Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Review Citation - WoS: 30Citation - Scopus: 33Molecular Separation by Using Active and Passive Microfluidic Chip Designs: a Comprehensive Review(Wiley, 2023) Ebrahimi, Aliakbar; Didarian, Reza; Shih, Chih-Hsin; Nasseri, Behzad; Ethan Li, Yi-Chen; Shih, Steven; İçöz, Kutay; Tarım, Ergün Alperay; Akpek, Ali; Çeçen, Berivan; Bal Öztürk, Ayça; Güleç, Kadri; Tarım, Burcu Sırma; Tekin, Hüseyin CumhurSeparation and identification of molecules and biomolecules such as nucleic acids, proteins, and polysaccharides from complex fluids are known to be important due to unmet needs in various applications. Generally, many different separation techniques, including chromatography, electrophoresis, and magnetophoresis, have been developed to identify the target molecules precisely. However, these techniques are expensive and time consuming. “Lab-on-a-chip” systems with low cost per device, quick analysis capabilities, and minimal sample consumption seem to be ideal candidates for separating particles, cells, blood samples, and molecules. From this perspective, different microfluidic-based techniques have been extensively developed in the past two decades to separate samples with different origins. In this review, “lab-on-a-chip” methods by passive, active, and hybrid approaches for the separation of biomolecules developed in the past decade are comprehensively discussed. Due to the wide variety in the field, it will be impossible to cover every facet of the subject. Therefore, this review paper covers passive and active methods generally used for biomolecule separation. Then, an investigation of the combined sophisticated methods is highlighted. The spotlight also will be shined on the elegance of separation successes in recent years, and the remainder of the article explores how these permit the development of novel techniques. © 2023 The Authors. Advanced Materials Interfaces published by Wiley-VCH GmbH.Article Citation - WoS: 17Citation - Scopus: 18Four Subtypes of Childhood Allergic Rhinitis Identified by Latent Class Analysis(Wiley, 2021) Yavuz, Süleyman Tolga; Öksel Karakuş, Ceyda; Custovic, Adnan; Kalaycı, ÖmerBackground Childhood allergic rhinitis (AR) is clinically heterogenous. We aimed to identify distinct phenotypes among children with AR using data-driven techniques and to ascertain their association with patterns of symptoms, allergic sensitization, and comorbidities. Methods We recruited 510 children with physician-diagnosed AR, of whom 205 (40%) had asthma. Latent class analysis (LCA) was performed to identify latent structure within the data set using 17 variables (allergic conjunctivitis, eczema, asthma, family history of asthma, family history of allergic rhinitis, skin sensitization to 8 common allergens, tonsillectomy, adenoidectomy). Results A four-class solution was selected as the optimal model based on statistical fit. We labeled latent classes as: (1) AR with grass mono-sensitization and conjunctivitis (n = 361, 70.8%); (2) AR with house dust mite sensitization and asthma (n = 75, 14.7%); (3) AR with pet and grass polysensitization and conjunctivitis (n = 35, 6.9%); and (4) AR among children with tonsils and adenoids removed (n = 39, 7.6%). Perennial AR was significantly more common among children in Class 2 (OR 5.83, 95% CI 3.42-9.94, p < .001) and Class 3 (OR 2.88, 95% CI 1.36-6.13, p = .006). Mild and intermittent AR symptoms were significantly more common in children in Class 2 compared to those in Class 1. AR was more severe in Class 1 compared to other 3 classes, indicating that upper respiratory symptoms are more severe among children with isolated seasonal rhinitis, than in those with rhinitis and coexisting asthma. Conclusion We have identified 4 phenotypes in school-age children with AR, which were associated with different patterns of clinical symptoms and comorbidities.Article Citation - WoS: 16Citation - Scopus: 18A Novel Thermostable Xylanase From Geobacillus Vulcani Gs90: Production, Biochemical Characterization, and Its Comparative Application in Fruit Juice Enrichment(Wiley, 2021) Algan, Müge; Sürmeli, Yusuf; Şanlı Mohamed, GülşahXylanases have great attention to act as a potential role in agro-industrial processes. In this study, production, characterization, and fruit juice application of novel xylanase from thermophilic Geobacillus vulcani GS90 (GvXyl) were performed. GvXyl was purified via acetone precipitation and gel-filtration chromatography. The results showed that GvXyl had 1,671.4 U/mg of specific activity and optimally worked at pH 8 and 55 degrees C. It was also active in a wide pH (3-9) and temperature (30-90oC) ranges. GvXyl was highly stable at 90oC and relatively stable at pH 3-9. The kinetic parameters of GvXyl were obtained as K-m, V-max, and k(cat); 10.2 mg/ml, 4,104 mu mol min(-1) mg(-1), and 3,542.6 s(-1), respectively. GvXyl had higher action than commercial xylanase in fruit juice enrichment. These results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability. Practical applications Polysaccharides include starch, pectin, and hemicellulose create problems by lowering fruit juice quality in beverages. To overcome this problem, various clarification processes might be applied to natural fruit juices. Even though chemicals are widely used for this purpose, recently enzymes including xylanases are preferred for obtaining high-quality products. In this study, we reported the production and biochemical characterization of novel thermostable xylanase from thermophilic G. vulcani GS90 (GvXyl). Also, apple and orange juice enrichment were performed with the novel xylanase to increase the quality in terms of yield, clarity, and reducing sugar substance. The improved quality features of apple and orange juices with GvXyl was then compared to commercially available beta-1,4-xylanase. The results revealed that GvXyl might possess a potential influence in fruit juice processing because of its high specific activity and great thermal stability.Conference Object Investigation of Antimicrobial Activity To Determine Mic Value of Cinnamon Bark Oil Against Helicobacter Pylori(Wiley, 2014) Güneş, Seda; Becerikli, T.; Tıhmınlıoğlu, Funda; Yılmaz, Özlem[No abstract available]Conference Object In Vitro Evaluation of Bioactive Chitosan Microspheres for Eradicating Helicobacter Pylori Biofilm(Wiley, 2016) Güneş, Seda; Arslan, Nur; Demiray Gürbüz, Ebru; Tıhmınlıoğlu, Funda; Yılmaz, ÖzlemCertain H. pylori strains can form biofilm both inside and outside human host to protect itself under environmental stress. Biofilm contributes to development of antimicrobial resistance by some kind of mechanisms like providing a barrier for diffusion and allowing resistance gene expression.Conference Object Determination of Biofilm Formation by Helicobacter Pylori(Wiley, 2016) Arslan, Nur; Güneş, Seda; Demiray Gürbüz, Ebru; Tıhmınlıoğlu, Funda; Yılmaz, ÖzlemBackground : Certain H. pylori strains form biofilm in laboratory experiments and also on the surface of gastric mucosa, suggesting possible reason for eradication failure by increasing resistance to antimicrobial agents and transmission. Aim : To examine the mature biofilm formation by H. pylori NCTC11637 standard strain in different incubation periods for H. pylori biofilm characterization.Article Citation - WoS: 5Citation - Scopus: 4Monitoring Neutropenia for Cancer Patients at the Point of Care(Wiley, 2017) İnan, Hakan; Kingsley, James L.; Özen, Mehmet O.; Tekin, Hüseyin Cumhur; Hoerner, Christian R.; Imae, Yoriko; Demirci, UtkanNeutrophils have a critical role in regulating the immune system. The immune system is compromised during chemotherapy, increasing infection risks and imposing a need for regular monitoring of neutrophil counts. Although commercial hematology analyzers are currently used in clinical practice for neutrophil counts, they are only available in clinics and hospitals, use large blood volumes, and are not available at the point of care (POC). Additionally, phlebotomy and blood processing require trained personnel, where patients are often admitted to hospitals when the infections are at late stage due to lack of frequent monitoring. Here, a reliable method is presented that selectively captures and quantifies white blood cells (WBCs) and neutrophils from a finger prick volume of whole blood by integrating microfluidics with high-resolution imaging algorithms. The platform is compact, portable, and easy to use. It captures and quantifies WBCs and neutrophils with high efficiency (> 95%) and specificity (> 95%) with an overall 4.2% bias compared to standard testing. The results from a small cohort of patients (N = 11 healthy, N = 5 lung and kidney cancer) present a unique disposable cell counter, demonstrating the ability of this tool to monitor neutrophil and WBC counts within clinical or in resource-constrained environments.