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Article Citation - WoS: 8Citation - Scopus: 8Surface Microbiota and Associated Staphylococci of Houseflies (musca Domestica) Collected From Different Environmental Sources(Academic Press Ltd- Elsevier Science Ltd, 2022) Sudagidan, Mert; Ozalp, Veli Cengiz; Can, Ozge; Eligul, Hakan; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Kocak, OnerHouseflies (Musca domestica) are important mechanical vectors for the transmission of pathogenic microorganisms. In this study, 129 houseflies (69 males and 60 females) were collected from 10 different environmental sources and a laboratory population was used. The surface microbiota of houseflies was identified by NextGeneration Sequencing. Staphylococci from the surfaces of houseflies were selectively isolated and their virulence genes, antibiotic susceptibilities, biofilm formation, and clonal relatedness were determined. Metagenomic analysis results demonstrated that Staphylococcus, Bacillus, and Enterococcus were mostly present on the surface of houseflies at the genus level. Additionally, the isolated 32 staphylococcal strains were identified as Staphylococcus sciuri (n = 11), S. saprophyticus (n = 9), S. arlettae (n = 6), S. xylosus (n = 4), S. epidermidis (n = 1) and S. gallinarum (n = 1). tetK, tetM, tetL, ermC, msrAB, and aad6 genes were found to carry by some of the staphylococcal strains. The strains were mostly resistant to oxacillin, penicillin, and erythromycin and three strains were multi-drug resistant. There was a statistical difference between housefly collection places and antibiotic resistance of isolated staphylococci to penicillin G, gentamicin, and erythromycin (p < 0.05). Biofilm test showed that 17 strains were strong biofilm formers, and it plays important role in the transmission of these bacteria on the surface of houseflies. Staphylococcal strains showed extracellular proteolytic and lipolytic activity in 31 and 12 strains, respectively. Closely related species were found in PFGE analysis from different environmental sources. By this study, surface microbiota and carriage of pathogenic staphylococci on the surfaces of houseflies and their virulence properties were elucidated.Article Citation - Scopus: 2The Effects of Paddy Cultivation and Microbiota Members on Arsenic Accumulation in Rice Grain(Mdpi, 2023) Ersoy Omeroglu, Esra; Bayer, Asli; Sudagidan, Mert; Ozalp, Veli Cengiz; Yasa, IhsanAccess to safe food is one of the most important issues. In this context, rice plays a prominent role. Because high levels of arsenic in rice grain are a potential concern for human health, in this study, we determined the amounts of arsenic in water and soil used in the rice development stage, changes in the arsC and mcrA genes using qRT-PCR, and the abundance and diversity (with metabarcoding) of the dominant microbiota. When the rice grain and husk samples were evaluated in terms of arsenic accumulation, the highest values (1.62 ppm) were obtained from areas where groundwater was used as irrigation water, whereas the lowest values (0.21 ppm) occurred in samples from the stream. It was observed that the abundance of the Comamonadaceae family and Limnohabitans genus members was at the highest level in groundwater during grain formation. As rice development progressed, arsenic accumulated in the roots, shoots, and rice grain. Although the highest arsC values were reached in the field where groundwater was used, methane production increased in areas where surface water sources were used. In order to provide arsenic-free rice consumption, the preferred soil, water source, microbiota members, rice type, and anthropogenic inputs for use on agricultural land should be evaluated rigorously.Article Selection of DNA Aptamers Against Parathyroid Hormone for Electrochemical Impedimetric Biosensor System Development(John Wiley and Sons Inc, 2025) Didarian, Reza; Bargh, Saharnaz; Gulerman, Almina; Ozalp, Veli Cengiz; Erel, Ozcan; Yildirim-Tirgil, NimetThis work presents the pioneering development of an aptamer-based electrochemical biosensor for real-time monitoring of parathyroid hormone (PTH) levels, with a focus on intraoperative assessment during parathyroid surgery. It introduces, for the first time, the selection and characterization of aptamers targeting distinct segments of the PTH peptide. The study demonstrates the feasibility and efficacy of the biosensing platform through a precisely designed experimental framework, including SELEX-based aptamer selection, aptamer-peptide interaction analysis, and biosensor fabrication. The SELEX process yields aptamers with notable binding affinities to different fragments of PTH, with the PTH (53-84) aptamer showing particularly sensitive binding to the hormone's C terminus, allowing for precise PTH analysis. Electrochemical characterization reveals significant changes in electrochemical impedance spectroscopy (EIS) signals upon exposure to varying PTH concentrations, highlighting the sensor's sensitivity and selectivity. The increase in charge transfer resistance (Rct) values with rising PTH concentrations underscores the biosensor's capability to detect PTH-induced structural changes, validating its potential for accurate measurement. The biosensor shows remarkable selectivity in the presence of common interferents in serum samples, ensuring precise PTH detection. Stability assessments over a 45-day storage period demonstrate the biosensor's robustness and long-term reliability, affirming its practical suitability. In summary, the developed aptamer-based biosensor represents a promising tool for sensitive and selective PTH detection, with potential applications in biomedical research and clinical diagnostics, particularly for intraoperative PTH analysis during parathyroidectomy. Continued research and optimization efforts hold promise for enhancing its performance and expanding its utility in diverse healthcare settings.Article Citation - WoS: 3Citation - Scopus: 3Paper-Based Aptasensor Assay for Detection of Food Adulterant Sildenafil(Mdpi, 2024) Kavruk, Murat; Ozalp, Veli CengizSildenafil is used to treat erectile dysfunction and pulmonary arterial hypertension but is often illicitly added to energy drinks and chocolates. This study introduces a lateral flow strip test using aptamers specific to sildenafil for detecting its illegal presence in food. The process involved using graphene oxide SELEX to identify high-affinity aptamers, which were then converted into molecular gate structures on mesoporous silica nanoparticles, creating a unique signaling system. This system was integrated into lateral flow chromatography strips and tested on buffers and chocolate samples containing sildenafil. The method simplifies the lateral flow assay (LFA) for small molecules and provides a tool for signal amplification. The detection limit for these strips was found to be 68.2 nM (31.8 mu g/kg) in spiked food samples.Article Citation - WoS: 24Citation - Scopus: 30High-Efficiency Application of Cts-Co Nps Mimicking Peroxidase Enzyme on Tmb(ox)(Pergamon-elsevier Science Ltd, 2022) Altuner, Elif Esra; Ozalp, Veli Cengiz; Yilmaz, M. Deniz; Bekmezci, Muhammed; Sen, FatihIn this study, analytical studies of Chitosan-Cobalt(II) (CTS-Co(II)) nanoparticles (CTS - Co NPs) by mimicking horseradish peroxidase (HRP) were evaluated. In the applications, it was observed that CTS-Co NPs 3,3 ' 5,5 ' tetramethylbenzidine (TMB) oxidized in the presence of hydrogen peroxide (H2O2). The required CTS-Co NPs were synthesized at 50 degrees C in 30 min and characterized using Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), inductively coupled plasma-optical emission spectroscopy (ICP-OES), and Xray photon spectroscopy (XPS) was done. CTS-Co NPs were studied to develop a selective TMB biosensor on TMB (ox) substrate. The synthesized CTS-Co NPs formed a catalytic reaction with 30% 0.2 mM H2O2 on 0.2 M TMB substrate. After the catalytic reaction, sensitive signals were obtained from the desired biosensor. Electrochemical measurements were taken as low limit of 10 mg and a high limit of 20 mg for the determination of CTSCo NPs to TMB(ox). In the microplate study; The sensors were applied on 1.5 mu g and 3 mu g CTS-Co NPs TMB(ox) substrate, respectively. CTS- Co NPs; for TMB(ox) determination, optical density (OD) measurement was taken as a low limit of 1.5 mu g and a high limit of 3 mu g. Electrochemical applications of particles and microplate reader results were compared with horseradish peroxidase (HRP) enzyme for sensor properties. According to the data obtained, it was observed that it behaved similarly to the CTS-Co NPs peroxidase enzyme. This work presents innovations for nanoparticle extraction and sensor study from chitosan and other naturally sourced polymers.Article Citation - WoS: 29Citation - Scopus: 40Development of Electrochemical Aptasensors Detecting Phosphate Ions on Tmb Substrate With Epoxy-Based Mesoporous Silica Nanoparticles(Pergamon-elsevier Science Ltd, 2022) Altuner, Elif Esra; Ozalp, Veli Cengiz; Yilmaz, M. Deniz; Sudagidan, Mert; Aygun, Aysenur; Acar, Elif Esma; Sen, FatihThis study, it is aimed to develop an electrochemical aptasensor that can detect phosphate ions using 3.3 & PRIME;5.5 & PRIME; tetramethylbenzidine (TMB). It is based on the principle of converting the binding affinity of the target molecule phosphate ion (PO43-) into an electrochemical signal with specific aptamer sequences for the aptasensor to be developed. The aptamer structure served as a gate for the TMB to be released and was used to trap the TMB molecule in mesoporous silica nanoparticles (MSNPs). The samples for this study were characterized by transmission electron spectroscopy (TEM), Brunner-Emmet-Teller, dynamic light scattering & electrophoretic light scattering, and induction coupled plasma atomic emission spectroscopy. According to TEM analysis, MSNPs have a morphologically hexagonal structure and an average size of 208 nm. In this study, palladium-carbon nano particles (Pd/C NPs) with catalytic reaction were used as an alternative to the biologically used horseradish peroxidase (HRP) enzyme for the release of TMB in the presence of phosphate ions. The limit of detection (LOD) was calculated as 0.983 mu M, the limit of determination (LOQ) was calculated as 3.276 mu M, and the dynamic linear phosphate range was found to be 50-1000 mu M. The most important advantage of this bio-based aptasensor assembly is that it does not contain molecules such as a protein that cannot be stored for a long time at room temperature, so its shelf life is very long compared to similar systems developed with antibodies. The proposed sensor shows good recovery in phosphate ion detection and is considered to have great potential among electrochemical sensors.Article Citation - WoS: 16Citation - Scopus: 18Exosomes as Biomarkers and Therapeutic Agents in Neurodegenerative Diseases: Current Insights and Future Directions(Springer, 2025) Dehghani, Sam; Ocakci, Ozgecan; Hatipoglu, Pars Tan; Ozalp, Veli Cengiz; Tevlek, AtakanNeurodegenerative diseases (NDs) like Alzheimer's, Parkinson's, and ALS rank among the most challenging global health issues, marked by substantial obstacles in early diagnosis and effective treatment. Current diagnostic techniques frequently demonstrate inadequate sensitivity and specificity, whilst conventional treatment strategies encounter challenges related to restricted bioavailability and insufficient blood-brain barrier (BBB) permeability. Recently, exosomes-nanoscale vesicles packed with proteins, RNAs, and lipids-have emerged as promising agents with the potential to reshape diagnostic and therapeutic approaches to these diseases. Unlike conventional drug carriers, they naturally traverse the BBB and can deliver bioactive molecules to affected neural cells. Their molecular cargo can influence cell signaling, reduce neuroinflammation, and potentially slow neurodegenerative progression. Moreover, exosomes serve as non-invasive biomarkers, enabling early and precise diagnosis while allowing real-time disease monitoring. Additionally, engineered exosomes, loaded with therapeutic molecules, enhance this capability by targeting diseased neurons and overcoming conventional treatment barriers. By offering enhanced specificity, reduced immunogenicity, and an ability to bypass physiological limitations, exosome-based strategies present a transformative advantage over existing diagnostic and therapeutic approaches. This review examines the multifaceted role of exosomes in NDDs, emphasizing their diagnostic capabilities, intrinsic therapeutic functions, and transformative potential as advanced treatment vehicles.Article Biotechnological Preparedness for Novel Pandemics: Diagnostic Performance of IVDS Against SARS-CoV(Wiley, 2025) Kavruk, Murat; Ercan, Meltem; Borsa, Baris Ata; Ozalp, Veli Cengiz; Hernandez, Frank J.Although the COVID-19 pandemic has created many challenges and negative impacts around the world, some of which will persist into the future, its technological challenge has created a unique opportunity in a globalized world. It is a rare event that almost all of humanity to be directed towards a single goal and to try to produce solutions, but the necessity of a similar global action in the future has begun to enter the agenda again. The predictions made on the basis of countries and institutions against the possibility of a pandemic, which is defined as Disease X, are shaped by the experience of the COVID-19 pandemic. Technologically, one of the know-how we have gained in this pandemic is the performance of IVD and test systems in terms of quality and quantity. A comprehensive analysis of the products produced by combining biotechnology with different strategies has not been conducted. In this context, we have analyzed the technical preferences, limitations, and other performance parameters of IVDs and test kits that could be developed against a future Disease X. The performance parameters of 2,882 biotechnological products listed for use in the European Union have been analyzed, and areas that could be targeted for increased effectiveness have been identified. Our study is the first of its kind in this field and can serve as a guide for those who want to work on detection methods, diagnostics, and novel technologies for deployment in future pandemics.Article Protective Role of Bromelain’s Antioxidant and Anti-Inflammatory Effects in Experimental Lower Limb Ischemia-Reperfusion Injury(Nature Portfolio, 2025) Sezen, Saban Cem; Demirtas, Huseyin; Yildirim, Alperen Kutay; Ozer, Abdullah; Dursun, Ali Dogan; Kucuk, Aysegul; Arslan, Mustafa; Ozalp, Veli Cengiz; Kucuk, Işın GunesIschemia-reperfusion (IR) injury is a multifaceted pathological process characterized by excessive oxidative stress and inflammatory responses upon restoration of blood flow. Bromelain, a proteolytic enzyme complex derived from pineapple, exhibits robust antioxidant and anti-inflammatory activities. This study aimed to evaluate the protective effects and underlying mechanisms of bromelain on oxidative stress and inflammation in an experimental rat model of lower limb ischemia-reperfusion injury. Twenty-four male Wistar Albino rats were randomly allocated into four groups: Sham-operated control (SHAM), Bromelain-only (BR), Ischemia-Reperfusion (IR), and Ischemia-Reperfusion with Bromelain treatment (IR + BR). Bromelain (40 mg/kg) was administered intraperitoneally before ischemia induction. The IR model involved 45 min of infrarenal abdominal aorta occlusion followed by 120 min of reperfusion. Oxidative biomarkers (total antioxidant status [TAS], total oxidant status [TOS], oxidative stress index [OSI]) and histopathological parameters (muscle atrophy, degeneration, leukocyte infiltration, internalization of nuclei, fragmentation, and hyalinization) were analyzed. Significant increases in muscle degeneration, leukocyte infiltration, nuclear internalization, fragmentation, and elevated oxidative stress biomarkers (increased TOS and OSI, decreased TAS) were observed in the IR group compared to controls. Bromelain treatment (IR + BR) significantly ameliorated these effects, reducing muscle tissue damage, inflammation, and oxidative imbalance compared to the untreated IR group. Bromelain effectively mitigates lower limb ischemia-reperfusion injury by reducing oxidative stress, restoring antioxidant capacity, and suppressing inflammatory responses. These protective effects suggest that bromelain holds potential as a therapeutic agent for managing oxidative and inflammatory damages associated with IR conditions, warranting further clinical investigation.Article Citation - WoS: 10Citation - Scopus: 12Detection of Viruses by Probe-Gated Silica Nanoparticles Directly From Swab Samples(Elsevier, 2022) Tuna, Bilge Guvenc; Durdabak, Dilara Buse; Ercan, Meltem Kazak; Dogan, Soner; Kavruk, Murat; Dursun, Ali Dogan; Ozalp, Veli CengizViral infection has been one of the major health issues for human life. The real-time reverse transcription polymerase chain reaction (RT-PCR)-based detection has primarily been used for virus detection as a highly reliable procedure. However, it is a relatively long and multi-stage process. In addition, required skilled personnel and complex instrumentation presents difficulties in large scale monitoring efforts. Therefore, we report here a direct and fast detection method for CoV-2 genome as applied in the nose-throat swab samples without any further processing. The detection principle is based on fluorescein-loaded mesoporous silica nanoparticles capped by specific gene sequences probes immobilized on the surface of the nanoparticles. Upon hybridization with the target viral genome, the fluorescein molecules were released from the mesopores. Testing with synthetic oligonucleotides, the NSP12 gene-based detection resulted in a strong signal. Target detection time could be optimized to 15 min and the limit of detection was 1.4 RFU with 84% sensitivity with clinical samples (n = 43).
