Medizinische und gesundheitsökonomische Bewertung der Radiochirurgie zur Behandlung von Hirnmetastasen

Background: Expressed Sequence Tags (ESTs) are in general used to gain a first insight into gene activities from a species of interest. Subsequently, and typically based on a combination of EST and genome sequences, microarray-based expression analyses are performed for a variety of conditions. In some cases, a multitude of EST and microarray experiments are conducted for one species, covering different tissues, cell states, and cell types. Under these circumstances, the challenge arises to combine results derived from the different expression profiling strategies, with the goal to uncover novel information on the basis of the integrated datasets. Findings: Using our new analysis tool, MediPlEx (MEDIcago truncatula multiPLe EXpression analysis), expression data from EST experiments, oligonucleotide microarrays and Affymetrix GeneChips® can be combined and analyzed, leading to a novel approach to integrated transcriptome analysis. We have validated our tool via the identification of a set of well-characterized AM-specific and AM-induced marker genes, identified by MediPlEx on the basis of in silico and experimental gene expression profiles from roots colonized with AM fungi. Conclusions: MediPlEx offers an integrated analysis pipeline for different sets of expression data generated for the model legume Medicago truncatula. As expected, in silico and experimental gene expression data that cover the same biological condition correlate well. The collection of differentially expressed genes identified via MediPlEx provides a starting point for functional studies in plant mutants

TRUNCATULIX – a data warehouse for the legume community

Henckel K, Runte KJ, Bekel T, et al. TRUNCATULIX - a data warehouse for the legume community. BMC Plant Biology. 2009;9(1):19

TRUNCATULIX – a data warehouse for the legume community

Henckel K, Runte KJ, Bekel T, et al. TRUNCATULIX - a data warehouse for the legume community. BMC Plant Biology. 2009;9(1):19

MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula

Henckel K, Küster H, Stutz L, Goesmann A. MediPlEx - a tool to combine in silico and experimental gene expression profiles of the model legume Medicago truncatula. BMC Research Notes. 2010;3(1): 262.BACKGROUND:Expressed Sequence Tags (ESTs) are in general used to gain a first insight into gene activities from a species of interest. Subsequently, and typically based on a combination of EST and genome sequences, microarray-based expression analyses are performed for a variety of conditions. In some cases, a multitude of EST and microarray experiments are conducted for one species, covering different tissues, cell states, and cell types. Under these circumstances, the challenge arises to combine results derived from the different expression profiling strategies, with the goal to uncover novel information on the basis of the integrated datasets.FINDINGS:Using our new application, MediPlEx (MEDIcago truncatula multiPLe EXpression analysis), expression data from EST experiments, oligonucleotide microarrays and Affymetrix GeneChips can be combined and analyzed, leading to a novel approach to integrated transcriptome analysis. We have validated our tool via the identification of a set of well-characterized AM-specific and AM-induced marker genes, identified by MediPlEx on the basis of in silico and experimental gene expression profiles from roots colonized with AM fungi.CONCLUSIONS:MediPlEx offers an integrated analysis pipeline for different sets of expression data generated for the model legume Medicago truncatula. As expected, in silico and experimental gene expression data that cover the same biological condition correlate well. The collection of differentially expressed genes identified via MediPlEx provides a starting point for functional studies in plant mutants. MediPlEx can freely be used at http://www.cebitec.uni-bielefeld.de/mediplex

Development of a software infrastructure to mine GeneChip expression data and to combine datasets from different Medicago truncatula expression profiling platforms

Henckel K. Development of a software infrastructure to mine GeneChip expression data and to combine datasets from different Medicago truncatula expression profiling platforms. Bielefeld (Germany): Bielefeld University; 2010.Medicago truncatula is a model plant for studying legume biology. The ability to interact with beneficial microbial organisms leading to the formation of nitrogen fixing root nodules and to phosphate-acquiring arbuscular mycorriza (AM) is one of the main distinctive features of this family of plants. The two different symbioses of Medicago truncatula are investigated by various international research projects. Oligonucleotide microarrays are a robust technique to examine the expression of thousands of genes in parallel. Affymetrix GeneChips®, more recently designed gene-specific chips, make it easier for the researcher to compare and evaluate gene expression and thus will most certainly lead to more accurate results. Not surprisingly, Medicago GeneChips® are moving into the focus of gene expression analysis research in this model plant. Software applications for the analysis of GeneChips® are mostly commercial, or implemented as command-line tools without a user interface. Furthermore, a comparison to the analyses of previously performed oligonucleotide microarrays is difficult, as analysis pipelines and methods differ in each application. In the scope of this thesis EMMA2, an application for the analysis of oligonucleotide microarrays, was extended to load, store and analyze Affymetrix GeneChips® as compareable as possible to oligonucleotide datasets. Databases for either sequence, annotation, or microarray experiment datasets are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, datasets from different sources develop their full capacities only when combined. The idea of a data warehouse directly addresses this problem and solves it by integrating all required data into one single database hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula there was no such single data warehouse that integrated all freely available gene sequences, the corresponding gene expression data, and annotation information. The TRUNCATULIX data warehouse is created in the scope of this thesis to store Medicago truncatula sequence, annotation, and expression datasets and offer these to the legume community. Different filtersteps allow a precise query for genes and expression values in a database of over 200.000 gene sequences and over 200 hybridizations. For the first time users can now quickly search for specific genes and gene expression datasets in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage. A multitude of EST and microarray experiments are conducted for Medicago truncatula covering different tissues, cell states, and cell types. Under these circumstances the challenge arises to integrate the results of the different expression analysis methods with the goal to discover novel information from the combined datasets. The application MediPlEx is designed to allow an integrated expression analysis for the Medicago truncatula datasets stored in SAMS and in the TRUNCATULIX data warehouse. After selecting genes of interest by their expression conditions, expression profiles are combined for a hierarchical clustering. The results are presented in a table, as a cluster dendrogram, and in an interactive 3D application. The three parts of the thesis have been published by Dondrup et al. (2009), Henckel et al. (2009), or are submitted (Henckel et al. (2010))

Mediplex - combining expression datasets of Medicago truncatula: Creating a software infrastructure to mine GeneChip expression data and to combine Medicago truncatula expression profiling datasets

Henckel K. Mediplex - combining expression datasets of Medicago truncatula: Creating a software infrastructure to mine GeneChip expression data and to combine Medicago truncatula expression profiling datasets. Germany: Suedwestdeutscher Verlag fuer Hochschulschriften; 2010.Medicago truncatula is a model plant for studying legume biology. The ability to interact with beneficial microbial organisms leading to the formation of nitrogen fixing root nodules and to phosphate-acquiring arbuscular mycorriza (AM) is one of the main distinctive features of this family of plants. The two different symbioses of Medicago truncatula are investigated by various international research projects. Oligonucleotide microarrays are a robust technique to examine the expression of thousands of genes in parallel. Affymetrix GeneChips®, more recently designed gene-specific chips, make it easier for the researcher to compare and evaluate gene expression and thus will most certainly lead to more accurate results. Not surprisingly, Medicago GeneChips® are moving into the focus of gene expression analysis research in this model plant. Software applications for the analysis of GeneChips® are mostly commercial, or implemented as command-line tools without a user interface. Furthermore, a comparison to the analyses of previously performed oligonucleotide microarrays is difficult, as analysis pipelines and methods differ in each application. In the scope of this thesis EMMA2, an application for the analysis of oligonucleotide microarrays, was extended to load, store and analyze Affymetrix GeneChips® as compareable as possible to oligonucleotide datasets. Databases for either sequence, annotation, or microarray experiment datasets are extremely beneficial to the research community, as they centrally gather information from experiments performed by different scientists. However, datasets from different sources develop their full capacities only when combined. The idea of a data warehouse directly addresses this problem and solves it by integrating all required data into one single database hence there are already many data warehouses available to genetics. For the model legume Medicago truncatula there was no such single data warehouse that integrated all freely available gene sequences, the corresponding gene expression data, and annotation information. The TRUNCATULIX data warehouse is created in the scope of this thesis to store Medicago truncatula sequence, annotation, and expression datasets and offer these to the legume community. Different filtersteps allow a precise query for genes and expression values in a database of over 200.000 gene sequences and over 200 hybridizations. For the first time users can now quickly search for specific genes and gene expression datasets in a huge database based on high-quality annotations. The results can be exported as Excel, HTML, or as csv files for further usage. A multitude of EST and microarray experiments are conducted for Medicago truncatula covering different tissues, cell states, and cell types. Under these circumstances the challenge arises to integrate the results of the different expression analysis methods with the goal to discover novel information from the combined datasets. The application MediPlEx is designed to allow an integrated expression analysis for the Medicago truncatula datasets stored in SAMS and in the TRUNCATULIX data warehouse. After selecting genes of interest by their expression conditions, expression profi les are combined for a hierarchical clustering. The results are presented in a table, as a cluster dendrogram, and in an interactive 3D application. The three parts of the thesis have been published by Dondrup et al. (2009), Henckel et al. (2009), or are submitted (Henckel et al. (2010))

'Rejected' vs. 'rejecting' transcriptomes in allogeneic challenged colonial urochordates

Oren M, Paz G, Douek J, et al. 'Rejected' vs. 'rejecting' transcriptomes in allogeneic challenged colonial urochordates. Mol Immunol. 2010;47(11-12):2083-2093.In botryllid ascidians, allogeneic contacts between histoincompatible colonies lead to inflammatory rejection responses, which eventually separate the interacting colonies. In order to elucidate the molecular background of allogeneic rejection in the colonial ascidian Botryllus schlosseri, we performed microarray assays verified by qPCR, and employed bioinformatic analyses of the results, revealing disparate transcription profiles of the rejecting partners. While only minor expression changes were documented during rejection when both interacting genotypes were pooled together, analyses performed on each genotype separately portrayed disparate transcriptome responses. Allogeneic interacting genotypes that developed the morphological markers of rejection (points of rejection; PORs), termed 'rejected' genotypes, showed transcription inhibition of key functional gene groups, including protein biosynthesis, cell structure and motility and stress response genes. In contrast, the allogeneic partners that did not show PORs, termed 'rejecting' genotypes, showed minor expression changes that were different from those of the 'rejected' genotypes. This data demonstrates that the observed morphological changes in the 'rejected' genotypes are not due to active transcriptional response to the immune challenge but reflect transcription inhibition of response elements. Based on the morphological and molecular outcomes we suggest that the 'rejected' colony activates an injurious self-destructive mechanism in order to disconnect itself from its histoincompatible neighboring colony

The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies

Bekel T, Henckel K, Küster H, et al. The Sequence Analysis and Management System - SAMS-2.0: Data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies. Journal of Biotechnology. 2009;140(1-2):3-12.DNA sequencing plays a more and more important role in various fields of genetics. This includes sequencing of whole genomes, libraries of cDNA clones and probes of metagenome communities. The applied sequencing technologies evolve permanently. With the emergence of ultrafast sequencing technologies, a new era of DNA sequencing has recently started. Concurrently, the needs for adapted bioinformatics tools arise. Since the ability to process current datasets efficiently is essential for modern genetics, a modular bioinformatics platform providing extensive sequence analysis methods, is designated to achieve well the constantly growing requirements. The Sequence Analysis and Management System (SAMS) is a bioinformatics software platform with a database backend designed to support the computational analysis of (1) whole genome shotgun (WGS) bacterial genome sequencing, (2) cDNA sequencing by reading expressed sequence tags (ESTs) as well as (3) sequence data obtained by ultrafast sequencing. It provides extensive bioinformatics analysis of sequenced single reads, sequencing libraries and fragments of arbitrary DNA sequences such as assembled contigs of metagenome reads for instance. The system has been implemented to cope with several thousands of sequences, efficiently processing them and storing the results for further analysis. With the project setup, SAMS automatically recognizes the data type

Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions

Mittard-Runte V, Bekel T, Blom J, et al. Practical Guide: Genomic Techniques and How to Apply Them to Marine Questions. In: Cock JM, Tessmar-Raible K, Boyen C, Viard F, eds. Introduction to Marine Genomics (Advances in Marine Genomics). Vol 1. Netherlands: Springer Netherlands; 2010: 315-396.Marine biology has always played an important role in biological research, being at the origin of many key advances. To a certain extent, the influence of marine biology on the biological sciences was overshadowed over a period of several years by the remarkable advances that were made using powerful model organisms from terrestrial environments. This situation is now changing again, however, due primarily to spectacular developments in genomic methodologies that have significantly accelerated research in a broad spectrum of marine biology disciplines ranging from biodiversity to developmental biology to biotechnology. The data generated by marine genomics projects have had an impact on questions as diverse as understanding planetary geochemical cycles, the impact of climate change on marine fauna and flora, the functioning of marine ecosystems, the discovery of new organisms and novel biomolecules, and investigation of the evolution of animal developmental complexity. This book represents the first attempt to document how genomic technologies are revolutionising these diverse domains of marine biology. Each chapter of this book looks at how these technologies are being employed in a specific domain of marine research and provides a summary of the major results obtained to date. The book as a whole provides an overview of marine genomics as a discipline and represents an ideal starting point for exploring this rapidly developing domain