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Biomedical subjects

T Werner

Publications and source records attributed to T Werner.

At least 19 recordsLinked to original sources
PubMed2006

New insights into the biology of cytokinin degradation.

A survey of recent results is presented concerning the role of cytokinin degradation in plants, which is catalyzed by cytokinin oxidase/dehydrogenase (CKX) enzymes. An overview of Arabidopsis CKX gene expression suggests that their differential regulation by biotic and abiotic factors contributes significantly to functional specification. Here, we show using reporter gene and semiquantitative RT-PCR analyses regulation of individual CKX genes by cytokinin, auxin, ABA, and phosphate starvation. Partially overlapping expression domains of CKX genes and cytokinin-synthesizing IPT genes in meristematic tissues and endo-reduplicating cells lend support for a locally restricted function of cytokinin. On the other hand, their expression in vascular tissue suggests a function in controlling transported cytokinin. Recent studies led to a model for the biochemical reaction mechanism of CKX-mediated catalysis, which was refined on the basis of the three-dimensional enzyme structure. Last but not least, the developmental functions of CKX enzymes are addressed. The recent identification of the rice OSCKX2 gene as an important novel breeding tool is highlighted. Together the results corroborate the relevance of metabolic control in determining cytokinin activity.

Arabidopsis↗
PubMed2005

MatInspector and beyond: promoter analysis based on transcription factor binding sites.

MOTIVATION: Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes. RESULTS: We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).

Algorithms↗
PubMed2005

Linking disease-associated genes to regulatory networks via promoter organization.

Pathway- or disease-associated genes may participate in more than one transcriptional co-regulation network. Such gene groups can be readily obtained by literature analysis or by high-throughput techniques such as microarrays or protein-interaction mapping. We developed a strategy that defines regulatory networks by in silico promoter analysis, finding potentially co-regulated subgroups without a priori knowledge. Pairs of transcription factor binding sites conserved in orthologous genes (vertically) as well as in promoter sequences of co-regulated genes (horizontally) were used as seeds for the development of promoter models representing potential co-regulation. This approach was applied to a Maturity Onset Diabetes of the Young (MODY)-associated gene list, which yielded two models connecting functionally interacting genes within MODY-related insulin/glucose signaling pathways. Additional genes functionally connected to our initial gene list were identified by database searches with these promoter models. Thus, data-driven in silico promoter analysis allowed integrating molecular mechanisms with biological functions of the cell.

Binding Sites↗
PubMed2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

SUMMARY: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. AVAILABILITY: The HNB portal is available at http://www.hnbioinfo.de

Algorithms↗
PubMed2003

[Teleteaching in otorhinolaryngology (part 1). Real-time transmission of a congress in picture and tone into the Internet].

The transmission of scientific seminars into the Internet represents a new application of modern technologies for teleteaching. We digitally recorded 74 seminars and discussions during the 8th annual meeting of the German Society of Skull Base Surgery with five cameras and eight microphones, and transformed the data live with the real-Producer using a video card.This transferred data stream was sent via ISDN (128 kbit/s) to a real-server at the university, which was used for distribution in the net. The seminars could be called up in the display format of 320x240 pixels with a delay of 3 min (minimum: 30 s, as a function of the connection of the user) at each computer with Internet entrance. Altogether,we registered 3,284 accesses to the presentations following the congress until June 2002. The quality of picture transmission (24-36 kbit/s) and the quality of tone (audio stream: 5 kbit/s) were sufficient to understand the contents of the slide, video or computer presentation. The transmission of scientific meetings into the Internet can increase, with a justifiable technical expenditure, their efficiency by the ubiquitous availability of the information and the extension of the audience.

Computer Systems↗
PubMed2003

[Teleteaching in otorhinolaryngology. Part 2: the European database "medicstream"].

Searching the medical literature is mainly characterized by the use of databases. The time for reviewing and printing a paper causes a delay between the first presentation of scientific results in a lecture and the appearance of the appropriate journal publication. Moreover, the possibilities for the integration of multimedia data are limited. Because of the development of new compression algorithms for audiovisual digitization software, the near simultaneous transmission of scientific presentations, both visually and aurally, has been possible since 1999. The section telemedicine of the interdisciplinary study group on image guided surgical navigation from the University of Leipzig has developed "medicstream" as a unique, audiovisual, scientific internetdatabase. It allows the documentation of presentations at congresses and courses, including the discussion,over a freely accessible, widely available homepage, using a home developed streaming technology. All presentations are examined by an authorized editorial committee consisting of representatives with different medical specializations for content before the admission to the data base. A total of 392 presentations from seven scientific meetings can be selected by an integrated search machine and viewed with Windows Media Player or Real Player using a conventional or faster internet connection to the homepage www.medicstream.de. The quality of the audiovisual transmission depends on the receiver-lateral data transmission rate,whereby the minimum variant of 56 kB/s is characterized by good detectability of the contents. In an analysis period of 242 days,we registered 44,199 accesses and 4,488 attendances. The telemedicine data base "medicstream" can optimize quality and extend medical education by live-streaming as well as by archiving scientific presentations as audiovisual data.

Congresses as Topic↗
PubMed2003

[Epidemiology and therapy of Lyme arthritis and other manifestations of Lyme borreliosis in Germany: results of a nation-wide survey].

AIM OF THE STUDY: Only little is known about the epidemiology of Lyme borreliosis in Germany. As an example, it is still unclear if there are regional differences in the incidence of Lyme disease in general or of certain clinical manifestations like Lyme arthritis. Moreover, standardization of diagnostic or therapeutic procedures does not exist. Therefore, a Germany-wide questionnaire-based survey was conducted in order to achieve more epidemiological data and to obtain more information about the diagnostic and therapeutic approaches of general practitioners and specialists. METHODS: A self-designed questionnaire was distributed along with two editions of the journal "Deutsches Arzteblatt" (which is delivered to every physician in Germany) and additionally by a pharmaceutical company. During the collection period from March 1, 1998 to February 28, 1999, patients with Lyme disease were reported and information was given about site of infection, diagnostic procedures, clinical symptoms, treatment, and outcome. RESULTS: Altogether 3935 patients were reported. Their mean age was 43.4 years with the peak incidences around the ages of 10 and 60 years. 37.3% of the questionnaires were sent in by general practitioners, 17.6% by dermatologists, 15.7% by pediatricians, 9.7% by internists, and 2.7% by neurologists. 83% of the patients did not have a special infecion risk. The most frequent clinical Lyme manifestation was erythema migrans (EM), which occurred in 50.9% of the patients. 21.3% suffered from general symptoms. Of special interest, 24.5% of the patients had Lyme arthritis (14.7% mon- or oligoarthritis, 9.8% polyarthritis). Therefore, arthritis was more frequently reported than neuroborreliosis (18.4%). Only 16% of the neuroborreliosis patients and 32% of the arthritis patients remembered having had an EM. 189 patients (4.8%) with lymphadenosis cutis benigna and 100 patients (2.5%) with acrodermatitis chronica atrophicans were reported. In 80.4% of the patients, positive Lyme serology was detected. In a few cases, the diagnosis was established by isolation of borreliae, PCR or histology. 3754 patients were treated by antibiotics. The most frequently used compounds were doxycycline (50.4%), followed by ceftriaxone (22.4%), amoxicillin (13.6%), penicillin (7%), and erythromycin (4.2%) with differences depending on clinical manifestations and specialization of the prescribing physician. In less than 10% of the cases, not evaluated or recommended therapeutic procedures were performed. DISCUSSION: Lyme disease is endemic throughuot Germany. The most frequent manifestations are EM, followed by Lyme arthritis and neuroborreliosis. Less than one third of patients suffering from disseminated or chronic Lyme disease remembered an EM. Most of the physicians taking part in this survey follow treatment recommendations concerning choice of antibiotics and treatment durations.

Adolescent↗
PubMed2002

Regulatory modules shared within gene classes as well as across gene classes can be detected by the same in silico approach.

Transcriptional regulation depends on the binding of transcription factors to their corresponding binding sites. The response to cellular signals is often mediated by the cooperative binding of transcription factors to well defined regulatory modules consisting of at least two transcription factor binding sites. Such regulatory modules can be responsible for the common regulation of genes within a gene class or confer a common function to promoters belonging to different gene classes. We developed in silico models representing a common framework of potential regulatory sites specific for one promoter class (actins). We also generated models for two different functional promoter modules both of which confer responsiveness to tumor necrosis factor (TNF) and interferon (IFN) to a variety of promoters. All models exhibited high selectivity, e.g. the mammalian muscle actin promoter model produced no false negatives in a database search.

Actins↗
PubMed2001

Regulation of plant growth by cytokinin.

Cytokinins are a class of plant-specific hormones that play a central role during the cell cycle and influence numerous developmental programs. Because of the lack of biosynthetic and signaling mutants, the regulatory roles of cytokinins are not well understood. We genetically engineered cytokinin oxidase expression in transgenic tobacco plants to reduce their endogenous cytokinin content. Cytokinin-deficient plants developed stunted shoots with smaller apical meristems. The plastochrone was prolonged, and leaf cell production was only 3-4% that of wild type, indicating an absolute requirement of cytokinins for leaf growth. In contrast, root meristems of transgenic plants were enlarged and gave rise to faster growing and more branched roots. These results suggest that cytokinins are an important regulatory factor of plant meristem activity and morphogenesis, with opposing roles in shoots and roots.

Cytokinins↗
PubMed2001

Molecular and in silico characterization of a promoter module and C/EBP element that mediate LPS-induced RANTES/CCL5 expression in monocytic cells.

The chemokine RANTES/CCL5 is a proinflammatory agent produced by a variety of tissues in response to specific stimuli. In human monocytes, RANTES/CCL5 transcription is up-regulated rapidly and transiently in response to LPS. We describe here two regions that help control LPS-driven transcription from the human RANTES/CCL5 promoter in monocytic cells. These sites were analyzed by using DNase I footprinting, transient transfection assays, site-directed mutagenesis, and EMSA. RANTES site E (R(E), -125/-99) constitutively binds C/EBP proteins in monocytic Mono Mac 6 cells. Mutation of region R(E) led to a significant (40%-50%) reduction in LPS-induced promoter reporter activity. Region R(AB) is composed of tandem kB-like elements R(A) and R(B) (-73/-34). These sites working in concert act as an LPS-responsive promoter module. R(A) constitutively binds Sp1, and Rel p50/p65 following LPS stimulation. Either factor can mediate transcriptional effects at R(A). Induced Rel p50/p50 binding to site R(B) is required for LPS regulation of RANTES/CCL5 transcription. A series of computer models based on the RANTES/CCL5 promoter were generated to represent the organization of these functional elements. The models could identify LPS-regulated promoters in human, other vertebrate, and viral sequences in various databases.

CCAAT-Enhancer-Binding Proteins↗
PubMed2001

Fluorimetric determination of copper(II) in aqueous solution using lucifer yellow CH as selective metal reagent.

Lucifer yellow CH is shown to be a highly selective fluorescent reagent for the determination of Cu(III) in the microg L(-1) concentration range. The fluorophore is statically quenched by Cu(II); the carbohydrazide group was assigned as the complexing part of the dye molecule. A total range of Cu(II) determination from 0.06 mg L(-1) (1 micromol L(-1)) to 6.3 mg L(-2) (100 micromol L(-1)) with a limit of detection of 0.019 mg L(-1) (0.3 micromol L(-1)) was obtained, along with surprisingly high selectivity. There was no interference from alkaline and earth alkaline metal ions. The cross sensitivity to heavy metal ions was evaluated by the separate solution method and by competitive binding experiments. Calibration plots are shown for Cu(II) determination at different pH and the dissociation constant was determined. The application of the reagent was demonstrated by the determination of the Cu(II) content of tap water samples.

Journal Article↗
PubMed2001

Experimental data of a single promoter can be used for in silico detection of genes with related regulation in the absence of sequence similarity.

Gene expression is presently a major focus in genome analysis, and the experimental data on regulatory mechanisms and functional transcription factor binding sites are steadily growing. However, the annotation of transcriptional regulation of sequences cannot keep pace with the exponential growth of sequence databases. Employing detailed experimental data of a single promoter or enhancer to predict genes with similar regulation would provide a powerful method to link the literature about transcriptional regulation and sequence databases. To this end, we used information on individual functional transcription factor binding sites to compose in silico promoter and enhancer models of muscle-specific genes and to analyze the rodents section of EMBL with these models. Exhaustive evaluation of all hits revealed every second to third match to be a muscle-associated gene. Moreover, functionally related regulatory regions were detected by our model-based approach even in the absence of sequence similarity. We believe that this new approach is a substanial extension to database analysis by BLAST or FASTA, which are restricted to sequence similarity.

Animals↗
PubMed2001

Comparative analysis of the genomic organization of Pax9 and its conserved physical association with Nkx2-9 in the human, mouse, and pufferfish genomes.

As a first step towards the identification of cis-regulatory elements of Pax9 by means of comparative genomics, we have analyzed genome regions encompassing the Pax9 gene in three vertebrate species, humans, mice (Mus musculus), and the Japanese pufferfish (Fugu rubripes). We show the genomic organization of Pax9 and its physical association with Nkx2-9 conserved in the three species. We discuss about possible implications of the conserved synteny between Pax9 and Nkx2-9 in a context of vertebrate evolution. This report also includes the first description of the primary structures of Fugu Pax9 and Nkx2-9. Furthermore, we report the identification of a novel upstream exon and putative transcription start sites in mouse Pax9. Our results suggest that transcription of Pax9 may be initiated at two alternative start sites and driven by TATA-less promoters.

Amino Acid Sequence↗
PubMed2001

Target gene identification from expression array data by promoter analysis.

DNA microchips and expression arrays yield enormous amounts of data linking cDNA sequences to gene expression patterns. This now allows the characterization of gene expression in normal and diseased tissues as well as the response of tissues to the application of therapeutic reagents. Software currently exists to analyze DNA array/chip data with respect to corresponding mRNA sequences, which facilitates the precise determination of when and where certain groups of genes are expressed. The information concerning transcriptional regulatory networks responsible for the observed expression patterns is not contained within the cDNA sequences used to generate the arrays, but resides often within the promoter sequences of the individual genes (and/or enhancers). The complete sequence of the human genome will provide the molecular basis for the identification of such regulatory regions. Promoter sequences for specific cDNAs can be obtained reliably from genomic sequences simply by exon mapping. Promoter prediction tools can also be used to locate promoters directly in the genomic sequence in many cases in which cDNAs are 5'-incomplete. Once sufficient numbers of promoter sequences have been obtained, the comparative promoter analysis of the co-regulated genes and groups of genes can be applied in order to generate models describing the higher order levels of the transcription factor binding site organization within these promoter regions. As evident from several examples, this approach can identify promoter modules responsible for the common regulation of promoters solely by the application of bioinformatics methods. Such modules represent the molecular mechanisms through which regulatory networks influence gene expression. Another advantage of this approach is that it also provides a powerful alternative for elucidating functional features of genes with no detectable sequence similarity, by linking them to other genes on the basis of their common promoter structures.

Computational Biology↗
PubMed2001

The promoter connection.

The availability of the complete genomic sequence of yeast now enables elucidation of molecular mechanisms governing gene expression patterns. New results from the yeast genome and recent advances in predicting and finding human promoters support the use of similar combinatorial approaches to study genome-wide transcriptional regulation in humans.

Binding Sites↗