Browsing by Author "Kavruk, Murat"

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Citation - WoS: 3
Citation - Scopus: 3
Aptamer decorated PDA@magnetic silica microparticles for bacteria purification
(Springer Wien, 2024) Kavruk, Murat; Babaie, Zahra; Kibar, Gunes; Cetin, Barbaros; Yesilkaya, Hasan; Amrani, Yassine; Ozalp, V. Cengiz; Basic Sciences; Nutrition and Dietetics
One significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.
Avrupa Birliği Ülkeleri ve Türkiye’nin 2010-2021 Dönemi Toplam Antibiyotik Tüketiminin Karşılaştırılması: Akılcı İlaç Kullanımı ve Pandeminin Etkileri
(Bilimsel Tip Yayinevi, 2023) Kavruk, Murat; Uçak, Samet; Sapmaz, Burcu; Demir, Canan Çiçek; Dursun, Ali Doğan; Basic Sciences; Nutrition and Dietetics
Giriş: Antibiyotik tüketimini düşürmek adına dünya genelinde pek çok uygulama yapılmaktadır fakat bu uygulamaların karşılaştırmalı analizi ve pandemi gibi geniş çaplı değişkenler karşısındaki durumu yeterince analiz edilmemektedir. Bu kapsamda; Türkiye ve Avrupa ülkelerinin ATC grubu J01 toplam antibiyotik tüketim eğilimleri ve ülkeler arasındaki farklılıklar incelenmiş olup son dönemde yaşanan pandeminin antibiyotik tüketim verilerindeki değişime etkisi sorgulanmıştır. Materyal ve Metod: Türkiye ve 19 Avrupa ülkesinin 2010-2021 yılları arasındaki ATC grubu J01 toplam antibiyotik tüketimi (hastane + toplum) verileri birleştirilerek karşılaştırıldı. Çalışma için Avrupa Hastalık Önleme ve Kontrol Merkezi (ECDC) ve Türkiye İlaç ve Tıbbi Cihaz Kurumu (TICKK) verileri kullanılmıştır. Antibiyotik tüketim verileri, günlük 1000 hasta başına tanımlanmış günlük doz (DDD) cinsinden temsil edildi. Bulgular: Türkiye, odaklanılan dönemde en yüksek antibiyotik tüketimine sahip olmasına rağmen 2010-2015 tarihleri arasında 41.43 günlük 1000 hasta başına tanımlanmış günlük doz (DDD) ve 2016-2021 tarihleri arasında 32.24 günlük 1000 hasta başına tanım- lanmış günlük doz (DDD) antibiyotik tüketim verisi ile istatistiksel olarak (p= 0.05) anlamlı bir düşüş gösterdi. COVID-19 pandemisinin etkili olduğu 2021 yılında Avrupa’da, çalışmaya konu olan 2010-2021 yılları arasındaki en düşük düzeyi olan 14.91 günlük 1000 hasta başına tanımlanmış günlük doz (DDD)’a gerilerken Türkiye’de 2020 yılındaki kaydedilen 24.39 günlük 1000 hasta başına tanımlanmış günlük doz (DDD) seviyesine düşen antibiyotik tüketimi, 2021 yılında 26.97 günlük 1000 hasta başına tanımlanmış günlük doz (DDD) seviyesine yükseldi. Sonuç: Akılcı ilaç kullanımı uygulamaları, Türkiye için antibiyotik tüketimini azaltmada etkili olmakla birlikte, 2021 tüketim verileri ile trendin bozulduğu gözlemlenmiştir. Avrupa ülkeleri antibiyotik tüketim miktarlarında farklılık gösterse de toplamda COVID-19 pandemisi ile azalan bir tüketim durumuna girdiği tespit edilmiştir.
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.; Basic Sciences; Nutrition and Dietetics
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.
Boza Mikrobiyotasının Fermantasyon Sürecindeki Değişimi
(2021) Kavruk, Murat; Yurt, Mediha Nur Zafer; Taşbaşı, Behiye Büşra; Acar, Elif Esma; Soyuçok, Ali; Altunbaş, Osman; Sudağıdan, Mert; Nutrition and Dietetics
Boza, insan sağlığı için yararlı mikroorganizmaları içeren fermente bir içecektir. Çalışmamızda boza üretiminde ham madde olarak kullanılan (mısır unu, buğday unu, mayşe) ve boza fermantasyonunun 1. günü, 3. günü ve 4. gün son ürün boza’nın içerdiği mikrobiyota Yeni Nesil DNA Dizileme yöntemi ve metagenomik analiz ile ortaya çıkarılmıştır. Örneklerden doğrudan cins düzeyinde yapılan analiz sonucunda, mısır unu ve buğday ununda dominant olarak Streptophyta ve Pleomorphobacterium bulunurken; bozanın 1. gün, 3. gün ve son ürün ile boza mayasında dominant bakterilerin Leuconostoc ve Lactococcus cinsine ait olduğu tespit edilmiştir. Ön zenginleştirme yapılan örneklerin analizinde, mısır ununda dominant bakteriler Enterococcus, Klebsiella ve Micromonospora, buğday ununda ise Pantoea ve Bacillus olduğu, boza mayası, 1. gün boza, 3. gün boza ve satışa sunulan son üründe dominant bakteri Lactococcus olarak belirlenmiştir. Çalışmamızda örnekler arasındaki bakteriyel çeşitlilik, benzerlik ve farklılıklar Principal Coordinate Analiz ve dendrogram oluşturulması ile ortaya konmuştur. Boza üretiminde kullanılan ham maddelerin bozanın fermantasyon aşamalarındaki ürünler ile fermantasyon sürecinde mikrobiyotasına nasıl değiştiği ve son ürüne olan katkıları, DNA düzeyinde yapılan metagenomik analizler ile belirlenmiştir.
Citation - WoS: 9
Citation - Scopus: 10
Detection 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 Cengiz; Basic Sciences; Nutrition and Dietetics
Viral 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).
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 Cengiz; Basic Sciences; Nutrition and Dietetics
Breast 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.
Citation - WoS: 4
Citation - Scopus: 5
Fluorescent and Electrochemical Detection of Nuclease Activity Associated With streptococcus Pneumoniae Using Specific Oligonucleotide Probes
(Royal Soc Chemistry, 2024) Goikoetxea, Garazi; Akhtar, Khadija-Tul Kubra; Prysiazhniuk, Alona; Borsa, Baris A.; Aldag, Mehmet Ersoy; Kavruk, Murat; Hernandez, Frank J.; Nutrition and Dietetics
Streptococcus pneumoniae (S. pneumoniae) represents a significant pathogenic threat, often responsible for community-acquired pneumonia with potentially life-threatening consequences if left untreated. This underscores the pressing clinical need for rapid and accurate detection of this harmful bacteria. In this study, we report the screening and discovery of a novel biomarker for S. pneumoniae detection. We used S. pneumoniae nucleases as biomarker and we have identified a specific oligonucleotide that works as substrate. This biomarker relies on a specific nuclease activity found on the bacterial membrane, forming the basis for the development of both fluorescence and electrochemical biosensors. We observed an exceptionally high sensitivity in the performance of the electrochemical biosensor, detecting as low as 10(2) CFU mL(-1), whereas the fluorescence sensor demonstrated comparatively lower efficiency, with a detection limit of 10(6) CFU mL(-1). Moreover, the specificity studies have demonstrated the biosensors' remarkable capacity to identify S. pneumoniae from other pathogenic bacteria. Significantly, both biosensors have demonstrated the ability to identify S. pneumoniae cultured from clinical samples, providing compelling evidence of the potential clinical utility of this innovative detection system.
Fluorescent and Electrochemical Detection of Nuclease Activity Associated With Streptococcus Pneumoniae Using Specific Oligonucleotide Probes
(Analyst, 2024) Goikoetxea, Garazi; Akhtar, Khadija-tul Kubra; Prysiazhniuk, Alona; Borsa, Barış A.; Aldağ, Mehmet Ersoy; Kavruk, Murat; Özalp, Veli Cengiz; Hernandez, Frank J.; Basic Sciences; Nutrition and Dietetics
Streptococcus pneumoniae (S. pneumoniae) represents a significant pathogenic threat, often responsible for community-acquired pneumonia with potentially life-threatening consequences if left untreated. This underscores the pressing clinical need for rapid and accurate detection of this harmful bacteria. In this study, we report the screening and discovery of a novel biomarker for S. pneumoniae detection. We used S. pneumoniae nucleases as biomarker and we have identified a specific oligonucleotide that works as substrate. This biomarker relies on a specific nuclease activity found on the bacterial membrane, forming the basis for the development of both fluorescence and electrochemical biosensors. We observed an exceptionally high sensitivity in the performance of the electrochemical biosensor, detecting as low as 102 CFU mL−1, whereas the fluorescence sensor demonstrated comparatively lower efficiency, with a detection limit of 106 CFU mL−1. Moreover, the specificity studies have demonstrated the biosensors’ remarkable capacity to identify S. pneumoniae from other pathogenic bacteria. Significantly, both biosensors have demonstrated the ability to identify S. pneumoniae cultured from clinical samples, providing compelling evidence of the potential clinical utility of this innovative detection system.
Global Insights Into Food Fraud From Location-Based Analysis: Food Adulteration in Turkey
(Wiley, 2025) Kavruk, Murat; Balci, Tugce Nur; Ozel, Irem Cagla; Ozalp, Veli Cengiz; Aydin, Ali; Nutrition and Dietetics; Basic Sciences
BackgroundFood fraud and adulteration pose critical global challenges impacting economic stability and public health. This study examines the prevalence and characteristics of food fraud incidents in Turkey, an international player in the food supply chain. Controls carried out from production to consumption reveal many fraudulent events worldwide.ResultsData collected by the Ministry of Agriculture and Forestry of T & uuml;rkiye from 2012 to 2022, covering 4007 incidents and 7180 specific cases of adulteration, form the basis of this analysis. The study categorizes food fraud by region, product group and type of fraud, revealing trends and patterns. Key findings indicate a higher incidence of fraud in milk, meat and vegetable oil products, including the detection of drug-based adulteration having potential for serious health consequences.ConclusionAt most importance, we demonstrated the importance of risk-based food inspections and the development of new detection technologies to enhance food safety. The results are fundamental for more effective food inspections in terms of risk-based conformity assessment approaches or developing new methods, devices and analysis kits in terms of scientific and technological approaches. Still, they can also significantly improve future food safety measures. These insights are aimed at informing global food safety strategies and policymaking, contributing to a safer and more transparent food supply chain. (c) 2025 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
Paper-Based Aptasensor Assay for Detection of Food Adulterant Sildenafil
(Mdpi, 2024) Kavruk, Murat; Ozalp, Veli Cengiz; Basic Sciences; Nutrition and Dietetics
Sildenafil 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.
Citation - WoS: 14
Citation - Scopus: 13
Real-Time Biosensing Bacteria and Virus With Quartz Crystal Microbalance: Recent Advances, Opportunities, and Challenges
(Taylor & Francis inc, 2023) Bonyadi, Farzaneh; Kavruk, Murat; Ucak, Samet; Cetin, Barbaros; Bayramoglu, Gulay; Dursun, Ali D. D.; Ozalp, Veli C. C.; Nutrition and Dietetics; Basic Sciences
Continuous monitoring of pathogens finds applications in environmental, medical, and food industry settings. Quartz crystal microbalance (QCM) is one of the promising methods for real-time detection of bacteria and viruses. QCM is a technology that utilizes piezoelectric principles to measure mass and is commonly used in detecting the mass of chemicals adhering to a surface. Due to its high sensitivity and rapid detection times, QCM biosensors have attracted considerable attention as a potential method for detecting infections early and tracking the course of diseases, making it a promising tool for global public health professionals in the fight against infectious diseases. This review first provides an overview of the QCM biosensing method, including its principle of operation, various recognition elements used in biosensor creation, and its limitations and then summarizes notable examples of QCM biosensors for pathogens, focusing on microfluidic magnetic separation techniques as a promising tool in the pretreatment of samples. The review explores the use of QCM sensors in detecting pathogens in various samples, such as food, wastewater, and biological samples. The review also discusses the use of magnetic nanoparticles for sample preparation in QCM biosensors and their integration into microfluidic devices for automated detection of pathogens and highlights the importance of accurate and sensitive detection methods for early diagnosis of infections and the need for point-of-care approaches to simplify and reduce the cost of operation.
Citation - WoS: 5
Citation - Scopus: 5
Surface Plasmon Resonance Aptasensor for Soluble Icam-1 Protein in Blood Samples
(Royal Soc Chemistry, 2022) Dursun, Ali Dogan; Dogan, Soner; Kavruk, Murat; Tasbasi, B. Busra; Sudagidan, Mert; Yilmaz, M. Deniz; Tuna, Bilge G.; Basic Sciences; Nutrition and Dietetics
Intercellular Adhesion Molecule-1 (ICAM-1) is considered to be a cancer biomarker in the assessment of metastatic potential in patients and an early indicator of atherosclerosis. A labelless biosensor based on the surface plasmon resonance (SPR) signal from the specific affinity interaction of an aptamer and a soluble ICAM-1 protein was developed for blood samples. The developed aptasensor provided real-time information on the concentration of the ICAM-1 protein in blood when integrated to a purification step based on a magnetic pull-down separation. The SPR aptasensor was highly specific with a limit of detection of 1.4/0.2 ng ml(-1), which was achieved through aptamer-functionalized silica-coated magnetic nanoparticles.