Soyer, Ferda
Loading...
Profile URL
Name Variants
Soyer Donmez, Ferda
Soyer, F.
Soyer, F
Soyer Dönmez, Ferda
Soyer, F.
Soyer, F
Soyer Dönmez, Ferda
Job Title
Email Address
ferdasoyer@iyte.edu.tr
Main Affiliation
04.03. Department of Molecular Biology and Genetics
Status
Current Staff
ORCID ID
Scopus Author ID
Turkish CoHE Profile ID
Google Scholar ID
WoS Researcher ID
Sustainable Development Goals
1NO POVERTY
0
Research Products
2ZERO HUNGER
9
Research Products
3GOOD HEALTH AND WELL-BEING
8
Research Products
4QUALITY EDUCATION
2
Research Products
5GENDER EQUALITY
0
Research Products
6CLEAN WATER AND SANITATION
11
Research Products
7AFFORDABLE AND CLEAN ENERGY
8
Research Products
8DECENT WORK AND ECONOMIC GROWTH
1
Research Products
9INDUSTRY, INNOVATION AND INFRASTRUCTURE
11
Research Products
10REDUCED INEQUALITIES
0
Research Products
11SUSTAINABLE CITIES AND COMMUNITIES
0
Research Products
12RESPONSIBLE CONSUMPTION AND PRODUCTION
9
Research Products
13CLIMATE ACTION
10
Research Products
14LIFE BELOW WATER
9
Research Products
15LIFE ON LAND
4
Research Products
16PEACE, JUSTICE AND STRONG INSTITUTIONS
0
Research Products
17PARTNERSHIPS FOR THE GOALS
0
Research Products
Documents
17
Citations
553
h-index
11
Documents
13
Citations
486
Scholarly Output
28
Articles
13
Views / Downloads
50852/11170
Supervised MSc Theses
10
Supervised PhD Theses
2
WoS Citation Count
427
Scopus Citation Count
487
Patents
0
Projects
10
WoS Citations per Publication
15.25
Scopus Citations per Publication
17.39
Open Access Source
24
Supervised Theses
12
| Journal | Count |
|---|---|
| International Journal of Food Science and Technology | 3 |
| ACS Omega | 2 |
| Biotechnology and Bioengineering | 1 |
| Current Microbiology | 1 |
| Current Proteomics | 1 |
Current Page: 1 / 3
Scopus Quartile Distribution
Competency Cloud
28 results
Scholarly Output Search Results
Now showing 1 - 10 of 28
Article Citation - WoS: 23Citation - Scopus: 29Physical Properties of Biopolymers Containing Natamycin and Rosemary Extract(John Wiley and Sons Inc., 2009) Türe, Hasan; Özen, Fatma Banu; Eroğlu, Erdal; Soyer, Ferda; Özen, Banu; Soyer, FerdaAntifungal biopolymers were prepared by incorporating natamycin (NA) and NA + rosemary extract (RE) into wheat gluten (WG) and methyl cellulose (MC) films. Interaction between antimicrobial agents and biopolymers was determined with mid-infrared spectroscopy and scanning electron microscopy (SEM). Water vapour permeability and mechanical properties of these films were also measured. Mid-infrared spectroscopy did not indicate any interaction. SEM observations showed that NA crystallises at high concentrations in biopolymers. There were no significant changes in water vapour permeabilities of biopolymers containing active agents at P < 0.05. While NA incorporation did not result in any changes in mechanical properties of WG films a reduction in tensile strength was observed for MC films containing high concentration of NA. In general, active agent incorporation into WG and MC films did not result in any considerable changes in their physical properties that could affect their application.Master Thesis Characterization of Outer Membrane Proteins of Salmonella Enteritidis in Response To Phenolic Acids Stress(Izmir Institute of Technology, 2012) Özdemir, Özgün Öykü; Soyer, Ferda; Soyer Dönmez, FerdaSalmonella enterica serovar Enteritidis (Salmonella Enteritidis) is one of the most reported foodborne pathogen bacterium throughout the world that causes large outbreaks and may result in deaths. Phenolic acids, synthesized in almost all plants, are important for plant metabolism and protection of plants. They can be thought as promising antimicrobial agents against Salmonella Enteritidis. Outer membrane proteins are unique structures to Gram-negative bacteria including Salmonella genus and they are the first targets to environmental changes. This study showed the antimicrobial effect of 3-HPAA, cinnamic acid and o-coumaric acid on Salmonella Enteritidis in vitro. Scanning electron microscopy was used for showing the changes in bacterial shapes. Their effects on the outer membrane protein profile were investigated via proteomic approach. According to results of 96-well microtiter plate assay used for antimicrobial effect determination, among these phenolic acids, 3-HPAA showed 100% growth inhibition and other phenolics retarded the bacterial growth. 30 mM was found as minimum inhibitory concentration (MIC) of 3-HPAA at 24th hour of the experiment. SEM results demonstrated that 3-HPAA causes bacteria to have collapses on cell surface while cinnamic acid and o-coumaric acid cause cells to elongate abnormally. SDS PAGE of the OMPs of bacteria who were exposed to phenolic acids showed changes in amounts of proteins in some protein bands compared to control OMPs. 2-D PAGE results of OMPs of control bacteria via OMPs of 3-HPAA, cinnamic acid and o-coumaric acid treated bacteria, changes in sizes of spots were observed.Master Thesis Investigation of Antimicrobial Properties of 4-Hydroxybenzoic Acid and Its Application in Bone Cement(01. Izmir Institute of Technology, 2022) Dokumacı, Ecem; Soyer Dönmez, FerdaThe bone cement is composed of polymethylmethacrylate powder and liquid methylmethacrylate which is commonly used in clinical applications. Nosocomial pathogens utilize the bone cement surface to induce infections, so that bone cements are loaded with various antibiotics to inhibit the infection. Nevertheless, the bacteria gain resistance against antibiotics since the antibiotics are released at slow rates. Phenolic acids are secondary metabolites of plants to prevent infections; thus, are promising antimicrobial chemicals against pathogens. The main aim of this study is the investigation of the antimicrobial effect of liquid and powder 4-hydroxybenzoic acid-loaded bone cement on Escherichia coli, methicillin-resistant and susceptible Staphylococcus aureus. Previously, liquid and powder vancomycin-loaded bone cement had been studied against MRSA and Candida albicans, caffeic acid-loaded bone cement is also investigated on the S. aureus. This study will be the first investigation that the antimicrobial effect of liquid and powder phenolic acid-loaded bone cement against pathogens. 4-HBA was added directly into polymethylmethacrylate powder and mixed with liquid methylmethacrylate. Cement discs were prepared by metal mold and the antimicrobial assay was carried out to determine the bacterial growth inhibition. The structural features of bone cements such as pores and surface were characterized SEM. The antimicrobial agent release of bone cement was also examined by spectrophotometer and HPLC was used for confirmation. Resistance development against 4-HBA was tested on MRSA and Acinetobacter haemolyticus by exposing them to the sub-inhibitory concentrations. The possible genes for the resistance were checked by ddPCR. The significant inhibition of bacterial growth by 4-HBA-loaded bone cement is expected and liquid 4-HBA is expected to be released at a higher rate. Therefore, the phenolic acids may be used as antimicrobial agents in bone cement to inhibit pathogenic bacterial growth.Master Thesis A Proteomic Analysis of the Response of Listeria Monocytogenes To the Stress Induced by O-Coumaric Acid and Ferulic Acid(Izmir Institute of Technology, 2013) Cerit, Ender Efe; Soyer Dönmez, FerdaPhenolic acids are known for their potential antimicrobial action, however their mechanisms of action are still unraveled. In this study, effect of phenolic acid stress on Listeria monocytogenes, a dangerous foodborne pathogen, was studied with a proteomic approach. Two phenolic acids found in olive oil, namely o-coumaric acid and ferulic acid, were applied on this bacterium via microtiter plate assay. The concentrations of these phenolic acids that inhibit the bacterial growth by 50% were determined as 7.5 mM for o-coumaric acid, and 8 mM for ferulic acid. Besides, minimum bactericidal concentration of o-coumaric acid was also found as 12 mM. Cellular proteomes of phenolic acid-treated and untreated bacteria were analysed with nanoLC-ESI-MS/MS system, and identified with MaxQuant/Andromeda bioinformatic toolbox. According to the results, both phenolic acids induced oxidative stress in L. monocytogenes cells. In addition to this, DNA replication and repair enzymes, nutrient uptake proteins and several proteins directly related with the virulence of L. monocytogenes were among the targets of phenolic acid stress. Last but not least, proteins associated with biosynthetic pathways were found to be predominantly downregulated. Moreover, the morphology of phenolic acid-treated and untreated cells was visualized with scanning electron microscope to support these findings. The images showed that lengths of treated cells were either abnormally elongated or shortened when compared to untreated cells. A possible reason for these abnormalities is the unequal fission promoted by two factors; excessive production of cell envelope biosynthesis and fission regulatory proteins, and repression of aforementioned DNA replication and repair enzymes.Article Citation - WoS: 4Citation - Scopus: 4Synthesis, Characterization, and Antimicrobial Activities of 3-Hpaa Nanoparticles(Techno Press, 2021) Özdemir, Özgün Öykü; Soyer, FerdaEncapsulation of bioactive compounds (e.g., phenolic acids) into nanoparticles is a well-received technique in the searching for new antimicrobial agents against multidrug-resistant pathogens. Encapsulation can be a good technique to maintain the stability of phenolic acids against environmental conditions. In this study, 3-hydroxyphenylacetic acid (3-HPAA) was encapsulated into alginate-chitosan nanoparticles with the ion gelation technique. The characterization of loaded and unloaded nanoparticles was performed via dynamic light scattering, Fourier transform infrared spectroscopy, and scanning electron microscopy. According to the results, 3-HPAA loaded nanoparticles have spherical shapes with a diameter range of 40-80 nm and an average hydrodynamic diameter of 361.0 +/- 69.8 nm. The loading of 3-HPAA was successfully achieved based on the Fourier transform infrared spectra and encapsulation percentage studies. The antimicrobial effect of the nanoparticles in solution forms was tested on P. aeruginosa, S. epidermidis, MRSA, and MSSA. The results demonstrated that the 3-HPAA loaded alginate chitosan nanoparticle solution showed elevated antimicrobial effect due to the pH change by treatment with 1% acetic acid, and it displayed bacteriocidal effects in a strain-specific and dose-dependent manner. Therefore, the 3-HPAA loaded alginate chitosan nanoparticle solution was produced successfully with the bacteriocidal effect against serious pathogenic bacteria.Master Thesis Antimicrobial and Antioxidant Activities of Turkish Extra Virgin Olive Oil From Different Varieties(Izmir Institute of Technology, 2009) Karaosmanoğlu, Hande; Soyer Dönmez, FerdaOlive oil is the main source of fat in Mediterranean diet. The major active components of olive oil include oleic acid, phenolic compounds and squalene which have different benefits such as cancer prevention, antimicrobial and antioxidant activities, and lowering the incidence of skin cancer, respectively. In recent years, the number of studies about the biochemical properties of different varieties of olive oils and their phenolic contents has dramatically increased.In this study, Turkish EVOO from different varieties and their phenolic compounds were investigated in terms of their antimicrobial and antioxidant properties as well as refined olive, hazelnut and canola oils. Antimicrobial activities of EVOOs and ten phenolic compounds were tested against three foodborne pathogenic bacteria, Escherichia coli O157:H7, Listeria monocytogenes and Salmonella Enteritidis which are the foremost bacterial cause of the largest number of outbreaks, cases and deaths in the world. While all EVOOs showed bactericidal effect the phenolics demonstrated slight antimicrobial activity with percent inhibition between 0-25 of growth rate of bacteria. Moreover, refined olive, hazelnut and canola oils did not show any antimicrobial activity.Finally, antioxidant activities of EVOOs, refined olive, hazelnut and canola oils were determined by B-carotene-linoleic acid model system and ABTS radical scavenging method. According to B-carotene-linoleic acid method, it was observed that antioxidant activities of oil samples varied between 21.19% and 64.54%. On the other hand, it was found that free radical scavenging activities varied between 1.21% and 21.97% as a result of ABTS method. These results were correlated with TPC values of oils.Master Thesis Molecular Characterization of Biofilm Properties of Listeria Monocytogenes in the Presence of O-Coumaric Acid and 4-Hydroxybenzoic Acid(Izmir Institute of Technology, 2013) Ekin, Umut; Soyer Dönmez, FerdaBiofilms in medical and food industries are difficult to deal with. The formation of biofilms on every type of surfaces, ability to withstand in biofilm structures against thousand folds of lethal antibiotic doses and reasoning for different kinds of chronic diseases prove dangerousness of biofilms. Food borne pathogens that survive in biofilms can contaminate foods and feeding tubes which results food poisonings, outbreaks and infections. Listeria monocytogenes EGDe is one of the dangerous food borne pathogens with ability to form biofilms and cause listeriosis among elderly people, immunocompromised patients or pregnant women, which results lethal consequences. In this study, 4-hydroxybenzoic acid and o-coumaric acid that have potential antimicrobial and antibiofilm effect on Listeria monocytogenes EGDe were examined. Furthermore, protein profiles were investigated in the presence of phenolic acids. The antimicrobial assays of selected phenolic acids revealed the MICs against Listeria monocytogenes EGDe which are 18 mM for 4-hydroxybenzoic acid and 10 mM for ocoumaric acid. In the presence of MICs, while o-coumaric acid reduced initial attachment at 58%, 4-hydroxybenzoic acid reduced 48%. 4-hydroxybenzoic acid and ocoumaric acid also showed inhibitory effects on preformed biofilms as 34% and 56% respectively. The inhibitory effects of selected phenolic acids were ensured by visualization with SEM and Flourescence Microscopy. Afterwards, Listeria monocytogenes EGDe was treated with MIC of phenolic acids for total protein isolation. Isolated proteins were subjected to in-gel digestion and analysed in nanoLC-ESIMS/ MS system to interpret the mode of actions of antimicrobial and antibiofilming propertiesMaster Thesis Efficacy of Natural Antimicrobials on Food-Borne Pathogens and Their Applications(Izmir Institute of Technology, 2008) Eroğlu, Erdal; Soyer Dönmez, FerdaMicrobial contamination of food products increases the risk of food-borne infections and intoxications. In recent years, more studies have been performed for development of natural alternatives to control the growth of pathogenic microorganisms in food rather than chemical origin. In the present study, natural antimicrobial agents from different sources, activated lactoferrin-(ALF), rosemary extract-(RE), jenseniin-G (JG) and natamycin-(NA) were used.The antimicrobial activity of agents (ALF-RE-JG) and their combinations against L. monocytogenes, E. coli O157:H7 and S. Enteritidis, and NA against A. niger and P. roquefortii was tested. These antimicrobials, found effective in vitro, applied also on meat and cheese samples. The minimum inhibitory concentrations (MIC) of ALF, RE and JG against pathogens were determined via disc diffusion and microtiter plate growth assay. Dipping method was applied on meat samples to test the efficacy of antimicrobials. MIC of NA was determined via disc diffusion assay. NA was applied on cheese samples to test the efficacy against both molds by dipping method.The data from microtiter well plate assay showed that ALF is effective on three pathogens. Rosemary extract inhibited only growth of L. monocytogenes and JG did not show any significant activity on the growth of same pathogens. RE enhanced the activity of ALF on E. coli O157:H7. Neither individual activity nor synergistic activity was determined by disc diffusion assay. The data from disc diffusion assay revealed that the effective NA concentration on both molds was 750 ppm. Some of dipping applications on both meat and cheese displayed promising results.Article Citation - WoS: 11Citation - Scopus: 13Pseudomonas Aeruginosa Presents Multiple Vital Changes in Its Proteome in the Presence of 3-Hydroxyphenylacetic Acid, a Promising Antimicrobial Agent(American Chemical Society, 2020) Özdemir, Özgün O.; Soyer, FerdaPseudomonas aeruginosa, a widely distributed opportunistic pathogen, is an important threat to human health for causing serious infections worldwide. Due to its antibiotic resistance and virulence factors, it is so difficult to combat this bacterium; thus, new antimicrobial agents are in search. 3-Hydroxyphenylacetic acid (3-HPAA), which is a phenolic acid mostly found in olive oil wastewater, can be a promising candidate with its dose-dependent antimicrobial properties. Elucidating the molecular mechanism of action is crucial for future examinations and the presentation of 3-HPAA as a new agent. In this study, the antimicrobial activity of 3-HPAA on P. aeruginosa and its action mechanism was investigated via shot-gun proteomics. The data, which are available via ProteomeXchange with identifier PXDO16243, were examined by STRING analysis to determine the interaction networks of proteins. KEGG Pathway enrichment analysis via the DAVID bioinformatics tool was also performed to investigate the metabolic pathways that undetected and newly detected groups of the proteins. The results displayed remarkable changes after 3-HPAA exposure in the protein profile of P. aeruginosa related to DNA replication and repair, RNA modifications, ribosomes and proteins, cell envelope, oxidative stress, as well as nutrient availability. 3-HPAA showed its antimicrobial action on P. aeruginosa by affecting multiple bacterial processes; hence, it could be categorized as a multitarget antimicrobial agent.Article Citation - WoS: 66Citation - Scopus: 81Effect of Biopolymers Containing Natamycin Against Aspergillus Niger and Penicillium Roquefortii on Fresh Kashar Cheese(John Wiley and Sons Inc., 2011) Türe, Hasan; Eroğlu, Erdal; Özen, Banu; Soyer, FerdaFungal spoilage during refrigerated storage is one of the main safety and quality-related problems for dairy products. The effect of wheat gluten (WG) and methyl cellulose (MC) biopolymers containing natamycin (NA) on the growth of Aspergillus niger and Penicillium roquefortii on the surface of fresh kashar cheese during storage at 10 C for 30 days was investigated. Wrapping of A. niger-inoculated cheese with MC films containing 5–20 mg NA per 10 g resulted in approximately 2-log reductions in spore count. Two mg NA per 10 g included into WG films was sufficient to eliminate A. niger on the surface of cheese. However, MC and WG films containing NA did not cause any significant decrease in P. roquefortii count on the cheese surface. Therefore, especially use WG films in dairy applications could be an effective way of controlling A. niger growth on these products.
- «
- 1 (current)
- 2
- 3
- »