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  • 84
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    Journal of molecular evolution 20 (1984), S. 128-134 
    ISSN: 1432-1432
    Keywords: Snake venom ; Neurotoxin ; Cytotoxin ; Evolution ; Circular dichroism
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    Notes: Summary The amino acid sequences of the 139 homologous “short” neurotoxins, “long” neurotoxins and cytotoxins so far characterised from elapid snake venoms were compared on the basis of the amino acid deletion/insertion events that have occurred during evolution. Systematic grouping of the toxins according to similarity suggests that the short neurotoxins resemble the cytotoxins more closely than they do the long neurotoxins. The significance of this finding is discussed in relation to the methodology, the conformations of the toxins (as represented by circular dichroism spectra) and the outcome of the study that would have been obtained had more traditional methods been used. It appears probable that the cytotoxins evolved relatively recently from neurotoxic ancestors.
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  • 85
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    Journal of molecular evolution 33 (1991), S. 464-469 
    ISSN: 1432-1432
    Keywords: Evolution ; tRNA ; Ribosome ; Peptide bond ; Catalytic RNA
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    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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  • 86
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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
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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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  • 87
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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
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    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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  • 88
    ISSN: 1432-1432
    Keywords: Evolution ; Teleostei ; Clupea harengus ; Esox lucius ; Fish ; Polymerase chain reaction ; Calcium binding
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    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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  • 89
    ISSN: 1432-1432
    Keywords: Ribonuclease ; Evolution ; Gene duplication ; Ruminants
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    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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    Journal of molecular evolution 37 (1993), S. 71-76 
    ISSN: 1432-1432
    Keywords: Evolution ; Catalase ; Phylogenetic tree
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    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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    Journal of molecular evolution 39 (1994), S. 13-21 
    ISSN: 1432-1432
    Keywords: Y chromosome ; Great ape ; Human ; Evolution ; DNA
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    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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  • 92
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    Journal of comparative physiology 170 (1992), S. 575-588 
    ISSN: 1432-1351
    Keywords: Moth ; Sensorimotor integration ; Neuroethology ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Summary 1. Certain species of tiger moths emit clicks when stimulated by bat-like sounds. These clicks are generated by modified thoracic episterna (tymbals) (Fig. 1) and constitute a rhythmic behaviour activated by simple sensory input. 2. Tymbal periods are indirectly related to stimulus intensity and periods (Fig. 3). Moths initiate sounds with the tymbal opposite to the stimulated ear and once a sequence commences it continues in an undisrupted fashion. 3. The tymbal is innervated by a pleural branch (IIIN2a) of the metathoracic leg nerve, a similar anatomy to that in the unmodified episterna of silent moths (Fig. 5). Backfills of the IIIN2a in Cycnia tenera reveal sensory fibres and a cluster of 5–9 motor neurons with densely overlying dendritic fields (Fig. 6). 4. Extracellular recordings of the IIIN2a reveal a large impulse preceding each tymbal sound (Fig. 7). I suggest that this impulse results from the synchronous firing of 2–3 motor neurons and is the motor output of the tymbal central pattern generator (CPG). The spikes alternate (Figs. 9, 10) and are bilaterally co-related (Fig. 11) but with an phase asymmetry of 2–3 ms (Fig. 12). 5. Normal motor output continues in the absence of tymbal sounds (Fig. 13) and when all nerve-tymbal connections are severed (Fig. 14, Table 1) therefore this CPG operates independent of sensory feedback. A model is proposed for the tymbal circuitry based upon the present data and the auditory organization of related noctuid moths (Fig. 15). I propose that the tymbal response in modern arctiids evolved from either flight or walking CPGs and that preadaptive circuitry ancestral to tymbal movements still exists in modern silent Lepidoptera.
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    Journal of comparative physiology 171 (1992), S. 171-181 
    ISSN: 1432-1351
    Keywords: Colour vision ; Flower colours ; Evolution ; Hymenoptera ; Pollination ecology
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    Topics: Biology , Medicine
    Notes: Summary The evolutionary tuning between floral colouration and the colour vision of flower-visiting Hymenoptera is quantified by evaluating the informational transfer from the signalling flower to the perceiving pollinator. The analysis of 180 spectral reflection spectra of angiosperm blossoms reveals that sharp steps occur precisely at those wavelengths where the pollinators are most sensitive to spectral differences. Straight-forward model calculations determine the optimal set of 3 spectral photoreceptor types for discrimination of floral colour signals on the basis of perceptual difference values. The results show good agreement with the sets of photoreceptors characterized electrophysiologically in 40 species of Hymenoptera.
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    Journal of comparative physiology 175 (1994), S. 289-302 
    ISSN: 1432-1351
    Keywords: Compound eye ; Open rhabdom ; Neural superposition ; Visual ecology ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract Observations of the infrared deep pseudopupil, optical determinations of the corneal nodal point, and histological methods were used to relate the visual fields of individual rhabdomeres to the array of ommatidial optical axes in four insects with open rhabdoms: the tenebrionid beetle Zophobas morio, the earwig Forficula auricularia, the crane fly Tipula pruinosa, and the backswimmer Notonecta glauca. The open rhabdoms of all four species have a central pair of rhabdomeres surrounded by six peripheral rhabdomeres. At night, a distal pigment aperture is fully open and the rhabdom receives light over an angle approximately six times the interommatidial angle. Different rhabdomeres within the same ommatidium do not share the same visual axis, and the visual fields of the peripheral rhabdomeres overlap the optical axes of several near-by ommatidia. During the day, the pigment aperture is considerably smaller, and all rhabdomeres share the same visual field of about two interommatidial angles, or less, depending on the degree of light adaptation. The pigment aperture serves two functions: (1) it allows the circadian rhythm to switch between the night and day sampling patterns, and (2) it works as a light driven pupil during the day. Theoretical considerations suggest that, in the night eye, the peripheral retinula cells are involved in neural pooling in the lamina, with asymmetric pooling fields matching the visual fields of the rhabdomeres. Such a system provides high sensitivity for nocturnal vision, and the open rhabdom has the potential of feeding information into parallel spatial channels with different tradeoffs between resolution and sensitivity. Modification of this operational principle to suit a strictly diurnal life, makes the contractile pigment aperture superfluous, and decreasing angular sensitivities together with decreasing pooling fields lead to a neural superposition eye.
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  • 95
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    Journal of molecular evolution 31 (1990), S. 3-9 
    ISSN: 1432-1432
    Keywords: Caenorhabditis elegans ; Caenorhabditis briggsae ; hsp70 ; grp78 ; Gene comparison ; Evolution ; Regulatory elements
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Caenorhabditis elegans andCaenorhabditis briggsae are two closely related nematode species that are nearly identical morphologically. Interspecific cross-hybridizing DNA appears to be restricted primarily to coding regions. We compared portions of thehsp-3 homologs two grp 78-like genes, fromC. elegans andC. briggsae and detected regions of DNA identity in the coding region, the 5′ flanking DNAs, and the introns. Thehsp-3 homologs share approximately 98% and 93% identity at the amino acid and nucleotide levels, respectively. Using the nucleotide substitution rate at the silent third position of the codons, we have estimated a lower limit for the date of divergence betweenC. elegans andC. briggsae to be approximately 23–32 million years ago. The 5′ flanking DNAs and one of the introns contain elements that are highly conserved betweenC. elegans andC. briggsae. Some of the regions of nucleotide identity in the 5′ flanking DNAs correspond to previously detected identities including viral enhancer sequences, a heat shock element, and an element present in the regulatory regions of mammalian grp78 and grp94 genes. We propose that a comparison ofC. elegans andC. briggsae sequences will be useful in the detection of potential regulatory and structural elements.
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  • 96
    ISSN: 1432-1432
    Keywords: Archaebacteria ; rRNA operons ; Secondary structure ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Several sequences flanking the large rRNA genes of several transcripts from extreme thermophiles, extreme halophiles, and methanogens were aligned and analyzed for the presence of common primary and secondary structural features, which would bear on the concept of monphyletic archaebacteria. Few sequences were common to all the archaebacterial transcripts, and these were confined to short regions generally flanking putative double helices. At a secondary structural level, however, in addition to the previously characterized processing stems of the 16S and 23S RNAs, four helices were detected that were common to the archaebacterial transcripts: two in the 16S RNA leader sequence and two in the 16S-23S RNA spacer. Although all of these helices vary in size and form from organism to organism, three of them contain double helical segments that are strongly supported by compensating base changes among the three archaebacterial groups. Three extreme halophiles exhibited two additional helices in their relatively large spacers and a further helix preceding the 5S RNA, which are also supported by compensating base changes. Ribosomal RNA transcripts from eubateria/chloroplasts and eukaryotes were also examined for secondary structural features with locations and forms corresponding to those of the archaebacteria, but none were detected. The analysis provides support for the monophyletic nature of the archaebacteria and reinforces their differences from eubacteria/chloroplasts and eukaryotes.
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  • 97
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    Journal of molecular evolution 18 (1982), S. 287-292 
    ISSN: 1432-1432
    Keywords: Evolution ; Endosymbiosis ; Gene transfer ; Transmembrane movement of proteins ; Receptors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary In the origin of the mitochondrion and plastid, gene transfer from the ancestral endosymbiont to the host was proposed to be a crucial event. For this genic integration to proceed, products of transferred genes had to return to and enter the endosymbionts. The limiting event was the crossing of the barrier presented by the two semipermeable membranes bounding the proto-organelle. In this paper it is suggested that spontaneous transport allowed transferred gene encoded proteins to enter the endosymbionts before receptors evolved. The effects of these events, including the degeneration of the endosymbiont genome, are discussed. Although the presumed gene transfer had profound effects on the metabolic relationships between host and endosymbionts it probably cannot account for all examples of organelle/cytoplasmic isozyme pairs or the absence of amino acid synthetic enzymes in animal cells.
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  • 98
    ISSN: 1432-1432
    Keywords: Retroposon ; Salmonid ; +RNA ; Evolution ; Average sequence divergence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary An in vitro runoff transcription assay of total genomic DNA was developed. As an example of use of this assay, analysis of a highly repetitive sequence in the cherry salmon (Oncorhynchus masou) is described. Total genomic DNA of the cherry salmon was completely digested with Hpa 1, whose site is known to be in the tRNA-unrelated region of the cherry salmon Hpa 1 family. On transcription of the digested DNA in a HeLa cell extract, a discrete-sized RNA of about 100 nucleotides, constituting 70% of the transcripts, was produced, whereas on transcription of the undigested total DNA, only smeared RNA was obtained. In a fingerprint, the oligonucleotides of the discrete transcript from the digested total DNA were very distinct and exactly corresponded to those of a transcript from an Hpa 1 digest of a cloned DNA, but with few extra oligonucleotides. These results showed that the cherry salmon Hpa 1 family constitutes a major repetitive family in the genome of the cherry salmon. For determination of the distribution of the salmonid Hpa 1 family in other salmonid species, the same analysis was applied to DNAs from the chum salmon (Oncorhynchus keta), brown trout (Salmo trutta), Japanese common charr (Salvelinus leucomaenis pluvius), and Japanese huchen (Hucho perryi). The results showed that the salmonid Hpa 1 family is widespread in the genomes of salmonid species. A method and equations are also presented for estimating the relationship between the ratio of a given repetitive family to all the Pol III genes and its average sequence divergence by calculating the molar ratio of the runoff transcript to all the in vitro Pol III transcripts.
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  • 99
    ISSN: 1432-1432
    Keywords: Phylogenetic tree ; Likelihood method ; RNA polymerase ; Archaebacteria ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The amino acid sequences of the largest subunits of the RNA polymerases I, II, and III from eukaryotes were compared with those of archaebacterial and eubacterial homologs, and their evolutionary relationships were analyzed in detail by a recently developed tree-making method, the likelihood method of protein phylogeny, as well as by the neighbor-joining method and the parsimony method, together with bootstrap analyses. It was shown that the best tree topologies predicted by the first two methods are identical, whereas the last one predicts a distinct tree. The maximum likelihood tree revealed that, after the separation from archaebacteria, the three eukaryotic RNA polymerases diverged from an ancestral precursor in the eukaryotic lineage. This result is contrasted with the published result showing multiple origins for the three eukaryotic polymerases. It was shown that eukaryotic RNA polymerase I evolved much more rapidly than RNA polymerases II and III: The N-terminal half of RNA polymerase I shows an extraordinarily high evolutionary rate, possibly due to relaxed functional constraints. In contrast the evolutionary rate of archaebacterial RNA polymerase is remarkably limited. In addition, including the second largest subunit of the RNA polymerase, a detailed analysis for the branching pattern of the three major groups of archaebacteria was carried out by the maximum likelihood method. It was shown that the three major groups of archaebacteria are likely to form a single cluster; that is, archaebacteria are likely to be monophyletic as originally proposed by Woese and his colleagues.
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  • 100
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    Journal of molecular evolution 33 (1991), S. 42-48 
    ISSN: 1432-1432
    Keywords: Satellite DNA ; Mouse ; Human chromosomes 13 and 21 ; Evolution ; Saltatory amplification ; Homogenization
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The hypothesis that highly reiterated satellite DNAs in present-day populations evolve by molecular mechanisms that create, by saltatory amplification steps, new long arrays of satellite DNA, and that such long arrays are used for homogenization purposes, has been tested both in mouse and in humans. In mouse, the data obtained are consistent with this hypothesis. This was tested in more detail on chromosomes 13 and 21 of the human genome. A Centre d'Etudes du Polymorphisme Humain family, which in some individuals exhibits strong supplementary DNA bands following TaqI restriction endonuclease digestion and conventional gel electrophoresis, was analyzed by pulse field gel electrophoresis following restriction by BamHI. The supplementary bands on chromosome 13 (18 times the basic alpha satellite DNA repeat) and on chromosome 21 (a 9.5-mer) segregated with centromeric alpha satellite DNA blocks of 5 and 5.3 megabases, respectively. These are by far the largest alpha satellite block lengths seen in all chromosome 13 and chromosome 21 centrometric sequences so far analyzed in this manner. The possibility that these supplementary alpha satellite sequences were created in single individuals by saltatory amplification steps is discussed in light of our own data and that published by others. It is proposed that deletion events and unequal cross-overs, which both occur in large satellite DNA arrays, contribute to the homogenization of size and sequence of the alpha satellite DNA on most chromosomes of humans.
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