385 research outputs found
Entwicklung und Charakterisierung von Komplexen aus Cetrorelix und biophilen Trägermaterialien
Die Dissertation beschreibt Arbeiten zur Herstellung neuer Cetrorelixkomplexe, zur Kinetik der dynamischen Liberation, zur Struktur von Aggregaten und Komplexen von Cetrorelix und zur Berechnung von Komplexeigenschaften mit Molecular Modeling.Presented are results about new complexes of cetrorelix, the kinetics of dynamical liberations, the structure of Cetrorelix aggregates and complexes and the computation of properties of complexes by molecular modeling
The evolutionary dynamics of protein-protein interaction networks inferred from the reconstruction of ancient networks
Cellular functions are based on the complex interplay of proteins, therefore
the structure and dynamics of these protein-protein interaction (PPI) networks
are the key to the functional understanding of cells. In the last years,
large-scale PPI networks of several model organisms were investigated.
Methodological improvements now allow the analysis of PPI networks of multiple
organisms simultaneously as well as the direct modeling of ancestral networks.
This provides the opportunity to challenge existing assumptions on network
evolution. We utilized present-day PPI networks from integrated datasets of
seven model organisms and developed a theoretical and bioinformatic framework
for studying the evolutionary dynamics of PPI networks. A novel filtering
approach using percolation analysis was developed to remove low confidence
interactions based on topological constraints. We then reconstructed the
ancient PPI networks of different ancestors, for which the ancestral proteomes,
as well as the ancestral interactions, were inferred. Ancestral proteins were
reconstructed using orthologous groups on different evolutionary levels. A
stochastic approach, using the duplication-divergence model, was developed for
estimating the probabilities of ancient interactions from today's PPI networks.
The growth rates for nodes, edges, sizes and modularities of the networks
indicate multiplicative growth and are consistent with the results from
independent static analysis. Our results support the duplication-divergence
model of evolution and indicate fractality and multiplicative growth as general
properties of the PPI network structure and dynamics
Hybrid de novo transcriptome assembly of poinsettia (Euphorbia pulcherrima Willd. Ex Klotsch) bracts
Background
Poinsettia is a popular and important ornamental crop, mostly during the Christmas season. Its bract coloration ranges from pink/red to creamy/white shades. Despite its ornamental value, there is a lack of knowledge about the genetics and molecular biology of poinsettia, especially on the mechanisms of color formation. We performed an RNA-Seq analysis in order to shed light on the transcriptome of poinsettia bracts. Moreover, we analyzed the transcriptome differences of red- and white-bracted poinsettia varieties during bract development and coloration. For the assembly of a bract transcriptome, two paired-end cDNA libraries from a red and white poinsettia pair were sequenced with the Illumina technology, and one library from a red-bracted variety was used for PacBio sequencing. Both short and long reads were assembled using a hybrid de novo strategy. Samples of red- and white-bracted poinsettias were sequenced and comparatively analyzed in three color developmental stages in order to understand the mechanisms of color formation and accumulation in the species.
Results
The final transcriptome contains 288,524 contigs, with 33% showing confident protein annotation against the TAIR10 database. The BUSCO pipeline, which is based on near-universal orthologous gene groups, was applied to assess the transcriptome completeness. From a total of 1440 BUSCO groups searched, 77% were categorized as complete (41% as single-copy and 36% as duplicated), 10% as fragmented and 13% as missing BUSCOs. The gene expression comparison between red and white varieties of poinsettia showed a differential regulation of the flavonoid biosynthesis pathway only at particular stages of bract development. An initial impairment of the flavonoid pathway early in the color accumulation process for the white poinsettia variety was observed, but these differences were no longer present in the subsequent stages of bract development. Nonetheless, GSTF11 and UGT79B10 showed a lower expression in the last stage of bract development for the white variety and, therefore, are potential candidates for further studies on poinsettia coloration.
Conclusions
In summary, this transcriptome analysis provides a valuable foundation for further studies on poinsettia, such as plant breeding and genetics, and highlights crucial information on the molecular mechanism of color formation
Comprehensive in silico prediction and analysis of chlamydial outer membrane proteins reflects evolution and life style of the Chlamydiae
<p>Abstract</p> <p>Background</p> <p>Chlamydiae are obligate intracellular bacteria comprising some of the most important bacterial pathogens of animals and humans. Although chlamydial outer membrane proteins play a key role for attachment to and entry into host cells, only few have been described so far. We developed a comprehensive, multiphasic <it>in silico </it>approach, including the calculation of clusters of orthologues, to predict outer membrane proteins using conservative criteria. We tested this approach using <it>Escherichia coli </it>(positive control) and <it>Bacillus subtilis </it>(negative control), and applied it to five chlamydial species; <it>Chlamydia trachomatis</it>, <it>Chlamydia muridarum</it>, <it>Chlamydia </it>(a.k.a. <it>Chlamydophila</it>) <it>pneumoniae</it>, <it>Chlamydia </it>(a.k.a. <it>Chlamydophila</it>) <it>caviae</it>, and <it>Protochlamydia amoebophila</it>.</p> <p>Results</p> <p>In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified, including 238 proteins not previously recognized to be located in the outer membrane. Analysis of their taxonomic distribution revealed an evolutionary conservation among <it>Chlamydiae</it>, <it>Verrucomicrobia</it>, <it>Lentisphaerae </it>and <it>Planctomycetes </it>as well as lifestyle-dependent conservation of the chlamydial outer membrane protein composition.</p> <p>Conclusion</p> <p>This analysis suggested a correlation between the outer membrane protein composition and the host range of chlamydiae and revealed a common set of outer membrane proteins shared by these intracellular bacteria. The collection of predicted chlamydial outer membrane proteins is available at the online database pCOMP <url>http://www.microbial-ecology.net/pcomp</url> and might provide future guidance in the quest for anti-chlamydial vaccines.</p
SIMAP: the similarity matrix of proteins
Similarity Matrix of Proteins (SIMAP) () provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith–Waterman algorithm. Our ProtInfo system allows querying by protein sequences covered by the SIMAP dataset as well as by fragments of these sequences, highly similar sequences and title words. Each sequence in the database is supplemented with pre-calculated features generated by detailed sequence analyses. By providing WWW interfaces as well as web-services, we offer the SIMAP resource as an efficient and comprehensive tool for sequence similarity searches
Gene3D: comprehensive structural and functional annotation of genomes
Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein–protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk
Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment
Enterobacter sakazakii is considered an opportunistic foodborne pathogen that is characterized by formation of yellow-pigmented colonies. Because of the lack of basic knowledge about Enterobacter sakazakii genetics, the BAC approach and the heterologous expression of the pigment in Escherichia coli were used to elucidate the molecular structure of the genes responsible for pigment production in Enterobacter sakazakii strain ES5. Sequencing and annotation of a 33.025 bp fragment revealed seven ORFs that could be assigned to the carotenoid biosynthesis pathway. The gene cluster had the organization crtE-idi-XYIBZ, with the crtE-idi-XYIB genes putatively transcribed as an operon and the crtZ gene transcribed in the opposite orientation. The carotenogenic nature of the pigment of Enterobacter sakazakii wt was ascertained by in situ analysis using visible microspectroscopy and resonance Raman microspectroscop
Genetic diversity of the obligate intracellular bacterium Chlamydophila pneumoniae by genome-wide analysis of single nucleotide polymorphisms: evidence for highly clonal population structure
<p>Abstract</p> <p>Background</p> <p><it>Chlamydophila pneumoniae </it>is an obligate intracellular bacterium that replicates in a biphasic life cycle within eukaryotic host cells. Four published genomes revealed an identity of > 99 %. This remarkable finding raised questions about the existence of distinguishable genotypes in correlation with geographical and anatomical origin.</p> <p>Results</p> <p>We studied the genetic diversity of <it>C. pneumoniae </it>by analysing synonymous single nucleotide polymorphisms (sSNPs) that are under reduced selection pressure. We conducted an in silico analysis of the four sequenced genomes, chose 232 representative sSNPs and analysed the loci in 38 <it>C. pneumoniae </it>isolates. We identified 15 different genotypes that were separated in four major clusters. Clusters were not associated with anatomical or geographical origin. However, animal lineages are basal on the <it>C. pneumomiae </it>phylogeny, suggesting a recent transmission to humans through successive bottlenecks some 150,000 years ago. A lack of detectable variation in 17 isolates emphasizes the extraordinary genetic conservation of this species and the high clonality of the population. Moreover, the largest cluster, which encompasses 80% of all analysed strains, is an extremely young clade, that went through an important population expansion some 3,300 years ago.</p> <p>Conclusion</p> <p>sSNPs have proven useful as a sensitive marker to gain new insights into genetic diversity, population structure and evolutionary history of <it>C. pneumoniae</it>.</p
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