02. Fen Fakültesi / Faculty of Science

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Citation - WoS: 3
Citation - Scopus: 4
1,2-Diboranes With Strong Donor Substitutes: Synthesis, Ovicidal and Larvicidal Effect on Important Vector Species
(Elsevier, 2024) Bursali, Fatma; Sahin, Yueksel; Aygun, Muhittin; Sevincek, Resul; Biyik, H. Halil; Özgener, Hüseyin; Gurbuz, Burcin
Novel control products are needed in the control of important insects like mosquitoes which are developing resistance to insecticides and larvicides currently in the market. Boron compounds have been demonstrated to exhibit antibacterial and anticancer effects. 1,2-diboranes with a long history and importance in boron chemistry have been described. These compounds are synthesized from reactions of 1,2-dichlordiborane derivatives with lidium amides (ArNHLi/Et2NLi, etc.). In addition to the three previously synthesized diborane compounds, five novel 1,2-diborane compounds were synthesized in good yield using the same method for the first time. The structures of the novel derivatives were characterized by nuclear magnetic resonance spectroscopy, and the molecular structure of one of them (2a) was also demonstrated using single crystal X-ray diffraction. In this preliminary study, the ovicidal and larvicidal effects of new 1,2-diamino-1,2-diborane derivatives against Aedes aegypti and Aedes albopictus eggs and larvae were investigated for the first time. Of these, 2a and 2e showed the highest ovicidal activity against both species, while 7, 4 and 2d showed particularly high larvicidal activity. Some 1,2-diborane derivatives were found to be significantly toxic, with LC50 values ranging from 14,930 to 27,975 mu g/mL. Some derivatives (6, 2a, 2c) were less effective against mosquito larvae. 1,2-Diborane derivatives have high ovicidal and larvicidal effects on mosquitoes and are therefore potential candidates for the development of new larvicides. Further studies are needed to evaluate its mode of action and safety. Understanding their mode of action against mosquito development is crucial to optimizing their use and reducing the potential development of resistance. Their potential effects on other mosquito species and non -target organisms need to be investigated.
Citation - WoS: 6
Citation - Scopus: 7
1,2-Diborolanes With Strong Donor Substituents: Synthesis and High Antimicrobial Activity
(Academic Press, 2021) Şahin, Yüksel; Poyrazoğlu Çoban, Esin; Sevinçek, Resul; Bıyık, Halil H.; Özgener, Hüseyin; Aygün, Muhittin
1,2-diborolanes with strong and without strong donor substituents have been described, and are also referred to as 1,2-diboracyclopentane. The 1,2-diaryl/alkyl-amino-1,2-diboracyclopentanes 2, 3, and 4 were obtained in good yield after the reaction of 1,2-dichloro-1,2-diboracyclopentane 1 with ArNHLi and Me3Si-NR2. The structures of these new derivatives were characterized by nuclear magnetic resonance spectroscopy. The molecular structures of 2b, 2c, 2e, 4, and 5f were also determined by single-crystal X-ray diffraction. The newly synthesized 1,2-borolanes are stable in air and showed particularly high activity against some Gram-positive bacteria. © 2020 Elsevier Inc.
Citation - WoS: 2
Citation - Scopus: 3
1-Octanol Is a Functional Impurity Modifying Particle Size and Photophysical Properties of Colloidal Zncdsse/Zns Nanocrystals
(American Chemical Society, 2021) Sevim Ünlütürk, Seçil; Çağır, Ali; Varlıklı, Canan; Özçelik, Serdar
Impurities in trioctylphophine (TOP) strongly affect nanocrystal synthesis. 1-Octanol among other contaminants in TOP is identified for the first time as a functional impurity by H-1 NMR. The deliberate addition of 1-octanol into trioctylphosphine reduced particle size and modified photophysical properties of ZnCdSSe/ZnS colloidal nanocrystals. NMR analysis furthermore revealed that 1-octanol is bonded to the nanocrystal surfaces. The ratio of integrals for the O-CH2 protons of 1-octanol, which is the lowest compared to the other ligands, suggests that 1-octanol plays a critical role to tune the particle size of nanocrystals. The increased amount of 1-octanol added into TOP reduces the particle size from 9.8 to 7.2 nm, causing a progressive blue shift in the UV-vis and PL spectra but leaving the alloy composition unaffected. The rate of nonradiative processes is enhanced with the amount of 1-octanol added into TOP, correlating with higher dislocation density observed in the nanocrystals. As a conclusion, 1-octanol is proposed as a functional impurity that varies particle size and nonradiative photophysical processes in the ZnCdSSe/ZnS colloidal nanocrystals.
Citation - Scopus: 4
44 Current Challenges in Mirnomics
(Humana Press, 2022) Akgül, Bünyamin; Stadler, Peter F.; Hawkins, Liam J.; Hadj-Moussa, Hanane; Storey, Kenneth B.; Ergin, Kemal; Allmer, Jens
Mature microRNAs (miRNAs) are short RNA sequences about 18–24 nucleotide long, which provide the recognition key within RISC for the posttranscriptional regulation of target RNAs. Considering the canonical pathway, mature miRNAs are produced via a multistep process. Their transcription (pri-miRNAs) and first processing step via the microprocessor complex (pre-miRNAs) occur in the nucleus. Then they are exported into the cytosol, processed again by Dicer (dsRNA) and finally a single strand (mature miRNA) is incorporated into RISC (miRISC). The sequence of the incorporated miRNA provides the function of RNA target recognition via hybridization. Following binding of the target, the mRNA is either degraded or translation is inhibited, which ultimately leads to less protein production. Conversely, it has been shown that binding within the 5? UTR of the mRNA can lead to an increase in protein product. Regulation of homeostasis is very important for a cell; therefore, all steps in the miRNA-based regulation pathway, from transcription to the incorporation of the mature miRNA into RISC, are under tight control. While much research effort has been exerted in this area, the knowledgebase is not sufficient for accurately modelling miRNA regulation computationally. The computational prediction of miRNAs is, however, necessary because it is not feasible to investigate all possible pairs of a miRNA and its target, let alone miRNAs and their targets. We here point out open challenges important for computational modelling or for our general understanding of miRNA-based regulation and show how their investigation is beneficial. It is our hope that this collection of challenges will lead to their resolution in the near future. © 2022, Springer Science+Business Media, LLC, part of Springer Nature.
Citation - Scopus: 3
Advances and Future Perspective of Graphene Field Effect Transistors (gfets) for Medical Diagnostics and Point-Of Tools
(World Scientific Publishing, 2022) İnanç, Dilce; Mutlu, Mustafa Umut; Karabacak, Soner; Yıldız, Ümit Hakan
Recently, major focus has been centered to enhance the capability of graphenebased devices and to facilitate utilization of graphene for biological applications by lowering its toxicity. In this chapter, from synthesis to applications, many of the conspicuous characteristics of graphene have been elaborately reviewed. We primarily focused on graphene-based field effect transistor (FET) for medical diagnostics and point-of-care applications. The device configurations and their application potential as well as sensing capability of various graphene FETs (GFETs) have been discussed. Here, we have also presented several aspects and advantages of GFETs in medical applications while discussing their pros and cons in commercialization. We address the advances and challenges for GFET-based sensing platforms for the medical applications and elaborate the combination strategy of GFETs with the existing commercial systems. © 2023 by World Scientific Publishing Co. Pte. Ltd.
Citation - WoS: 3
Citation - Scopus: 3
Amperometric Detection of Nh3 by Aromatic Sam-Modified Graphene
(IEEE, 2023) Yağmurcukardeş, Nesli; Bayram, Abdullah; Aydın, Hasan; Can, Mustafa; Demiç, Şerafettin; Açıkbaş, Yaşar; Çelebi, Cem
Ammonia (NH3) is a toxic substance resulting in various acute and chronic effects on individuals. NH3 detection, monitoring methods, and detection tools are desperately needed. In this work, we improved the NH3 sensing capabilities of grapheme (GP) films deposited by chemical vapor deposition (CVD) by modifying aromatic self-assembled monolayer (SAM) molecules such as 5-[(3-methylphenyl) (phenyl) amino] isophthalic acid (MeIPA) and 5-(diphenyl)amino] isophthalic acid (PhIPA) on amperometric detection method. Morphological investigations of the films were carried out by optical and scanning electron microscopy (SEM). Surface potential was characterized with Kelvin probe force microscopy (KPFM), and vibrational properties were characterized with Raman spectroscopy. MeIPA modification increased NH3 uptake by two times compared to unmodified GP. The results indicated that the SAM modification enhanced NH3 molecule adsorption and improved its periodic reversible and reproducible response using the amperometric detection system, indicating that SAM molecules might be a feasible probe for NH3. © 2001-2012 IEEE.
Citation - WoS: 9
Citation - Scopus: 12
Analysis of European Hazelnut (corylus Avellana) Reveals Loci for Cultivar Improvement and the Effects of Domestication and Selection on Nut and Kernel Traits
(Springer Verlag, 2019) Frary, Amy; Öztürk, Süleyman Can; Balık, Hüseyin İrfan; Kayalak Balık, Selda; Kızılcı, Gökhan; Doğanlar, Sami; Frary, Anne
Turkey is a rich source of European hazelnut (Corylus avellana) germplasm with nearly 400 accessions in the national collection. This genetic material encompasses cultivars, landraces and wild genotypes which were characterized for 12 nut and 13 kernel traits over 2years in the 1990s. Analysis of these attributes revealed both the positive and negative impacts that human selection and breeding have had on hazelnut. Thus, while selection has resulted in larger nuts and kernels, cultivars have fewer nuts per cluster and kernels with larger internal cavities. Breeding has also resulted in a propensity for cultivars to have higher proportions of double kernels and empty nuts, two traits which reduce quality and yield. In addition, it is clear that while selection has successfully increased hazelnut fat content it has not impacted overall flavor, a much more complex trait. The nut and kernel phenotypic data were combined with genotypic data from 406 simple sequence repeat marker alleles for association mapping of the quantitative trait loci (QTL) for the traits. A total of 78 loci were detected in the population with the highest proportions for nut (24%) and kernel (26%) appearance parameters followed by quality (19%), shell thickness (16%) and yield-related (15%) traits. It is hoped that some of the identified QTL will be useful for future breeding of hazelnut for improved nut and kernel yield and quality.
Citation - WoS: 13
Citation - Scopus: 13
Analysis of Illumination Dependent Electrical Characteristics of Α- Styryl Substituted Bodipy Dye-Based Hybrid Heterojunction
(Springer, 2021) Kaplan, Nazmiye; Taşcı, Enis; Emrullahoğlu, Mustafa; Gökçe, Halil; Tuğluoğlu, Nihat; Eymur, Serkan
The alpha-styryl substituted BODIPY compound (BDP-Sty) was synthesized and characterized. The optimize ground state structure, HOMO and LUMO simulations, MEP surface map, and various molecular descriptors of the isolated BDP-Sty compound were investigated by Density Functional Theory at the B3LYP/6-311G (d,p) level. The reverse and forward bias current-voltage (I-V) characteristics of the Au/BDP-Sty/n-Si/In diode showed Schottky diode-like characteristics. An ideality factor (n) and barrier height (phi(b)) values of prepared diode for dark were found as 2.32 and 0.828, respectively. The series resistance (R-s) values were attained from the dV/dln(I) plot and Cheung's H(I) function and their values found for dark as 4.95 k omega and 4.59 k omega, respectively. The lnI - lnV and ln(I-R) - V-R(1/2) characteristics of the Au/BDP-Sty/n-Si/In diode reveal that the conduction mechanism is ohmic at low voltage and that of trap-filled space charge limited current and space charge limited current at higher voltage. The characteristic photodiode parameters of the prepared diode such as open circuit voltage (V-oc), short circuit current density (J(sc)), and photosensitivity (S) have also been investigated. All these results indicate the applicability for Au/BDP-Sty/n-Si/In diode in the field optoelectronic device applications.
Citation - WoS: 16
Citation - Scopus: 17
Antiproliferative Activity of (r)-4 '-methylklavuzon on Hepatocellular Carcinoma Cells and Epcam(+)/Cd133(+) Cancer Stem Cells Via Sirt1 and Exportin-1 (crm1) Inhibition
(Elsevier Ltd., 2019-10) Delman, Murat; Avcı, Sanem Tercan; Akçok, İsmail; Kanbur, Tuğçe; Erdal, Esra; Çağır, Ali
Cytotoxic effects of (R)-4'-methylklavuzon were investigated on hepatocellular carcinoma cells (HuH-7 and HepG2) and HuH-7 EpCAM(+)/CD133(+) cancer stem cells. IC50 of (R)-4'-methylklavuzon was found as 1.25 mu M for HuH-7 parental cells while it was found as 2.50 mu M for HuH-7 EpCAM(+)/CD133(+) cancer stem cells. (R)-4'-methylklavuzon tended to show more efficient in vitro cytotoxicity with its lower IC50 values on hepatocellular carcinoma cell lines compared to its lead molecule, goniothalamin and FDA-approved drugs, sorafenib and regorafenib. Cell-based Sirtuin/HDAC enzyme activity measurements revealed that endogenous Sirtuin/HDAC enzymes were reduced by 40% compared to control. SIRT1 protein levels were upregulated indicating triggered DNA repair mechanism. p53 was overexpressed in HepG2 cells. (R)-4'methylklavuzon inhibited CRM1 protein providing increased retention of p53 and RIOK2 protein in the nucleus. HuH-7 parental and EpCAM(+)/CD133(+) cancer stem cell spheroids lost intact morphology. 3D HepG2 spheroid viabilities were decreased in a correlation with upregulation in p53 protein levels. (C) 2019 Elsevier Masson SAS. All rights reserved.
Citation - WoS: 3
Citation - Scopus: 4
Applicability of Low-Intensity Vibrations as a Regulatory Factor on Stem and Progenitor Cell Populations
(Bentham Science Publishers, 2020) Baskan, Öznur; Karadaş, Özge; Meşe, Gülistan; Özçivici, Engin
Persistent and transient mechanical loads can act as biological signals on all levels of an organism. It is therefore not surprising that most cell types can sense and respond to mechanical loads, similar to their interaction with biochemical and electrical signals. The presence or absence of mechanical forces can be an important determinant of form, function and health of many tissue types. Along with naturally occurring mechanical loads, it is possible to manipulate and apply external physical loads on tissues in biomedical sciences, either for prevention or treatment of catabolism related to many factors, including aging, paralysis, sedentary lifestyles and spaceflight. Mechanical loads consist of many components in their applied signal form such as magnitude, frequency, duration and intervals. Even though high magnitude mechanical loads with low frequencies (e.g. running or weight lifting) induce anabolism in musculoskeletal tissues, their applicability as anabolic agents is limited because of the required compliance and physical health of the target population. On the other hand, it is possible to use low magnitude and high frequency (e.g. in a vibratory form) mechanical loads for anabolism as well. Cells, including stem cells of the musculoskeletal tissue, are sensitive to high frequency, low-intensity mechanical signals. This sensitivity can be utilized not only for the targeted treatment of tissues, but also for stem cell expansion, differentiation and biomaterial interaction in tissue engineering applications. In this review, we reported recent advances in the application of low-intensity vibrations on stem and progenitor cell populations. Modulation of cellular behavior with low-intensity vibrations as an alternative or complementary factor to biochemical and scaffold induced signals may represent an increase of capabilities in studies related to tissue engineering.
Citation - WoS: 1
Citation - Scopus: 1
Applications of Class Numbers and Bernoulli Numbers To Harmonic Type Sums
(Korean Mathematical Society, 2021) Göral, Haydar; Sertbaş, Doğa Can
Divisibility properties of harmonic numbers by a prime number p have been a recurrent topic. However, finding the exact p-adic orders of them is not easy. Using class numbers of number fields and Bernoulli numbers, we compute the exact p-adic orders of harmonic type sums. Moreover, we obtain an asymptotic formula for generalized harmonic numbers whose p-adic orders are exactly one.
Arithmetic Progressions in Certain Subsets of Finite Fields
(Elsevier, 2023) Eyidoğan, Sadık; Göral, Haydar; Kutlu, Mustafa Kutay
In this note, we focus on how many arithmetic progressions we have in certain subsets of finite fields. For this purpose, we consider the sets Sp = {t2 : t & ISIN; Fp} and Cp = {t3 : t & ISIN; Fp}, and we use the results on Gauss and Kummer sums. We prove that for any integer k & GE; 3 and for an odd prime number p, the number of k-term arithmetic progressions in Sp is given by p2 2k + R, where and ck is a computable constant depending only on k. The proof also uses finite Fourier analysis and certain types of Weil estimates. Also, we obtain some formulas that give the exact number of arithmetic progressions of length  in the set Sp when  & ISIN; {3,4, 5} and p is an odd prime number. For  = 4, 5, our formulas are based on the number of points on
Citation - WoS: 1
Citation - Scopus: 1
Association Mapping of Plant Structure and Yield Traits in Faba Bean (vicia Faba L.)
(John Wiley and Sons Inc., 2023) Abuzayed, M.A.; Baytar, A.A.; Yanar, E.G.; Doğanlar, Sami; Frary, Anne
Tens of thousands of faba bean accessions are available in germplasm collections throughout the world. Morphological characterization of these materials can enrich these collections and aid in the selection of genotypes for use in breeding programs. Results: In this study, 26 morphological characters were analyzed for 61 faba bean landraces and 53 cultivars over two seasons in Izmir, Turkey. The genotypes had high diversity for several yield traits including number of pods per plant, dry seed yield, and 100-seed weight. Association mapping was conducted for the morphological characters using 651 alleles from 100 simple sequence repeat (SSR) markers and a general linear model based on the Q matrix. A false discovery rate of 0.20 was used to test the significance of marker–trait associations resulting in 75 loci detected for 20 of the morphological characters (p ≤ 0.001). Conclusion: Overall, 44% of the quantitative trait loci (QTLs) were for seed traits, with 24%, 15%, and 17% of QTL identified for vegetative, inflorescence, and pod traits, respectively. The phenotypic data and marker–trait associations generated by this work can help breeding programs in the selection and improvement of faba bean. © 2023 Society of Chemical Industry.
Citation - Scopus: 1
Automated Analysis of Phase-Contrast Optical Microscopy Time-Lapse Images: Application To Wound Healing and Cell Motility Assays of Breast Cancer
(Elsevier, 2023) Erdem, Yusuf Sait; Ayanzadeh, Aydın; Mayalı, Berkay; Balıkçı, Muhammed; Belli, Özge Nur; Uçar, Mahmut; Yalçın Özuysal, Özden; Pesen Okvur, Devrim; Önal, Sevgi; Morani, Kenan; Iheme, Leonardo Obinna; Töreyin, Behçet Uğur
This chapter describes a workflow for analyzing phase-contrast microscopy (PCM) data from two fundamental types of biomedical assays: assays for cell motility and assays for wound healing. The workflow of the analysis is composed of the methods for acquiring, restoring, segmenting, and quantifying biomedical data. In the literature, there have been separate methods aimed at specific stages of PCM data analysis. Nonetheless, there has never been a complete workflow for all stages of analysis. This work is an innovation that proposes an end-to-end workflow for image pre-processing, deep learning segmentation, tracking, and quantification stages in cell motility and wound healing assay analyses. The findings indicate that domain knowledge can be used to make simple but significant improvements to the results of cutting-edge methods. Furthermore, even for deep learning-based methods, pre-processing is clearly a necessary step in the workflow. © 2023 Elsevier Inc. All rights reserved.
Citation - WoS: 17
Citation - Scopus: 19
Bacterial Surface, Biofilm and Virulence Properties of Listeriamonocytogenes Strains Isolated From Smoked Salmon and Fish Food Contact Surfaces
(Elsevier, 2021) Sudağıdan, Mert; Özalp, Veli Cengiz; Öztürk, Orhan; Yurt, Mediha Nur Zafer; Yavuz, Orhan; Taşbaşı, Behiye Busra; Uçak, Samet; Mavili, Zehra Seda; Çoban, Ayşen
Biofilm formation is one of the defense mechanisms of bacteria against disinfectants and antimicrobials. The aim of this study was to determine biofilm-forming L.monocytogenes from fish processing and salmon surfaces. Biofilm formation at 15, 25, 37, and 40 degrees C from 1 to 6-days period, adhesion to glass, polypropylene and stainless-steel surfaces, bacterial surface charge and hydrophobicity was determined. Adhesion behavior of the strains was evaluated using Surface Plasmon Resonance (SPR) technique. Totally 32 L.monocytogenes strains belonging to serogroups IIa (n:17), IIc(n:14) and IVb(n:1) were detected from 1320 swabs and 16 smoked salmons. Biofilm formation tests revealed that 21 strains form biofilm on microplate by increasing time and temperature. Although all strains strongly formed biofilm on glass surfaces, two strains slightly adhered polypropylene surfaces. High surface roughness of stainless-steel FeCrNi alloy (Ra = 4.15 nm) and CoCrMo alloy (Ra = 10.75 nm) increased biofilm formation of L.monocytogenes on stainless-steel surfaces. Zeta potential results showed that non-biofilm formers were more negatively charged after 6-days and hydrophobicity couldn't give a distinct distribution among biofilm formers and non-formers. SPR analysis method was evaluated to distinguish biofilm formers to adhere SPR gold chip surfaces. PCR results revealed that all strains were positive for hylA, iap, actA, plcA, plcB, fri, flaA, inlA, inlB, inlC, inlJ, and lmo1386 genes. Additionally, all strains were susceptible to penicillin, ampicillin, meropenem, erythromycin and trimethoprim-sulfamethoxazole. Biofilm-forming, virulence properties of L. monocytogenes strains isolated from fish processing surfaces and smoked salmons were evaluated and SPR was used to differentiate biofilm formers as a sensitive technique for biofilm studies.
Citation - WoS: 27
Citation - Scopus: 31
Ballistic Thermoelectric Transport Properties of Two-Dimensional Group Iii-Vi Monolayers
(American Physical Society, 2021) Çınar, Mustafa Neşet; Özbal Sargın, Gözde; Sevim, Koray; Özdamar, Burak; Kurt, Gizem; Sevinçli, Haldun
Ballistic transport and thermoelectric properties of group III-VI compounds (XY: X = B, Al, Ga, In, Tl; Y = O, S, Se, Te, Po) are investigated based on first-principles calculations and Landauer formalism. This large family is composed of 25 compounds which stands out with their unique electronic band structures. Mexican hat shaped valence band, which exhibits quartic energy-momentum relation gives rise to a sharp peak in the density of states as well as a steplike electronic transmission spectrum near the valence band edge. The intriguing electronic band structure and transport properties motivate us to explore thermoelectric properties of group III-VI monolayers. We find that, in addition to the stepwise transmission at the band edge, flat bands, valley degeneracy, and band degeneracy are the factors that enhance thermoelectric efficiencies. For heavier compounds, better thermoelectric efficiencies are possible for both n-type and p-type carriers.
Citation - WoS: 26
Citation - Scopus: 28
Biocomposite Scaffolds for 3d Cell Culture: Propolis Enriched Polyvinyl Alcohol Nanofibers Favoring Cell Adhesion
(John Wiley and Sons Inc., 2021-05) Bilginer, Rumeysa; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
The objective of this work is generation of propolis/polyvinyl alcohol (PVA) scaffold by electrospinning for 3D cell culture. Here, PVA used as co-spinning agent since propolis alone cannot be easily processed by electrospinning methodology. Propolis takes charge in maximizing biological aspect of scaffold to facilitate cell attachment and proliferation. Morphological analysis showed size of the electrospun nanofibers varied between 172-523 nm and 345-687 nm in diameter, for non-crosslinked and crosslinked scaffolds, respectively. Incorporation of propolis resulted in desired surface properties of hybrid matrix, where hybrid scaffolds highly favored protein adsorption. To examine cell compatibility, NIH-3T3 and HeLa cells were seeded on propolis/PVA hybrid scaffold. Results confirmed that integration of propolis supported cell adhesion and cell proliferation. Also, results indicated electrospun propolis/PVA hybrid scaffold provide suitable microenvironment for cell culturing. Therefore, developed hybrid scaffold could be considered as potential candidate for 3D cell culture and tissue engineering.
Citation - WoS: 34
Citation - Scopus: 35
Biomimetic Hybrid Scaffold Consisting of Co-Electrospun Collagen and Pllcl for 3d Cell Culture
(Elsevier Ltd., 2019) Türker, Esra; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
Electrospun collagen is commonly used as a scaffold in tissue engineering applications since it mimics the content and morphology of native extracellular matrix (ECM) well. This report describes "toxic solvent free" fabrication of electrospun hybrid scaffold consisting of Collagen (Col) and Poly(L-lactide-co-epsilon-caprolactone) (PLLCL) for three-dimensional (3D) cell culture. Biomimetic hybrid scaffold was fabricated via co-spinning approach where simultaneous electrospinning of PLLCL and Collagen was mediated by polymer sacrificing agent Polyvinylpyrrolidone (PVP). Acidified aqueous solution of PVP was used to solubilize collagen without using toxic solvents for electrospinning, and then PVP was readily removed by rinsing in water. Mechanical characterizations, protein adsorption, as well as biodegradation analysis have been conducted to investigate feasibility of biomimetic hybrid scaffold for 3D cell culture applications. Electrospun biomimetic hybrid scaffold, which has 3D-network structure with 300-450 nm fiber diameters, was found to be maximizing cell adhesion through assisting NIH 3T3 mouse fibroblast cells. 3D cell culture studies confirmed that presence of collagen in biomimetic hybrid scaffold have created a major impact on cell proliferation compared to conventional 2D systems on long-term, also cell viability increased with the increasing amount of collagen. (c) 2019 Elsevier B.V. All rights reserved.
Citation - WoS: 2
Citation - Scopus: 3
Biquandle Brackets and Knotoids
(World Scientific Publishing, 2021) Güğümcü, Neslihan; Nelson, Sam; Oyamaguchi, Natsumi
Biquandle brackets are a type of quantum enhancement of the biquandle counting invariant for oriented knots and links, defined by a set of skein relations with coefficients which are functions of biquandle colors at a crossing. In this paper, we use biquandle brackets to enhance the biquandle counting matrix invariant defined by the first two authors in (N. Gügümcü and S. Nelson, Biquandle coloring invariants of knotoids, J. Knot Theory Ramif. 28(4) (2019) 1950029). We provide examples to illustrate the method of calculation and to show that the new invariants are stronger than the previous ones. As an application we show that the trace of the biquandle bracket matrix is an invariant of the virtual closure of a knotoid.
Citation - WoS: 5
Citation - Scopus: 6
Boosting Up Printability of Biomacromolecule Based Bio-Ink by Modulation of Hydrogen Bonding Pairs
(Elsevier Ltd., 2020) Köksal, Büşra; Önbaş, Rabia; Başkurt, Mehmet; Şahin, Hasan; Arslan Yıldız, Ahu; Yıldız, Ümit Hakan
This study describes low dose UV curable and bioprintable new bioink made of hydrogen bond donor-acceptor adaptor molecule 2-isocyanatoethyl methacrylate (NCO)modified gelatin (NCO-Gel). Our theoretical calculations demonstrate that insertion of 2-isocyanatoethyl methacrylate doubles the interaction energy (500 meV) between gelatin chains providing significant contribution in interchain condensation and self-organization as compared to methacrylic anhydride modified gelatin (GelMA). The NCO-Gel exhibits peak around 1720 cm?1 referring to bidentate hydrogen bonding between H-NCO and its counterpart O[dbnd]CN[sbnd]H. These strong interchain interactions drive chains to be packed and thereby facilitating UV crosslinking. The NCO-Gel is exhibiting a rapid, 10 s gelation process by the exposure of laser (3 W, 365 nm). The dynamic light scattering characterization also reveals that NCO-Gel has faster sol to gel transition as compared to GelMA depending on the UV curing time. The NCO-Gel was found to be more firm and mechanically strong that provides advantages in molding as well as bioprinting processes. Bioprinted NCO-Gel has shown sharp borders and stable 3D geometry as compared to GelMA ink under 10 s UV curing time. The cell viability tests confirm that NCO-Gel facilitates cell proliferation and supports cell viability. We foresee that NCO-Gel bioink formulation provides a promising opportunity when low dose UV curing and rapid printing are required. © 2020 Elsevier Ltd

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