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Publication Open Access 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients(Public Library of Science, 2019) Dinçer, Cansu; Kaya, Tuğba; Tunçbağ, Nurcan; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; 26605; 8745Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor. Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies. In this study, we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas (TCGA) and applied a systems level approach based on biophysical characteristics of mutations and their organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights. Approximately 10% of the mutations are located in "patches" which are defined as the set of residues spatially in close proximity that are mutated across multiple patients. Grouping mutations as 3D patches reduces the heterogeneity across patients. There are multiple patches that are relatively small in oncogenes, whereas there are a small number of very large patches in tumor suppressors. Additionally, different patches in the same protein are often located at different domains that can mediate different functions. We stratified the patients into five groups based on their potentially affected pathways, revealed from the patient-specific subnetworks. These subnetworks were constructed by integrating mutation profiles of the patients with the interactome data. Network-guided clustering showed significant association between each group and patient survival (P-value = 0.0408). Also, each group carries a set of signature 3D mutation patches that affect predominant pathways. We integrated drug sensitivity data of GBM cell lines with the mutation patches and the patient groups to analyze the therapeutic outcome of these patches. We found that Pazopanib might be effective in Group 3 by targeting CSF1R. Additionally, inhibiting ATM that is a mediator of PTEN phosphorylation may be ineffective in Group 2. We believe that from mutations to networks and eventually to clinical and therapeutic data, this study provides a novel perspective in the network-guided precision medicine.Publication Open Access A cartridge based sensor array platform for multiple coagulation measurements from plasma(Royal Society of Chemistry (RSC), 2015) Bulut, Serpil; Yaralioglu, G. G.; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Çakmak, Onur; Ermek, Erhan; Kılınç, Necmettin; Barış, İbrahim; Kavaklı, İbrahim Halil; Ürey, Hakan; PhD Student; Other; Researcher; Teaching Faculty; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; 109991; N/A; 111629; 40319; 8579This paper proposes a MEMS-based sensor array enabling multiple clot-time tests for plasma in one disposable microfluidic cartridge. The versatile LoC (Lab-on-Chip) platform technology is demonstrated here for real-time coagulation tests (activated Partial Thromboplastin Time (aPTT) and Prothrombin Time (PT)). The system has a reader unit and a disposable cartridge. The reader has no electrical connections to the cartridge. This enables simple and low-cost cartridge designs and avoids reliability problems associated with electrical connections. The cartridge consists of microfluidic channels and MEMS microcantilevers placed in each channel. The microcantilevers are made of electroplated nickel. They are actuated remotely using an external electro-coil and the read-out is also conducted remotely using a laser. The phase difference between the cantilever oscillation and the coil drive is monitored in real time. During coagulation, the viscosity of the blood plasma increases resulting in a change in the phase read-out. The proposed assay was tested on human and control plasma samples for PT and aPTT measurements. PT and aPTT measurements from control plasma samples are comparable with the manufacturer's datasheet and the commercial reference device. The measurement system has an overall 7.28% and 6.33% CV for PT and aPTT, respectively. For further implementation, the microfluidic channels of the cartridge were functionalized for PT and aPTT tests by drying specific reagents in each channel. Since simultaneous PT and aPTT measurements are needed in order to properly evaluate the coagulation system, one of the most prominent features of the proposed assay is enabling parallel measurement of different coagulation parameters. Additionally, the design of the cartridge and the read-out system as well as the obtained reproducible results with 10 mu l of the plasma samples suggest an opportunity for a possible point-of-care application.
Publication Metadata only A facile method for cross-linking of methacrylated wood fibers for engineered wood composites(Elsevier B.V., 2023) Bengü, Başak; Biçer, Aziz; Yarıcı, Tugay; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Sarıoğlu, Ebru; Turhan, Emine Ayşe; Karaz, Selcan; Erkey, Can; Şenses, Erkan; PhD Student; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM), Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 29633; 280298Chemical modifications are widely used to enhance the properties of wood composites and create a strong bonding mechanism for enhancing the dimensional stability, water resistance as well as decreasing carcinogenic formaldehyde emission. Esterification is the most-known modification way to enhance the durability of wood composites, but it does not improve mechanical performance. In this work, we demonstrated a two-step, easy and quick wood surface modification strategy based on microwave heating and UV crosslinking. Firstly, the fiber surface was reacted with methacrylic anhydride, then using methacrylated groups on wood, the fibers are covalently linked. As a proof-of-concept the fibers cross-linked within five minutes under UV radiation using benzophenone solution. Then, the effect of crosslinked wood fiber on the properties of mechanical and swelling of fiberboard were studied. Using SEM, FTIR-ATR, and swelling tests, we investigated the wood-based products' reaction mechanism, morphology, and internal bonding strength. The chemical cross-linking gives stronger bonding, compared to hydrogen bonding, between fibers even in wet conditions, resulting in a cross-linked foam-like structure. Also, wood panels were fabricated, compared to unmodified fibers, the internal bond strength and dimensional stability of fiberboards increased slightly. Overall, these results show that chemical cross-linking of wood fibers can be a fast and promising way to produce multi-functional wood composites.Publication Metadata only A model to predict maximum tolerable temperatures of metal-oxide-supported 1-n-butyl-3-methylimidazolium based ionic liquids(Elsevier, 2015) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Akçay, Aslı; Babucci, Melike; Balci, Volkan; Uzun, Alper; Master Student; PhD Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; 59917The thermal stability limits of metal-oxide-supported ionic liquids (Its) with 1-n-butyl-3-methylimidazolium cation, [BMIM](+), on most commonly used metal-oxides, SiO2, TiO2, gamma-Al2O3, and MgO are determined. Data show that stability limits of bulk and metal-oxide-supported ILs linearly increase with increasing acidity of C2 proton on imidazolium ring, controlling the inter-ionic interaction strength. Moreover, data also show that the presence of metal-oxide lowers the stability limits considerably. This effect becomes more significant as the surface acidity of the metal-oxide decreases from SiO2 to MgO This decrease in stability limits with increasing point of zero charge (PZC) of metal-oxide indicates that the interaction between IL and metal-oxide becomes the dominant factor rather than the inter-ionic interactions. Based on these findings a simple mathematical expression was developed as a function of PZC and inter-ionic interaction strength probed by nu(C2H) to predict the stability limits of [BMIM](+)-based ILs immobilized on metal-oxides. Performance of the model was tested on several different ILs supported on different metal-oxides, including Fe2O3 and CeO2. Results show that the model successfully predicts the maximum operating or tolerable temperatures of supported-[BMIM](+)-based ILs with an average relative error less than 4.3%. We suggest that the model developed here can help to choose proper ILs that can tolerate the operating conditions of systems including ILs immobilized on metal oxides, such as in solid catalysts with ionic liquid layer (SCILL) or in supported ionic liquid phase (SILP) catalysts. (C) 2014 Elsevier Ltd. All rights reserved.Publication Metadata only A molecular dynamics study of allosteric transitions in Leishmania mexicana pyruvate kinase(Cell Press, 2015) Naithani, Ankita; Taylor, Paul; Walkinshaw, Malcolm D.; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997A comparative molecular dynamics analysis of the pyruvate kinase from Leishmania mexicana is presented in the absence and presence of the allosteric effector fructose 2,6-bisphosphate. Comparisons of the simulations of the large 240 kDa apo and holo tetramers show that binding of fructose 2,6-bisphosphate cools the enzyme and reduces dynamic movement, particularly of the B-domain. The reduced dynamic movement of the holo form traps the pyruvate kinase tetramer in its enzymatically active state with the B-domain acting as a lid to cover the active site. The simulations are also consistent with a transition of the mobile active-site alpha 6' helix, which would adopt a helical conformation in the active R-state and a less structured coil conformation in the inactive T-state. Analysis of the rigid body motions over the trajectory highlights the concerted anticorrelated rigid body rocking motion of the four protomers, which drives the T to R transition. The transitions predicted by these simulations are largely consistent with the Monod-Wyman-Changeux model for allosteric activation but also suggest that rigidification or cooling of the overall structure upon effector binding plays an additional role in enzyme activation.Publication Open Access A multi-state coarse grained modeling approach for an intrinsically disordered peptide(American Institute of Physics (AIP) Publishing, 2017) Department of Chemical and Biological Engineering; N/A; Sayar, Mehmet; Dalgıçdır, Cahit; Ramezanghorbani, Farhad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 109820; N/A; N/AMany proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LK alpha 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LK alpha 14 is disordered in dilute solutions; however, it strictly adopts the alpha-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an alpha-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.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 Metadata only A new dataset of non-redundant protein/protein interfaces(Biophysical Society, 2003) Tsai, CJ; Wolfson, H; Nussinov, R; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605Publication Metadata only A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications(Wiley, 2004) Tsai, CJ; Wolfson, H; Nussinov, R; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605Here, we present a diverse, structurally nonredundant data set of two-chain protein–protein interfaces derived from the PDB. Using a sequence order-independent structural comparison algorithm and hierarchical clustering, 3799 interface clusters are obtained. These yield 103 clusters with at least five nonhomologous members. We divide the clusters into three types. In Type I clusters, the global structures of the chains from which the interfaces are derived are also similar. This cluster type is expected because, in general, related proteins associate in similar ways. In Type II, the interfaces are similar; however, remarkably, the overall structures and functions of the chains are different. The functional spectrum is broad, from enzymes/inhibitors to immunoglobulins and toxins. The fact that structurally different monomers associate in similar ways, suggests “good” binding architectures. This observation extends a paradigm in protein science: It has been well known that proteins with similar structures may have different functions. Here, we show that it extends to interfaces. In Type III clusters, only one side of the interface is similar across the cluster. This structurally nonredundant data set provides rich data for studies of protein–protein interactions and recognition, cellular networks and drug design. In particular, it may be useful in addressing the difficult question of what are the favorable ways for proteins to interact.Publication Metadata only A novel alkali activated magnesium silicate as an effective and mechanically strong adsorbent for methylene blue removal(Elsevier, 2022) Kaya Özkiper, Kardelen; Soyer Uzun, Sezen; Department of Chemical and Biological Engineering; Uzun, Alper; Faculty Member; Department of Chemical and Biological Engineering; 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); College of Engineering; 59917A novel, cheap, and easy-to-synthesize sepiolite-based alkali-activated material (Sep-AAM), synthesized by the reaction of a magnesium silicate source, sepiolite, with sodium silicate solution, demonstrating high mechanical strength and methylene blue (MB) removal performance is introduced. Kinetics data indicated that MB adsorption occurs through pseudo-second-order adsorption kinetics model, while the Langmuir isotherm model provided a better fit to adsorption isotherms. The Sep-AAM provided a removal capacity of 99.92 mg g-1 at 50 degrees C, setting a new benchmark value among the materials used for this purpose. Thermodynamical parameters indicated that the adsorption of MB onto Sep-AAM was endothermic and the interaction between Sep-AAM and MB included weak chemical bonding. Regenerability of the Sep-AAM in powder and monolith forms was confirmed up to four-cycles. Structural parameters determined by several characterization tools demonstrated that the surface hydroxyl groups are responsible for the superior MB adsorption performance. The mechanical strength measurements showed that Sep-AAM in monolith form displayed a remarkable compressive strength value of 40 MPa. To establish a new approach forward on the development of AAMs for wastewater treatment, this study shows that sepiolite can effectively be utilized and Sep-AAM provides a sustainable solution for dye removal with advanced mechanical properties.