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Öğe Detection strategies of infectious diseases via peptide-based electrochemical biosensors(Elsevier Science Sa, 2024) Hanoglu, Simge Balaban; Harmanci, Duygu; Evran, Serap; Timur, SunaInfectious diseases have threatened human life for as long as humankind has existed. One of the most crucial aspects of fighting against these infections is diagnosis to prevent disease spread. However, traditional diagnostic methods prove insufficient and time-consuming in the face of a pandemic. Therefore, studies focusing on detecting viruses causing these diseases have increased, with a particular emphasis on developing rapid, accurate, specific, user-friendly, and portable electrochemical biosensor systems. Peptides are used integral components in biosensor fabrication for several reasons, including various and adaptable synthesis protocols, long-term stability, and specificity. Here, we discuss peptide-based electrochemical biosensor systems that have been developed over the last decade for the detection of infectious diseases. In contrast to other reports on peptidebased biosensors, we have emphasized the following points i) the synthesis methods of peptides for biosensor applications, ii) biosensor fabrication approaches of peptide-based electrochemical biosensor systems, iii) the comparison of electrochemical biosensors with other peptide-based biosensor systems and the advantages and limitations of electrochemical biosensors, iv) the pros and cons of peptides compared to other biorecognition molecules in the detection of infectious diseases, v) different perspectives for future studies with the shortcomings of the systems developed in the past decade.Öğe Dye-Loaded Polymersome-Based Lateral Flow Assay: Rational Design of a COVID-19 Testing Platform by Repurposing SARS-CoV-2 Antibody Cocktail and Antigens Obtained from Positive Human Samples(Amer Chemical Soc, 2021) Ghorbanizamani, Faezeh; Tok, Kerem; Moulahoum, Hichem; Harmanci, Duygu; Hanoglu, Simge Balaban; Durmus, Ceren; Zihnioglu, FigenThe global pandemic of COVID-19 continues to be an important threat, especially with the fast transmission rate observed after the discovery of novel mutations. In this perspective, prompt diagnosis requires massive economical and human resources to mitigate the disease. The current study proposes a rational design of a colorimetric lateral flow immunoassay (LFA) based on the repurposing of human samples to produce COVID-19-specific antigens and antibodies in combination with a novel dye-loaded polymersome for naked-eye detection. A group of 121 human samples (61 serums and 60 nasal swabs) were obtained and analyzed by RT-PCR and ELISA. Pooled samples were used to purify antibodies using affinity chromatography, while antigens were purified via magnetic nanoparticles-based affinity. The purified proteins were confirmed for their specificity to COVID-19 via commercial LFA, ELISA, and electrochemical tests in addition to sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. Polymersomes were prepared using methoxy polyethylene glycol-b-polycaprolactone (mPEG-b-PCL) diblock copolymers and loaded with a Coomassie Blue dye. The polymersomes were then functionalized with the purified antibodies and applied for the preparation of two types of LFA (antigen test and antibody test). Overall, the proposed diagnostic tests demonstrated 93 and 92.2% sensitivity for antigen and antibody tests, respectively. The repeatability (92-94%) and reproducibility (96-98%) of the tests highlight the potential of the proposed LFA. The LFA test was also analyzed for stability, and after 4 weeks, 91-97% correct diagnosis was observed. The current LFA platform is a valuable assay that has great economical and analytical potential for widespread applications.Öğe Evaluation of the first Turkish in vitro diagnostic symposium(Walter De Gruyter Gmbh, 2017) Kose, Fadime Aydin; Celebi, Serap; Cengiz, Hakan; Harmanci, Duygu; Kocak, Ayse; Canbay, Erhan; Aslan, Diler; Sezer, Ebru; Pabuccuoglu, Aysun; Kocdor, HilalIn vitro diagnostic (IVD) medical laboratory devices, tests and equipment are closely related with public health, patient safety and the safety of all who utilize these tools in laboratories. The close monitoring of the process from the production line to the end-point user is crucial so that IVD devices and tests do not pose a risk to individuals and society. Based on this background, the "First Turkish in vitro Diagnostic Symposium: Medical Laboratory Tests" was held in February, 2016. The symposium was organized by the cooperation of Turkish Biochemical Society, Izmir Branch and Dokuz Eylul University Health Sciences Institute along with the contributions of TurkLab Calibration Association. It was intended that the meeting would shed light on questions such as, 'What is the place and importance of IVD in Turkey?', 'What are the responsibilities of educational institutions?', 'What is the role of Ministry of Health?', with the aim that the answers would help to determine the infrastructure needed for successful production of IVD medical devices in Turkey. At the end of the symposium, feedback from participants were collected via a questionnaire. This article presents the general evaluation of the symposium based on the results of this survey.Öğe Indiscriminate SARS-CoV-2 multivariant detection using magnetic nanoparticle-based electrochemical immunosensing(Elsevier, 2022) Durmus, Ceren; Harmanci, Duygu; Moulahoum, Hichem; Tok, Kerem; Ghorbanizamani, Faezeh; Sanli, Serdar; Zihnioglu, FigenThe increasing mutation frequency of the SARS-CoV-2 virus and the emergence of successive variants have made correct diagnosis hard to perform. Developing efficient and accurate methods to diagnose infected patients is crucial to effectively mitigate the pandemic. Here, we developed an electrochemical immunosensor based on SARS-CoV-2 antibody cocktail-conjugated magnetic nanoparticles for the sensitive and accurate detection of the SARS-CoV-2 virus and its variants in nasopharyngeal swabs. The application of the antibody cocktail was compared with commercially available anti-SARS-CoV-2 S1 (anti-S1) and anti-S2 monoclonal antibodies. After optimization and calibration, the limit of detection (LOD) determination demonstrated a LOD = 0.53-0.75 ng/ mL for the antibody cocktail-based sensor compared with 0.93 ng/mL and 0.99 ng/mL for the platforms using anti-S1 and anti-S2, respectively. The platforms were tested with human nasopharyngeal swab samples pre diagnosed with RT-PCR (10 negatives and 40 positive samples). The positive samples include the original, alpha, beta, and delta variants (n = 10, for each). The polyclonal antibody cocktail performed better than commercial anti-S1 and anti-S2 antibodies for all samples reaching 100% overall sensitivity, specificity, and accuracy. It also showed a wide range of variants detection compared to monoclonal antibody-based platforms. The present work proposes a versatile electrochemical biosensor for the indiscriminate detection of the different variants of SARS-CoV-2 using a polyclonal antibody cocktail. Such diagnostic tools allowing the detection of variants can be of great efficiency and economic value in the fight against the ever-changing SARS-CoV-2 virus.Öğe Magnetic Nanoparticle-Based Electrochemical Sensing Platform Using Ferrocene-Labelled Peptide Nucleic Acid for the Early Diagnosis of Colorectal Cancer(Mdpi, 2022) Hanoglu, Simge Balaban; Man, Ezgi; Harmanci, Duygu; Ruzgar, Serife Tozan; Sanli, Serdar; Keles, Nazim Arda; Ayden, AtakanDiagnostic biomarkers based on epigenetic changes such as DNA methylation are promising tools for early cancer diagnosis. However, there are significant difficulties in directly and specifically detecting methylated DNA regions. Here, we report an electrochemical sensing system based on magnetic nanoparticles that enable a quantitative and selective analysis of the methylated septin9 (mSEPT9) gene, which is considered a diagnostic marker in early stage colorectal cancer (CRC). Methylation levels of SEPT9 in CRC samples were successfully followed by the selective recognition ability of a related peptide nucleic acid (PNA) after hybridization with DNA fragments in human patients' serums and plasma (n = 10). Moreover, this system was also adapted into a point-of-care (POC) device for a one-step detection platform. The detection of mSEPT9 demonstrated a limit of detection (LOD) value of 0.37% and interference-free measurement in the presence of branched-chain amino acid transaminase 1 (BCAT1) and SRY box transcription factor 21 antisense divergent transcript 1 (SOX21-AS1). The currently proposed functional platform has substantial prospects in translational applications of early CRC detection.Öğe Rapid Fibroblast Cell Culture Characterization with Impedimetric Label-free Heat Shock Protein-47 Biosensor(Wiley-V C H Verlag Gmbh, 2020) Harmanci, Duygu; Uygun, Zihni Onur; Sezgin, Ayse Kocak; Demirdover, Cenk; Sagin, Ferhan Girgin; Akdogan, GulIn this study, for the first time in literature, an impedimetric biosensor technology was developed to determine Heat Shock Protein-47 (HSP-47) for the characterization of primary skin fibroblast cells. Gold nanoparticle electrodes (GNPE) were modified with amino-functionalized graphene oxide layers and anti-HSP-47 were immobilized on this layer. the performance of the biosensor was tested with real samples as cell lysates. the low detection limit (LOD) and the linear detection limit (LOQ) of the biosensor were calculated as 9.47 pg/mL and 3.23 pg/mL, respectively. Linear measurement range was obtained between 10-160 pg/mL HSP-47. the reproducibility of the biosensor was good.Öğe Recent Approaches in Magnetic Nanoparticle-Based Biosensors of miRNA Detection(MDPI, 2023) Balaban Hanoglu, Simge; Harmanci, Duygu; Ucar, Nursima; Evran, Serap; Timur, SunaIn recent years, magnetic nanoparticles (MNPs) have been widely used in many fields due to their advantageous properties, such as biocompatibility, easy modifiability, and high chemical stability. One of these areas is the detection of cancer. It is essential to use existing biomarkers, such as microRNAs (miRNAs), for the early diagnosis of this disease. miRNAs are challenging to distinguish and detect in biological samples because they are small, circulating molecules. It is necessary to use more sensitive and feature-rich systems. Thanks to their large surface areas and magnetic moments, MNPs allow easy separation of miRNA at low concentrations from complex samples (urine and blood) and rapid and specific detection in biosensing systems. Here, we discussed the synthesis and characterization methods of MNPs, their stabilization, and MNP-based biosensors in terms of miRNA detection. We considered the challenges and prospects of these biosensor systems in evaluating the development stages, sensitivity, and selectivity.Öğe Simple workflow to repurpose SARS-CoV-2 swab/serum samples for the isolation of cost-effective antibody/antigens for proteotyping applications and diagnosis(Springer Heidelberg, 2021) Tok, Kerem; Moulahoum, Hichem; Ghorbanizamani, Faezeh; Harmanci, Duygu; Hanoglu, Simge Balaban; Durmus, Ceren; Evran, SerapSupply shortage for the development and production of preventive, therapeutic, and diagnosis tools during the COVID-19 pandemic is an important issue affecting the wealthy and poor nations alike. Antibodies and antigens are especially needed for the production of immunological-based testing tools such as point-of-care tests. Here, we propose a simple and quick magnetic nanoparticle (MNP)-based separation/isolation approach for the repurposing of infected human samples to produce specific antibodies and antigen cocktails. Initially, an antibody cocktail was purified from serums via precipitation and immunoaffinity chromatography. Purified antibodies were conjugated onto MNPs and used as an affinity matrix to separate antigens. The characterization process was performed by ELISA, SDS-PAGE, electrochemistry, isothermal titration calorimetry, and LC-Q-TOF-MS/MS analyses. The MNP-separated peptides can be used for mass spectrometry-based as well as paper-based lateral flow assay diagnostic. The exploitation of the current workflow for the development of efficient diagnostic tools, specific treatments, and fundamental research can significantly impact the present or eventual pandemic. This workflow can be considered as a two birds, one stone-like strategy.
