24626
2021
eng
9
11
article
1
--
2021-09-18
--
Metabolite ratios as quality indicators for pre-analytical variation in serum and EDTA plasma
In clinical diagnostics and research, blood samples are one of the most frequently used materials. Nevertheless, exploring the chemical composition of human plasma and serum is challenging due to the highly dynamic influence of pre-analytical variation. A prominent example is the variability in pre-centrifugation delay (time-to-centrifugation; TTC). Quality indicators (QI) reflecting sample TTC are of utmost importance in assessing sample history and resulting sample quality, which is essential for accurate diagnostics and conclusive, reproducible research. In the present study, we subjected human blood to varying TTCs at room temperature prior to processing for plasma or serum preparation. Potential sample QIs were identified by Ultra high pressure liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) based metabolite profiling in samples from healthy volunteers (n = 10). Selected QIs were validated by a targeted MS/MS approach in two independent sets of samples from patients (n = 40 and n = 70). In serum, the hypoxanthine/guanosine (HG) and hypoxanthine/inosine (HI) ratios demonstrated high diagnostic performance (Sensitivity/Specificity > 80%) for the discrimination of samples with a TTC > 1 h. We identified several eicosanoids, such as 12-HETE, 15-(S)-HETE, 8-(S)-HETE, 12-oxo-HETE, (±)13-HODE and 12-(S)-HEPE as QIs for a pre-centrifugation delay > 2 h. 12-HETE, 12-oxo-HETE, 8-(S)-HETE, and 12-(S)-HEPE, and the HI- and HG-ratios could be validated in patient samples.
Metabolites
2218-1989
10.3390/metabo11090638
urn:nbn:de:bvb:20-opus-246261
2021-10-01T17:47:56+00:00
sword
swordwue
attachment; filename=deposit.zip
73a07a587073ba5c5a98638747ee4328
Metabolites (2021) 11:9, 638. https://doi.org/10.3390/metabo11090638
Interdisciplinary Bank of Biological Material and Data Würzburg (IBDW)
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Sven Heiling
Nadine Knutti
Franziska Scherr
Jörg Geiger
Juliane Weikert
Michael Rose
Roland Jahns
Uta Ceglarek
André Scherag
Michael Kiehntopf
eng
uncontrolled
quality indicators
eng
uncontrolled
biomarker
eng
uncontrolled
hypoxanthine
eng
uncontrolled
inosine
eng
uncontrolled
guanosine
eng
uncontrolled
eicosanoids
eng
uncontrolled
time-to-centrifugation
eng
uncontrolled
pre-analytical variation
Medizin und Gesundheit
open_access
Medizinische Fakultät
Import
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/24626/metabolites-11-00638-v2.pdf
18958
2016
eng
13 Seiten
2
6
article
1
2019-10-22
--
--
The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable
Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.
Interface Focus
10.1098/rsfs.2015.0103
urn:nbn:de:bvb:20-opus-189584
Interface Focus (2016) 6:2, 20150103. https://doi.org/10.1098/rsfs.2015.0103
true
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
David Nickerson
Koray Atalag
Bernard de Bono
Jörg Geiger
Carole Goble
Susanne Hollmann
Joachim Lonien
Wolfgang Müller
Babette Regierer
Natalie J. Stanford
Martin Golebiewski
Peter Hunter
eng
uncontrolled
Human Physiome
eng
uncontrolled
standards
eng
uncontrolled
repositories
eng
uncontrolled
service infrastructure
eng
uncontrolled
reproducible science
eng
uncontrolled
managing big data
Medizin und Gesundheit
open_access
Medizinische Fakultät
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/18958/Nickerson_InterfaceFocus_2016.pdf
14182
2011
eng
169-176
2
384
article
1
2016-12-14
--
--
Quantification of cAMP and cGMP analogs in intact cells: pitfalls in enzyme immunoassays for cyclic nucleotides
Immunoassays are routinely used as research tools to measure intracellular cAMP and cGMP concentrations. Ideally, this application requires antibodies with high sensitivity and specificity. The present work evaluates the cross-reactivity of commercially available cyclic nucleotide analogs with two non-radioactive and one radioactive cAMP and cGMP immunoassay. Most of the tested cyclic nucleotide analogs showed low degree competition with the antibodies; however, with Rp-cAMPS, 8-Br-cGMP and 8-pCPT-cGMP, a strong cross-reactivity with the corresponding cAMP and cGMP, respectively, immunoassays was observed. The determined EIA-binding constants enabled the measurement of the intracellular cyclic nucleotide concentrations and revealed a time- and lipophilicity-dependent cell membrane permeability of the compounds in the range of 10–30% of the extracellular applied concentration, thus allowing a more accurate prediction of the intracellular analog levels in a given experiment.
Naunyn-Schmiedeberg's Archives of Pharmacology
10.1007/s00210-011-0662-6
urn:nbn:de:bvb:20-opus-141828
Naunyn-Schmiedeberg's Arch Pharmacol (2011) 384:169–176
Katharina Werner
Frank Schwede
Hans-Gottfried Genieser
Jörg Geiger
Elke Butt
eng
uncontrolled
Cyclic nucleotides
eng
uncontrolled
Enzyme immunoassay
eng
uncontrolled
Lipophilicity
eng
uncontrolled
Cell permeability
Medizin und Gesundheit
open_access
Institut für Klinische Biochemie und Pathobiochemie
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/14182/119_Werner_Naunyn-Schmiedeberg's-Archieves-of-Pharmacology.pdf
5972
2011
eng
article
1
2012-06-30
--
--
Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation
Background: Hemostasis is a critical and active function of the blood mediated by platelets. Therefore, the prevention of pathological platelet aggregation is of great importance as well as of pharmaceutical and medical interest. Endogenous platelet inhibition is predominantly based on cyclic nucleotides (cAMP, cGMP) elevation and subsequent cyclic nucleotide-dependent protein kinase (PKA, PKG) activation. In turn, platelet phosphodiesterases (PDEs) and protein phosphatases counterbalance their activity. This main inhibitory pathway in human platelets is crucial for countervailing unwanted platelet activation. Consequently, the regulators of cyclic nucleotide signaling are of particular interest to pharmacology and therapeutics of atherothrombosis. Modeling of pharmacodynamics allows understanding this intricate signaling and supports the precise description of these pivotal targets for pharmacological modulation. Results: We modeled dynamically concentration-dependent responses of pathway effectors (inhibitors, activators, drug combinations) to cyclic nucleotide signaling as well as to downstream signaling events and verified resulting model predictions by experimental data. Experiments with various cAMP affecting compounds including antiplatelet drugs and their combinations revealed a high fidelity, fine-tuned cAMP signaling in platelets without crosstalk to the cGMP pathway. The model and the data provide evidence for two independent feedback loops: PKA, which is activated by elevated cAMP levels in the platelet, subsequently inhibits adenylyl cyclase (AC) but as well activates PDE3. By multi-experiment fitting, we established a comprehensive dynamic model with one predictive, optimized and validated set of parameters. Different pharmacological conditions (inhibition, activation, drug combinations, permanent and transient perturbations) are successfully tested and simulated, including statistical validation and sensitivity analysis. Downstream cyclic nucleotide signaling events target different phosphorylation sites for cAMP- and cGMP-dependent protein kinases (PKA, PKG) in the vasodilator-stimulated phosphoprotein (VASP). VASP phosphorylation as well as cAMP levels resulting from different drug strengths and combined stimulants were quantitatively modeled. These predictions were again experimentally validated. High sensitivity of the signaling pathway at low concentrations is involved in a fine-tuned balance as well as stable activation of this inhibitory cyclic nucleotide pathway. Conclusions: On the basis of experimental data, literature mining and database screening we established a dynamic in silico model of cyclic nucleotide signaling and probed its signaling sensitivity. Thoroughly validated, it successfully predicts drug combination effects on platelet function, including synergism, antagonism and regulatory loops.
urn:nbn:de:bvb:20-opus-69145
6914
BMC Systems Biology (2011) 5:178, doi:10.1186/1752-0509-5-178
Gaby Wangorsch
Elke Butt
Regina Mark
Katharina Hubertus
Jörg Geiger
Thomas Dandekar
Marcus Dittrich
deu
swd
Vasodilatator-stimuliertes Phosphoprotein
deu
uncontrolled
VASP
eng
uncontrolled
cyclic nucleotide signaling
eng
uncontrolled
silico model
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2011
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/5972/dandekar_1752_0509_5_178.pdf