Biomedical subjects

Martin Schindler

Publications and source records attributed to Martin Schindler.

7 recordsLinked to original sources

PubMed2006

AthaMap web tools for the analysis and identification of co-regulated genes.

The AthaMap database generates a map of cis-regulatory elements for the whole Arabidopsis thaliana genome. This database has been extended by new tools to identify common cis-regulatory elements in specific regions of user-provided gene sets. A resulting table displays all cis-regulatory elements annotated in AthaMap including positional information relative to the respective gene. Further tables show overviews with the number of individual transcription factor binding sites (TFBS) present and TFBS common to the whole set of genes. Over represented cis-elements are easily identified. These features were used to detect specific enrichment of drought-responsive elements in cold-induced genes. For identification of co-regulated genes, the output table of the colocalization function was extended to show the closest genes and their relative distances to the colocalizing TFBS. Gene sets determined by this function can be used for a co-regulation analysis in microarray gene expression databases such as Genevestigator or PathoPlant. Additional improvements of AthaMap include display of the gene structure in the sequence window and a significant data increase. AthaMap is freely available at http://www.athamap.de/.

Arabidopsis↗

PubMed2006

PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses.

Plants react to pathogen attack by expressing specific proteins directed toward the infecting pathogens. This involves the transcriptional activation of specific gene sets. PathoPlant, a database on plant-pathogen interactions and signal transduction reactions, has now been complemented by microarray gene expression data from Arabidopsis thaliana subjected to pathogen infection and elicitor treatment. New web tools enable identification of plant genes regulated by specific stimuli. Sets of genes co-regulated by multiple stimuli can be displayed as well. A user-friendly web interface was created for the submission of gene sets to be analyzed. This results in a table, listing the stimuli that act either inducing or repressing on the respective genes. The search can be restricted to certain induction factors to identify, e.g. strongly up- or down-regulated genes. Up to three stimuli can be combined with the option of induction factor restriction to determine similarly regulated genes. To identify common cis-regulatory elements in co-regulated genes, a resulting gene list can directly be exported to the AthaMap database for analysis. PathoPlant is freely accessible at http://www.pathoplant.de.

Arabidopsis↗

PubMed2006

AthaMap: from in silico data to real transcription factor binding sites.

AthaMap generates a map for cis-regulatory sequences for the whole Arabidopsis thaliana genome. AthaMap was initially developed by matrix-based detection of putative transcription factor binding sites (TFBS) mostly determined from random binding site selection experiments. Now, also experimentally verified TFBS have been included for 48 different Arabidopsis thaliana transcription factors (TF). Based on these sequences, 89,416 very similar putative TFBS were determined within the genome of A. thaliana and annotated to AthaMap. Matrix- and single sequence-based binding sites can be included in colocalization analysis for the identification of combinatorial cis-regulatory elements. As an example, putative target genes of the WRKY18 transcription factor that is involved in plant-pathogen interaction were determined. New functions of AthaMap include descriptions for all annotated Arabidopsis thaliana genes and direct links to TAIR, TIGR and MIPS. Transcription factors used in the binding site determination are linked to TAIR and TRANSFAC databases. AthaMap is freely available at http://www.athamap.de.

Arabidopsis↗

PubMed2005

AthaMap web tools for database-assisted identification of combinatorial cis-regulatory elements and the display of highly conserved transcription factor binding sites in Arabidopsis thaliana.

The AthaMap database generates a map of cis-regulatory elements for the Arabidopsis thaliana genome. AthaMap contains more than 7.4 x 10(6) putative binding sites for 36 transcription factors (TFs) from 16 different TF families. A newly implemented functionality allows the display of subsets of higher conserved transcription factor binding sites (TFBSs). Furthermore, a web tool was developed that permits a user-defined search for co-localizing cis-regulatory elements. The user can specify individually the level of conservation for each TFBS and a spacer range between them. This web tool was employed for the identification of co-localizing sites of known interacting TFs and TFs containing two DNA-binding domains. More than 1.8 x 10(5) combinatorial elements were annotated in the AthaMap database. These elements can also be used to identify more complex co-localizing elements consisting of up to four TFBSs. The AthaMap database and the connected web tools are a valuable resource for the analysis and the prediction of gene expression regulation at http://www.athamap.de.

Arabidopsis↗

PubMed2004

AthaMap: an online resource for in silico transcription factor binding sites in the Arabidopsis thaliana genome.

Gene expression is controlled mainly by the binding of transcription factors to regulatory sequences. To generate a genomic map for regulatory sequences, the Arabidopsis thaliana genome was screened for putative transcription factor binding sites. Using publicly available data from the TRANSFAC database and from publications, alignment matrices for 23 transcription factors of 13 different factor families were used with the pattern search program Patser to determine the genomic positions of more than 2.4 x 10(6) putative binding sites. Due to the dense clustering of genes and the observation that regulatory sequences are not restricted to upstream regions, the prediction of binding sites was performed for the whole genome. The genomic positions and the underlying data were imported into the newly developed AthaMap database. This data can be accessed by positional information or the Arabidopsis Genome Initiative identification number. Putative binding sites are displayed in the defined region. Data on the matrices used and on the thresholds applied in these screens are given in the database. Considering the high density of sites it will be a valuable resource for generating models on gene expression regulation. The data are available at http://www.athamap.de.

Arabidopsis↗

PubMed2004

Acute otitis externa: efficacy and tolerability of N-chlorotaurine, a novel endogenous antiseptic agent.

OBJECTIVE: The study's objective was to test the tolerability and efficacy of the endogenous antiseptic N-chlorotaurine (NCT) in comparison with a standard clinical treatment according to a phase IIb clinical trial protocol. STUDY DESIGN: The antimicrobial agent NCT was compared with the antibiotic component drops Otosporin (containing neomycin, polymyxin B, and hydrocortisone) for topical treatment of acute otitis externa in a randomized and rater-blinded clinical study. METHODS: Fifty patients suffering from acute otitis externa were divided into two groups according to a randomized list. The test group was treated with 1 mL of 1% aqueous NCT solution, the reference group with 1 mL of Otosporin. The substances were applied to the external ear canal at one daily session until the signs of infection disappeared. Efficacy and tolerability were evaluated daily by visual analogue scale and a six-step infection score. In addition, smears were analyzed to identify the causative pathogens. RESULTS: Both medications were equally well tolerated by the patients. The treatment was successful for all patients of the NCT group, whereas in one patient from the reference group, the infection did not disappear. The inflammation score improved more rapidly in the NCT group, which resulted in an earlier termination of the therapy. This difference became highly significant on days 4 to 7 (P <.01 each). Time needed for disappearance of inflammation (score 0) was 5.6 +/- 1.6 (mean +/- SD, range 3-9) days in the NCT group and 7.4 +/- 1.6 (range 4-10) days in the Otosporin group (P <.001). As expected, microbiologic cultures from ear swabs revealed Pseudomonas aeruginosa (58%) followed by Staphylococcus aureus (18%) as the main causative pathogens. CONCLUSIONS: NCT appears to be well tolerated and more effective than the therapy using antibiotic component drops. Because of its endogenous nature and its higher efficacy, NCT appears to be a good choice for topical treatment of acute otitis externa.

Acute Disease↗

PubMed2004

PathoPlant: a database on plant-pathogen interactions.

Pathogen recognition and signal transduction during plant pathogenesis is essential for the activation of plant defense mechanisms. To facilitate easy access to published data and to permit comparative studies of different pathogen response pathways, a database is indispensable to give a broad overview of the components and reactions so far known. PathoPlant has been developed as a relational database to display relevant components and reactions involved in signal transduction related to plant-pathogen interactions. On the organism level, the tables 'plant', 'pathogen' and 'interaction' are used to describe incompatible interactions between plants and pathogens or diseases. On the molecular level, plant pathogenesis related information is organized in PathoPlant's main tables 'molecule', 'reaction' and 'location'. Signal transduction pathways are modeled as consecutive sequences of known molecules and corresponding reactions. PathoPlant entries are linked to associated internal records as well as to entries in external databases such as SWISS-PROT, GenBank, PubMed, and TRANSFAC. PathoPlant is available as a web-based service at http://www.pathoplant.de.

Computational Biology↗