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Article Enhanced Doxorubicin Cytotoxicity on Breast Cancer Spheroids by Aptamer Targeted Co-Delivery With Hyaluronidase(Wiley, 2025) Kavruk, Murat; Demirel, Dide Su; Bonyadi, Farzaneh; Guner, Buket Cakmak; Dursun, Ali Dogan; Vakifahmetoglu, Cekdar; Ozalp, Veli CengizBreast cancer is one of the most prevalent solid tumors in women and can be classified into subtypes based on molecular characteristics, such as hormone receptor status and HER2 expression. Aptamers, highly specific affinity molecules, are extensively studied for targeted drug delivery using nanocarriers to enhance anti-cancer efficacy. This study focused on HER2-responsive co-delivery of doxorubicin and hyaluronidase via aptamer-gated mesoporous silica nanoparticles to improve therapeutic outcomes in solid tumors. SK-BR-3 spheroids are employed as a model for resistant tumor environments in solid tumors. Previous research is shown that conjugating cytotoxic drugs with nanoparticles or cells enhances drug penetration into tumor spheroids. In this work, doxorubicin is loaded into mesoporous silica nanoparticles and capped with HER2-specific aptamers, while the particle surface is functionalized with hyaluronidase. This dual-functionalized nanocarrier system achieves an approximate to 8.5-fold increase in cytotoxicity compared to aptamer-targeted delivery lacking hyaluronidase. The enhanced effect is attributed to hyaluronidase-mediated loosening of the spheroid structure, facilitating nanoparticle penetration and localized release of doxorubicin at high concentrations on HER2-positive cells.Article Citation - WoS: 9Citation - Scopus: 12Exosomes 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 Enhancement of Paclitaxel Therapeutic Effect by Aptamer Targeted Delivery in Plga Nanoparticles(2021) Dursun, Ali; Dursun, Ali Doğan; Ucak, Samet; Özalp, Veli Cengiz; Poyraz, Fatma Sayan; Yilmaz, Elif; Mansuroglu, Banu; Ozalp, Veli Cengiz; Dursun, Ali Doğan; Özalp, Veli Cengiz; Basic Sciences; Basic SciencesObjectives: Paclitaxel is a drug molecule used in the therapy of various cancer types, including breast cancer. It is one of the preferred chemotherapy agent due to its high efficacy. However, many side effects have been observed associ- ated with paclitaxel use such as allergy, hair loss, diarrhea and pain. Methods: We evaluated therapeutic efficacy of paclitaxel when it is actively targeted to breast cancer tumours inside a polymeric nanoparticle. Targeted delivery of paclitaxel to tumour sites has been reported as an improved cytotoxicity strategy with a variety of nanoparticles. In this study, poly Lactic-co-Glycolic Acid (PLGA) nanoparticles were used as drug carrier and nucleolin aptamers as affinity targeting agents. Results: Paclitaxel molecules were entrapped during the synthesis of PLGA nanoparticles of 238 nm in diameter. The encapsulation and loading efficiencies of paclitaxel was 97% and 21% respectively. The paclitaxel loaded PLGA nanoparticles were functionalized with nucleolin aptamers and their targeting ability to cultured mouse cancer cells was determined for two cell lines (E0771 and 4T1). E0771 cell line was chosen for the preparation of allograph breast cancer mouse models. Evaluations of the targeted paclitaxel in PLGA nanoparticles showed 38% better performance in inhibiting tumour growth compared to free paclitaxel treatment groups of mouse models. Conclusion: The chemotherapeutic effect of cancer drugs like paclitaxel can be increased by loading inside tumour targeted polymeric nanoparticlesArticle 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 Citation - WoS: 3Citation - Scopus: 4Identification of Bacterial Diversity of Bee Collected Pollen and Bee Bread Microbiota by Metagenomic Analysis(Aves, 2022) Arserim Ucar, Dilhun Keriman; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Yegin, Zeynep; Ozalp, Veli Cengiz; Sudagidan, MertThis study investigated the bacterial diversities of bee-collected pollen and bee bread of Apis mellifera in Turkey. The bacterial community structure of 14 bee pollen from Bingol, Konya, and Hakkari and 11 bee bread samples from Bingol were studied using 16 S rRNA amplicon sequencing and metagenomic analysis. The dominant bacterial phylum in pollen and bee bread samples was Firmicutes, followed by Proteobacteria. In pollen and bee bread samples, Bacillaceae, Clostridiaceae, Enterococcaceae, and Enterobacteriaceae were identified as dominant bacterial families. At the genus level, Bacillus, Clostridium sensu stricto, and Enterococcus were dominant bacteria in both pollen and bee bread samples. The most abundant species was Clostridium perfringens in both pollen and bee bread samples. Escherichia vulneris, Enterococcus faecalis, Bacillus cereus, Enterococcus casseliflavus, and Cronobacter malonaticus were identified with high reads in pollen samples. In bee bread samples, E. faecalis, Clostridium bifermentans, and Pantoea calida were abundant bacterial species. Alpha diversity showed that pol-3 sample had the highest diversity. Beta-diversity plots separated the pollen samples into four main groups and bee bread samples into three main groups. Our results indicated that the culture-independent metagenomic analysis will be a valuable tool for determining the microbial diversity of bee products produced in Bingol-Turkey one of the important centers of apiculture.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: 2Citation - Scopus: 2Paper-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 Identification of Bacterial Vaginal Microbiota Via Metagenomic Approach(Galenos Publ House, 2022) Ucak, Samet; Sudagidan, Mert; Yurt, Mediha Nur Zafer; Tasbasi, Behiye Busra; Acar, Elif Esma; Tuna, Bilge Guvenc; Ozalp, Veli CengizAim: The aim of the current study was to identify vaginal bacterial microbiota of 38 Turkish women using the high -throughput next -generation sequencing and metagenomic approach at different taxonomic levels from the kingdom to the species level. Materials and Methods: Vaginal swab samples (n=38) were collected in the DNA/RNA shield collection tubes at Yeditepe University Hospital, Department of Obstetrics and Gynecology in June 2021 and DNA extraction was performed by ZymoBIOMICS DNA miniprep kit. The information related to age, marital status, preliminary diagnosis and anamnesis status of patients were collected. To determine the vaginal microbiota, a metagenomic approach was applied using 16S rRNA amplicon sequencing. Results: The dominant phylum Firmicutes was followed by Proteobacteria, Actinobacteria, Tenericutes, Fusobacteria, and Synergistetes in the vaginal samples. Lactobacillus was the most abundant genus followed by Prevotella, Enterobacter, Gardnerella, and Dialister. Lactobacillus iners was dominant at the species level in vaginal swab samples, followed by Gardnerella vaginalis, Enterobacter tabaci, Prevotella timonensis, Prevotella bivia, and Lactobacillus jensenii. Canonical correspondence analysis (CCA) showed that Proteobacteria and Fusobacteria were mainly related to married/single variable with the highest percentages, whereas Actinobacteria and Tenericutes were related to age variable at the phylum level. Campylobacter , Atopobium , Enterobacter , and Lactococcus were mainly found in married/single variable with the highest percentages, whereas Anaerococcus, Streptococcus, Sutterella , and Veillonella were related to age. Moreover, CCA showed that Campylobacter ureolyticus, Lb. jensenii , and Atopobium vaginae were associated with married/single variable, whereas Lactobacillus johnsonii and G. vaginalis were found in age variable with the highest percentages at the species level. Conclusion: Vaginal diseases are still a major public health concern. The vaginal microbiota, which has been studied in more depth in recent years, has been discovered to be more complicated than previously imagined thanks to technological developments. More patient investigations are needed to confirm and develop these findings.
