Reconstruction of the temporal signaling network in salmonella infected human cells

2016
Budak, Güngör
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) approach and the Integer Linear Programming (ILP) based edge inference approach by integrating a published temporal phosphoproteomic dataset of Salmonella-infected human cells and the human interactome. The final temporal signaling network conserves the information about temporality and directionality, while showing hidden entities in the signaling, such as the SNARE binding, mTOR signaling, immune response, cytoskeleton organization, and apoptosis pathways. Although the targets of Salmonella effectors such as CDC42, RHOA, 14-3-3δ, Syntaxin family, Oxysterol-binding proteins were not present in the phosphoproteomic dataset, they were revealed in the reconstructed signaling network. Structural analysis of these targets also revealed binding preferences of their neighbors. The application of such integrated approaches has a high potential to identify the clinical targets in infectious diseases, especially in the Salmonella infections.

Suggestions

Reconstruction of the temporal signaling network in Salmonella-infected human cells
Budak, Gungor; Ozsoy, Oyku Eren; Aydın Son, Yeşim; Can, Tolga; Tunçbağ, Nurcan (2015-07-20)
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 principl...
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...
Investigation of cytocidal effect of K5 type yeast killer protein on sensitive microbial cells
Sertkaya, Abdullah; İzgü, Kadri Fatih; Department of Biology (2005)
Some yeasts secrete polypeptide toxins, which are lethal to other sensitive yeast cells, gram-positive pathogenic bacteria and pathogenic fungi. Therefore these are designated as killer toxins. Killer toxins are suggested as potent antimicrobial agents especially for the protection of fermentation process against contaminating yeasts, biological control of undesirable yeasts in the preservation of foods. Moreover they are promising antimicrobial agents in the medical field; due to immune system suppressing ...
THE INFLUENCE OF A CELLULASE BEARING ENZYME COMPLEX FROM ANAEROBIC FUNGI ON BREAD STALING
YURDUGÜL, SEYHUN; Pancevska, Natalija-Atanasova; YILDIZ, GÜLGEZ GÖKÇE; Bozoglu, Faruk (2012-01-01)
The digestive system of the ruminants possesses anaerobic fungi, which are responsible for the degradation of cellulose and cell wall structures by their enzyme systems. An enzyme complex, bearing cellulase activity from Neocallimastix spp. which belongs to anaerobic rumen fungi, was partially isolated and its effect at various concentrations on bread quality was tested. The addition of enzyme complex into bread dough resulted in a decrease of hardness, gumminess and chewiness, providing a softer crumb, ind...
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, “Reconstruction of the temporal signaling network in salmonella infected human cells,” M.S. - Master of Science, Middle East Technical University, 2016.