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Publication Open Access Birt-Hogg-Dube syndrome: diagnostic journey of three cases from skin to gene(Korean Dermatological Association, 2022) Hasal, Eda; Başkan, Emel Bülbül; Dilektaşlı, Aslı Görek; Sağ, Şebnem Özemri; Adird, Saduman Balaban; Temel, Şehime Gülsün; Department of Chemical and Biological Engineering; Gül, Şeref; Researcher; Department of Chemical and Biological Engineering; College of EngineeringBirt-Hogg-Dube syndrome (BHDS) is a rare disorder characterized by the triad of cutaneous lesions, renal tumors, lung cysts and inactivation of the gene folliculin (FLCN). Here, we present three female patients diagnosed with BHDS. First case a 55-year-old female had flesh moles histopathology compatible with angiofibroma, multiple cysts in the lung and kidneys, FLCN gene mutations ('c.1285dupC [p.His429Profs*]' 11th exon and 'c.653G>A [p.Arg258His]' 7th exon). The second case a 76-year-old female had trichodiscoma on her skin, multiple cysts in the lung, spontaneous pneumothorax, FLCN gene mutation 'c.1285dupC (p.His429Profs*27) 11th exon' and, her son had renal carcinoma history under 50 years of age. Our third case, also the daughter of case 2, had dermal papules histopathology compatible with trichodiscoma, spontaneous pneumothorax, FLCN gene mutation 'c.1285dupC (p.His429Profs*27) 11th exon' and, parotid oncocytoma. Through our cases, we document the first case of two mutations ('c.1285dupC [p.His429Profs*]' 11th exon and 'c.653G>A [p.Arg258His]' 7th exon) in the same FLCN gene and the 11th known case of parotid oncocytoma associated with BHDS in the light of the literature.Publication Open Access CO2 absorption into primary and secondary amine aqueous solutions with and without copper ions in a bubble column(TÜBİTAK, 2022) Güler, Cansu; Uzunlar, Erdal; Department of Chemical and Biological Engineering; Erkey, Can; Yousefzadeh, Hamed; Faculty Member; Researcher; Department of Chemical and Biological Engineering; College of Engineering; 29633; N/AChemical absorption of CO2 into aqueous amine solutions using a nonstirred bubble column was experimentally investigated. The performance of CO2 absorption of four different primary and secondary amines including monoethanolamine (MEA), piperazine (PZ), 2-piperidineethanol (2PE), and homopiperazine (HPZ) were compared. The effects of initial concentration of amine, the inlet mole fraction of CO2, and solution temperature on the rate of CO2 absorption and CO2 loading (mol CO2/mol amine) were studied in the range of 0.02–1 M, 0.10–0.15, and 25–40 °C, respectively. The effect of the presence of copper ions in the amine solution on CO2 loading was also studied. By comparison of the breakthrough curves of the amines at different operational conditions, it was revealed that the shortest and longest time for the appearance of the breakthrough point was observed for MEA and HPZ solutions, respectively. CO2 loading of MEA, 2PE, PZ, and HPZ aqueous solutions at 25 °C, 0.2 M of initial concentration of amine, and 0.15 of inlet mole fraction of CO2 were 1.06, 1.14, 1.13, and 1.18 mol CO2/mol amine, respectively. By decreasing the inlet mole fraction of CO2 from 0.15 to 0.10, CO2 loading slightly decreased. As the initial concentration of amine and temperature decreased, CO2 loading increased. Also, the presence of copper ions in the absorbent solution resulted in a decrease in the CO2 loading of MEA and HPZ aqueous solutions. In case of PZ and 2PE amines, adding copper ions led to precipitation even at low copper ion concentrations.
Publication Metadata only Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis(2022) Kutnu, Meltem; İşlerel, Elif Tekin; Özcengiz, Gülay; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 245513The Gram-positive bacterium Bacillus subtilis produces a diverse range of secondary metabolites with different structures and activities. Among them, bacilysin is an enzymatically synthesized dipeptide that consists of L-alanine and L-anticapsin. Previous research by our group has suggested bacilysin’s role as a pleiotropic molecule in its producer, B. subtilis PY79. However, the nature of protein interactions in the absence of bacilysin has not been defined. In the present work, we constructed a protein–protein interaction subnetwork by using Omics Integrator based on our recent comparative proteomics data obtained from a bacilysin-silenced strain, OGU1. Functional enrichment analyses on the resulting networks pointed to certain putatively perturbed pathways such as citrate cycle, quorum sensing and secondary metabolite biosynthesis. Various molecules, which were absent from the experimental data, were included in the final network. We believe that this study can guide further experiments in the identification and confirmation of protein–protein interactions in B. subtilis.Publication Metadata only Competitive hydrogen bonding in aspirin-aspirin and aspirin-leucine interactions(Scientific Technical Research Council Turkey-Tubitak, 2012) Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Yurtsever, Zeynep; Erman, Burak; Yurtsever, İsmail Ersin; Undergraduate Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; College of Sciences; College of Engineering; College of Sciences; N/A; 179997; 7129Aspirin-aspirin and aspirin-leucine interactions are studied by the density functional theory (DFT) and high level ab initio calculations with second order Moller-Plesset perturbation theory (MP2). The rotational isomers of aspirin are identified by their relative stability both in gaseous phase and in water using the polarizable continuum method (PCM). Local minima of aspirin monomers in water are found to be all highly populated compared to the gas phase behavior. Homodimers of aspirin form hydrogen bonds with bond energies of 10 kcal/mol. Weak hydrogen bonds utilizing phenyl and methyl groups are also found. The interaction between aspirin and leucine is stronger with relatively short bond lengths compared to homodimeric aspirin interactions. The potential energy surface has several minima with comparable stability. This study shows the significance of diverse bonding schemes, which are important for understanding complete interaction mechanisms of aspirin.Publication Open Access Effects of timolol treatment on pancreatic antioxidant enzymes in streptozotocin-induced diabetic rats: an experimental and computational study(Sciendo, 2019) Gök, Müslüm; Turan, Belma; N/A; Department of Chemical and Biological Engineering; Ulusu, Nuriye Nuray; Erman, Burak; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; School of Medicine; College of Engineering; 6807; 179997Background: the study aimed to investigate whether timolol-treatment has a beneficial effect on pentose phosphate pathway enzyme activities such as glucose-6-phosphate dehydrogenase (G6PD), 6-phosphogluconate dehydrogenase (6PGDH) enzyme activities and cAMP level in streptozotocin-induced diabetic rats in pancreatic tissues. Methods: diabetes was induced by streptozotocin (STZ) in 3-month old male Wistar rats. The diabetic rats were treated with timolol (5 mg/kg body weight, for 12 weeks) while the control group received saline. Enzyme activities were determined in pancreas tissue. To support our results, we performed in silico calculations, using Protein Data Bank structures. Results: timolol treatment of STZ-induced diabetic rats had no noteworthy effect on high blood-glucose levels. However, this treatment induced activities of G6PD and 6PGDH in diabetic rats. Timolol treatment significantly increased cAMP level in diabetic pancreatic tissue. We found that timolol cannot bind strongly to either G6PD or 6PGD, but there is a relatively higher binding affinity to adenylyl cyclase, responsible for cAMP production, serving as a regulatory signal via specific cAMP-binding proteins. Conclusions: our data point out that timolol treatment has beneficial effects on the antioxidant defence mechanism enzymes in the pancreas of STZ-induced diabetic rats. / Uvod: cilj istrazivanja je bio da se utvrdi da li tretman timololom ima pozitivan efekat na aktivnosti enzima pentoze fosfata, kao sto su aktivnosti glukoze-6-fosfat dehidrogenaze (G6PD), enzimske aktivnosti 6-fosfoglukonat dehidrogenaze i cAMP nivo u tkivu pankreasa kod pacova kojima je dijabetes izazvan streptozotocionom. Metode: dijabetes je izazvan streptozotocionom (STZ) kod tromesecnih muzjaka vistar pacova. Pacovi sa dijabetesom su tretirani timololom (5 mg/kg telesne tezine tokom 12 nedelja), dok je kontrolna grupa primila fizioloski rastvor. Enzimske aktivnosti su utvrivane u tkivu pankreasa. Da bismo potkrepili nase rezultate, sproveli smo in silico racunanja koristeci strukture Proteinske baze podataka. Rezultati: tretman timololom na pacovima kojima je dijabetes izazvan putem STZ-a nije imao znacajan uticaj na visoke nivoe glukoze u krvi. Medutim, kod takvih pacova ovaj tretman je indukovao aktivnosti G6PD i 6PGDH. Lecenje timololom znacajno je povecalo nivo cAMP-a u dijabeticnom tkivu pankreasa. Utvrdili smo da se timolol ne moze snazno vezati ni za G6PD, ni za 6PGD, ali da postoji relativno veci afinitet vezivanja za adenilil ciklazu, odgovornu za proizvodnju cAMP, koja sluzi kao regulatorni signal putem odredenih cAMP vezivnih proteina. Zakljucak: nasi podaci ukazuju da tretman timololom ima pozitivne efekte na antioksidantne enzime od brambenog sistema u pankreasu pacova sa dijebetesom izazvanim putem STZ-a.Publication Open Access Experimental and theoretical study of NH3 adsorption and desorption over a Cu-chabazite NH3-SCR catalyst(TÜBİTAK, 2018) Şimşek, Mutlu; Demir, Onur; Yıldız, Deniz Şanlı; Özener, Hüseyin Barkın; Hisar, Gökhan; Department of Chemical and Biological Engineering; Erkey, Can; Bozbağ, Selmi Erim; Faculty Member; Researcher; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; 29633; N/ANH3 adsorption and desorption behavior of a commercial Cu-chabazite (CHA) NH3 selective catalytic reduction (NH3-SCR) catalyst was studied in the presence and absence of H2O. NH3 uptake values at various adsorption temperatures were obtained during various steps of the adsorption and temperature-programmed desorption (TPD) experiments. Total NH3 uptake decreased from 4.6 to 1.6 g NH3/L catalyst when the adsorption temperature was increased from 50 to 300 degrees C. Three major adsorption sites for NH(3)adsorption could be identified and quantified using TPD experiments, namely loosely, moderately, and strongly bound NH3 with peak centers at around 147, 266, and 447 degrees C. The total NH3 uptake was significantly affected by the presence of H2O in the feed. This resulted in a significant uptake loss (nearly 60%) for the loosely bound NH3. Three single-site and one three-site model were developed and compared in terms of NH3 uptake and release. The effects of site density values and thermodynamic restrictions in one-site models were investigated. The model using site density values obtained during the TPD phase resulted in the best fit among one-site models. The three-site model, which uses site density values obtained using dry adsorption of NH3, best represented the experimental data.Publication Metadata only Improved coating of pancreatic islets with regulatory T cells to create local immunosuppression by using the biotin-polyethylene glycol-succinimidyl valeric acid ester molecule(Elsevier Science Inc, 2014) Golab, K.; Hara, M.; Zielinski, M.; Grose, R.; Savari, O.; Wang, X. -J.; Wang, L. -J.; Tibudan, M.; Krzystyniak, A.; Marek-Trzonkowska, N.; Millis, J. M.; Trzonkowski, P.; Witkowski, P.; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kızılel, Seda; Bal, Tuğba; Faculty Member; PhD. Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 28376; N/ABackground. We showed that T regulatory (Treg) cells can be attached to the surface of pancreatic islets providing local immunoprotection. Further optimization of the method can improve coating efficiency, which may prolong graft survival. In this study, we compared the effectiveness of two different molecules used for binding of the Tregs to the surface of pancreatic islets. Our aim was to increase the number of Treg cells attached to islets without compromising islets viability and function. Methods. The cell surface of human Treg cells and pancreatic islets was modified using biotin-polyethylene glycol-N-hydroxylsuccinimide (biotin-PEG-NHS) or biotin-PEG-succinimidyl valeric acid ester (biotin-PEG-SVA). Then, islets were incubated with streptavidin as islet/Treg cells binding molecule. Treg cells were stained with Cell Tracker CM-DiL dye and visualized using a Laser Scanning Confocal Microscope. The number of Treg cells attached per islets surface area was analyzed by Imaris software. The effect of coating on islet functionality was determined using the glucose-stimulated insulin response (GSIR) assay. Results. The coating procedure with biotin-PEG-SVA allowed for attaching 40% more Treg cells per 1 mu m(2) of islet surface. Although viability was comparable, function of the islets after coating using the biotin-PEG-SVA molecule was better preserved than with NHS molecule. GSIR was 62% higher for islets coated with biotin-PEG-SVA compared to biotin-PEG-NHS. Conclusion. Coating of islets with Treg cells using biotin-PEG-SVA improves effectiveness with better preservation of the islet function. Improvement of the method of coating pancreatic islets with Treg cells could further facilitate the effectiveness of this novel immunoprotective approach and translation into clinical settings.Publication Open Access Investigation of performances of commercial diesel oxidation catalysts for CO, C3H6, and NO oxidation(TÜBİTAK, 2021) Yıldız, Deniz Şanlı; Özener, Hüseyin Barkın; Hisar, Gökhan; Department of Chemical and Biological Engineering; Güneş, Hande; Bozbağ, Selmi Erim; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; 29633Four commercial monolithic diesel oxidation catalysts (DOCs) with two different platinum group metal (PGM) loadings and Pt:Pd ratios of 1:0, 2:1, 3:1 (w/w) were investigated systematically for CO, C3H6, and NO oxidation, CO-C3H6 co-oxidation, and CO-C3H6-NO oxidation reactions via transient activity measurements in a simulated diesel engine exhaust environment. As PGM loading increased, light-off curves shifted to lower temperatures for individual and co-oxidation reactions of CO and C3H6. CO and C3H6 were observed to inhibit the oxidation of themselves and each other. Addition of Pd to Pt was found to enhance CO and C3H6 oxidation performance of the catalysts while the presence and amount of Pd was found to increase the extent of self-inhibition of NO oxidation. NO inhibited CO and C3H6 oxidation reactions while NO oxidation performance was enhanced in the presence of CO and C3H6 probably due to the occurrence of reduced Pt and Pd sites during CO and C3H6 oxidations. The optimum Pt:Pd ratio for individual and co-oxidations of CO, C3H6, and NO was found to be Pt:Pd = 3:1 (w/w) in the range of experimental conditions investigated in this study.Publication Metadata only Modeling of an industrial delayed coker unit(Elsevier B.V., 2023) Firstauthor, Anne; Secondauthor, Tim B.; Thirdauthora, James Q.; Department of Chemical and Biological Engineering; Kuşoğlu, Gizem Kaya; Arkun, Yaman; Department of Chemical and Biological Engineering; College of EngineeringDelayed Coker Unit (DCU) converts the vacuum residual feedstock to lighter and more valuable products such as motor fuels and eliminates the low-order and environment-damaging streams. Thus, optimal operation of this unit provides great economic return. In this direction, we have modeled an industrial DCU which exists in the TUPRAS Refinery. The steady-state model consists of the furnace and coke drums and implemented using MATLAB. Physical properties are determined by Aspen HYSYS. The obtained model was used for predicting the coke level in the coke drums where the reaction takes place and the distribution of the products. Both furnace and coke drum models were verified by comparing obtained results with actual plant data. © 2023 Elsevier B.V.Publication Open Access ModiBodies: a computational method for modifying nanobodies in nanobody-antigen complexes to improve binding affinity and specificity(Springer, 2020) Department of Chemical and Biological Engineering; Hacısüleyman, Aysima; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 179997Nanobodies are special derivatives of antibodies, which consist of single domain fragments. They have become of considerable interest as next-generation biotechnological tools for antigen recognition. They can be easily engineered due to their high stability and compact size. Nanobodies have three complementarity-determining regions, CDRs, which are enlarged to provide a similar binding surface to that of human immunoglobulins. Here, we propose a benchmark testing algorithm that uses 3D structures of already existing protein-nanobody complexes as initial structures followed by successive mutations on the CDR domains. The aim is to find optimum binding amino acids for hypervariable residues of CDRs. We use molecular dynamics simulations to compare the binding energies of the resulting complexes with that of the known complex and accept those that are improved by mutations. We use the MDM4-VH9 complex, (PDB id 2VYR), fructose-bisphosphate aldolase from Trypanosoma congolense (PDB id 5O0W) and human lysozyme (PDB id 4I0C) as benchmark complexes. By using this algorithm, better binding nanobodies can be generated in a short amount of time. We suggest that this method can complement existing immune and synthetic library-based methods, without a need for extensive experimentation or large libraries.