Over the past decades, quantitative methods linking theory and observation became increasingly important in many areas of life science. Subsequently, a large number of mathematical and computational models has been developed. The BioModels database alone lists more than 140,000 Systems Biology Markup Language (SBML) models. However, while the exchange within specific model classes has been supported by standardisation and database efforts, the generic application and especially the re-use of models is still limited by practical issues such as easy and straight forward model execution. MAGPIE, a Modeling and Analysis Generic Platform with Integrated Evaluation, closes this gap by providing a software platform for both, publishing and executing computational models without restrictions on the programming language, thereby combining a maximum on flexibility for programmers with easy handling for non-technical users. MAGPIE goes beyond classical SBML platforms by including all models, independent of the underlying programming language, ranging from simple script models to complex data integration and computations. We demonstrate the versatility of MAGPIE using four prototypic example cases. We also outline the potential of MAGPIE to improve transparency and reproducibility of computational models in life sciences. A demo server is available at magpie.imb.medizin.tu-dresden.de.

Aquakultur ist essentiell um den heutigen Bedarf an Fisch als Nahrungsmittel zu decken. Einsatz von Antibiotika und Kontaminationen mit Schadstoffen in der Vergangenheit haben das Vertrauen von Verbrauchern in Fischprodukte aus Aquakulturproduktion massiv geschwächt. Zeitgleich sind die Ansprüche der Verbraucher an Qualität, Frische und Sicherheit von Lebensmitteln, aber auch das Bewusstsein, negative Auswirkungen der Lebensmittelproduktion auf die Umwelt zu minimieren, erheblich gestiegen. In der Dissertation wurde der Einsatz einer natürlichen organischen Substanz (Fulvosäure) auf die Fischgesundheit und das Immunsystem untersucht. Dabei wurde gezeigt, dass die Zugabe zum Haltungswasser bei Salmoniden und Cypriniden zu verbesserter Stressresistenz und einer Anregung des Immunsystems führte. Dies hilft den Tieren sich auf natürliche Weise gegen Krankheitserreger zu verteidigen, reduziert den Einsatz umweltschädlicher Therapeutika und steigert gleichzeitig das Tierwohl. Weiterhin führte der Zusatz der Fulvosäure zu einer signifikanten Verbesserung der Futterumsatzrate, was sich ebenfalls in gesteigertem Wachstum der Tiere widerspiegelte. Huminstoffe, zu denen die Fulvosäure zählt, sind natürlicher Bestandteil aller aquatischen Ökosysteme. Die Zugabe zum Haltungswasser stellt daher nicht nur eine umweltfreundliche, sondern auch die ursprüngliche Expositionsroute mit diesen Immunstimulanzien für aquatischen Lebewesen dar. Weiterhin besteht mit diesem innovativen Ansatz erstmals die Option die extrem empfindlichen Embryo- und Larvenstadien ohne Zusatz von Antibiotika vor Krankheiten zu schützen. Zeitgleich wird der Metabolismus stimuliert und die Larven im Schlupf und Wachstum unterstützt. Da die Sterblichkeit in diesen Stadien bei über 80 % liegen kann, eröffnen die Ergebnisse der Dissertation ein immenses Potenzial den Tierschutz zu verbessern, und sowohl die Nachhaltigkeit als auch gesellschaftliche Akzeptanz und Konkurrenzfähigkeit der Aquakultur zu steigern. / Aquaculture has become imperative to cover the dietary demand for fish as food. The use of antibiotics and contaminations with harmful substances in the past have caused a lot of prejudices for fish products from aquaculture production. At the same time, consumer standards for quality, freshness and safety of food, as well as the awareness to minimize negative impacts of food production on the environment, have increased significantly. In the dissertation, the use of a natural organic substance (fulvic acid) on the health and immune system of fish was determined. Supplementing the water resulted in improved stress resistance and a stimulation of the immune system in salmonids and cyprinids. This helps the animals to defend themselves against pathogens in a natural way, thereby reduces the use of environmentally harmful therapeutics and at the same time increases animal welfare. Furthermore, the addition of fulvic acid led to a significant improvement in feed conversion rate, which was also reflected in increased growth of the animals. Humic substances, which include fulvic acid, are a natural component of all aquatic ecosystems. Therefore, the addition to the holding water represents not only an environmentally friendly but also the original route of exposure to these immunostimulants for aquatic organisms. Furthermore, this innovative approach provides for the first time the option to protect the extremely sensitive embryo and larval stages from disease without the need of antibiotics. At the same time, the metabolism is stimulated and larvae are supported in hatching and growth. Since the mortality in these stages can be more than 80 %, the results of the dissertation show an immense potential to improve animal welfare and to increase sustainability as well as social acceptance and competitive

Heparan sulfate Proteoglycans (HSPG) are ubiquitous molecules with indispensable functions in various biological processes. Glypicans are a family of HSPG’s, characterized by a Gpi-anchor which directs them to the cell surface and/or extracellular matrix where they regulate growth factor signaling during development and disease. We report the identification and expression pattern of glypican genes from zebrafish. The zebrafish genome contains 10 glypican homologs, as opposed to six in mammals, which are highly conserved and are phylogenetically related to the mammalian genes. Some of the fish glypicans like Gpc1a, Gpc3, Gpc4, Gpc6a and Gpc6b show conserved synteny with their mammalian cognate genes. Many glypicans are expressed during the gastrulation stage, but their expression becomes more tissue specific and defined during somitogenesis stages, particularly in the developing central nervous system. Existence of multiple glypican orthologs in fish with diverse expression pattern suggests highly specialized and/or redundant function of these genes during embryonic development.

Plastid genomes of photosynthetic flowering plants are usually highly conserved in both structure and gene content. However, the plastomes of parasitic and mycoheterotrophic plants may be released from selective constraint due to the reduction or loss of photosynthetic ability. Here we present the greatly reduced and highly divergent, yet functional, plastome of the nonphotosynthetic holoparasite Hydnora visseri (Hydnoraceae, Piperales). The plastome is 27 kb in length, with 24 genes encoding ribosomal proteins, ribosomal RNAs, tRNAs and a few non-bioenergetic genes, but no genes related to photosynthesis. The inverted repeat and the small single copy region are only ~1.5 kb, and intergenic regions have been drastically reduced. Despite extreme reduction, gene order and orientation are highly similar to the plastome of Piper cenocladum, a related photosynthetic plant in Piperales. Gene sequences in Hydnora are highly divergent and several complementary approaches using the highest possible sensitivity were required for identification and annotation of this plastome. Active transcription is detected for all of the protein coding genes in the plastid genome, and one of two introns is appropriately spliced out of rps12 transcripts. The whole genome shotgun read depth is 1,400X coverage for the plastome, while the mitochondrial genome is covered at 40X and the nuclear genome at 2X. Despite the extreme reduction of the genome and high sequence divergence, the presence of syntenic, long transcriptionally-active open reading frames with distant similarity to other plastid genomes and a high plastome stoichiometry relative to the mitochondrial and nuclear genomes suggests that the plastome remains functional in Hydnora visseri. A four stage model of gene reduction, including the potential for complete plastome loss, is proposed to account for the range of plastid genomes in nonphotosynthetic plants.

Aims: To study the β-adrenoceptor subtypes involved in the relaxation responses to (-)-isoprenaline in carbachol-pre-contracted (CCh) mouse detrusor muscle with intact and denuded mucosa. Methods: Isolated muscle strips from the urinary bladder of male C57BL6 mice or β2-adrenoceptor knockout mice were pre-contracted with CCh, 1 µM and relaxed with increasing concentrations of the β-adrenoceptor (β-AR) agonist (-)-isoprenaline and forskolin. For estimating the β-AR subtypes involved, subtype-selective receptor blockers were used, that is, CGP 20712A (β1-ARs), ICI 118,551 (β2-ARs), and L748,337 (β3-ARs). Results: Unlike in KCl-pre-contracted muscle, the mucosa did not affect the sensitivity of the relaxation response to (-)-isoprenaline in CCh-pre-contracted murine detrusor strips. Increasing concentrations of (-)-isoprenaline produced a biphasic concentration-relaxation response without any difference both during the presence and absence of mucosa. The relaxation fraction produced by low (-)-isoprenaline concentrations was mediated by β2-AR as evidenced by a shift of the concentration-response curve to higher concentrations with ICI 118,551, but not with CGP 20712A and L748,337, and by the absence of this fraction in β2-AR-KO mice. The relaxation response with low sensitivity to (-)-isoprenaline was not affected by any of the β-AR subtype-selective blockers and was the only response detected in detrusor strips from β2-AR-KO mice. Conclusions: In CCh-pre-contracted mouse detrusor, β2-ARs are responsible for the relaxation component with high sensitivity to (-)-isoprenaline as indicated by the conversion of a biphasic into a monophasic CRC with ICI 118,551 or by its absence in β2-AR KO mice. The mucosa does not impair relaxation under these conditions. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

In a study looking for risk factors of atherosclerosis in families with combined hyperlipidemia and hypertension, clinical and biochemical data of 1,149 persons were analyzed to develop two hypothetical multivariate scores concerning the degree to which a patient is affected by the metabolic syndrome. The scores are based on a structural model for low-density cholesterol (LDL) and high-density cholesterol (HDL), triglycerides, uric acid, creatinine, glucose, insulin, systolic blood pressure and waist-to-hip ratio. Age, gender and body mass index were used for adjusting all variables. In segregation analyses of 42 pedigrees without using genotype information, estimations of the heritabilities and environmentally caused variance and covariance components were computed for the individual score values of the two latent factors. The first score shows a heritability of 42%; the environment component disappeared. The score mainly reflects the HDL, LDL and triglyceride levels. The second score shows a heritability of 16% with an environment component of 7%. It includes mainly insulin, uric acid and creatinine. In the search for genetic causes, both scores could be a basis for further phenotypic classification of the metabolic syndrome. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Analysis of donor chimerism has become a routine method for the documentation of engraftment after allogeneic hematopoietic stem cell transplantation (HSCT). In recent years several groups have also focused on the application of this technique for the detection of relapsing disease after allogeneic HSCT. This review addresses technical issues (sensitivity, specificity) and discusses the advantages and limitations of methods currently used for chimerism analysis and their usefulness for the detection of MRD. In addition, the potential impact of novel procedures, e.g. subset chimerism or real-time PCR-based procedures, is discussed. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Effective prevention, or treatment, of invasive fungal infection in the neutropenic patient has hitherto been unsatisfactory because of either an inadequate anti-fungal spectrum of the agent or important toxicity. Itraconazole is effective against a broad spectrum of the opportunistic pathogens seen in Europe and North America. Prior problems with absorption, e.g. in the marrow transplant recipient, have been overcome with the introduction of an oral solution and an i.v. preparation. The deliberations of an expert meeting held in June, 1998 include recommendations on which patient requires one of these new preparations based on clinical trials, the dose and route. Important drug interactions are also detailed. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

We report on a stem cell-transplanted patient with B cell chronic lymphatic leukemia who presented with a subacute onset of focal neurological deficits, gait abnormalities, emotional lability and dementia. Progressive multifocal leukoencephalopathy was diagnosed by magnetic resonance imaging (MRI) of the brain and detection of JC virus genome in the cerebrospinal fluid. Cidofovir and the 5HT2A receptor antagonist chlorpromazine were subsequently administered. A follow-up MRI of the brain 2 weeks after initiation of the antiviral therapy displayed progress of the demyelination, and the patient died 3 months after onset of the neurological symptoms. This report highlights the need for the development of novel and potent strategies for treatment of progressive multifocal leukoencephalopathy. / Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.

Dieser Beitrag ist mit Zustimmung des Rechteinhabers aufgrund einer (DFG-geförderten) Allianz- bzw. Nationallizenz frei zugänglich.