Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Citation - Scopus: 3Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform(Elsevier, 2024) Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, AhuPlasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)Article Citation - WoS: 9Citation - Scopus: 9Fabrication and Development of a Microfluidic Paper-Based Immunosorbent Assay Platform (μpisa) for Colorimetric Detection of Hepatitis C(Royal Society of Chemistry, 2023) Özefe, Fatih; Arslan Yıldız, AhuPaper-based microfluidics is an emerging analysis tool used in various applications, especially in point-of-care (PoC) diagnostic applications, due to its advantages over other types of microfluidic devices in terms of simplicity in both production and operation, cost-effectiveness, rapid response time, low sample consumption, biocompatibility, and ease of disposal. Recently, various techniques have been developed and utilized for the fabrication of paper-based microfluidics, such as photolithography, micro-embossing, wax and PDMS printing, etc. In this study, we offer a fabrication methodology for a microfluidic paper-based immunosorbent assay (μPISA) platform and the detection of Hepatitis C Virus (HCV) was carried out to validate this platform. A laser ablation technique was utilized to form hydrophobic barriers easily and rapidly, which was the major advantage of the developed fabrication methodology. The characterization of the μPISA platform was performed in terms of micro-channel properties using bright-field (BF) microscopy, and surface properties using scanning electron microscopy (SEM). At the same time, sample volume and liquid handling capacity were analyzed quantitatively. Ablation speed (S) and laser power (P) were optimized, and it was shown that one combination (10P60S) provided minimal deviation in micro-channel dimensions and prevented deterioration of hydrophobic barriers. Also, the minimum hydrophobic barrier width, which prevents cross-barrier bleeding, was determined to be 255.92 ± 10.01 μm. Furthermore, colorimetric HCV NS3 detection was implemented to optimize and validate the μPISA platform. Here, HCV NS3 in both PBS and human blood plasma was successfully detected by the naked eye at concentrations as low as 1 ng mL−1 and 10 ng mL−1, respectively. Moreover, the limit of detection (LoD) values for HCV NS3 were acquired as 0.796 ng mL−1 in PBS and 2.203 ng mL−1 in human blood plasma with a turnaround time of 90 min. In comparison with conventional ELISA, highly sensitive and rapid HCV NS3 detection was accomplished colorimetrically on the developed μPISA platform.Article Citation - WoS: 7Citation - Scopus: 7Neo-Clerodanes From Teucrium Divaricatum Subsp. Divaricatum and Their Biological Activity Assessment(Elsevier, 2023) Aydoğan, Fadime; Ali, Zülfiqar; Zülfiqar, Fazila; Karaalp, Canan; Khan, Ikhlas A.; Bedir, ErdalFifteen neo-clerodane diterpenoids (1–15), including two undescribed glycosides, teudivaricosides A (1) and B (2), together with a known iridoid glycoside (16) and a phenylpropanoid glycoside (17) from the whole plant of Teucrium divaricatum subsp. divaricatum were isolated. Their structures were determined by spectral data analysis including 1D and 2D NMR and HRESIMS. Neo-clerodane diterpenoids were evaluated for their anti-inflammatory, and antimicrobial activities. None of them showed significant antimicrobial activity against various bacterial and fungal strains (up to 20 µg/mL). All tested compounds were inactive up to the highest tested concentration of 50 µM on iNOS inhibitory activity.Article Citation - WoS: 3Citation - Scopus: 3Structural and Functional Analyses of Gh51 Alpha-L of Geobacillus Vulcani Gs90 Reveal Crucial Residues for Catalytic Activity and Thermostability(Wiley, 2022) Sürmeli, Yusuf; Şanlı Mohamed, GülşahAlpha-L-arabinofuranosidase (Abf) is of big interest in various industrial areas. Directed evolution is a powerful strategy to identify significant residues underlying Abf properties. Here, six active variants from GH51 Abf of Geobacillus vulcani GS90 (GvAbf) by directed evolution were overproduced, extracted, and analyzed at biochemical and structural levels. According to the activity and thermostability results, the most-active and the least-active variants were found as GvAbf51 and GvAbf52, respectively. GvAbf63 variant was more active than parent GvAbf by 20% and less active than GvAbf51. Also, the highest thermostability belonged to GvAbf52 with 80% residual activity after 1 h. Comparative sequence and structure analyses revealed that GvAbf51 possessed L307S displacement. Thus, this study suggested that L307 residue may be critical for GvAbf activity. GvAbf63 had H30D, Q90H, and L307S displacements, and H30 was covalently bound to E29 catalytic residue. Thus, H30D may decrease the positive effect of L307S on GvAbf63 activity, preventing E29 action. Besides, GvAbf52 possessed S215N, L307S, H473P, and G476C substitutions and S215 was close to E175 (acid–base residue). S215N may partially disrupt E175 action. Overall effect of all substitutions in GvAbf52 may result in the formation of the C–C bond between C171 and C213 by becoming closer to each other.Article Citation - WoS: 1Citation - Scopus: 1Exploring the Heterogeneity of Ige-Mediated Food Allergy Through Latent Class Analysis(S. Karger AG, 2022) Akarsu, Ayşegül; Öksel Karakuş, Ceyda; Ocak, Melike; Oral, Nihan; Bilgi, Eyüp; Şahiner, Ümit Murat; Soyer, Özge; Şekerel, Bülent EnisIntroduction: Food allergy (FA) is a heterogeneous disease with multiple morbidities and a huge burden for patients and healthcare systems. Variable manifestations, comorbidities (atopic dermatitis [AD], asthma, and/or allergic rhinitis [AR]), severity (anaphylaxis), and outcomes suggest the existence of different endotypes that cluster analyses may reveal. In this study, we aimed to investigate distinct subgroups among patients with FAs using data from 524 children/adolescents. Methods: 524 patients with IgE-mediated FA (353 male [67%]; median age 4.4 years [IQR:3.0-6.8]), 354 (68%) had multiple FA. The history of AD, asthma, AR, and anaphylaxis was recorded in 59.4%, 35.5%, 24.2%, and 51.2% of the patients, respectively. Latent class analysis was carried out to distinguish clinical FA phenotypes using five potential markers of allergy severity (single/multiple FA, never/inactive/current asthma and AD, AR, and anaphylaxis). Results: Three distinct phenotypes were identified: (1) multiple FA with eczema and respiratory multimorbidity (42%), (2) multiple FA with persistent eczema (34%), and (3) single FA with respiratory multimorbidity without eczema (24%). Compared with the single FA cluster, the prevalence of AD was significantly higher in multiple FA groups. Cluster 1 had the highest frequency of AR and allergic asthma, and the lowest rate of total tolerance of FA. Discussion: We put forward the hypothesis of underlying pathogenesis according to the clinical phenotypes. While skin barrier defect may play a dominant role in the pathogenesis in Cluster 2, immune dysregulation may be dominant in Cluster 3. In Cluster 1, the most severe group, a combination of both skin barrier defects and immune dysregulation may be responsible for the clinical features.Article Citation - WoS: 25Citation - Scopus: 30Fabrication of 3d Printed Poly(lactic Acid) Strut and Wet-Electrospun Cellulose Nano Fiber Reinforced Chitosan-Collagen Hydrogel Composite Scaffolds for Meniscus Tissue Engineering(SAGE Publications, 2022) Güneş, Oylum Çolpankan; Kara, Aylin; Baysan, Gizem; Hüsemoğlu, Reşit Buğra; Akokay, Pınar; Ziylan Albayrak, Aylin; Ergür, Bekir Uğur; Havitçioğlu, HasanThe main goal of the study was to produce chitosan-collagen hydrogel composite scaffolds consisting of 3D printed poly(lactic acid) (PLA) strut and nanofibrous cellulose for meniscus cartilage tissue engineering. For this purpose, first PLA strut containing microchannels was incorporated into cellulose nanofibers and then they were embedded into chitosan-collagen matrix to obtain micro- and nano-sized topographical features for better cellular activities as well as mechanical properties. All the hydrogel composite scaffolds produced by using three different concentrations of genipin (0.1, 0.3, and 0.5%) had an interconnected microporous structure with a swelling ratio of about 400% and water content values between 77 and 83% which is similar to native cartilage extracellular matrix. The compressive strength of all the hydrogel composite scaffolds was found to be similar (∼32 kPa) and suitable for cartilage tissue engineering applications. Besides, the hydrogel composite scaffold comprising 0.3% (w/v) genipin had the highest tan δ value (0.044) at a frequency of 1 Hz which is around the walking frequency of a person. According to the in vitro analysis, this hydrogel composite scaffold did not show any cytotoxic effect on the rabbit mesenchymal stem cells and enabled cells to attach, proliferate and also migrate through the inner area of the scaffold. In conclusion, the produced hydrogel composite scaffold holds great promise for meniscus tissue engineering.Article Citation - WoS: 6Citation - Scopus: 7Designing Robust Xylan/Chitosan Composite Shells Around Drug-Loaded Msns: Stability in Upper Git and Degradation in the Colon Microbiota(Elsevier, 2023) Zeybek, Nüket; Büyükkileci, Ali Oğuz; Güleç, Şükrü; Polat, Mehmet; Polat, Hürriyetong residence times, near-neutral pH values, and release triggered by the enzymatic action of the resident microbiota offer unique opportunities for improved drug delivery in the colon. The fact that a delivery agent must also pass through the complete GI tract without degradation presents a challenge due to widely changing pH conditions. In this study, a promising colon-targeted drug delivery system was composed of a xylan/chitosan composite shell formed on curcumin-loaded mesoporous silica nanoparticles (MSNs). A novel synthesis approach was employed to facilitate precipitation of negatively charged xylan on negatively charged MSNs by concurrent chitosan polymerization. Curcumin-loaded xylan/chitosan-coated MSNs (C-MSNs) were determined to contain nearly 42% xylan by the inclusion of chitosan in a one-to-one ratio with xylan. The xylan/chitosan composite shell demonstrated excellent stability in the acidic upper GI tract. The hydrolysis of glycosidic bonds by resident microbiota was the triggering mechanism for xylan degradation and curcumin release in the colon. The presence of xylan has the further benefit of increasing the number of beneficial bacteria and improving short-chain fatty acid production for improved colon health.Article Citation - WoS: 17Citation - Scopus: 18Development of a Hydrocolloid Bio-Ink for 3d Bioprinting(Royal Society of Chemistry, 2022) Yıldırım, Özüm; Arslan Yıldız, AhuA new generation of bio-inks that are soft, viscous enough, stable in cell culture, and printable at low printing pressures is required in the current state of 3D bioprinting technology. Hydrogels can meet these features and can mimic the microenvironment of soft tissues easily. Hydrocolloids are a group of hydrogels which have a suitable gelling capacity and rheological properties. According to the literature, polysaccharide-based hydrocolloids are used in the food industry, wound healing technologies, and tissue engineering. Quince seed hydrocolloids (QSHs), which consist of mostly glucuronoxylan, can easily be obtained from quince seeds by water extraction. In this study, the use of a QSH as a bio-ink was investigated. The suitability of QSH for the printing process was assessed by rheological, uniformity and pore factor analyses. Appropriate printing parameters were determined and the characterization of the bioprinted QSHs was performed by SEM analysis, water uptake capacity measurement, and protein adsorption assay. The bioprinted QSHs had excellent water uptake capacity and showed suitable protein adsorption behaviour. Analyses of the biocompatibility and cellular viability of bioprinted QSHs were conducted using NIH-3T3 fibroblast cells and the results were found to be high during short and long-term cell culture periods. It was proved that QSH is a highly promising bio-ink for 3D bioprinting and further tissue engineering applications.Article Citation - WoS: 8Citation - Scopus: 9Neuroprotective Metabolites Via Fungal Biotransformation of a Novel Sapogenin, Cyclocephagenol(Nature Research, 2022) Küçüksolak, Melis; Üner, Göklem; Ballar Kırmızıbayrak, Petek; Bedir, ErdalCyclocephagenol (1), a novel cycloartane-type sapogenin with tetrahydropyran unit, is only encountered in Astragalus species. This rare sapogenin has never been a topic of biological activity or modification studies. The objectives of this study were; (i) to perform microbial transformation studies on cyclocephagenol (1) using Astragalus endophyte, Alternaria eureka 1E1BL1, followed by isolation and structural characterization of the metabolites; (ii) to investigate neuroprotective activities of the metabolites; (iii) to understand structure–activity relationships towards neuroprotection. The microbial transformation of cyclocephagenol (1) using Alternaria eureka resulted in the production of twenty-one (2–22) previously undescribed metabolites. Oxidation, monooxygenation, dehydration, methyl migration, epoxidation, and ring expansion reactions were observed on the triterpenoid skeleton. Structures of the compounds were established by 1D-, 2D-NMR, and HR-MS analyses. The neuroprotective activities of metabolites and parent compound (1) were evaluated against H2O2-induced cell injury. The structure–activity relationship (SAR) was established, and the results revealed that 1 and several other metabolites had potent neuroprotective activity. Further studies revealed that selected compounds reduced the amount of ROS and preserved the integrity of the mitochondrial membrane. This is the first report of microbial transformation of cyclocephagenol.Article Citation - WoS: 4Citation - Scopus: 6Rational Design of Thermophilic Cyp119 for Progesterone Hydroxylation by in Silico Mutagenesis and Docking Screening(Elsevier, 2023) Kestevur Doğru, Ekin; Güralp, Gülce; Uyar, Arzu; Sürmeli, Nur BaşakSteroid-based chemicals can affect the metabolism, immune functions, and development of sexual characteristics. Because of these effects, steroid derivatives are widely used in the pharmaceutical industry. Progesterone is a steroid-based hormone that mainly controls the ovulation period of women but is also a precursor molecule for the synthesis of important hormones like testosterone and cortisone. Cytochrome P450 (CYP) enzymes are important for the production of hydroxyprogesterones in the industry since they can catalyze regio- and enantioselective hydroxylation reactions. Although human CYP enzymes can catalyze hydroxyprogesterone synthesis with high selectivity, these enzymes are membrane bound, which limits their application for industrial production. CYP119 is a soluble and thermophilic enzyme from the archaea Sulfolobus acidocaldarius. Even though the native substrate of the enzyme is not known, CYP119 can catalyze styrene epoxidation, lauric acid hydroxylation, and Amplex®Red peroxidation. In this work, an in silico mutagenesis approach was used to design CYP119 mutants with high progesterone affinity. Energy scores of progesterone docking simulations were used for the design and elimination of single, double, and triple mutants of CYP119. Among designed 674 mutants, five of them match the criteria for progesterone hydroxylation. The most common mutation of these five mutants, L69G mutant was analyzed using independent molecular dynamics (MD) simulations in comparison with the wild-type (WT) enzyme. L69G CYP119, was expressed and isolated from Escherichia coli; it showed 800-fold higher affinity for progesterone compared to WT CYP119. L69G CYP119 also catalyzed progesterone hydroxylation. The novel designed enzyme L69G CYP119 is a potential versatile biocatalyst for progesterone hydroxylation that is expected to be stable under industrial production conditions.