Reconstruction of the temporal signaling network in Salmonella-infected human cells

2015-07-20
Budak, Gungor
Ozsoy, Oyku Eren
Aydın Son, Yeşim
Can, Tolga
Tunçbağ, Nurcan
Show full item record
Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.
231
views
133
downloads
Salmonella enterica is a bacterial pathogen that usually infects its host through food sources. Translocation of the pathogen proteins into the host cells leads to changes in the signaling mechanism either by activating or inhibiting the host proteins. Given that the bacterial infection modifies the response network of the host, a more coherent view of the underlying biological processes and the signaling networks can be obtained by using a network modeling approach based on the reverse engineering principles. In this work, we have used a published temporal phosphoproteomic dataset of Salmonella-infected human cells and reconstructed the temporal signaling network of the human host by integrating the interactome and the phosphoproteomic dataset. We have combined two well-established network modeling frameworks, the Prize-collecting Steiner Forest (PCSF) approach and the Integer Linear Programming (ILP) based edge inference approach. The resulting network conserves the information on temporality, direction of interactions, while revealing hidden entities in the signaling, such as the SNARE binding, mTOR signaling, immune response, cytoskeleton organization, and apoptosis pathways. Targets of the Salmonella effectors in the host cells such as CDC42, RHOA, 14-3-3 delta, Syntaxin family, Oxysterol-binding proteins were included in the reconstructed signaling network although they were not present in the initial phosphoproteomic data. We believe that integrated approaches, such as the one presented here, have a high potential for the identification of clinical targets in infectious diseases, especially in the Salmonella infections.
Phosphoproteomic, Network reconstruction, Salmonella infection, Temporal data integration, Pathway analysis
https://hdl.handle.net/11511/30841
FRONTIERS IN MICROBIOLOGY
Graduate School of Informatics, Article

Suggestions

Reconstruction of the temporal signaling network in salmonella infected human cells
Budak, Güngör; Aydın Son, Yeşim; Tunçbağ, Nurcan; Department of Bioinformatics (2016)
Salmonella enterica is a bacterial pathogen whose mechanism of infection is usually through food sources. The pathogen proteins are translocated into the host cells to change the host signaling mechanisms either by activating or inhibiting the host proteins. In order to obtain a more complete view of the biological processes and the signaling networks and to reconstruct the temporal signaling network of the human host, we have used two network modeling approaches, the Prize-collecting Steiner Forest (PCSF) ...
Development of rapid dipstick assay for food pathogens, Salmonella, by optimized parameters
Çam, Dilek; Öktem, Hüseyin Avni (Springer Science and Business Media LLC, 2018-10-25)
Salmonella is among the very important pathogens threating the human and animal health. Rapid and easy detection of these pathogens is crucial. In this context, antibody (Ab) based lateral flow assays (LFAs) which are simple immunochromatographic point of care test kits were developed by gold nanoparticles (GNPs) as labelling agent for Salmonella detection. For that purpose some critical parameters such as reagent concentrations on the capture zones, conjugate concentrations and ideal membrane type needed f...
Subtyping of salmonella isolated from human clinical and animal non-clinical cases, as well as different food samples using pulsed field gel electrophoresis (PFGE) /
Bulut, Ece; Soyer, Yeşim; Özcengiz, Gülay; Department of Biotechnology (2014)
Salmonella is one of the most reported pathogens in foodborne outbreaks worldwide. In order to ensure safety of foods, farm-to-fork surveillance and control systems must be utilized. Development of numerous typing methods have improved the ability to detect salmonellosis outbreaks, enabling to trace the contaminated source from farm to fork. Facilitating prevention and regulation of techniques, knowledge of the epidemiology, genetics and ecology of Salmonella infections depend on the information provided by...
Development of immunoaffinity based detection platforms for food pathogens
Çam, Dilek; Öktem, Hüseyin Avni; Department of Biology (2016)
Salmonella and E.coli, food pathogens, are among the very important pathogens threating the health. Rapid and easy detection of these pathogens is crucial. In this context, lateral flow assay (LFA) platform prepared by gold nanoparticles (GNPs) based on antibody for Salmonella and E.coli O157:H7 was developed in the first part of this study. In second part, single chain variable fragments (scFv) and SNAP-Tagged full IgG (fusion protein) of se155-4 antibody specific to Salmonella were genetically produced. T...
Molecular evaluation and antimicrobial susceptibility testing of Escherichia coli isolates from food products in Turkey
Kyere, Emmanuel Owusu; Bulut, Ece; AVŞAROĞLU ERKAN, MÜRŞİDE DİLEK; Soyer, Yeşim (Springer Science and Business Media LLC, 2015-06-01)
Some strains of Escherichia coli can be important food borne pathogens. Characterization and antimicrobial resistance testing of 28 E. coli isolates from random food samples obtained in Van, Turkey were performed. Primers for 6 indicator genes (fliC, stx1, stx2, eae, hlyA, and rfbE) for shiga toxin-producing E. coli and 5 indicator genes for each pathogroup (bfpA, aggR, ipaH, daaD, st, and lt) were used. E. coli isolates were also typed using pulsed field gel electrophoresis with the XbaI restriction enzyme...
Citation Formats
G. Budak, O. E. Ozsoy, Y. Aydın Son, T. Can, and N. Tunçbağ, “Reconstruction of the temporal signaling network in Salmonella-infected human cells,” FRONTIERS IN MICROBIOLOGY, pp. 0–0, 2015, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/30841.
METU IIS - Integrated Information Service open@metu.edu.tr