Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Advances in Optical Biosensors: Technologies and Trends in Point of Care Applications(Academic Press Inc., 2025) Sözmen, A.B.; Bayraktar, A.E.; Ülker, Ö.; Arslan-Yildiz, A.A sensor detects changes in its environment and converts them into readable data using three key components: a receptor to sense changes, a transducer to generate a signal, and a detection system to output the signal. Optical sensors are devices that use a receptor and optical transducer to produce signals corresponding to an analyte, and optical biosensors combine a biological sensing element with an optical transducer to detect and quantify specific analytes. They offer easy-to-read, real-time signals, such as color changes or light emission, sometimes even detectable by the naked eye, reducing the need for external devices and providing versatile Point-of-Care (PoC) applicability. Their portability and rapid response time enable remote testing and monitoring, further improving accessibility. They allow sensitive and selective detection of various analytes, making them utile in areas like glucose monitoring, drug testing, and pathogen detection. Many of these sensors provide label-free and non-invasive detection, further enhancing patient comfort and safety. This chapter provides an overview of optical biosensors; it starts with categorizing them by biorecognition elements, transducers, and detection modes. It investigates biosensors that utilize nanomaterials, polymers, and engineered biorecognition elements are discussed, with examples from literature. Technologies such as miniaturization, multiplexing, and wearable designs, which enhance PoC feasibility, are also examined. Lastly, challenges in development and operation are addressed, and future research directions for advancing optical biosensors in PoC diagnostics are discussed. © 2025Book Part Toward Accurate in Silico Prediction of Antigen Binding Affinities for Antibody Engineering(Academic Press Inc., 2025) Uluçay, T.; Arslan, M.; Döşeme, H.; Kalyoncu, S.; Kale, S.In clinical applications and life sciences research, antibodies represent an important diagnostic and therapeutic potential thanks to their high target affinity, specificity, and broad developability. While the antigen affinity, one of the primary success assessors of an antibody, can be measured at reasonably high precision and reliability, the scalability of the measurements can be cumbersome and limited. This is troubling because the affinity must be monitored throughout all steps of the developability approaches such as affinity maturation and humanization of an antibody. In this context, in silico approaches present a lucrative opportunity at a fraction of the cost and time typically invested in a comparable wet lab undertaking. In addition to their high-throughput potential, in silico approaches can provide an invaluable side product, i.e., identifying the molecular driving forces behind affinity. Here, we investigated the performance of six different high-throughput servers in two settings common in antibody engineering applications: (i) de novo prediction of the experimental antibody-antigen binding constants, and (ii) the free energy change in binding due to single point mutations. We find that the accuracy of these tools can be significantly low in the two regimes relevant to antibody development: (i) prediction of high-affinity binding, and (ii) prediction of favorable mutations. These issues are intricately related to the training sets used in the underlying models of these tools where high-affinity complexes and favorable point mutations are typically underrepresented. We showed that biophysical characteristics of single point mutations, especially changes in bulkiness and hydrophobicity, increase the prediction error. We argue that while the prediction of mutational impact can be predicted within one kcal per mol using re-parameterized versions of the present in silico tools, the de novo prediction of the affinity likely requires revisiting the underlying physical models behind these tools. © 2025Article Citation - WoS: 1Citation - Scopus: 1Lithium Treatment Rescues Dysfunctional Autophagy in the Cell Models of Tay-Sachs Disease(Academic Press Inc., 2024) Basirli,H.; Can,M.; Sengul,T.; Seyrantepe,V.Tay-Sachs disease is a rare lysosomal storage disorder (LSD) caused by a mutation in the HexA gene coding β-hexosaminidase A enzyme. The disruption of the HexA gene causes the accumulation of GM2 ganglioside resulting in progressive neurodegeneration in humans. Surprisingly, Hexa−/− mice did not show neurological phenotypes. Our group recently generated a murine model of Tay-Sachs disease exhibiting excessive GM2 accumulation and severe neuropathological abnormalities mimicking Tay-Sachs patients. Previously, we reported impaired autophagic flux in the brain of Hexa/-Neu3−/− mice. However, regulation of autophagic flux using inducers has not been clarified in Tay-Sachs disease cells. Here, we evaluated the effects of lithium treatment on dysfunctional autophagic flux using LC3 and p62 in the fibroblast and neuroglia of Hexa−/-Neu3−/− mice and Tay-Sachs patients. We discovered the clearance of accumulating autophagosomes, aggregate-prone metabolites, and GM2 ganglioside under lithium-induced conditions. Our data suggest that targeting autophagic flux with an autophagy inducer might be a rational therapeutic strategy for the treatment of Tay-Sachs disease. © 2024 Elsevier Inc.Article Citation - WoS: 6Citation - Scopus: 6Biomolecular Fingerprints of the Effect of Zoledronic Acid on Prostate Cancer Stem Cells: Comparison of 2d and 3d Cell Culture Models(Academic Press Inc., 2024) Güler,G.; Acikgoz,E.; Mukhtarova,G.; Oktem,G.Revealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research. © 2024 Elsevier Inc.Article Citation - WoS: 5Citation - Scopus: 9Antilisterial Effects of Lysozyme-Nisin Combination at Temperature and Ph Ranges Optimal for Lysozyme Activity: Test of Key Findings To Inactivate Listeria in Raw Milk(Academic Press Inc., 2021) Sözbilen, Gözde Seval; Yemenicioğlu, AhmetThis study aimed to determine antilisterial potential of lysozyme (LYS)-nisin (NIS) combination at temperatures and pHs optimal for LYS activity. Tests in buffers at pH 4.5 and 6.0 showed that heating at 50 or 60 °C combined with LYS-NIS caused higher Listeria innocua inactivation (- 6.2 to >6.6 log) than heating alone (- 0.05 to 5.5 log), or heating combined with LYS (- 4.34 to 6.0 log) or NIS (3.9 to >6.6). The antimicrobial performance of LYS-NIS in buffer at 50 °C was not pH-dependant (5.8–5.9 logs) while heating at 60 °C with LYS-NIS at pH 6.0 (>6.6 logs) caused higher Listeria reduction than that at pH 4.5 (5.7 logs). Heating at 50 °C for 45 min alone or in combination with LYS-NIS caused 0 and 5.5 logs Listeria reduction in milk, respectively. In contrast, Listeria inactivation in milk at 60 °C occurred mainly by heat (5.5 logs) with limited contribution of LYS and/or NIS. Milk heated at 50 °C maintained 73% of NIS and 63% of LYS activity. Application of LYS-NIS at 50 °C provides an opportunity to improve milk safety with less destruction of milk enzyme and microbial flora necessary to obtain desired ripening periods, and aroma and flavour in traditional cheeses. © 2020 Elsevier LtdArticle Citation - WoS: 26Citation - Scopus: 26Multi-Route - Multi-Pathway Exposure To Trihalomethanes and Associated Cumulative Health Risks With Response and Dose Addition(Academic Press Inc., 2019) Genişoğlu, Mesut; Ergi Kaytmaz, Ceyda; Sofuoğlu, Sait CemilCumulative health risk estimation for exposure to mixtures is a current issue, which would present a useful tool for environmental and public health management. Cumulative risks were estimated with response and dose addition methods for individual multi-route - multi-pathway exposure to trihalomethanes and associated carcinogenic toxic risks in Izmir, Turkey. Exposure levels were estimated for ingestion, dermal, and inhalation routes using measured tap water and bottled water THM concentrations. Drinking, showering, hand and dish washing were the considered pathways. THM concentrations in air during the showering were modeled with two-resistance theory using tap water concentration data. The estimated carcinogenic risk levels for ingestion route were in the range of safe (< 10(-6)) to low priority (< 10(-4)), for dermal route all were in the safe zone (< 10(-6)), and for inhalation route were in the range of safe to high priority (> 10(-4)) zones, indicating ingestion and inhalation routes were of similar significance ahead of dermal exposure. Cumulative carcinogenic risks of THM compounds were estimated using simple (response) addition and dose addition using cumulative relative potency factor (CRPF) methods. CRPF method estimated the risks at lower levels compared to the simple addition, which originated from the use two different risk factor values for the index chemical in the method. Cumulative chronic-toxic risks were also assessed, rendering below the threshold risk levels for all routes. This study showed that multi-route - multi-pathway exposure assessment and cumulative risk assessment should together be considered for better environmental and public health management.