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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Hydrothermal-electrochemical growth of heterogeneous zno: co films(SpringerOpen, 2017) Department of Chemistry; Akkaya, Ceren Yılmaz; 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; Graduate School of Sciences and EngineeringBACKGROUND: Central venous cannulation is a necessary invasive procedure for fluid management, haemodynamic monitoring and vasoactive drug therapy. The right internal jugular vein (RIJV) is the preferred site. Enlargement of the jugular vein area facilitates catheterization and reduces complication rates. Common methods to enlarge the RIJV cross-sectional area are the Trendelenburg position and the Valsalva maneuver. OBJECTIVE: Compare the Trendelenburg position with upper-extremity venous return blockage using the tourniquet technique. DESIGN: Prospective clinical study. SETTING: University hospital. SUBJECTS AND METHODS: Healthy adult volunteers (American Society of Anesthesiologists class I) aged 18-45 years were included in the study. The first measurement was made when the volunteers were in the supine position. The RIJV diameter and cross-sectional area were measured from the apex of the triangle formed by the clavicle and the two ends of the sternocleidomastoid muscle, which is used for the conventional approach. The second measurement was performed in a 20 degrees Trendelenburg position. After the drainage of the veins using an Esbach bandage both arms were cuffed. The third measurement was made when tourniquets were inflated. MAIN OUTCOME MEASURE(S): Hemodynamic measurements and RIJV dimensions. RESULTS: In 65 volunteers the diameter and cross-sectional area of the RIJV were significantly widened in both Trendelenburg and tourniquet measurements compared with the supine position (P<.001 for both measures). Measurements using the upper extremity tourniquet were significantly larger than Trendelenburg measurements (P=.002 and <.001 for cross-sectional area and diameter, respectively). CONCLUSION: Channelling of the upper-extremity venous return to the jugular vein was significantly superior when compared with the Trendelenburg position and the supine position. LIMITATIONS: No catheterization and study limited to healthy volunteers.Publication Open Access Lead halide perovskite quantum dots for photovoltaics and photocatalysis: a review(American Chemical Society (ACS), 2022) Department of Chemistry; Peighambardoust, Naeimeh Sadat; Sadeghi, Ebrahim; Aydemir, Umut; Researcher; PhD Student; Faculty Member; Department of Chemistry; Koç University AKKİM Boron-Based Materials _ High-technology Chemicals Research _ Application Center (KABAM) / Koç Üniversitesi AKKİM Bor Tabanlı Malzemeler ve İleri Teknoloji Kimyasallar Uygulama ve Araştırma Merkezi (KABAM); College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; 58403Lead halide-based perovskite quantum dots (PQDs) have recently emerged as an important class of nanocrystal (NC) materials for optoelectronic and photoelec-trochemical applications. Thanks to their intriguing features including tunable band gap, narrow emission, high charge carrier mobility, remarkable light-absorbing factors, and long charge diffusion length, there has been a surge in research on lead halide-based PQDs and their applications. In this review, we showcase the fundamentals of PQDs and two principal applications including PQD solar cells (PQDSCs) and photocatalytic conversion. First, a thorough discussion on PQDSCs, their structure, surface treat-ment, and interface engineering along with their recent progress are presented. It is highlighted that the improvement of the efficiency of PQDSCs from below 10% to beyond 16% in a matter of a few years has turned them into promising candidates for future SC applications. Subsequently, the application of PQDs in photocatalytic reactions such as hydrogen production, CO2 reduction, and organic compounds' degradation is summarized. Not to mention that, despite the remarkable properties of PQDs in SCs and photocatalysis, the inferior stability of PV devices based thereon under operation as well as their poor tolerance under air, water, light, and heat impede their widespread application. For this, the practical efforts and possible solutions are extensively addressed. Finally, an outlook is provided, addressing further merits, and demerits of each application as well as prospective opportunities.Publication Open Access Stability trends in ono-metallic 3d layered double hydroxides(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Mohammadi, Saeedeh; Esmailpour, Ayoub; Assadi, Mohammad Hussein Naseef; Department of Chemistry; Doustkhah, Esmail; Teaching Faculty; Department of Chemistry; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); School of SciencesLayered double hydroxides (LDHs) constitute a unique group of 2D materials that can deliver exceptional catalytic, optical, and electronic performance. However, they usually suffer from low stability compared to their oxide counterparts. Using density functional calculations, we quantitatively demonstrate the crucial impact of the intercalants (i.e., water, lactate, and carbonate) on the stability of a series of common LDHs based on Mn, Fe, and Co. We found that intercalation with the singly charged lactate results in higher stability in all these LDH compounds, compared to neutral water and doubly charged carbonate. Furthermore, we show that the dispersion effect aids the stability of these LDH compounds. This investigation reveals that certain intercalants enhance LDH stability and alter the bandgap favourably.Publication Open Access Activity-based photosensitizers with optimized triplet state characteristics toward cancer cell selective and image guided photodynamic therapy(American Chemical Society (ACS), 2022) Elmazoğlu, Zübeyir; Kepil, Dilay; Etienne, Thibaud; Marion, Antoine; Günbaş, Görkem; Department of Chemistry; Kılıç, Eda; Almammadov, Toghrul; Kölemen, Safacan; Researcher; Faculty Member; Department of Chemistry; 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; College of Sciences; N/A; N/A; 272051Activity-based theranostic photosensitizers are highly attractive in photodynarnic therapy as they offer enhanced therapeutic outcome on cancer cells with an imaging opportunity at the same time. However, photosensitizers (PS) cores that can be easily converted to activity-based photosensitizers (aPSs) are still quite limited in the literature. In this study, we modified the dicyanomethylene-4H-chromene (DCM) core with a heavy iodine atom to get two different PSs (DCMo-I, I-DCMo-Cl) that can be further converted to aPS after simple modifications. The effect of iodine positioning on singlet oxygen generation capacity was also evaluated through computational studies. DCMo-I showed better performance in solution experiments and further proved to be a promising phototheranostic scaffold via cell culture studies. Later, a cysteine (Cys) activatable PS based on the DCMo-I core (DCMo-I-Cys) was developed, which induced selective photocytotoxicity along with a fluorescence turn-on response in Cys rich cancer cells.Publication Open Access Nanometer-scale siRNA carriers incorporating peptidomimetic oligomers: physical characterization and biological activity(Dove Medical Press, 2014) Kirshenbaum, Kent; Zuckermann, Ronald N.; Department of Chemistry; Konca, Yeliz Utku; Teaching Faculty; Department of Chemistry; College of Sciences; 111280Synthetic short interfering RNA (siRNA) oligonucleotides can trigger the RNA interference pathway and lead to selective gene silencing. Despite considerable enthusiasm and investment, formidable challenges remain that may deter translating this breakthrough discovery into clinical applications. In particular, the development of efficient, nontoxic, nonimmunogenic methods for delivering siRNA in vivo has proven to be exceptionally challenging. Thorough analysis of the relationship between the structure and function of siRNA carrier systems, both in isolation and in complex with RNA, will facilitate the design of efficient nonviral siRNA delivery vehicles. In this study, we explore the relationship between the physicochemical characteristics and the biological activity of "lipitoid" compounds as potent siRNA delivery vehicles. Lipitoids are cationic peptidomimetic oligomers incorporating a peptoid and a phospholipid moiety. Lipitoids can associate with siRNA oligonucleotides and self-assemble into spherical lipitoid-based nanoparticles (LNPs), with dimensions that are dependent upon the medium and the stoichiometric ratio between the cationic monomers of the lipitoid and anionic siRNA oligonucleotides. The morphology, gene silencing efficiency, and cytotoxicity of the siRNA-loaded LNPs are similarly sensitive to the stoichiometry of the complexes. The medium in which the LNPs are formed affects the assembled cargo particles' characteristics such as particle size, transfection efficiency, and stability. Formation of the LNPs in the biological, serum-free medium OptiMEM resulted in LNPs an order of magnitude larger than LNPs formed in water, and were twice as efficient in siRNA transfection compared to LNPs formed in water. Inhibitor studies were conducted to elucidate the efficiency of lysosomal escape and the uptake mechanism of the siRNA-loaded LNPs. Our results suggest that these lipitoid-based, siRNA-loaded spherical LNPs are internalized through a lipid raft-dependent and dynaminmediated pathway, circumventing endosomal and lysosomal encapsulation. The lipitoid-siRNA nanospheres proved to be suitable platforms for investigating the critical parameters determining the efficiency of transfection agents, revealing the necessity for conducting characterization studies in biological media. The investigation of the LNP internalization pathway points to an alternative uptake route that bypasses the lysosome, explaining the surprisingly high efficiency of LNPs and suggesting that the uptake mechanism should be probed rather than assumed for the next generation of rationally designed -transfection agents.Publication Open Access Emission tunable, cyto/hemocompatible, near-IR-emitting Ag2S quantum dots by aqueous decomposition of DMSA(Royal Society of Chemistry (RSC), 2014) Sevrin, Chantal; Department of Chemistry; Department of Physics; Birer, Özgür; Hocaoğlu, İbrahim; Kiraz, Alper; Acar, Havva Funda Yağcı; Duman, Fatma Demir; Researcher; PhD Student; Faculty Member; Department of Chemistry; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; N/A; 22542; N/A; 178902Size tunable aqueous Ag2S quantum dots emitting in the near-infrared region were synthesized through decomposition of meso-2,3-dimercaptosuccinic acid (DMSA) in water. The resulting NIR QDs are highly cyto- and hemocompatible, have quantum yields as high as 6.5% and are effective optical imaging agents based on in vitro evaluation.Publication Open Access Single glycerol/water microdroplets standing on a superhydrophobic surface: optical microcavities promising original applications(Society of Photo-optical Instrumentation Engineers (SPIE), 2007) Department of Physics; Department of Chemistry; Kiraz, Alper; Dündar, Mehmet Ali; Demirel, Adem Levent; Doğanay, Sultan; Kurt, Adnan; Sennaroğlu, Alphan; Yüce, Mehdi Yavuz; Faculty Member; Faculty Member; Undergraduate Student; Teaching Faculty; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; 22542; N/A; 6568; N/A; 194455; 23851; N/AGlycerol/water microdroplets take almost spherical shapes when standing on a superhydrophobic surface. Hence they are suitable to function as optical microcavities. Using Rhodamine B doped water microdroplets, large spectral tunability of the whispering gallery modes (WGMs) (>5 nm) was observed. Tunability was achieved by evaporation/condensation in a current controlled mini humidity chamber. Experiments revealed a mechanism stabilizing the volume of these microdroplets with femtoliter resolution. The mechanism relied on the interplay between the condensation rate that was kept constant and the size dependent laser induced heating. The radii of individual water microdroplets (>5 mu m) stayed within a few nanometers during long time periods (several minutes). By blocking the laser excitation for 500 msec, the stable volume of individual microdroplets were changed stepwise. Laser emission was also observed from Rhodamine B doped glycerol/water microdroplets using a pulsed, frequency-doubled Nd:YAG laser (lambda=532 nm) as the excitation source. The observed largely tunable WGMs and laser emission can pave way for novel applications in optical communication systems. Besides due to the sensitivity of the WGMs to the size and shape of the microdroplets, the results can find applications in characterizing superhydrophobic surfaces and investigating liquid-solid surfaces.Publication Open Access Cetuximab-Ag2S quantum dots for fluorescence imaging and highly effective combination of ALA-based photodynamic/chemo-therapy of colorectal cancer cells(Royal Society of Chemistry (RSC), 2021) Mohammad Hadi, Layla; Yaghini, Elnaz; Loizidou, Marilena; MacRobert, Alexander J.; Department of Chemistry; N/A; Department of Physics; Acar, Havva Funda Yağcı; Bayır, Ali; Hashemkhani, Mahshid; Demirci, Gözde; Muti, Abdullah; Sennaroğlu, Alphan; Researcher; PhD Student; Master Student; PhD Student; Faculty Member; Department of Chemistry; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; Graduate School of Sciences and Engineering; 178902; N/A; N/A; N/A; N/A; 23851Colorectal cancer (CRC) has a poor prognosis and urgently needs better therapeutic approaches. 5-Aminolevulinic acid (ALA) induced protoporphyrin IX (PpIX) based photodynamic therapy (PDT) is already used in the clinic for several cancers but not yet well investigated for CRC. Currently, systemic administration of ALA offers a limited degree of tumour selectivity, except for intracranial tumours, limiting its wider use in the clinic. The combination of effective ALA-PDT and chemotherapy may provide a promising alternative approach for CRC treatment. Herein, theranostic Ag2S quantum dots (AS-2MPA) optically trackable in near-infrared (NIR), conjugated with endothelial growth factor receptor (EGFR) targeting Cetuximab (Cet) and loaded with ALA for PDT monotherapy or ALA/5-fluorouracil (5FU) for the combination therapy are proposed for enhanced treatment of EGFR(+) CRC. AS-2MPA-Cet exhibited excellent targeting of the high EGFR expressing cells and showed a strong intracellular signal for NIR optical detection in a comparative study performed on SW480, HCT116, and HT29 cells, which exhibit high, medium and low EGFR expression, respectively. Targeting provided enhanced uptake of the ALA loaded nanoparticles by strong EGFR expressing cells and formation of higher levels of PpIX. Cells also differ in their efficiency to convert ALA to PpIX, and SW480 was the best, followed by HT29, while HCT116 was determined as unsuitable for ALA-PDT. The therapeutic efficacy was evaluated in 2D cell cultures and 3D spheroids of SW480 and HT29 cells using AS-2MPA with either electrostatically loaded, hydrazone or amide linked ALA to achieve different levels of pH or enzyme sensitive release. Most effective phototoxicity was observed in SW480 cells using AS-2MPA-ALA-electrostatic-Cet due to enhanced uptake of the particles, fast ALA release and effective ALA-to-PpIX conversion. Targeted delivery reduced the effective ALA concentration significantly which was further reduced with codelivery of 5FU. Delivery of ALA via covalent linkages was also effective for PDT, but required a longer incubation time for the release of ALA in therapeutic doses. Phototoxicity was correlated with high levels of reactive oxygen species (ROS) and apoptotic/necrotic cell death. Hence, both AS-2MPA-ALA-Cet based PDT and AS-2MPA-ALA-Cet-5FU based chemo/PDT combination therapy coupled with strong NIR tracking of the nanoparticles demonstrate an exceptional therapeutic effect on CRC cells and excellent potential for synergistic multistage tumour targeting therapy.Publication Open Access Treatment of breast cancer with autophagy inhibitory microRNAs carried by AGO2-conjugated nanoparticles(BioMed Central, 2020) Akkoç, Yunus; Koçak, Muhammed; Nalbat, Esra; Doğan-Ekici, Asiye Işın; N/A; Department of Chemistry; Ünal, Özlem; Acar, Havva Funda Yağcı; Gözüaçık, Devrim; PhD Student; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Sciences; N/A; 178902; N/ANanoparticle based gene delivery systems holds great promise. Superparamagnetic iron oxide nanoparticles (SPIONs) are being heavily investigated due to good biocompatibility and added diagnostic potential, rendering such nanoparticles theranostic. Yet, commonly used cationic coatings for efficient delivery of such anionic cargos, results in significant toxicity limiting translation of the technology to the clinic. Here, we describe a highly biocompatible, small and non-cationic SPION-based theranostic nanoparticles as novel gene therapy agents. We propose for the first-time, the usage of the microRNA machinery RISC complex component Argonaute 2 (AGO2) protein as a microRNA stabilizing agent and a delivery vehicle. In this study, AGO2 protein-conjugated, anti-HER2 antibody-linked and fluorophore-tagged SPION nanoparticles were developed (SP-AH nanoparticles) and used as a carrier for an autophagy inhibitory microRNA, MIR376B. These functionalized nanoparticles selectively delivered an effective amount of the microRNA into HER2-positive breast cancer cell lines in vitro and in a xenograft nude mice model of breast cancer in vivo, and successfully blocked autophagy. Furthermore, combination of the chemotherapy agent cisplatin with MIR376B-loaded SP-AH nanoparticles increased the efficacy of the anti-cancer treatment both in vitro in cells and in vivo in the nude mice. Therefore, we propose that AGO2 protein conjugated SPIONs are a new class of theranostic nanoparticles and can be efficiently used as innovative, non-cationic, non-toxic gene therapy tools for targeted therapy of cancer.