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Article ; Online: An innovative method for the detection of alpha synuclein, a potential biomarker of Parkinson's disease: quartz tuning fork-based mass sensitive immunosensor design.

Sonuç Karaboğa, Münteha Nur / Ünal, Mehmet Altay / Arı, Fikret / Sezgintürk, Mustafa Kemal / Özkan, Sibel Ayşıl

Physical chemistry chemical physics : PCCP

2024 Volume 26, Issue 6, Page(s) 5106–5114

Abstract: An innovative biosensing fabrication strategy has been demonstrated for the first time using a quartz tuning fork (QTF) to develop a practical immunosensor for sensitive, selective and practical analysis of alpha synuclein protein (SYN alpha), a ... ...

Abstract	An innovative biosensing fabrication strategy has been demonstrated for the first time using a quartz tuning fork (QTF) to develop a practical immunosensor for sensitive, selective and practical analysis of alpha synuclein protein (SYN alpha), a potential biomarker of Parkinson's disease. Functionalization of gold-coated QTFs was carried out in 2 steps by forming a self-assembled monolayer with 4-aminothiophenol (4-ATP) and conjugation of gold nanoparticles (AuNPs). The selective determination range for SYN alpha of the developed biosensor system is 1-500 ng mL
MeSH term(s)	Humans ; alpha-Synuclein ; Parkinson Disease ; Gold/chemistry ; Quartz ; Biosensing Techniques/methods ; Immunoassay ; Metal Nanoparticles/chemistry ; Electrochemical Techniques/methods ; Biomarkers
Chemical Substances	alpha-Synuclein ; Gold (7440-57-5) ; Quartz (14808-60-7) ; Biomarkers
Language	English
Publishing date	2024-02-07
Publishing country	England
Document type	Journal Article
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/d3cp04527g
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Article ; Online: Ultrasensitive electrochemical immunosensor system for determination of autologous SOX2 antibody.

Özçelikay-Akyıldız, Göksu / Ünal, Mehmet Altay / Atakan, Şükrü / Gülden, Seçil / Kızılelma, Bilal / Aydın, Safa / Ozkan, Sibel A

Journal of pharmaceutical and biomedical analysis

2024 Volume 241, Page(s) 115992

Abstract: Lung cancer is mainly seen as the cancer type in the world. Lung cancer causes the death of many people. It is classified as large-cell neuroendocrine carcinoma (LCNEC), small-cell lung cancer (SCLC), and adenocarcinoma by the World Health Organization ( ... ...

Abstract	Lung cancer is mainly seen as the cancer type in the world. Lung cancer causes the death of many people. It is classified as large-cell neuroendocrine carcinoma (LCNEC), small-cell lung cancer (SCLC), and adenocarcinoma by the World Health Organization (WHO) in 2015. Small cell lung cancer (SCLC) is a highly aggressive type of cancer, accounting for approximately 20% of all cases. By performing the serological analysis of expression cDNA libraries (SEREX), the humoral immune response of SCLC patients is determined. SEREX of SCLC cell lines using pooled sera of SCLC patients led to the isolation of SOX2 genes. The between SOX2 antigen expression intensity and autologous antibody presence has a significant correlation because SOX2 is the main antigen eliciting anti-SOX responses. Electrochemical biosensors take much attention because of their simplicity, selectivity, and sensitivity in clinical analysis. Antibody-based surface recognizes antibody-specific antigens. This work aims to fabricate an immunosensor for determining autologous SOX2 antibodies using a multi-walled carbon nanotube-modified screen-printed electrode (DRP-MWCNT). All immobilization processes were evaluated with cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The critical parameters were optimized, such as EDC/NHS concentration and time, SOX2 protein concentration and incubation time, BSA ratio, BSA blocking time, and anti-SOX2 antibody incubation time. The developed immunosensor, under optimal conditions, shows a linear response of autologous SOX2 antibody between 0.005 ng.mL
MeSH term(s)	Humans ; Immunoassay/methods ; Biosensing Techniques/methods ; Antibodies ; Enzyme-Linked Immunosorbent Assay ; Lung Neoplasms ; Small Cell Lung Carcinoma ; Electrochemical Techniques ; Electrodes ; Limit of Detection ; Gold ; SOXB1 Transcription Factors
Chemical Substances	Antibodies ; Gold (7440-57-5) ; SOX2 protein, human ; SOXB1 Transcription Factors
Language	English
Publishing date	2024-01-20
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	604917-5
ISSN	1873-264X ; 0731-7085
ISSN (online)	1873-264X
ISSN	0731-7085
DOI	10.1016/j.jpba.2024.115992
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Article ; Online: Effect of Disulfide Bonds on the Thermal Stability of Pediocin: In-silico Screening Using Molecular Dynamics Simulation.

Unal, Mehmet Altay / Kaymaz, Ozlem / Gunes Altuntas, Evrim / Juneja, Vijay K / Elmali, Ayhan

Journal of food protection

2023 Volume 86, Issue 9, Page(s) 100107

Abstract: The thermal stability properties of pediocin at 310, 313, 323, 333, 343, and 348 K (37, 40, 50, 60, 70, and 75°C, respectively) are reported in this study. A theoretical approach, such as the molecular dynamics method, was used to analyze the structure. ... ...

Abstract	The thermal stability properties of pediocin at 310, 313, 323, 333, 343, and 348 K (37, 40, 50, 60, 70, and 75°C, respectively) are reported in this study. A theoretical approach, such as the molecular dynamics method, was used to analyze the structure. Molecular dynamics simulation confirms the stability of molecules with Cys. Furthermore, this study reveals that Cys residues play an essential role in structure stability at high temperatures. To understand the structural basis for the stability of pediocin, a detailed in-silico analysis using molecular dynamics simulations to explore the thermal stability profiles of the compounds was conducted. This study shows that thermal effects fundamentally alter the functionally crucial secondary structure of pediocin. However, as previously reported, pediocin's activity was strictly conserved due to the disulfide bond between Cys residues. These findings reveal, for the first time, the dominant factor behind the thermodynamic stability of pediocin.
MeSH term(s)	Pediocins ; Molecular Dynamics Simulation ; Protein Structure, Secondary ; Disulfides/chemistry
Chemical Substances	Pediocins ; Disulfides
Language	English
Publishing date	2023-05-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	243284-5
ISSN	1944-9097 ; 0362-028X
ISSN (online)	1944-9097
ISSN	0362-028X
DOI	10.1016/j.jfp.2023.100107
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Article ; Online: Electrochemical detection of lactate produced by foodborne presumptive lactic acid bacteria.

Ozoglu, Ozum / Uzunoglu, Aytekin / Unal, Mehmet Altay / Gumustas, Mehmet / Ozkan, Sibel Aysıl / Korukluoglu, Mihriban / Gunes Altuntas, Evrim

Journal of bioscience and bioengineering

2023 Volume 135, Issue 4, Page(s) 313–320

Abstract: The detection of lactate is an important indicator of the freshness, stability, and storage stability of products as well as the degree of fermentation in the food industry. In addition, it can be used as a diagnostic tool in patients' healthcare since ... ...

Abstract	The detection of lactate is an important indicator of the freshness, stability, and storage stability of products as well as the degree of fermentation in the food industry. In addition, it can be used as a diagnostic tool in patients' healthcare since it is known that the lactate level in blood increases in some pathological conditions. Thus, the determination of lactate level plays an important role in not only the food industry but also in health fields. As a result, biosensor technologies, which are quick, cheap, and easy to use, have become important for lactate detection. In the current study, amperometric lactate biosensors based on lactate oxidase immobilization (with Nafion 5% wt) were designed and the limit of detection, linear range, and sensitivity values were determined to be 31 μM, 50-350 μM, and 0.04 μA μM
MeSH term(s)	Humans ; Lactic Acid/metabolism ; Enzymes, Immobilized/metabolism ; Biosensing Techniques/methods ; Food Industry ; Fermentation
Chemical Substances	Lactic Acid (33X04XA5AT) ; Enzymes, Immobilized
Language	English
Publishing date	2023-02-23
Publishing country	Japan
Document type	Journal Article
ZDB-ID	1465387-4
ISSN	1347-4421 ; 1389-1723
ISSN (online)	1347-4421
ISSN	1389-1723
DOI	10.1016/j.jbiosc.2022.12.014
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Article ; Online: A novel SLC35D1 variant causing milder phenotype of Schneckenbecken dysplasia in a large pedigree.

Özer, Leyla / Aktuna, Suleyman / Unsal, Evrim / Ünal, Mehmet Altay / Sahin, Guler / Baltaci, Volkan

American journal of medical genetics. Part A

2022 Volume 188, Issue 10, Page(s) 3078–3083

Abstract: SLC35D1 gene encodes UDP-glucuronic acid/UDP-n-acetylgalactosamine dual transporter protein and transports organic or inorganic molecules across cellular membranes. SLC35D1 gene pathogenic variants causes Schneckenbecken dysplasia (SHNKND) which is a ... ...

Abstract	SLC35D1 gene encodes UDP-glucuronic acid/UDP-n-acetylgalactosamine dual transporter protein and transports organic or inorganic molecules across cellular membranes. SLC35D1 gene pathogenic variants causes Schneckenbecken dysplasia (SHNKND) which is a rare lethal autosomal recessive disorder characterized by the snail-like pelvis, flattening of vertebral bodies, short and broad long bones with a dumbbell-like appearance, thoracic hypoplasia. Only six cases with homozygous SLC35D1 variants have been reported to date, and all of these cases were lost in the perinatal period. Here we report different family members with a novel SLC35D1 variant who presented a milder phenotype of SHNKND. The affected patients have common clinical features such as short stature, mild mesomelia, shortening of the lower extremity, genu valgum, and narrow thorax. Exome sequencing of the proband revealed a homozygous missense variant of SLC35D1 gene, c.401 T > C (p. Met134Thr). The affected siblings, their two cousins, and their paternal uncle with a similar phenotype were also homozygous for the variant. This is the first case report of a family with a novel likely pathogenic variant (p. Met134Thr) and mild phenotypic features. It has the largest family with different ages of patients (ages ranged 4-31 years old) reported to date. The present report supports the evidence that the p. Met134Thr variant is responsible for a milder phenotype than previously reported cases with SLC35D1 pathogenic variants.
MeSH term(s)	Female ; Humans ; Monosaccharide Transport Proteins/genetics ; Osteochondrodysplasias/genetics ; Pedigree ; Phenotype ; Pregnancy ; Uridine Diphosphate
Chemical Substances	Monosaccharide Transport Proteins ; SLC35D1 protein, human ; Uridine Diphosphate (58-98-0)
Language	English
Publishing date	2022-08-07
Publishing country	United States
Document type	Case Reports
ZDB-ID	2108614-X
ISSN	1552-4833 ; 0148-7299 ; 1552-4825
ISSN (online)	1552-4833
ISSN	0148-7299 ; 1552-4825
DOI	10.1002/ajmg.a.62939
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Zs.A 1376/A: Show issues

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Article ; Online: Ultrasensitive Determination of Glial-Fibrillary-Acidic-Protein (GFAP) in Human Serum-Matrix with a Label-Free Impedimetric Immunosensor.

Ozcelikay, Goksu / Mollarasouli, Fariba / Unal, Mehmet Altay / Gucuyener, Kıvılcım / Ozkan, Sibel A

Biosensors

2022 Volume 12, Issue 12

Abstract: In this work, immobilizing anti-GFAP antibodies via covalent attachment onto L-cysteine/gold nanoparticles that were modified with screen-printed carbon electrodes (Anti-GFAP/L-cys/AuNps/SPCE) resulted in the development of a sensitive label-free ... ...

Abstract	In this work, immobilizing anti-GFAP antibodies via covalent attachment onto L-cysteine/gold nanoparticles that were modified with screen-printed carbon electrodes (Anti-GFAP/L-cys/AuNps/SPCE) resulted in the development of a sensitive label-free impedance immunosensor for the detection of Glial Fibrillary Acidic Protein (GFAP). The immunosensor's stepwise construction was studied using cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). L-cysteine was chosen as the linker between GFAP antibodies and Au NPs/SPCE because it enables the guided and stable immobilization of GFAP antibodies, thus resulting in increased immunosensor sensitivity. As a redox probe, 5 mM of [Fe(CN)6]3-/4- was used to measure the electron-transfer resistance (Ret), which was raised by the binding of antigens to the immobilized anti-GFAP on the surface of the modified electrode. A linear correlation between Rct and GFAP concentration was achieved under optimum conditions in the range of 1.0-1000.0 pg/mL, with an extraordinarily low detection limit of 51.0 fg/mL. The suggested immunosensor was successfully used to detect the presence of GFAP in human blood serum samples, yielding good findings. As a result, the proposed platform may be utilized to monitor central nervous system injuries.
Language	English
Publishing date	2022-12-14
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662125-3
ISSN	2079-6374 ; 2079-6374
ISSN (online)	2079-6374
ISSN	2079-6374
DOI	10.3390/bios12121165
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Article ; Online: Emerging 2D materials for antimicrobial applications in the pre- and post-pandemic era.

Gokce, Cemile / Gurcan, Cansu / Besbinar, Omur / Unal, Mehmet Altay / Yilmazer, Acelya

Nanoscale

2022 Volume 14, Issue 2, Page(s) 239–249

Abstract: Infectious diseases caused by viral or bacterial pathogens are one of the most serious threats to humanity. Moreover, they may lead to pandemics, as we have witnessed severely with the coronavirus disease 2019 (COVID-19). Nanotechnology, including ... ...

Abstract	Infectious diseases caused by viral or bacterial pathogens are one of the most serious threats to humanity. Moreover, they may lead to pandemics, as we have witnessed severely with the coronavirus disease 2019 (COVID-19). Nanotechnology, including technological developments of nano-sized materials, has brought great opportunities to control the spreading of such diseases. In the family of nano-sized materials, two-dimensional (2D) materials with intrinsic physicochemical properties can efficiently favor antimicrobial activity and maintain a safer environment to protect people against pathogens. For this purpose, they can be used alone or combined for the disinfection process of microbes, antiviral or antibacterial surface coatings, air filtering of medical equipment like face masks, or antimicrobial drug delivery systems. At the same time, they are promising candidates to deal with the issues of conventional antimicrobial approaches such as low efficacy and high cost. This review covers the antiviral or antibacterial activities of 2D materials and highlights their current and possible future applications. Considering their intrinsic properties, 2D materials will become part of the leading antimicrobial technologies for combating future pandemics anytime soon.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Infective Agents/pharmacology ; COVID-19 ; Humans ; Pandemics ; SARS-CoV-2
Chemical Substances	Anti-Bacterial Agents ; Anti-Infective Agents
Language	English
Publishing date	2022-01-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2515664-0
ISSN	2040-3372 ; 2040-3364
ISSN (online)	2040-3372
ISSN	2040-3364
DOI	10.1039/d1nr06476b
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Article ; Online: SnO

Bilge, Selva / Dogan Topal, Burcu / Gokhan Caglayan, Mehmet / Altay Unal, Mehmet / Nazır, Hasan / Bellur Atici, Esen / Sınağ, Ali / Ozkan, Sibel A

Bioelectrochemistry (Amsterdam, Netherlands)

2022 Volume 150, Page(s) 108329

Abstract: This present study is the first investigation of pazopanib-dsDNA binding using bare and modified GCE. The interaction was mainly evaluated based on the decrease of voltammetric signal of deoxyadenosine by differential pulse voltammetry using three ... ...

Abstract	This present study is the first investigation of pazopanib-dsDNA binding using bare and modified GCE. The interaction was mainly evaluated based on the decrease of voltammetric signal of deoxyadenosine by differential pulse voltammetry using three different ways, including the incubated solutions, dsDNA biosensor, and nanobiosensor. The nanobiosensor was fabricated with the help of SnO
MeSH term(s)	Humans ; Carbon/chemistry ; Molecular Docking Simulation ; Masks ; Pandemics ; COVID-19 ; Antineoplastic Agents ; Nanoparticles/chemistry ; DNA/chemistry ; Biosensing Techniques/methods ; Electrodes ; Electrochemical Techniques/methods
Chemical Substances	Carbon (7440-44-0) ; pazopanib (7RN5DR86CK) ; Antineoplastic Agents ; DNA (9007-49-2)
Language	English
Publishing date	2022-12-07
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2010650-6
ISSN	1878-562X ; 0302-4598 ; 1567-5394
ISSN (online)	1878-562X
ISSN	0302-4598 ; 1567-5394
DOI	10.1016/j.bioelechem.2022.108329
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Zs.A 1178: Show issues

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Article ; Online: Human hair rich in pyridinic nitrogen-base DNA biosensor for direct electrochemical monitoring of palbociclib-DNA interaction.

Bilge, Selva / Dogan Topal, Burcu / Caglayan, Mehmet Gokhan / Unal, Mehmet Altay / Nazır, Hasan / Atici, Esen Bellur / Sınağ, Ali / Ozkan, Sibel A

Bioelectrochemistry (Amsterdam, Netherlands)

2022 Volume 148, Page(s) 108264

Abstract: Carbon material derived from the waste-based biomass human hair (H), which is naturally rich in pyridinic nitrogen, provides a significant benefit in biosensor applications with its dominant conductivity character. The carbon material was synthesized ... ...

Abstract	Carbon material derived from the waste-based biomass human hair (H), which is naturally rich in pyridinic nitrogen, provides a significant benefit in biosensor applications with its dominant conductivity character. The carbon material was synthesized from human hair waste by the hydrothermal carbonization (HTC) method, which is a promising green synthesis. A morphological characterization of the carbon materials was performed. In this study, H and amine-functionalized multi-walled carbon nanotubes (NH
MeSH term(s)	Amines ; Biosensing Techniques ; DNA/chemistry ; Deoxyadenosines ; Deoxyguanosine ; Electrochemical Techniques/methods ; Electrodes ; Hair ; Humans ; Nanotubes, Carbon/chemistry ; Nitrogen/chemistry ; Pharmaceutical Preparations ; Piperazines ; Pyridines
Chemical Substances	Amines ; Deoxyadenosines ; Nanotubes, Carbon ; Pharmaceutical Preparations ; Piperazines ; Pyridines ; DNA (9007-49-2) ; Deoxyguanosine (G9481N71RO) ; palbociclib (G9ZF61LE7G) ; Nitrogen (N762921K75)
Language	English
Publishing date	2022-09-13
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2010650-6
ISSN	1878-562X ; 0302-4598 ; 1567-5394
ISSN (online)	1878-562X
ISSN	0302-4598 ; 1567-5394
DOI	10.1016/j.bioelechem.2022.108264
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Article ; Online: Functional analyses of three different mutations in the AVP-NPII gene causing familial neurohypophyseal diabetes insipidus.

Türkmen, Merve Özcan / Karaduman, Tugce / Tuncdemir, Beril Erdem / Ünal, Mehmet Altay / Mergen, Hatice

Endocrine

2021 Volume 74, Issue 3, Page(s) 658–665

Abstract: Purpose: Familial neurohypophyseal diabetes insipidus (FNDI), a rare disorder, which is clinically characterized by polyuria and polydipsia, results from mutations in the arginine vasopressin-neurophysin II (AVP-NPII) gene. The aim of this study was to ... ...

Abstract	Purpose: Familial neurohypophyseal diabetes insipidus (FNDI), a rare disorder, which is clinically characterized by polyuria and polydipsia, results from mutations in the arginine vasopressin-neurophysin II (AVP-NPII) gene. The aim of this study was to perform functional analyses of three different mutations (p.G45C, 207_209delGGC, and p.G88V) defined in the AVP-NPII gene of patients diagnosed with FNDI, which are not included in the literature. Methods: For functional analysis studies, the relevant mutations were created using PCR-based site-directed mutagenesis and restriction fragment replacement strategy and expressed in Neuro2A cells. AVP secretion into the cell culture medium was determined by radioimmunoassay (RIA) analysis. Fluorescence imaging studies were conducted to determine the differences in the intracellular trafficking of wild-type (WT) and mutant AVP-NPII precursors. Molecular dynamics (MD) simulations were performed to determine the changing of the conformational properties of domains for both WT and 207-209delGGC mutant structures and dynamics behavior of residues. Results: Reduced levels of AVP in the supernatant culture medium of p.G45C and p.G88V transfected cells compared to 207_209delGGC and WT cells were found. Fluorescence imaging studies showed that a substantial portion of the mutant p.G45C and p.G88V AVP-NPII precursors appeared to be located in the endoplasmic reticulum (ER), whereas 207_209delGGC and WT AVP-NPII precursors were distributed throughout the cytoplasm. Conclusions: The mutations p.G45C and p.G88V cause a failure in the intracellular trafficking of mutant AVP-NPII precursors. However, 207_209delGGC mutation does not result in impaired cellular trafficking, probably due to not having any significant effect in processes such as the proper folding, gain of three-dimensional structure, or processing. These results will provide valuable information for understanding the influence of mutations on the function of the AVP precursor hormone and cellular trafficking. Therefore, this study will contribute to elucidate the mechanisms of the molecular pathology of AVP-NPII mutations.
MeSH term(s)	Diabetes Insipidus ; Diabetes Insipidus, Neurogenic/genetics ; Diabetes Mellitus ; Humans ; Mutation ; Neurophysins/genetics ; Neurophysins/metabolism ; Pedigree
Chemical Substances	Neurophysins
Language	English
Publishing date	2021-07-07
Publishing country	United States
Document type	Journal Article
ZDB-ID	1194484-5
ISSN	1559-0100 ; 1355-008X ; 0969-711X
ISSN (online)	1559-0100
ISSN	1355-008X ; 0969-711X
DOI	10.1007/s12020-021-02803-0
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