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Article: Repurposing Fc gamma receptor I (FcγRI, CD64) for site-oriented monoclonal antibody capture: A proof-of-concept study for real-time detection of tumor necrosis factor-alpha (TNF -α).

Çapkın, Eda / Kutlu, Aslı / Yüce, Meral

2023 Volume 9, Issue 9, Page(s) e19469

Abstract: The controlled orientation of biomolecules on the sensor surface is crucial for achieving high sensitivity and accurate detection of target molecules in biosensing. FcγRI is an immune cell surface receptor for recognizing IgG-coated targets, such as ... ...

Abstract	The controlled orientation of biomolecules on the sensor surface is crucial for achieving high sensitivity and accurate detection of target molecules in biosensing. FcγRI is an immune cell surface receptor for recognizing IgG-coated targets, such as opsonized pathogens or immune complexes. It plays a crucial role in T cell activation and internalization of the cargos, leading downstream signaling cascades. In this study, we repurposed the FcγRI as an analytical ligand molecule for site-oriented ADA capture, a monoclonal antibody-based biosimilar drug, on a plasmonic sensor surface and demonstrated the real-time detection of the corresponding analyte molecule, TNF-α. The study encompasses the analysis of comparative ligand behaviors on the surface, biosensor kinetics, concentration-dependent studies, and sensor specificity assays. The findings of this study suggest that FcγRI has a significant potential to serve as a universal ligand molecule for site-specific monoclonal antibody capture, and it can be used for biosensing studies, as it represents low nanomolar range affinity and excellent selectivity towards the target. However, there is still room for improvement in the surface stability and sensing response, and further studies are needed to reveal its performance on the monoclonal antibodies with various antigen binding sites and glycoforms.
Language	English
Publishing date	2023-08-26
Publishing country	England
Document type	Journal Article
ZDB-ID	2835763-2
ISSN	2405-8440
ISSN	2405-8440
DOI	10.1016/j.heliyon.2023.e19469
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Article ; Online: Repurposing Fc gamma receptor I (FcγRI, CD64) for site-oriented monoclonal antibody capture

Eda Çapkın / Aslı Kutlu / Meral Yüce

Heliyon, Vol 9, Iss 9, Pp e19469- (2023)

A proof-of-concept study for real-time detection of tumor necrosis factor-alpha (TNF -α)

2023

Abstract	The controlled orientation of biomolecules on the sensor surface is crucial for achieving high sensitivity and accurate detection of target molecules in biosensing. FcγRI is an immune cell surface receptor for recognizing IgG-coated targets, such as opsonized pathogens or immune complexes. It plays a crucial role in T cell activation and internalization of the cargos, leading downstream signaling cascades. In this study, we repurposed the FcγRI as an analytical ligand molecule for site-oriented ADA capture, a monoclonal antibody-based biosimilar drug, on a plasmonic sensor surface and demonstrated the real-time detection of the corresponding analyte molecule, TNF-α. The study encompasses the analysis of comparative ligand behaviors on the surface, biosensor kinetics, concentration-dependent studies, and sensor specificity assays. The findings of this study suggest that FcγRI has a significant potential to serve as a universal ligand molecule for site-specific monoclonal antibody capture, and it can be used for biosensing studies, as it represents low nanomolar range affinity and excellent selectivity towards the target. However, there is still room for improvement in the surface stability and sensing response, and further studies are needed to reveal its performance on the monoclonal antibodies with various antigen binding sites and glycoforms.
Keywords	Fc gamma receptor I ; Monoclonal antibody ; TNF-α biosensor ; Surface plasmon resonance ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
Subject code	570
Language	English
Publishing date	2023-09-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Nanomaterials to tackle the COVID-19 pandemic.

Pishva, Parsa / Yüce, Meral

Emergent materials

2021 Volume 4, Issue 1, Page(s) 211–229

Abstract: The rapid worldwide spread of the COVID-19 pandemic, caused by the severe acute respiratory SARS-CoV-2, has created an urgent need for its diagnosis and treatment. As a result, many researchers have sought to find the most efficient and appropriate ... ...

Abstract	The rapid worldwide spread of the COVID-19 pandemic, caused by the severe acute respiratory SARS-CoV-2, has created an urgent need for its diagnosis and treatment. As a result, many researchers have sought to find the most efficient and appropriate methods to detect and treat the SARS-CoV-2 virus over the past few months. Real-time reverse-transcriptase polymerase chain reaction (RT-PCR) testing is currently used as one of the most reliable methods to detect the new virus; however, this method is time-consuming, labor-intensive, and requires trained laboratory workers. Moreover, despite its high sensitivity and specificity, false negatives are reported, especially in non-nasopharyngeal swab samples that yield lower viral loads. Therefore, designing and employing faster and more reliable methods seems necessary. In recent years, many attempts have been made to fabricate various nanomaterial-based biosensors to detect viruses and bacteria in clinical samples. The use of nanomaterials plays a significant role in improving the performance of biosensors. Plasmonic biosensors, field-effect transistor (FET)-based biosensors, electrochemical biosensors, and reverse transcription loop-mediated isothermal amplification (RT-LAMP) methods are only some of the effective ways to detect viruses. However, to use these biosensors to detect the SARS-CoV-2 virus, modifications must be performed to increase sensitivity and speed of testing due to the rapidly spreading nature of SARS-CoV-2, which requires an early point of care detection and treatment for pandemic control. Several studies have been carried out to show the nanomaterial-based biosensors' performance and success in detecting the novel virus. The limit of detection, accuracy, selectivity, and detection speed are some vital features that should be considered during the design of the SARS-CoV-2 biosensors. This review summarizes various nanomaterials-based sensor platforms to detect the SARS-CoV-2, and their design, advantages, and limitations.
Language	English
Publishing date	2021-02-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2522-574X
ISSN (online)	2522-574X
DOI	10.1007/s42247-021-00184-8
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Article ; Online: Nanotechnology in food and water security: on-site detection of agricultural pollutants through surface-enhanced Raman spectroscopy.

Yılmaz, Deniz / Günaydın, Beyza Nur / Yüce, Meral

Emergent materials

2022 Volume 5, Issue 1, Page(s) 105–132

Abstract: Agricultural pollutants are harmful components threatening human health, wildlife, the environment, and the ecosystem. To avoid their exposure, developing prevention and detection systems with high sensitivity and selectivity is required. Most ... ...

Abstract	Agricultural pollutants are harmful components threatening human health, wildlife, the environment, and the ecosystem. To avoid their exposure, developing prevention and detection systems with high sensitivity and selectivity is required. Most conventional methods, including molecular and chromatographic techniques, cannot be adopted for outdoor on-site detection even though they can provide sensitive and selective detection. Thus, detection platforms that can provide on-site detection via miniaturized and high throughput systems should be developed. As an alternative method, surface-enhanced Raman scattering (SERS) provides unique information about the substances in the presence of plasmonic nanostructures, and it can be portable with the use of portable detection systems and spectrometers. In this study, on-site detection of agricultural pollutants through SERS is reviewed. Three different types of agricultural pollutants were pointed out. On-site detection of biological pollutants, including bacteria and viruses, is reviewed as the first type of pollutant. As a second type, the detection of pesticides, antibiotics, and additives are focused on as chemical pollutants. The third group includes the detection of microplastics and also nanoparticles from the environment.
Language	English
Publishing date	2022-03-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ISSN	2522-574X
ISSN (online)	2522-574X
DOI	10.1007/s42247-022-00376-w
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Article ; Online: Material and Design Toolkit for Drug Delivery: State of the Art, Trends, and Challenges.

Rad, Monireh Esmaeili / Soylukan, Caner / Kulabhusan, Prabir Kumar / Günaydın, Beyza Nur / Yüce, Meral

ACS applied materials & interfaces

2023 Volume 15, Issue 48, Page(s) 55201–55231

Abstract: The nanomaterial and related toolkit have promising applications for improving human health and well-being. Nanobased drug delivery systems use nanoscale materials as carriers to deliver therapeutic agents in a targeted and controlled manner, and they ... ...

Abstract	The nanomaterial and related toolkit have promising applications for improving human health and well-being. Nanobased drug delivery systems use nanoscale materials as carriers to deliver therapeutic agents in a targeted and controlled manner, and they have shown potential to address issues associated with conventional drug delivery systems. They offer benefits for treating various illnesses by encapsulating or conjugating biological agents, chemotherapeutic drugs, and immunotherapeutic agents. The potential applications of this technology are vast; however, significant challenges exist to overcome such as safety issues, toxicity, efficacy, and insufficient capacity. This article discusses the latest developments in drug delivery systems, including drug release mechanisms, material toolkits, related design molecules, and parameters. The concluding section examines the limitations and provides insights into future possibilities.
MeSH term(s)	Humans ; Drug Delivery Systems ; Nanostructures ; Drug Carriers ; Nanoparticles
Chemical Substances	Drug Carriers
Language	English
Publishing date	2023-11-23
Publishing country	United States
Document type	Journal Article ; Review
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c10065
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Article ; Online: Nanomaterial surface modification toolkit: Principles, components, recipes, and applications.

Kaymaz, Sümeyra Vural / Nobar, Hediyeh Malekzadsani / Sarıgül, Hasan / Soylukan, Caner / Akyüz, Lalehan / Yüce, Meral

Advances in colloid and interface science

2023 Volume 322, Page(s) 103035

Abstract: Surface-functionalized nanostructures are at the forefront of biotechnology, providing new opportunities for biosensors, drug delivery, therapy, and bioimaging applications. The modification of nanostructures significantly impacts the performance and ... ...

Abstract	Surface-functionalized nanostructures are at the forefront of biotechnology, providing new opportunities for biosensors, drug delivery, therapy, and bioimaging applications. The modification of nanostructures significantly impacts the performance and success of various applications by enabling selective and precise targeting. This review elucidates widely practiced surface modification strategies, including click chemistry, cross-coupling, silanization, aldehyde linkers, active ester chemistry, maleimide chemistry, epoxy linkers, and other protein and DNA-based methodologies. We also delve into the application-focused landscape of the nano-bio interface, emphasizing four key domains: therapeutics, biosensing, environmental monitoring, and point-of-care technologies, by highlighting prominent studies. The insights presented herein pave the way for further innovations at the intersection of nanotechnology and biotechnology, providing a useful handbook for beginners and professionals. The review draws on various sources, including the latest research articles (2018-2023), to provide a comprehensive overview of the field.
MeSH term(s)	Nanostructures/chemistry ; Nanotechnology/methods ; Biosensing Techniques/methods ; Biotechnology ; Proteins
Chemical Substances	Proteins
Language	English
Publishing date	2023-11-03
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	210507-x
ISSN	1873-3727 ; 0001-8686
ISSN (online)	1873-3727
ISSN	0001-8686
DOI	10.1016/j.cis.2023.103035
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Article ; Online: Microwave-assisted green synthesis of silver nanoparticles using dried extracts of Chlorella vulgaris and antibacterial activity studies

Torabfam Milad / Yüce Meral

Green Processing and Synthesis, Vol 9, Iss 1, Pp 283-

2020 Volume 293

Abstract: Green synthesis of metallic nanoparticles (NPs) is acquiring considerable attention due to its environmental and economic superiorities over other methods. This study describes the practical synthesis of silver nanoparticles (AgNPs) through the reduction ...

Abstract	Green synthesis of metallic nanoparticles (NPs) is acquiring considerable attention due to its environmental and economic superiorities over other methods. This study describes the practical synthesis of silver nanoparticles (AgNPs) through the reduction of silver nitrate solution using an algal source, Chlorella vulgaris, as the reducing as well as the stabilizing agent. The energy required for this synthesis was supplied by microwave radiation. The ultraviolet-visible spectroscopy exhibited a single peak related to the surface plasmon absorbance of AgNPs at 431 nm. The AgNPs with high stability (a zeta potential of −17 mV), hydrodynamic size distribution of 1–50 nm, and mostly spherical shape were obtained through a 10 min process. Fourier transform infrared spectroscopy analysis revealed that several functional groups, including carbonyl groups of C. vulgaris, play a significant role in the formation of functional NPs. Antibacterial features of the produced AgNPs were verified against those of Salmonella enterica subsp. enterica serovar typhimurium and Staphylococcus aureus, demonstrating a considerable growth inhibition at increasing concentrations of the NPs. As a result, the formed AgNPs can be used as a promising agent against bacterial diseases.
Keywords	green synthesis ; microwave synthesis ; silver nanoparticles ; algae ; chlorella vulgaris ; antimicrobial activity ; Chemistry ; QD1-999
Subject code	540
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	De Gruyter
Document type	Article ; Online
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Article ; Online: SELEX against whole-cell bacteria resulted in lipopolysaccharide binding aptamers.

Yılmaz, Deniz / Muslu, Tuğdem / Parlar, Ayhan / Kurt, Hasan / Yüce, Meral

Journal of biotechnology

2022 Volume 354, Page(s) 10–20

Abstract: Nucleic acid aptamers are target-specific oligonucleotides selected from combinatorial libraries through an iterative in vitro screening process known as Systemic Evolution of Ligands by Exponential Enrichment (SELEX). In this report, the selection of ... ...

Abstract	Nucleic acid aptamers are target-specific oligonucleotides selected from combinatorial libraries through an iterative in vitro screening process known as Systemic Evolution of Ligands by Exponential Enrichment (SELEX). In this report, the selection of bacteria differentiating ssDNA aptamer candidates from a combinatorial library through the whole-cell SELEX method was performed. The enriched SELEX pool was sequenced using Illumina Next-Generation Sequencing (NGS) technology and analyzed for the most abundant sequences using CLC Genomics Workbench. The sequencing data resulted in several oligonucleotide families from which three individual sequences were chosen per SELEX based on the copy numbers. The binding performance of the selected aptamers was assessed by flow cytometry and fluorescence spectroscopy, and the binding constants were estimated using binding saturation curves. Varying results were obtained from two independent SELEX procedures where the SELEX against the model gram-negative bacterium Escherichia coli provided more selective sequences while the SELEX library used against gram-positive bacterium Listeria monocytogenes did not evolve as expected. The sequences that emerged from E. coli SELEX were shown to bind Lipopolysaccharide residues (LPS) and inhibit LPS-induced macrophage polarization. Thus, it can be said that, performed whole-cell SELEX could be resulted as the selection of aptamers which can bind LPS and inhibit LPS induced inflammation response and thus can be candidates for the inhibition of bacterial infections. In future studies, the selected aptamer sequences could be structurally and chemically modified and exploited as potential diagnostic tools and therapeutic agents as LPS antagonists.
MeSH term(s)	Aptamers, Nucleotide/chemistry ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Gene Library ; Humans ; Ligands ; Lipopolysaccharides ; SELEX Aptamer Technique/methods
Chemical Substances	Aptamers, Nucleotide ; Ligands ; Lipopolysaccharides
Language	English
Publishing date	2022-06-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	843647-2
ISSN	1873-4863 ; 0168-1656 ; 1389-0352
ISSN (online)	1873-4863
ISSN	0168-1656 ; 1389-0352
DOI	10.1016/j.jbiotec.2022.06.001
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Zs.A 2299: Show issues

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Article ; Online: COVID-19 diagnosis -A review of current methods.

Yüce, Meral / Filiztekin, Elif / Özkaya, Korin Gasia

Biosensors & bioelectronics

2020 Volume 172, Page(s) 112752

Abstract: A fast and accurate self-testing tool for COVID-19 diagnosis has become a prerequisite to comprehend the exact number of cases worldwide and to take medical and governmental actions accordingly. SARS-CoV-2 (formerly, 2019-nCoV) infection was first ... ...

Abstract	A fast and accurate self-testing tool for COVID-19 diagnosis has become a prerequisite to comprehend the exact number of cases worldwide and to take medical and governmental actions accordingly. SARS-CoV-2 (formerly, 2019-nCoV) infection was first reported in Wuhan (China) in December 2019, and then it has rapidly spread around the world, causing
MeSH term(s)	Antibodies, Viral/analysis ; Antigens, Viral/analysis ; Biosensing Techniques/instrumentation ; Biosensing Techniques/methods ; COVID-19/diagnosis ; COVID-19/immunology ; COVID-19/virology ; COVID-19 Nucleic Acid Testing/instrumentation ; COVID-19 Nucleic Acid Testing/methods ; COVID-19 Serological Testing/instrumentation ; COVID-19 Serological Testing/methods ; COVID-19 Testing/instrumentation ; COVID-19 Testing/methods ; Genome, Viral ; Humans ; Pandemics ; SARS-CoV-2/chemistry ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology
Chemical Substances	Antibodies, Viral ; Antigens, Viral
Keywords	covid19
Language	English
Publishing date	2020-10-24
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2020.112752
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Article: Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents.

Kumar Kulabhusan, Prabir / Hussain, Babar / Yüce, Meral

Pharmaceutics

2020 Volume 12, Issue 7

Abstract: Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer ... ...

Abstract	Aptamers are synthetic single-stranded DNA or RNA sequences selected from combinatorial oligonucleotide libraries through the well-known in vitro selection and iteration process, SELEX. The last three decades have witnessed a sudden boom in aptamer research, owing to their unique characteristics, like high specificity and binding affinity, low immunogenicity and toxicity, and ease in synthesis with negligible batch-to-batch variation. Aptamers can specifically bind to the targets ranging from small molecules to complex structures, making them suitable for a myriad of diagnostic and therapeutic applications. In analytical scenarios, aptamers are used as molecular probes instead of antibodies. They have the potential in the detection of biomarkers, microorganisms, viral agents, environmental pollutants, or pathogens. For therapeutic purposes, aptamers can be further engineered with chemical stabilization and modification techniques, thus expanding their serum half-life and shelf life. A vast number of antagonistic aptamers or aptamer-based conjugates have been discovered so far through the in vitro selection procedure. However, the aptamers face several challenges for its successful clinical translation, and only particular aptamers have reached the marketplace so far. Aptamer research is still in a growing stage, and a deeper understanding of nucleic acid chemistry, target interaction, tissue distribution, and pharmacokinetics is required. In this review, we discussed aptamers in the current diagnostics and theranostics applications, while addressing the challenges associated with them. The report also sheds light on the implementation of aptamer conjugates for diagnostic purposes and, finally, the therapeutic aptamers under clinical investigation, challenges therein, and their future directions.
Keywords	covid19
Language	English
Publishing date	2020-07-09
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527217-2
ISSN	1999-4923
ISSN	1999-4923
DOI	10.3390/pharmaceutics12070646
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