Kooperativer Bibliotheksverbund

Berlin Brandenburg

and
and

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
Filter
Language
Year
  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 17 February 2015, Vol.112(7), pp.2058-63
    Description: Phylogenomics heavily relies on well-curated sequence data sets that comprise, for each gene, exclusively 1:1 orthologos. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe restriction of the data sets is not necessary. Building upon recent advances in mathematical phylogenetics, we demonstrate that gene duplications convey meaningful phylogenetic information and allow the inference of plausible phylogenetic trees, provided orthologs and paralogs can be distinguished with a degree of certainty. Starting from tree-free estimates of orthology, cograph editing can sufficiently reduce the noise to find correct event-annotated gene trees. The information of gene trees can then directly be translated into constraints on the species trees. Although the resolution is very poor for individual gene families, we show that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees, even in the presence of horizontal gene transfer.
    Keywords: Cograph ; Gene Tree ; Orthology ; Paralogy ; Species Tree ; Genomics ; Phylogeny
    ISSN: 00278424
    E-ISSN: 1091-6490
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 2
    Language: English
    In: Molecular Phylogenetics and Evolution, March 2013, Vol.66(3), pp.811-823
    Description: ► We use near intron pairs (NIPs) for phylogenetic inference concerning metazoans. ► We could reliably detect shared intron gain events via NIPs. ► The application to a broad collection of genomes reveals a plausible phylogeny. Gene structure data can substantially advance our understanding of metazoan evolution and deliver an independent approach to resolve conflicts among existing hypotheses. Here, we used changes of spliceosomal intron positions as novel phylogenetic marker to reconstruct the animal tree. This kind of data is inferred from orthologous genes containing mutually exclusive introns at pairs of sequence positions in close proximity, so-called near intron pairs (NIPs). NIP data were collected for 48 species and utilized as binary genome-level characters in maximum parsimony (MP) analyses to reconstruct deep metazoan phylogeny. All groupings that were obtained with more than 80% bootstrap support are consistent with currently supported phylogenetic hypotheses. This includes monophyletic Chordata, Vertebrata, Nematoda, Platyhelminthes and Trochozoa. Several other clades such as Deuterostomia, Protostomia, Arthropoda, Ecdysozoa, Spiralia, and Eumetazoa, however, failed to be recovered due to a few problematic taxa such as the mite and the warty comb jelly . The corresponding unexpected branchings can be explained by the paucity of synapomorphic changes of intron positions shared between some genomes, by the sensitivity of MP analyses to long-branch attraction (LBA), and by the very unequal evolutionary rates of intron loss and intron gain during evolution of the different subclades of metazoans. In addition, we obtained an assemblage of Cnidaria, Porifera, and Placozoa as sister group of Bilateria + Ctenophora with medium support, a disputable, but remarkable result. We conclude that NIPs can be used as phylogenetic characters also within a broader phylogenetic context, given that they have emerged regularly during evolution irrespective of the large variation of intron density across metazoan genomes.
    Keywords: Intron Evolution ; Molecular Phylogenetics ; Maximum Parsimony ; Metazoan Phylogeny ; Ecdysozoa ; Rare Genomic Changes ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 3
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 27 September 2016, Vol.113(39), pp.10818-23
    Description: It is widely assumed that one of the fundamental properties of spoken language is the arbitrary relation between sound and meaning. Some exceptions in the form of nonarbitrary associations have been documented in linguistics, cognitive science, and anthropology, but these studies only involved small subsets of the 6,000+ languages spoken in the world today. By analyzing word lists covering nearly two-thirds of the world's languages, we demonstrate that a considerable proportion of 100 basic vocabulary items carry strong associations with specific kinds of human speech sounds, occurring persistently across continents and linguistic lineages (linguistic families or isolates). Prominently among these relations, we find property words ("small" and i, "full" and p or b) and body part terms ("tongue" and l, "nose" and n). The areal and historical distribution of these associations suggests that they often emerge independently rather than being inherited or borrowed. Our results therefore have important implications for the language sciences, given that nonarbitrary associations have been proposed to play a critical role in the emergence of cross-modal mappings, the acquisition of language, and the evolution of our species' unique communication system.
    Keywords: Cognitive Sciences ; Iconicity ; Language Evolution ; Linguistics ; Sound Symbolism ; Language ; Sound
    ISSN: 00278424
    E-ISSN: 1091-6490
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 4
    Language: English
    In: Journal of Theoretical Biology, Nov 7, 2013, Vol.336, p.61(14)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.jtbi.2013.07.012 Byline: Christian Arnold, Peter F. Stadler, Sonja J. Prohaska Abstract: Eukaryotic histones carry a diverse set of specific chemical modifications that accumulate over the life-time of a cell and have a crucial impact on the cell state in general and the transcriptional program in particular. Replication constitutes a dramatic disruption of the chromatin states that effectively amounts to partial erasure of stored information. To preserve its epigenetic state the cell reconstructs (at least part of) the histone modifications by means of processes that are still very poorly understood. A plausible hypothesis is that the different combinations of reader and writer domains in histone-modifying enzymes implement local rewriting rules that are capable of "recomputing" the desired parental modification patterns on the basis of the partial information contained in that half of the nucleosomes that predate replication. To test whether such a mechanism is theoretically feasible, we have developed a flexible stochastic simulation system (available at http://www.bioinf.uni-leipzig.de/Software/StoChDyn) for studying the dynamics of histone modification states. The implementation is based on Gillespie's approach, i.e., it models the master equation of a detailed chemical model. It is efficient enough to use an evolutionary algorithm to find patterns across multiple cell divisions with high accuracy. We found that it is easy to evolve a system of enzymes that can maintain a particular chromatin state roughly stable, even without explicit boundary elements separating differentially modified chromatin domains. However, the success of this task depends on several previously unanticipated factors, such as the length of the initial state, the specific pattern that should be maintained, the time between replications, and chemical parameters such as enzymatic binding and dissociation rates. All these factors also influence the accumulation of errors in the wake of cell divisions. Author Affiliation: (a) Computational EvoDevo Group, Department of Computer Science, Universitat Leipzig, Hartelstra[sz]e 16-18, 04107 Leipzig, Germany (b) Interdisciplinary Center for Bioinformatics, Universitat Leipzig, Hartelstra[sz]e 16-18, 04107 Leipzig, Germany (c) Bioinformatics Group, Department of Computer Science, Universitat Leipzig, Hartelstra[sz]e 16-18, 04107 Leipzig, Germany (d) Harvard University, Department of Human Evolutionary Biology, 11 Divinity Avenue, Cambridge, MA 02138, USA (e) Max-Planck-Institute for Mathematics in the Sciences, Inselstra[sz]e 22, 04103 Leipzig, Germany (f) Fraunhofer Institut fur Zelltherapie und Immunologie Perlickstra[sz]e 1, 04103 Leipzig, Germany (g) Department of Theoretical Chemistry University of Vienna, Wahringerstra[sz]e 17, 1090 Wien, Austria (h) Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA Article History: Received 19 March 2013; Revised 2 July 2013; Accepted 15 July 2013
    Keywords: Chromatin
    ISSN: 0022-5193
    Source: Cengage Learning, Inc.
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 5
    Language: English
    In: PLoS ONE, 2012, Vol.7(4), p.e34780
    Description: Hard combinatorial optimization problems deal with the search for the minimum cost solutions (ground states) of discrete systems under strong constraints. A transformation of state variables may enhance computational tractability. It has been argued that these state encodings are to be chosen invertible to retain the original size of the state space. Here we show how redundant non-invertible encodings enhance optimization by enriching the density of low-energy states. In addition, smooth landscapes may be established on encoded state spaces to guide local search dynamics towards the ground state.
    Keywords: Research Article ; Biology ; Computer Science ; Mathematics ; Physics ; Computer Science ; Evolutionary Biology ; Physics ; Mathematics
    E-ISSN: 1932-6203
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 6
    Language: English
    In: Molecular Phylogenetics and Evolution, November 2013, Vol.69(2), pp.328-338
    Description: ► The organisation of mitochondrial genomes is similar but not identical among animals. ► Several different rearrangement operations shape animal mitogenomes. ► Differences in genome structure are reflected in the mito-transcriptome. Many years of extensive studies of metazoan mitochondrial genomes have established differences in gene arrangements and genetic codes as valuable phylogenetic markers. Understanding the underlying mechanisms of replication, transcription and the role of the control regions which cause e.g. different gene orders is important to assess the phylogenetic signal of such events. This review summarises and discusses, for the Metazoa, the general aspects of mitochondrial transcription and replication with respect to control regions as well as several proposed models of gene rearrangements. As whole genome sequencing projects accumulate, more and more observations about mitochondrial gene transfer to the nucleus are reported. Thus occurrence and phylogenetic aspects concerning nuclear mitochondrial-like sequences (NUMTS) is another aspect of this review.
    Keywords: Genetic Code ; Gene Content ; Chromosome Structure ; Replication ; Transcriptome ; Phylogenomics ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 7
    Language: English
    In: Molecular Phylogenetics and Evolution, November 2013, Vol.69(2), pp.320-327
    Description: ► Review and comparison of methods for analysing metazoan mitochondrial genomes. ► Data bases. ► Genome annotation, in particular tRNAs. ► Model based and model free gene order comparison. ► Models of sequence evolution. In this review we provide an overview of various bioinformatics methods and tools for the analysis of metazoan mitochondrial genomes. We compare available dedicated databases and present current tools for accurate genome annotation, identification of protein coding genes, and determination of tRNA and rRNA models.We also evaluate various tools and models for phylogenetic tree inference using gene order or sequence based data. As for gene order based methods, we compare rearrangement based and gene cluster based methods for gene order rearrangement analysis. As for sequence based methods, we give special emphasis to substitution models or data treatment that reduces certain systematic biases that are typical for metazoan mitogenomes such as within genome and/or among lineage compositional heterogeneity.
    Keywords: Bioinformatics ; Mitochondria ; Genome Rearrangements ; Substitution Models ; Gene Annotation ; Biology
    ISSN: 1055-7903
    E-ISSN: 1095-9513
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 8
    Language: English
    In: Nature, 28 January 2016, Vol.529(7587), pp.496-501
    Description: Bacteria express many small RNAs for which the regulatory roles in pathogenesis have remained poorly understood due to a paucity of robust phenotypes in standard virulence assays. Here we use a generic 'dual RNA-seq' approach to profile RNA expression simultaneously in pathogen and host during Salmonella enterica serovar Typhimurium infection and reveal the molecular impact of bacterial riboregulators. We identify a PhoP-activated small RNA, PinT, which upon bacterial internalization temporally controls the expression of both invasion-associated effectors and virulence genes required for intracellular survival. This riboregulatory activity causes pervasive changes in coding and noncoding transcripts of the host. Interspecies correlation analysis links PinT to host cell JAK-STAT signalling, and we identify infection-specific alterations in multiple long noncoding RNAs. Our study provides a paradigm for a sensitive RNA-based analysis of intracellular bacterial pathogens and their hosts without physical separation, as well as a new discovery route for hidden functions of pathogen genes.
    Keywords: Gene Expression Regulation -- Genetics ; Host-Pathogen Interactions -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Untranslated -- Genetics ; Salmonella Typhimurium -- Genetics
    ISSN: 00280836
    E-ISSN: 1476-4687
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 9
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 28 June 2016, Vol.113(26), pp.7237-42
    Description: RNA structures are fundamentally important for RNA function. Dynamic, condition-dependent structural changes are able to modulate gene expression as shown for riboswitches and RNA thermometers. By parallel analysis of RNA structures, we mapped the RNA structurome of Yersinia pseudotuberculosis at three different temperatures. This human pathogen is exquisitely responsive to host body temperature (37 °C), which induces a major metabolic transition. Our analysis profiles the structure of more than 1,750 RNAs at 25 °C, 37 °C, and 42 °C. Average mRNAs tend to be unstructured around the ribosome binding site. We searched for 5'-UTRs that are folded at low temperature and identified novel thermoresponsive RNA structures from diverse gene categories. The regulatory potential of 16 candidates was validated. In summary, we present a dynamic bacterial RNA structurome and find that the expression of virulence-relevant functions in Y. pseudotuberculosis and reprogramming of its metabolism in response to temperature is associated with a restructuring of numerous mRNAs.
    Keywords: RNA Structure ; RNA Thermometer ; Temperature ; Translational Control ; Virulence ; Temperature ; RNA, Bacterial -- Genetics ; Yersinia Pseudotuberculosis -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
  • 10
    Language: English
    In: Nucleic acids research, July 2011, Vol.39(Web Server issue), pp.W149-54
    Description: Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure and function. Most sRNAs act as post-transcriptional regulators by means of specific base pairing interactions with the 5'-untranslated region of mRNA transcripts, thereby modifying the stability of the target transcript and/or its ability to be translated. Here, we present RNApredator, a web server for the prediction of sRNA targets. The user can choose from a set of over 2155 genomes and plasmids from 1183 bacterial species. RNApredator then uses a dynamic programming approach, RNAplex, to compute putative targets. Compared to web servers with a similar task, RNApredator takes the accessibility of the target during the target search into account, improving the specificity of the predictions. Furthermore, enrichment in Gene Ontology terms, cellular pathways as well as changes in accessibilities along the target sequence can be done in fully automated post-processing steps. The predictive performance of the underlying dynamic programming approach RNAplex is similar to that of more complex methods, but needs at least three orders of magnitude less time to complete. RNApredator is available at http://rna.tbi.univie.ac.at/RNApredator.
    Keywords: Software ; RNA, Bacterial -- Chemistry ; RNA, Small Untranslated -- Chemistry
    ISSN: 03051048
    E-ISSN: 1362-4962
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. Further information can be found on the KOBV privacy pages