PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 21Citation - Scopus: 23Engineering of Xylanases for the Development of Biotechnologically Important Characteristics(Wiley, 2023) Sürmeli, Yusuf; Şanlı Mohamed, GülşahXylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.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: 2Citation - Scopus: 2High-Throughput Analysis of Tetragonal Transition Metal Xenes(Royal Society of Chemistry, 2022) Šabani, Denis; Milošević, Milorad V.; Yorulmaz, Uğur; Yağmurcukardeş, Mehmet; Sevik, CemWe report a high-throughput first-principles characterization of the structural, mechanical, electronic, and vibrational properties of tetragonal single-layer transition metal Xenes (t-TMXs). Our calculations revealed 22 dynamically, mechanically and chemically stable structures among the 96 possible free-standing layers present in the t-TMX family. As a fingerprint for their structural identification, we identified four characteristic Raman active phonon modes, namely three in-plane and one out-of-plane optical branches, with various intensities and frequencies depending on the material in question. Spin-polarized electronic calculations demonstrated that anti-ferromagnetic (AFM) metals, ferromagnetic (FM) metals, AFM semiconductors, and non-magnetic semiconductor materials exist within this family, evidencing the potential of t-TMXs for further use in multifunctional heterostructures.Article Citation - WoS: 6Citation - Scopus: 8Intervention for Hepatic and Pulmonary Metastases in Breast Cancer Patients: Prospective, Multi-Institutional Registry Study-Imet, Protocol Mf 14-02(Springer, 2022) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, Lütfi; Şenol, Kazım; Dağ, Ahmet; Karanlık, Hasan; Aytaç, Özgür; Karadeniz Çakmak, Güldeniz; Dalcı, Kubilay; Doğan, Mutlu; Sezer, Atakan Y.; Gökgöz, Şehsuvar; Özyar, Enis; Sezgin, EfeBackground: One fourth of early-stage breast cancer cases become metastatic during the follow-up period. Limited metastasis is a metastatic disease condition in which the number of metastatic sites and the extent of the disease both are limited, and the disease is amenable to metastatic intervention. This prospective study aimed to evaluate intervention for limited metastases in the lung, liver, or both. Methods: The study enrolled luminal A/B and/or human epidermal growth factor receptor 2 (HER2)-neu+ patients with operable lung and/or liver metastases in the follow-up assessment after completion of primary breast cancer treatment and patients with a diagnosis of metastasis after 2014. Demographic, clinical, tumor-specific, and metastasis detection-free interval (MDFI) data were collected. Bone metastasis in addition to lung and liver metastases also was included in the analysis. The patients were divided into two groups according to the method of treatment for metastases: systemic therapy alone (ST) group or intervention (IT) group.Article Citation - WoS: 7Citation - Scopus: 7Connexin 32 Overexpression Increases Proliferation, Reduces Gap Junctional Intercellular Communication, Motility and Epithelial-To Transition in Hs578t Breast Cancer Cells(Springer, 2022) Uğur, Deniz; Güngül, Taha Buğra; Yücel, Simge; Özçivici, Engin; Yalçın Özuysal, Özden; Meşe Özçivici, GülistanConnexins (Cx) are primary components of gap junctions that selectively allow molecules to be exchanged between adjacent cells, regulating multiple cellular functions. Along with their channel forming functions, connexins play a variety of roles in different stages of tumorigenesis and their roles in tumor initiation and progression is isoform- and tissue-specific. While Cx26 and Cx43 were downregulated during breast tumorigenesis, Cx32 was accumulated in the cytoplasm of the cells in lymph node metastasis of breast cancers and Cx32 was further upregulated in metastasis. Cx32's effect on cell proliferation, gap junctional communication, hemichannel activity, cellular motility and epithelial-to-mesenchymal transition (EMT) were investigated by overexpressing Cx32 in Hs578T and MCF7 breast cancer cells. Additionally, the expression and localization of Cx26 and Cx43 upon Cx32 overexpression were examined by Western blot and immunostaining experiments, respectively. We observed that MCF7 cells had endogenous Cx32 while Hs578T cells did not and when Cx32 was overexpressed in these cells, it caused a significant increase in the percentages of Hs578T cells at the S phase in addition to increasing their proliferation. Further, while Cx32 overexpression did not induce hemichannel activity in either cell, it decreased gap junctional communication between Hs578T cells. Additionally, Cx32 was mainly observed in the cytoplasm in both cells, where it did not form gap junction plaques but Cx32 overexpression reduced Cx43 levels without affecting Cx26. Moreover, migration and invasion potentials of Hs578T and migration in MCF7 were reduced upon Cx32 overexpression. Finally, the protein level of mesenchymal marker N-cadherin decreased while epithelial marker ZO-1 and E-cadherin increased in Hs578T cells. We observed that Cx32 overexpression altered cell proliferation, communication, migration and EMT in Hs578T, suggesting a tumor suppressor role in these cells while it had minor effects on MCF7 cells.Article Citation - WoS: 1Citation - Scopus: 1Investigating Triple Superphosphate for Lead Removal From Aqueous Solutions(Taylor & Francis, 2022) Souley Garba, Mahamane Chapiou; Kaya, Erol; Gökelma, Mertol; Seyrankaya, AbdullahThe aim of this research is to investigate monocalcium phosphate monohydrate [Ca(H2PO4)2. H2O] also called triple superphosphate (TSP) for the removal of lead (Pb) from aqueous solutions. In this study, TSP was selected amongst various phosphate-based materials and fertilizers to act as the source of orthophosphate (PO43-) which is a powerful tool for metal fixation in soil and water. Thermodynamic equilibrium dissolution-precipitation relationships for the systems of Pb-H2O and Pb-PO43--H2O were drawn with the aid of Eh-pH stability diagrams to determine the predominance areas of different species. The lead phosphate compounds, identified through the stability area diagrams, were verified with the batch precipitation tests performed with standard solutions of lead and TSP at different conditions. It was observed that, depending upon solution conditions, TSP can precipitate 99.9% of the lead from the solution. Lead precipitates, analyzed by x-ray diffraction, showed the formation of lead phosphate compounds. The mechanism of TSP for the removal of lead from aqueous solutions is discussed.Article Generating Plan Layouts: a Case Study on Visualization of Implicit Knowledge by “doctor Architects”(SAGE Publications, 2022) Kasalı, AltuğAim: This article presents an opportunistic case with particular focus on instances from an extended procurement operation in which medical professionals run a proactive process involving the generation of layouts through distinct modes of representational practices without any actual collaboration with designers. The questions of inquiry involve an analysis on how the visualizations came into being and a discussion into the content of drawings that was shaped by individuals without any formal design education. Background: Although the literature introduces examples of genuine participation, particularly in healthcare design practices, the instances in which nondesigners demonstrate accomplished skills in spatial reasoning and representation are limited. Method: The research was formulated as a qualitative case study including a series of observations of the activities of the participants followed by interviews recorded at different locations. The investigation also focuses on the features of these authentic graphics which illustrate the intentions of the medical professionals concerning the function of spaces. Results: In this research, the participants went through a labor intensive and elaborate effort to produce “architectural representations” with the intention to convey their implicit professional expertise in the domain. The layouts were introduced to be the vital elements to visualize the implicit knowledge regarding the functioning of space. Conclusions: The productive and creative engagement of clinicians within this research makes the case for a multidisciplinary approach that reframes the limits and potential contributions of participants alongside drawings, which are exclusively claimed by and strategically employed by architects as negotiation devices within participatory design processes.Article Citation - WoS: 4Citation - Scopus: 3Hg(ii)-Mediated Intramolecular Cyclization of Alkynyl Hydrazones: Towards a New Reaction-Based Sensing Approach for Hg(ii) Ions(Wiley, 2022) Tütüncü, Büşra Buse; Cebeci, Miray; Emrullahoğlu, MustafaDrawing upon an intramolecular cyclization/annulation reaction sequence mediated by Hg2+ ions, a BODIPY-based fluorescent probe decorated with an alkynyl hydrazone motif responds rapidly and selectively to Hg2+ ions, with a detection limit of 29 nM and a fluorescence turn-on ratio of 15-fold. With the addition of Hg2+ ions, the BODIPY-based alkynyl hydrazone transforms into a pyrazole ring to mediate a turn-on emission response clearly observable to the naked eye under visible light excitation.Article Citation - WoS: 8Citation - Scopus: 8Association Analysis of Germination Level Cold Stress Tolerance and Candidate Gene Identification in Upland Cotton (gossypium Hirsutum L.)(Springer, 2022) Akköse Baytar, Asena; Peynircioğlu, Ceng; Sezener, Volkan; Frary, Anne; Doğanlar, SamiCotton originated from ancestors in the Gossypium genus that grew in semi-desert habitats. As a result, it is adversely affected by low temperatures especially during germination and the first weeks of growth. Despite this, there are relatively few molecular studies on cold stress in cotton. This limitation may present a future breeding handicap, as recent years have witnessed increased low temperature damage to cotton production. Cold tolerance is a sustainable approach to obtain good production in case of extreme cold. In the present study, 110 Upland cotton (Gossypium hirsutum) genotypes were evaluated for cold tolerance at the germination stage. We identified vigorous genotypes with cold-related parameters that outperformed the panel’s average performance (x¯ = 76.9% CG, 83.9% CSI, 167.5 CWVI). Molecular genetic diversity analysis with 101 simple sequence repeat (SSR) markers yielding 416 loci was used to select tolerant genotypes that could be important materials for breeding this trait. A total of 16 marker-cold tolerance trait associations (p < 0.005) were identified with 10 of them having major effects (PVE > 10%). Based on the positions of these markers, candidate genes for cold tolerance in the G. hirsutum genome were identified. Three of these markers (BNL0569, CIR081 and CIR202) are important candidates for use in marker-assisted breeding for cold tolerance because they mapped to genes previously associated with cold tolerance in other plant species such as Arabidopsis thaliana, rice and tomato.Article Citation - WoS: 7Citation - Scopus: 7Synthesis and Characterization of Single-Walled Carbon Nanotube: Cyto-Genotoxicity in Allium Cepa Root Tips and Molecular Docking Studies(Wiley, 2022) İnce Yardımcı, Atike; İstifli, Erman Salih; Açıkbaş, Yaser; Liman, Recep; Yağmurcukardeş, Nesli; Yılmaz, Selahattin; Ciğerci, İbrahim HakkıHerein, single-walled carbon nanotubes (SWCNTs) were synthesized by the thermal chemical vapor deposition (CVD) method, and characterized by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDX), transmission electron microscopy (TEM), Raman spectroscopy, dynamic light scattering (DLS), and thermo-gravimetric analysis (TGA). The results indicated that obtained nanotubes were SWCNTs with high crystallinity and their average diameter was 10.15 ± 3 nm. Allium cepa ana–telophase and comet assays on the root meristem were employed to evaluate the cytotoxic and genotoxic effects of SWCNTs by examining mitotic phases, mitotic index (MI), chromosomal aberrations (CAs), and DNA damage. A. cepa root tip cells were exposed to SWCNTs at concentrations of 12.5, 25, 50, and 100 μg/ml for 4 h. Distilled water and methyl methanesulfonate (MMS, 10 μg/ml) were used as the negative and positive control groups, respectively. It was observed that MIs decreased statistically significantly for all applied doses. Besides, CAs such as chromosome laggards, disturbed anaphase–telophase, stickiness and bridges and also DNA damage increased in the presence of SWCNTs in a concentration-dependent manner. In the molecular docking study, the SWCNT were found to be a strong DNA major groove binder showing an energetically very favorable binding free energy of −21.27 kcal/mol. Furthermore, the SWCNT interacted effectively with the nucleotides on both strands of DNA primarily via hydrophobic π and electrostatic interactions. As a result, cytotoxic and genotoxic effects of SWCNTs in A. cepa root meristematic cells which is a reliable system for assessment of nanoparticle toxicology were demonstrated in this study.