Publications with Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
Browse
45 results
Search Results
Publication Open Access CdTe quantum dot sensitized hexaniobate nanoscrolls and their photoelectrochemical properties(Royal Society of Chemistry (RSC), 2012) Department of Chemistry; Öztuna, Feriha Eylül Saraç; Akkaya, Ceren Yılmaz; Acar, Havva Funda Yağcı; Ünal, Uğur; PhD Student; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; N/A; N/A; 178902; N/AWe have constructed hybrid quantum dot-layered niobate films with an electrophoretic deposition method. The structure and photoelectrochemical behaviour were demonstrated.Publication Open Access Comprehensive research on past and future therapeutic strategies devoted to treatment of amyotrophic lateral sclerosis(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Sever, Belgin; Sever, Hilal; Ocak, Firdevs; Yuluğ, Burak; Tateishi, Hiroshi; Tateishi, Takahisa; Otsuka, Masami; Mikako, Fujita; Department of Molecular Biology and Genetics; Başak, Ayşe Nazlı; Çiftçi, Halil İbrahim; Demirci, Hasan; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Sciences; 1512; N/A; 307350Amyotrophic lateral sclerosis (ALS) is a rapidly debilitating fatal neurodegenerative disorder, causing muscle atrophy and weakness, which leads to paralysis and eventual death. ALS has a multifaceted nature affected by many pathological mechanisms, including oxidative stress (also via protein aggregation), mitochondrial dysfunction, glutamate-induced excitotoxicity, apoptosis, neuroinflammation, axonal degeneration, skeletal muscle deterioration and viruses. This complexity is a major obstacle in defeating ALS. At present, riluzole and edaravone are the only drugs that have passed clinical trials for the treatment of ALS, notwithstanding that they showed modest benefits in a limited population of ALS. A dextromethorphan hydrobromide and quinidine sulfate combination was also approved to treat pseudobulbar affect (PBA) in the course of ALS. Globally, there is a struggle to prevent or alleviate the symptoms of this neurodegenerative disease, including implementation of antisense oligonucleotides (ASOs), induced pluripotent stem cells (iPSCs), CRISPR-9/Cas technique, non-invasive brain stimulation (NIBS) or ALS-on-a-chip technology. Additionally, researchers have synthesized and screened new compounds to be effective in ALS beyond the drug repurposing strategy. Despite all these efforts, ALS treatment is largely limited to palliative care, and there is a strong need for new therapeutics to be developed. This review focuses on and discusses which therapeutic strategies have been followed so far and what can be done in the future for the treatment of ALS.Publication Open Access Effect of methylation of ionic liquids on the gas separation performance of ionic liquid/metal-organic framework composites(Royal Society of Chemistry (RSC), 2018) Department of Chemical and Biological Engineering; Nozari, Vahid; Keskin, Seda; Uzun, Alper; Zeeshan, Muhammad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; N/A; 40548; 59917; N/A1-N-Butyl-3-methylimidazolium hexafluorophosphate, [BMIM]ijPF6], and its methylated form, 1-N-butyl2,3-dimethylimidazolium hexafluorophosphate, [BMMIM]ijPF6], were incorporated into CuBTC to examine the effect of methylation of ionic liquids (ILs) on the gas separation performance of the corresponding IL/ metal–organic framework (MOF) composites. Spectroscopic analysis revealed that the interactions of the methylated ILs with CuBTC were weaker compared to those of its non-methylated counterpart. Gas uptake measurements illustrated that this difference in the interactions influences the gas separation performance of the composites. Accordingly, the CO2/N2: 15/85 and CH4/N2: 50/50 selectivities increased by 37% and 60% for [BMMIM]ijPF6]/CuBTC and 34% and 50% for [BMIM]ijPF6]/CuBTC, respectively, compared to the corresponding selectivities of pristine CuBTC at 1000 mbar. The results revealed another structural parameter controlling the performance of the IL/MOF composites, a novel type of material with rapidly expanding application areas.Publication Open Access One-step aqueous synthesis of anionic and cationic AgInS2 quantum dots and their utility in improving the efficacy of ALA-based photodynamic therapy(American Chemical Society (ACS), 2022) Loizidou, Marilena; MacRobert, Alexander J.; Department of Chemistry; Acar, Havva Funda Yağcı; Hashemkhani, Mahshid; PhD Student; Department of Chemistry; College of Sciences; Graduate School of Sciences and Engineering; 178902; N/ASilver-indium-sulfide quantum dots (AIS QDs) have potential applications in many areas, including biomedicine. Their lack of regulated heavy metals, unlike many commercialized QDs, stands out as an advantage, but the necessity for alloyed or core-shell structures and related costly and sophisticated processes for the production of stable and high quantum yield aqueous AIS QDs are the current challenges. The present study demonstrates the one-step aqueous synthesis of simple AgInS2 QD compositions utilizing for the first time either a polyethyleneimine/2-mercaptopropionic acid (AIS-PEI/2MPA) mixture or only 2-mercaptopropionic acid (AIS-2MPA) as the stabilizing molecules, providing a AgInS2 portfolio consisting of cationic and anionic AIS QDs, respectively, and tuneable emission. Small AIS QDs with long-term stability and high quantum yields (19-23%) were achieved at a molar ratio of Ag/In/S 1/10/10 in water without any dopant or a semiconductor shell. The theranostic potential of these cationic and anionic AIS QDs was also evaluated in vitro. Non-toxic doses were determined, and fluorescence imaging potential was demonstrated. More importantly, these QDs were electrostatically loaded with zwitterionic 5-aminolevulinic acid (ALA) as a prodrug to enhance the tumor availability of ALA and to improve ALA-induced porphyrin photodynamic therapy (PDT). This is the first study investigating the influence of nanoparticle charge on ALA binding, release, and therapeutic efficacy. Surface charge was found to be more critical in cellular internalization and dark toxicity rather than drug loading and release. Both QDs provided enhanced ALA release at acidic pH but protected the prodrug at physiological pH, which is critical for tumor delivery of ALA, which suffers from low bioavailability. The PDT efficacy of the ALA-loaded AIS QDs was tested in 2D monolayers and 3D constructs of HT29 and SW480 human colon adenocarcinoma cancer cell lines. The incorporation of ALA delivery by the AIS QDs, which on their own do not cause phototoxicity, elicited significant cell death due to enhanced light-induced ROS generation and apoptotic/necrotic cell death, reducing the IC50 for ALA dramatically to about 0.1 and 0.01 mM in anionic and cationic AIS QDs, respectively. Combined with simple synthetic methods, the strong intracellular photoluminescence of AIS QDs, good biocompatibility of especially the anionic AIS QDs, and the ability to act as drug carriers for effective PDT signify that the AIS QDs, in particular AIS-2MPA, are highly promising theranostic QDs.Publication Open Access Finger-actuated microneedle array for sampling body fluids(Multidisciplinary Digital Publishing Institute (MDPI), 2021) Ahmadpour, Abdollah; Yetişen, Ali K.; Department of Mechanical Engineering; Taşoğlu, Savaş; Sarabi, Misagh Rezapour; Faculty Member; Department of Mechanical Engineering; KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Sciences and Engineering; 291971; N/AThe application of microneedles (MNs) for minimally invasive biological fluid sampling is rapidly emerging, offering a user-friendly approach with decreased insertion pain and less harm to the tissues compared to conventional needles. Here, a finger-powered microneedle array (MNA) integrated with a microfluidic chip was conceptualized to extract body fluid samples. Actuated by finger pressure, the microfluidic device enables an efficient approach for the user to collect their own body fluids in a simple and fast manner without the requirement for a healthcare worker. The processes for extracting human blood and interstitial fluid (ISF) from the body and the flow across the device, estimating the amount of the extracted fluid, were simulated. The design in this work can be utilized for the minimally invasive personalized medical equipment offering a simple usage procedure.Publication Open Access Synthesis and characterization of mesoporous zirconium oxide thin films(Institute of Physics (IOP) Publishing, 2010) Department of Chemistry; Miko, Annamaria; Demirel, Adem Levent; Somer, Mehmet Suat; Teaching Faculty; Faculty Member; Faculty Member; Department of Chemistry; College of Sciences; N/A; 6568; 178882Zirconium oxide (ZrO2) has generated wide interest because of its potential in applications such as solid oxide fuel cells, catalysts and optical devices. In these applications, it is important to control the grain size of the material and increase the surface area by introducing porosity with tailored pore size. This paper presents a synthesis route for the preparation of mesoporous zirconia using spin-coating method combined with block copolymer templating evaporation induced self assembly (EISA). The hybrid mesophase was formed by zirconium oxychloride precursor ZrOCl2 center dot 8H(2)O and Brij 700 poly-ethylene oxide based block copolymer template C18H37(OCH2CH2). FT-IR and Raman measurements of the hybrid mesophase provided information on the possible intermolecular interactions between the precursor and the copolymer template. The results indicate a weak ion-dipole interaction between the inorganic precursor and the organic template after the solvent evaporation, possibly directly between the zirconium and the oxygen of the poly-ethylene oxide chain. The removal of the organic block copolymer by heat treatment resulted in mesoporous zirconia with pore size of similar to 4-8 nm and crystalline grain size of similar to 10-17 nm. The morphology in thin films depended significantly on the solvent quality and the block copolymer concentration. Tailoring the surface morphology and the grain size resulted in super-hydrophilic mesoporous zirconia thin films in contrast to water contact angle of 50 degrees on conventional tetragonal zirconium oxide.Publication Open Access Silk-hydrogel lenses for light-emitting diodes(Nature Publishing Group (NPG), 2017) Melikov, Rustamzhon; Press, Daniel Aaron; Kumar, Baskaran Ganesh; Dogru, Itir Bakis; Sadeghi, Sadra; Chirea, Mariana; Department of Chemistry; Department of Electrical and Electronics Engineering; Yılgör, İskender; Nizamoğlu, Sedat; Faculty Member; Faculty Member; Department of Chemistry; Department of Electrical and Electronics Engineering; College of Sciences; College of Engineering; 24181; 130295Today the high demand for electronics leads to massive production of waste, thus green materials based electronic devices are becoming more important for environmental protection and sustainability. The biomaterial based hydrogels are widely used in tissue engineering, but their uses in photonics are limited. In this study, silk fibroin protein in hydrogel form is explored as a bio-friendly alternative to conventional polymers for lens applications in light-emitting diodes. The concentration of silk fibroin protein and crosslinking agent had direct effects on optical properties of silk hydrogel. The spatial radiation intensity distribution was controlled via dome- and crater-type silk-hydrogel lenses. The hydrogel lens showed a light extraction efficiency over 0.95 on a warm white LED. The stability of silk hydrogel lens is enhanced approximately three-folds by using a biocompatible/biodegradable poly(ester-urethane) coating and more than three orders of magnitude by using an edible paraffin wax coating. Therefore, biomaterial lenses show promise for green optoelectronic applications.Publication Open Access Chronically radiation-exposed survivor glioblastoma cells display poor response to Chk1 inhibition under hypoxia(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Molecular Biology and Genetics; Değirmenci, Nareg Pınarbaşı; Sur, İlknur Erdem; Akçay, Vuslat; Bölükbaşı, Yasemin; Selek, Uğur; Solaroğlu, İhsan; Önder, Tuğba Bağcı; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; College of Sciences; School of Medicine; Koç University Hospital; N/A; N/A; N/A; 216814; 27211; 102059; 184359Glioblastoma is the most malignant primary brain tumor, and a cornerstone in its treatment is radiotherapy. However, tumor cells surviving after irradiation indicates treatment failure; therefore, better understanding of the mechanisms regulating radiotherapy response is of utmost importance. In this study, we generated clinically relevant irradiation-exposed models by applying fractionated radiotherapy over a long time and selecting irradiation-survivor (IR-Surv) glioblastoma cells. We examined the transcriptomic alterations, cell cycle and growth rate changes and responses to secondary radiotherapy and DNA damage response (DDR) modulators. Accordingly, IR-Surv cells exhibited slower growth and partly retained their ability to resist secondary irradiation. Concomitantly, IR-Surv cells upregulated the expression of DDR-related genes, such as CHK1, ATM, ATR, and MGMT, and had better DNA repair capacity. IR-Surv cells displayed downregulation of hypoxic signature and lower induction of hypoxia target genes, compared to naive glioblastoma cells. Moreover, Chk1 inhibition alone or in combination with irradiation significantly reduced cell viability in both naive and IR-Surv cells. However, IR-Surv cells' response to Chk1 inhibition markedly decreased under hypoxic conditions. Taken together, we demonstrate the utility of combining DDR inhibitors and irradiation as a successful approach for both naive and IR-Surv glioblastoma cells as long as cells are refrained from hypoxic conditions.Publication Open Access A new class of porous materials for efficient CO2 separation: ionic liquid/graphene aerogel composites(Elsevier, 2021) Department of Chemical and Biological Engineering; N/A; Department of Chemistry; Zeeshan, Muhammad; Yalçın, Kaan; Keskin, Seda; Uzun, Alper; Öztuna, Feriha Eylül Saraç; Ünal, Uğur; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; N/A; 40548; 59917; N/A; 42079Here, we report a new post-synthesis modification strategy for functionalizing reduced graphene aerogels (rGAs) towards an exceptional CO2 separation performance. 1-N-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) was impregnated on a rGA, prepared by reducing GA at 700 degrees C, at various ionic liquid (IL) loadings of 5, 10, 30, and 50 wt%. The resulting composites were characterized in deep detail by X-ray photoelectron spectroscopy, X-ray diffraction, N-2 physical adsorption measurements, scanning electron microscopy, Fourier transform infrared and Raman spectroscopies, and thermogravimetric analysis. Results indicated the presence of interactions between the rGA surface and the anion of the IL, potentially improving the CO2 affinity. Volumetric gas adsorption measurements using these materials showed that the deposition of [BMIM][PF6] on rGA surface at an IL loading of 50 wt% boosts the CO2/CH4 selectivity by more than 20-times, exceeding an absolute value of 120, a remarkably higher CO2/CH4 selectivity compared to that of other functionalized materials under similar operating conditions. Tunability of both the IL structure and the surface characteristics of rGA offer a tremendous degree of flexibility for the rational design of these IL/rGA composites towards high performance in gas separation applications.Publication Open Access CRISPR-Cas-Integrated LAMP(Multidisciplinary Digital Publishing Institute (MDPI), 2022) N/A; Department of Mechanical Engineering; Özdalgıç, Berin; Taşoğlu, Savaş; Yığcı, Defne; Atçeken, Nazente; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; 291971; N/A; N/APathogen-specific point-of-care (PoC) diagnostic tests have become an important need in the fight against infectious diseases and epidemics in recent years. PoC diagnostic tests are designed with the following parameters in mind: rapidity, accuracy, sensitivity, specificity, and ease of use. Molecular techniques are the gold standard for pathogen detection due to their accuracy and specificity. There are various limitations in adapting molecular diagnostic methods to PoC diagnostic tests. Efforts to overcome limitations are focused on the development of integrated molecular diagnostics by utilizing the latest technologies available to create the most successful PoC diagnostic platforms. With this point of view, a new generation technology was developed by combining loop-mediated isothermal amplification (LAMP) technology with clustered regularly interspaced short palindromic repeat (CRISPR)-associated (CRISPR-Cas) technology. This integrated approach benefits from the properties of LAMP technology, namely its high efficiency, short turnaround time, and the lack of need for a complex device. It also makes use of the programmable function of CRISPR-Cas technology and the collateral cleavage activity of certain Cas proteins that allow for convenient reporter detection. Thus, this combined technology enables the development of PoC diagnostic tests with high sensitivity, specificity, and ease of use without the need for complicated devices. In this review, we discuss the advantages and limitations of the CRISPR/Cas combined LAMP technology. We review current limitations to convert CRISPR combined LAMP into pathogen-specific PoC platforms. Furthermore, we point out the need to design more useful PoC platforms using microfabrication technologies by developing strategies that overcome the limitations of this new technology, reduce its complexity, and reduce the risk of contamination.