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  • 1
    Keywords: Virology. ; Evolution (Biology). ; Evolutionary genetics. ; Virology. ; Evolutionary Biology. ; Evolutionary Genetics.
    Description / Table of Contents: Theoretical analysis of the evolution of viral populations in sequence space, and empirical fitness landscapes -- Self-organized maps to derive fitness landscapes from deep sequencing data -- Mutations to overcome viral resistance in plants -- The role of recombination in the generation of new begomovirus phenotypes -- Plant virus adaptation to new hosts -- Viral fitness, host interactions, and resistance to antiviral agents -- Viral fitness and evolution of hepatitis C virus -- Population dynamics and fitness variations of hemorrhagic RNA viruses -- Coronavirus genome sequences, variation, and disease implications -- Epilogue: viral populations from a theoretical and experimental perspective.
    Abstract: This book unifies general concepts of plant and animal virus evolution and covers a broad range of topics related to theoretical and experimental aspects of virus population dynamics and viral fitness. Timely topics such as viral mechanisms to cope with antiviral agents, the adaptability of the virus to new hosts, emergence of new viral phenotypes, and the connections between short- and long-term virus evolution are included. By comparing plant and animal viruses, universal mechanisms responsible for fitness variations, viral emergence and disease mechanisms are explored. Although emphasis is put on specific plant and human viral pathogens, relevant similarities and differences to other viruses are highlighted. Additionally, readers will learn more about the adaptability of coronaviruses, including the recently emerged SARS-CoV-2, the causative agent of the COVID-19 pandemic. The book is aimed at students and scientists interested in basic and applied aspects of plant and animal virus population dynamics and evolution.
    Type of Medium: Online Resource
    Pages: X, 344 p. 80 illus., 74 illus. in color. , online resource.
    Edition: 1st ed. 2023.
    ISBN: 9783031156403
    Series Statement: Current Topics in Microbiology and Immunology, 439
    DDC: 579.2
    Language: English
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  • 2
    Call number: MR 90.0184
    Type of Medium: Monograph available for loan
    Pages: 225 S.
    Language: German
    Location: Upper compact magazine
    Branch Library: GFZ Library
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. ; Stafa-Zurich, Switzerland
    Solid state phenomena Vol. 97-98 (Apr. 2004), p. 27-36 
    ISSN: 1662-9779
    Source: Scientific.Net: Materials Science & Technology / Trans Tech Publications Archiv 1984-2008
    Topics: Physics
    Notes: Autocatalytic chemical reactions may lead to spatio-temporal patterns if processed under non-equilibrium conditions. The patterns disappear when the conditions change and information stored in these non-equilibrium structures is lost since precise reconstructions are impossible. Replication of molecules, in particular of polynucleotides RNA or DNA, is an autocatalytic process too. The storage of information in polynucleotide sequences, however, allows for reconstruction ofthe molecules under suitable conditions. Conservation of information in polymer sequences constitutes the basic difference between chemical and biological self-organization. Evolution of RNA molecules is considered as pattern formation in sequence space, which manifests itself as another pattern in the space of minimum-free-energy structures. In addition, optimization of RNA structures and properties is visualized as an evolutionary trial-and-error process. This process can beinterpreted as a simple form of learning at the level of ensembles or populations of molecules. Evolutionary optimization of RNA molecules occurs in steps: Short adaptive periods are interrupted by long epochs of quasi-stationarity during which the mean replication rate of the populations is essentially constant. Understanding of evolution is largely facilitated through consideration of sequence-structure relation as a many-to-one or non-invertible mapping from sequence space into structure space. Neutrality of sequences with respect to structure formation is highly relevant for evolutionary optimization on rugged fitness landscapes
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Journal of mathematical biology 32 (1994), S. 545-562 
    ISSN: 1432-1416
    Keywords: Map dynamics ; Bifurcation theory ; Deterministic chaos ; Poincaré section ; Replicator system ; Autocatalytic networks
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Mathematics
    Notes: Abstract Processes of replication and mutation pivotal to molecular evolution may be modelled by a set of coupled nonlinear differential equations descriptive of autocatalytic networks. Solutions of the four dimensional system reveal aperiodic behaviours and chaos, punctuated by regions of periodic oscillations of the population variables. This complicated dynamics is encapsulated in terms of polynomial mappings which cast the relevant features of these behaviours in compact form and reproduces many of the fine details of the sequences of bifurcations. The equations descriptive of replication are topologically equivalent to generalized Lotka-Volterra equations, and thus the present map dynamics analysis finds a corresponding broader range of potential future application.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Biological cybernetics 40 (1981), S. 9-15 
    ISSN: 1432-0770
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Computer Science , Physics
    Notes: Abstract A discussion of the game dynamics for asymmetric contest between two animal populations is presented by means of qualitative analysis.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Biological cybernetics 40 (1981), S. 1-8 
    ISSN: 1432-0770
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Computer Science , Physics
    Notes: Abstract The ordinary differential equation which transformes the game theoretical model of Maynard-Smith into a dynamical system is discussed and some important theorems and applications to symmetric contests in animal societies are presented.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    European biophysics journal 23 (1994), S. 29-38 
    ISSN: 1432-1017
    Keywords: Activation energy landscape ; RNA folding ; RNA melting ; RNA secondary structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that. assigns structure dependent overall rate constants of melting (or refolding) to a sequence. This induces a “landscape” of reaction rates, or activation energies, over the space of sequences with fixed length. We study the distribution and the correlation structure of these activation energies.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1432-1017
    Keywords: Key words RNA structural motifs ; GNRA tetraloops ; Conformational search ; Solvent effects ; Electrostatic continuum model ; AbbreviationsMC-SYM Macromolecular conformations by symbolic programming ; JUMNA Junction minimization of nucleic acids ; AMBER Assisted model building with energy refinement ; RF Reaction field ; FIESTA Field integrated electrostatic approach ; FD Finite difference ; sc Synclinal ; ac Anticlinal ; ap Antiperiplanar ; ED Electrostatic damping
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Physics
    Notes: Abstract The protocol of conformational analysis applied here to ribonucleotide oligomers combines conformational search in the space of torsion angles and energy minimization using the AMBER4.1 force field with a continuum treatment of electrostatic solute-solvent interactions. RNA fragments with 5′-GGGCGNNAGCCU-3′ sequences commonly fold into hairpins with four-membered loops. The combinatorial search for acceptable conformations using the MC-SYM program was restricted to loop nucleotides and yielded roughly 1500 structures being compatible with a double-stranded stem. After energy minimization by the JUMNA program (without applying any experimental constraints), these structures converged into an ensemble of 74 different conformers including 26 structures which contained the sheared G-A base pair observed in experimental studies of GNRA tetraloops. Energetic analysis shows that inclusion of solvent electrostatic effects is critically important for the selection of conformers that agree with experimentally determined structures. The continuum model accounts for solvent polarization by means of the electrostatic reaction field. In the case of GNRA loop sequences, the contributions of the reaction field shift relative stabilities towards conformations showing most of the structural features derived from NMR studies. The agreement of computed conformations with the experimental structures of GAAA, GCAA, and GAGA tetraloops suggests that the continuum treatment of the solvent represents a definitive improvement over methods using simple damping models in electrostatic energy calculations. Application of the procedure described here to the evaluation of the relative stabilities of conformers resulting from searching the conformational space of RNA structural motifs provides some progress in (non-homology based) RNA 3D-structure prediction.
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 109 (1998), S. 1833-1844 
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: The structural and electronic properties of homoatomic chains consisting of up to five Br-atoms are studied by means of the linear combination of Gaussian-type orbitals–local spin density method including nonlocal corrections to the exchange and correlation energy. A highly flexible basis set is used and the effects of introducing additional diffuse basis functions are examined. By comparison of the results for atomic Br and Br2 with those from very accurate correlated ab initio calculations the quality of the present method is established. Based on these results neutral and singly charged Br3, Br4 and Br5 are investigated, for which very few accurate data exist in literature. Geometries, harmonic vibrational frequencies, ionization potentials, electron affinities and charge distributions are reported and found in satisfactory agreement with available experimental data. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 92 (1988), S. 6881-6891 
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
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