27122
2022
eng
5
11
article
1
--
2022-04-28
--
Cisplatin-induced reproductive toxicity and oxidative stress: ameliorative effect of kinetin
Cisplatin is a commonly used chemotherapeutic agent; however, its potential side effects, including gonadotoxicity and infertility, are a critical problem. Oxidative stress has been implicated in the pathogenesis of cisplatin-induced testicular dysfunction. We investigated whether kinetin use at different concentrations could alleviate gonadal injury associated with cisplatin treatment, with an exploration of the involvement of its antioxidant capacity. Kinetin was administered in different doses of 0.25, 0.5, and 1 mg/kg, alone or along with cisplatin for 10 days. Cisplatin toxicity was induced via a single IP dose of 7 mg/kg on day four. In a dose-dependent manner, concomitant administration of kinetin with cisplatin significantly restored testicular oxidative stress parameters, corrected the distorted sperm quality parameters and histopathological changes, enhanced levels of serum testosterone and testicular StAR protein expression, as well as reduced the up-regulation of testicular TNF-α, IL-1β, Il-6, and caspase-3, caused by cisplatin. It is worth noting that the testicular protective effect of the highest kinetin dose was comparable/more potent and significantly higher than the effects of vitamin C and the lowest kinetin dose, respectively. Overall, these data indicate that kinetin may offer a promising approach for alleviating cisplatin-induced reproductive toxicity and organ damage, via ameliorating oxidative stress and reducing inflammation and apoptosis.
Antioxidants
2076-3921
10.3390/antiox11050863
urn:nbn:de:bvb:20-opus-271223
2022-05-09T06:54:26+00:00
sword
swordwue
attachment; filename=deposit.zip
8a2724b8ddc2c3935ce284b68c429946
Antioxidants (2022) 11:5, 863. doi:10.3390/antiox11050863
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Rania Abdel-Latif
Moustafa Fathy
Hend Ali Anwar
Muhammad Naseem
Thomas Dandekar
Eman M. Othman
eng
uncontrolled
cytokinins
eng
uncontrolled
kinetin
eng
uncontrolled
cisplatin
eng
uncontrolled
reproductive toxicity
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Import
Förderzeitraum 2022
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/27122/antioxidants-11-00863-v2.pdf
16269
2016
eng
baw118
2016
article
1
2018-06-08
--
--
Mining biomedical images towards valuable information retrieval in biomedical and life sciences
Biomedical images are helpful sources for the scientists and practitioners in drawing significant hypotheses, exemplifying approaches and describing experimental results in published biomedical literature. In last decades, there has been an enormous increase in the amount of heterogeneous biomedical image production and publication, which results in a need for bioimaging platforms for feature extraction and analysis of text and content in biomedical images to take advantage in implementing effective information retrieval systems. In this review, we summarize technologies related to data mining of figures. We describe and compare the potential of different approaches in terms of their developmental aspects, used methodologies, produced results, achieved accuracies and limitations. Our comparative conclusions include current challenges for bioimaging software with selective image mining, embedded text extraction and processing of complex natural language queries.
Database - The Journal of Biological Databases and Curation
10.1093/database/baw118
PMC4990152
urn:nbn:de:bvb:20-opus-162697
Database, 2016, 1–17 doi: 10.1093/database/baw118
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Zeeshan Ahmed
Saman Zeeshan
Thomas Dandekar
eng
uncontrolled
humans
eng
uncontrolled
software
eng
uncontrolled
image processing
eng
uncontrolled
animals
eng
uncontrolled
computer-assisted
eng
uncontrolled
data mining/methods
eng
uncontrolled
natural language processing
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/16269/Ahmed_Database_2016.pdf
12010
2014
eng
bau077
2014
article
1
2015-10-12
--
--
‘Isotopo’ a database application for facile analysis and management of mass isotopomer data
The composition of stable-isotope labelled isotopologues/isotopomers in metabolic products can be measured by mass spectrometry and supports the analysis of pathways and fluxes. As a prerequisite, the original mass spectra have to be processed, managed and stored to rapidly calculate, analyse and compare isotopomer enrichments to study, for instance, bacterial metabolism in infection. For such applications, we provide here the database application ‘Isotopo’. This software package includes (i) a database to store and process isotopomer data, (ii) a parser to upload and translate different data formats for such data and (iii) an improved application to process and convert signal intensities from mass spectra of \(^{13}C\)-labelled metabolites such as tertbutyldimethylsilyl-derivatives of amino acids. Relative mass intensities and isotopomer distributions are calculated applying a partial least square method with iterative refinement for high precision data. The data output includes formats such as graphs for overall enrichments in amino acids. The package is user-friendly for easy and robust data management of multiple experiments.
Database
10.1093/database/bau077
PMC4158277
urn:nbn:de:bvb:20-opus-120102
Zeeshan Ahmed
Saman Zeeshan
Claudia Huber
Michael Hensel
Dietmar Schomburg
Richard Münch
Eva Eylert
Wolfgang Eisenreich
Thomas Dandekar
eng
uncontrolled
stable-isotope
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/12010/076_Ahmed_Database.pdf
20266
2019
eng
15711
9
article
1
2020-04-09
--
--
C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1
Protein-protein interaction (PPI) studies are gaining momentum these days due to the plethora of various high-throughput experimental methods available for detecting PPIs. Proteins create complexes and networks by functioning in harmony with other proteins and here in silico network biology hold the promise to reveal new functionality of genes as it is very difficult and laborious to carry out experimental high-throughput genetic screens in living organisms. We demonstrate this approach by computationally screening C. elegans conserved homologs of already reported human tumor suppressor and aging associated genes. We select by this nhr-6, vab-3 and gst-23 as predicted longevity genes for RNAi screen. The RNAi results demonstrated the pro-longevity effect of these genes. Nuclear hormone receptor nhr-6 RNAi inhibition resulted in a C. elegans phenotype of 23.46% lifespan reduction. Moreover, we show that nhr-6 regulates oxidative stress resistance in worms and does not affect the feeding behavior of worms. These findings imply the potential of nhr-6 as a common therapeutic target for aging and cancer ailments, stressing the power of in silico PPI network analysis coupled with RNAi screens to describe gene function.
Scientific Reports
10.1038/s41598-019-51649-0
urn:nbn:de:bvb:20-opus-202666
Scientific Reports (2019) 9:15711. https://doi.org/10.1038/s41598-019-51649-0
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Bashir A. Akhoon
Shishir K. Gupta
Sudeep Tiwari
Laxmi Rathor
Aakanksha Pant
Nivedita Singh
Shailendra K. Gupta
Thomas Dandekar
Rakesh Pandey
eng
uncontrolled
Computer modelling
eng
uncontrolled
Embryonic induction
eng
uncontrolled
RNAi
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2019
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/20266/Akhoon_ScientificReports_2019.pdf
25006
2021
eng
12
10
article
1
--
2021-11-23
--
An in vitro and in silico study of the enhanced antiproliferative and pro-oxidant potential of Olea europaea L. cv. Arbosana leaf extract via elastic nanovesicles (spanlastics)
The olive tree is a venerable Mediterranean plant and often used in traditional medicine. The main aim of the present study was to evaluate the effect of Olea europaea L. cv. Arbosana leaf extract (OLE) and its encapsulation within a spanlastic dosage form on the improvement of its pro-oxidant and antiproliferative activity against HepG-2, MCF-7, and Caco-2 human cancer cell lines. The LC-HRESIMS-assisted metabolomic profile of OLE putatively annotated 20 major metabolites and showed considerable in vitro antiproliferative activity against HepG-2, MCF-7, and Caco-2 cell lines with IC\(_{50}\) values of 9.2 ± 0.8, 7.1 ± 0.9, and 6.5 ± 0.7 µg/mL, respectively. The encapsulation of OLE within a (spanlastic) nanocarrier system, using a spraying method and Span 40 and Tween 80 (4:1 molar ratio), was successfully carried out (size 41 ± 2.4 nm, zeta potential 13.6 ± 2.5, and EE 61.43 ± 2.03%). OLE showed enhanced thermal stability, and an improved in vitro antiproliferative effect against HepG-2, MCF-7, and Caco-2 (IC\(_{50}\) 3.6 ± 0.2, 2.3 ± 0.1, and 1.8 ± 0.1 µg/mL, respectively) in comparison to the unprocessed extract. Both preparations were found to exhibit pro-oxidant potential inside the cancer cells, through the potential inhibitory activity of OLE against glutathione reductase and superoxide dismutase (IC\(_{50}\) 1.18 ± 0.12 and 2.33 ± 0.19 µg/mL, respectively). These inhibitory activities were proposed via a comprehensive in silico study to be linked to the presence of certain compounds in OLE. Consequently, we assume that formulating such a herbal extract within a suitable nanocarrier would be a promising improvement of its therapeutic potential.
Antioxidants
2076-3921
10.3390/antiox10121860
urn:nbn:de:bvb:20-opus-250064
2021-12-01T14:44:11+00:00
sword
swordwue
attachment; filename=deposit.zip
e3774d750670cb832e52b4abdefd283c
Antioxidants (2021) 10:12, 1860. https://doi.org/10.3390/antiox10121860
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Taghreed S. Alnusaire
Ahmed M. Sayed
Abeer H. Elmaidomy
Mohammad M. Al-Sanea
Sarah Albogami
Mha Albqmi
Bassam F. Alowaiesh
Ehab M. Mostafa
Arafa Musa
Khayrya A. Youssif
Hesham Refaat
Eman M. Othman
Thomas Dandekar
Eman Alaaeldin
Mohammed M. Ghoneim
Usama Ramadan Abdelmohsen
eng
uncontrolled
olive
eng
uncontrolled
metabolomic profiling
eng
uncontrolled
antiproliferative
eng
uncontrolled
pro-oxidant
eng
uncontrolled
encapsulation
eng
uncontrolled
spanlastic
eng
uncontrolled
nanocarrier
eng
uncontrolled
docking
eng
uncontrolled
molecular dynamics simulation
eng
uncontrolled
Olea
Medizin und Gesundheit
open_access
Theodor-Boveri-Institut für Biowissenschaften
Import
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/25006/antioxidants-10-01860-v2.pdf
15753
2017
eng
282
18
article
1
2018-02-13
--
--
Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence
Background:
Commensal bacteria like Neisseria meningitidis sometimes cause serious disease. However, genomic comparison of hyperinvasive and apathogenic lineages did not reveal unambiguous hints towards indispensable virulence factors. Here, in a systems biological approach we compared gene expression of the invasive strain MC58 and the carriage strain α522 under different ex vivo conditions mimicking commensal and virulence compartments to assess the strain-specific impact of gene regulation on meningococcal virulence.
Results:
Despite indistinguishable ex vivo phenotypes, both strains differed in the expression of over 500 genes under infection mimicking conditions. These differences comprised in particular metabolic and information processing genes as well as genes known to be involved in host-damage such as the nitrite reductase and numerous LOS biosynthesis genes. A model based analysis of the transcriptomic differences in human blood suggested ensuing metabolic flux differences in energy, glutamine and cysteine metabolic pathways along with differences in the activation of the stringent response in both strains. In support of the computational findings, experimental analyses revealed differences in cysteine and glutamine auxotrophy in both strains as well as a strain and condition dependent essentiality of the (p)ppGpp synthetase gene relA and of a short non-coding AT-rich repeat element in its promoter region.
Conclusions:
Our data suggest that meningococcal virulence is linked to transcriptional buffering of cryptic genetic variation in metabolic genes including global stress responses. They further highlight the role of regulatory elements for bacterial virulence and the limitations of model strain approaches when studying such genetically diverse species as N. meningitidis.
BMC Genomics
10.1186/s12864-017-3616-7
urn:nbn:de:bvb:20-opus-157534
BMC Genomics (2017) 18:282. DOI: 10.1186/s12864-017-3616-7
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Biju Joseph Ampattu
Laura Hagmann
Chunguang Liang
Marcus Dittrich
Andreas Schlüter
Jochen Blom
Elizaveta Krol
Alexander Goesmann
Anke Becker
Thomas Dandekar
Tobias Müller
Christoph Schoen
eng
uncontrolled
neisseria meningitidis
eng
uncontrolled
MITE
eng
uncontrolled
virulenceregulatory evolution
eng
uncontrolled
systems biology
eng
uncontrolled
metabolism
eng
uncontrolled
cryptic
eng
uncontrolled
genetic variation
eng
uncontrolled
stringent response
eng
uncontrolled
relA
Medizin und Gesundheit
open_access
Institut für Hygiene und Mikrobiologie
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2017
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/15753/Ampattu_BMC_Genomics.pdf
2836
1994
eng
article
1
2009-04-07
--
--
Delineating the main chain topology of four-helix bundle proteins using the genetic algorithm and knowledge based on the amino acid sequence alone
No abstract available
urn:nbn:de:bvb:20-opus-33807
3380
Bohr,H. und Brunak,S. (Hrsg.): Protein Structure Distance Analysis. IOS Press, Amsterdam (1994) 302-314. - ISBN: 90-5199-161-4
P. Argos
Thomas Dandekar
deu
swd
Proteine
deu
swd
Strukturanalyse
deu
swd
Abstandsmessung
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/2836/Dandekar_Delineating_topology.pdf
26031
2021
eng
1
11
article
1
2022-03-15
--
--
Modeling of stringent-response reflects nutrient stress induced growth impairment and essential amino acids in different Staphylococcus aureus mutants
Stapylococcus aureus colonises the nose of healthy individuals but can also cause a wide range of infections. Amino acid (AA) synthesis and their availability is crucial to adapt to conditions encountered in vivo. Most S. aureus genomes comprise all genes required for AA biosynthesis. Nevertheless, different strains require specific sets of AAs for growth. In this study we show that regulation inactivates pathways under certain conditions which result in these observed auxotrophies. We analyzed in vitro and modeled in silico in a Boolean semiquantitative model (195 nodes, 320 edges) the regulatory impact of stringent response (SR) on AA requirement in S. aureus HG001 (wild-type) and in mutant strains lacking the metabolic regulators RSH, CodY and CcpA, respectively. Growth in medium lacking single AAs was analyzed. Results correlated qualitatively to the in silico predictions of the final model in 92% and quantitatively in 81%. Remaining gaps in our knowledge are evaluated and discussed. This in silico model is made fully available and explains how integration of different inputs is achieved in SR and AA metabolism of S. aureus. The in vitro data and in silico modeling stress the role of SR and central regulators such as CodY for AA metabolisms in S. aureus.
Scientific Reports
10.1038/s41598-021-88646-1
urn:nbn:de:bvb:20-opus-260313
publish
Scientific Reports (2021) 11:1, 9651. https://doi.org/10.1038/s41598-021-88646-1
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Christof Audretsch
Fabio Gratani
Christiane Wolz
Thomas Dandekar
eng
uncontrolled
bacteriology
eng
uncontrolled
cellular signalling networks
Mikroorganismen, Pilze, Algen
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2021
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/26031/s41598-021-88646-1.pdf
30126
2022
eng
1
12
article
1
--
--
--
Motif and conserved module analysis in DNA (promoters, enhancers) and RNA (lncRNA, mRNA) using AlModules
Nucleic acid motifs consist of conserved and variable nucleotide regions. For functional action, several motifs are combined to modules. The tool AIModules allows identification of such motifs including combinations of them and conservation in several nucleic acid stretches. AIModules recognizes conserved motifs and combinations of motifs (modules) allowing a number of interesting biological applications such as analysis of promoter and transcription factor binding sites (TFBS), identification of conserved modules shared between several gene families, e.g. promoter regions, but also analysis of shared and conserved other DNA motifs such as enhancers and silencers, in mRNA (motifs or regulatory elements e.g. for polyadenylation) and lncRNAs. The tool AIModules presented here is an integrated solution for motif analysis, offered as a Web service as well as downloadable software. Several nucleotide sequences are queried for TFBSs using predefined matrices from the JASPAR DB or by using one’s own matrices for diverse types of DNA or RNA motif discovery. Furthermore, AIModules can find TFBSs common to two or more sequences. Demanding high or low conservation, AIModules outperforms other solutions in speed and finds more modules (specific combinations of TFBS) than alternative available software. The application also searches RNA motifs such as polyadenylation site or RNA–protein binding motifs as well as DNA motifs such as enhancers as well as user-specified motif combinations (https://bioinfo-wuerz.de/aimodules/; alternative entry pages: https://aimodules.heinzelab.de or https://www.biozentrum.uni-wuerzburg.de/bioinfo/computing/aimodules). The application is free and open source whether used online, on-site, or locally.
Scientific Reports
10.1038/s41598-022-21732-0
urn:nbn:de:bvb:20-opus-301268
@articleAydinli.2022, author = Aydinli, Muharrem and Liang, Chunguang and Dandekar, Thomas, year = 2022, title = Motif and conserved module analysis in DNA (promoters, enhancers) and RNA (lncRNA, mRNA) using AlModules, pages = 17588, volume = 12, number = 1, journal = Scientific reports, doi = 10.1038/s41598-022-21732-0,
md5:7380e89b101a9be2d73d428852d8a4b3
2023-01-25T15:20:43+00:00
/tmp/phpK9qWsg
bibtex
63d148cb2152f3.61730211
Scientific Reports 2022, 12(1):17588. DOI: 10.1038/s41598-022-21732-0
false
true
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Muharrem Aydinli
Chunguang Liang
Thomas Dandekar
eng
uncontrolled
AIModules
eng
uncontrolled
nucleic acid motifs
eng
uncontrolled
DNA
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Förderzeitraum 2022
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/30126/Scientific_Reports_Aydinli.pdf
23037
2020
eng
21
article
1
2021-03-10
--
--
Comparison of the central human and mouse platelet signaling cascade by systems biological analysis
Background
Understanding the molecular mechanisms of platelet activation and aggregation is of high interest for basic and clinical hemostasis and thrombosis research. The central platelet protein interaction network is involved in major responses to exogenous factors. This is defined by systemsbiological pathway analysis as the central regulating signaling cascade of platelets (CC).
Results
The CC is systematically compared here between mouse and human and major differences were found. Genetic differences were analysed comparing orthologous human and mouse genes. We next analyzed different expression levels of mRNAs. Considering 4 mouse and 7 human high-quality proteome data sets, we identified then those major mRNA expression differences (81%) which were supported by proteome data. CC is conserved regarding genetic completeness, but we observed major differences in mRNA and protein levels between both species. Looking at central interactors, human PLCB2, MMP9, BDNF, ITPR3 and SLC25A6 (always Entrez notation) show absence in all murine datasets. CC interactors GNG12, PRKCE and ADCY9 occur only in mice. Looking at the common proteins, TLN1, CALM3, PRKCB, APP, SOD2 and TIMP1 are higher abundant in human, whereas RASGRP2, ITGB2, MYL9, EIF4EBP1, ADAM17, ARRB2, CD9 and ZYX are higher abundant in mouse. Pivotal kinase SRC shows different regulation on mRNA and protein level as well as ADP receptor P2RY12.
Conclusions
Our results highlight species-specific differences in platelet signaling and points of specific fine-tuning in human platelets as well as murine-specific signaling differences.
BMC Genomics
10.1186/s12864-020-07215-4
urn:nbn:de:bvb:20-opus-230377
publish
BMC Genomics (2020) 21:897 https://doi.org/10.1186/s12864-020-07215-4
CC BY: Creative-Commons-Lizenz: Namensnennung 4.0 International
Johannes Balkenhol
Kristin V. Kaltdorf
Elmina Mammadova-Bach
Attila Braun
Bernhard Nieswandt
Marcus Dittrich
Thomas Dandekar
eng
uncontrolled
interspecies comparison
eng
uncontrolled
transcriptome
eng
uncontrolled
proteome
eng
uncontrolled
platelet
eng
uncontrolled
network
eng
uncontrolled
signaling
eng
uncontrolled
mouse
eng
uncontrolled
human
eng
uncontrolled
interactome
eng
uncontrolled
cascade
Biowissenschaften; Biologie
open_access
Theodor-Boveri-Institut für Biowissenschaften
Rudolf-Virchow-Zentrum
Institut für Experimentelle Biomedizin
Förderzeitraum 2020
Universität Würzburg
https://opus.bibliothek.uni-wuerzburg.de/files/23037/s12864-020-07215-4.pdf